profnet-1.0.22/0000755015075101507510000000000012021415652012545 5ustar lkajanlkajanprofnet-1.0.22/src-phd/0000755015075101507510000000000012021415607014105 5ustar lkajanlkajanprofnet-1.0.22/src-phd/exa/0000755015075101507510000000000012021362702014657 5ustar lkajanlkajanprofnet-1.0.22/src-phd/exa/1crn.hssp0000644015075101507510000003325612021362702016432 0ustar lkajanlkajanHSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 1.0 1991 PDBID 1crn DATE file generated on 9-Aug-98 SEQBASE RELEASE 36.0 OF EMBL/SWISS-PROT WITH 74019 SEQUENCES PARAMETER SMIN: -0.5 SMAX: 1.0 PARAMETER gap-open: 3.0 gap-elongation: 0.1 PARAMETER conservation weights: YES PARAMETER InDels in secondary structure allowed: YES PARAMETER alignments sorted according to :DISTANCE THRESHOLD according to: t(L)=(290.15 * L ** -0.562) + 5 REFERENCE Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991). CONTACT e-mail (INTERNET) Schneider@EMBL-Heidelberg.DE or Sander@EMBL-Heidelberg.DE / fax +49-6221-387306 AVAILABLE Free academic use. Commercial users must apply for license. AVAILABLE No inclusion in other databanks without permission. HEADER PLANT SEED PROTEIN COMPND CRAMBIN SOURCE ABYSSINIAN CABBAGE (CRAMBE ABYSSINICA) SEED AUTHOR W.A.HENDRICKSON,M.M.TEETER SEQLENGTH 46 NCHAIN 1 chain(s) in 1crn data set NALIGN 11 NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry NOTATION : %IDE: percentage of residue identity of the alignment NOTATION : %SIM (%WSIM): (weighted) similarity of the alignment NOTATION : IFIR/ILAS: first and last residue of the alignment in the test sequence NOTATION : JFIR/JLAS: first and last residue of the alignment in the alignend protein NOTATION : LALI: length of the alignment excluding insertions and deletions NOTATION : NGAP: number of insertions and deletions in the alignment NOTATION : LGAP: total length of all insertions and deletions NOTATION : LSEQ2: length of the entire sequence of the aligned protein NOTATION : ACCNUM: SwissProt accession number NOTATION : PROTEIN: one-line description of aligned protein NOTATION : SeqNo,PDBNo,AA,STRUCTURE,BP1,BP2,ACC: sequential and PDB residue numbers, amino acid (lower case = Cys), secondary NOTATION : structure, bridge partners, solvent exposure as in DSSP (Kabsch and Sander, Biopolymers 22, 2577-2637(1983) NOTATION : VAR: sequence variability on a scale of 0-100 as derived from the NALIGN alignments NOTATION : pair of lower case characters (AvaK) in the alignend sequence bracket a point of insertion in this sequence NOTATION : dots (....) in the alignend sequence indicate points of deletion in this sequence NOTATION : SEQUENCE PROFILE: relative frequency of an amino acid type at each position. Asx and Glx are in their NOTATION : acid/amide form in proportion to their database frequencies NOTATION : NOCC: number of aligned sequences spanning this position (including the test sequence) NOTATION : NDEL: number of sequences with a deletion in the test protein at this position NOTATION : NINS: number of sequences with an insertion in the test protein at this position NOTATION : ENTROPY: entropy measure of sequence variability at this position NOTATION : RELENT: relative entropy, i.e. entropy normalized to the range 0-100 NOTATION : WEIGHT: conservation weight ## PROTEINS : EMBL/SWISSPROT identifier and alignment statistics NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN 1 : cram_craab 1AB1 1.00 1.00 1 46 1 46 46 0 0 46 P01542 CRAMBIN. 2 : thn_pyrpu 0.53 0.60 2 46 2 47 45 1 1 47 P07504 THIONIN. 3 : thn_dencl 0.53 0.69 2 44 2 44 43 0 0 46 P01541 DENCLATOXIN B. 4 : thn3_visal 0.49 0.65 2 46 28 72 45 0 0 111 P01538 VISCOTOXIN A3 PRECURSOR. 5 : thn_pholi 0.47 0.61 2 46 2 46 45 0 0 46 P01540 LIGATOXIN A. 6 : thnb_visal 0.44 0.61 2 46 8 52 45 0 0 103 P08943 VISCOTOXIN B PRECURSOR (FRAGMENT). 7 : thn5_horvu 0.44 0.61 2 46 30 74 45 0 0 137 P09617 DG3). 8 : y4ik_rhisn 0.54 0.37 8 46 180 207 28 1 11 232 P55494 HYPOTHETICAL 26.8 KD PROTEIN Y4IK. 9 : dp87_dicdi 0.47 0.26 9 44 234 314 36 2 45 555 Q04503 PRESPORE PROTEIN DP87 PRECURSOR. 10 : thn2_visal 0.43 0.61 2 41 2 41 40 0 0 46 P32880 VISCOTOXIN A2. 11 : thn6_horvu 0.40 0.57 2 46 30 74 45 0 0 137 P09618 LEAF-SPECIFIC THIONIN PRECURSOR (CLONE BT ## ALIGNMENTS 1 - 11 SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7 1 1 T 0 0 77 1 0 T 2 2 T E -A 34 0A 21 9 22 TSSSSSS SS 3 3 C E -A 33 0A 0 9 0 CCCCCCC CC 4 4 C - 0 0 0 9 0 CCCCCCC CC 5 5 P S S+ 0 0 52 9 26 PRPPPPK PK 6 6 S S > S- 0 0 48 9 34 SNTNSNN ND 7 7 I H > S+ 0 0 123 9 24 ITTTTTT TT 8 8 V H > S+ 0 0 98 10 45 VWATTTTV TL 9 9 A H > S+ 0 0 6 11 21 AAAGAGGSAGA 10 10 R H X S+ 0 0 55 11 0 RRRRRRRRRRR 11 11 S H X S+ 0 0 63 11 39 SNNNNNNLPNN 12 12 N H X S+ 0 0 82 11 56 NCQIIICEPIC 13 13 F H X S+ 0 0 5 11 24 FYYYYYYMHYY 14 14 N H X S+ 0 0 87 11 0 NNNNNNNNNNN 15 15 V H >< S+ 0 0 99 11 42 VVIATTAPLTT 16 16 C H 3<>S+ 0 0 18 11 16 CCCCCCCNCCC 17 17 R H ><5S+ 0 0 94 11 0 RRRRRRRRRRR 18 18 L T <<5S+ 0 0 144 11 33 LLLLLLFSGFF 19 19 P T 3 5S- 0 0 107 11 42 PPPTTGAPFGA 20 20 G T < 5 + 0 0 53 11 9 GGGGGGGEGGG 21 21 T < - 0 0 37 10 32 TTTATGG.CGG 22 22 P >> - 0 0 81 10 32 PIPPSSS.PSS 23 23 E H 3> S+ 0 0 70 10 37 EsRRRRR.ERR 24 24 A H 3> S+ 0 0 63 10 35 AePPPEP.gEP 25 25 I H <> S+ 0 0 99 10 39 IIVTTRV.nVV 26 26 C H X S+ 0 0 0 10 0 CCCCCCC.CCC 27 27 A H X S+ 0 0 12 10 8 AAAAAAA.GAA 28 28 T H < S+ 0 0 120 10 41 TKAKSST.PSG 29 29 Y H < S+ 0 0 176 10 53 YKLLLLA.GLA 30 30 T H < S- 0 0 24 10 38 TCSSSSC.YSC 31 31 G S < S+ 0 0 35 10 31 GDGGGGG.IGR 32 32 C - 0 0 5 11 0 CCCCCCCCCCC 33 33 I E -A 3 0A 51 11 40 IKKKKKKITKK 34 34 I E -A 2 0A 78 11 16 IIIIIIIRIII 35 35 I - 0 0 34 11 0 IIIIIIIIIII 36 36 P S S+ 0 0 143 11 29 PSSSSSSPNSS 37 37 G S S- 0 0 41 11 24 GGGGGAGLGAG 38 38 A S S+ 0 0 80 11 41 ATTSSSPAhSP 39 39 T - 0 0 127 11 24 TTGTTTTTrTK 40 40 C - 0 0 46 11 7 CCCCCCCSCCC 41 41 P > - 0 0 53 11 8 PPPPBPPPPPP 42 42 G G > S+ 0 0 75 10 41 GSPSSSRDH S 43 43 D G 3 S+ 0 0 116 10 9 DDGDGDDDD D 44 44 Y G < S+ 0 0 66 10 3 YYYYWYYYY Y 45 45 A < 0 0 70 8 31 AP PBPPA P 46 46 N 0 0 76 8 37 NK KHKKS K ## SEQUENCE PROFILE AND ENTROPY SeqNo PDBNo V L I M F W Y G A P S T C H R K Q E N D NOCC NDEL NINS ENTROPY RELENT WEIGHT 1 1 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00 2 2 0 0 0 0 0 0 0 0 0 0 89 11 0 0 0 0 0 0 0 0 9 0 0 0.349 16 1.00 3 3 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.34 4 4 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.34 5 5 0 0 0 0 0 0 0 0 0 67 0 0 0 0 11 22 0 0 0 0 9 0 0 0.849 39 0.82 6 6 0 0 0 0 0 0 0 0 0 0 22 11 0 0 0 0 0 0 56 11 9 0 0 1.149 52 0.78 7 7 0 0 11 0 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 0 9 0 0 0.349 16 0.97 8 8 20 10 0 0 0 10 0 0 10 0 0 50 0 0 0 0 0 0 0 0 10 0 0 1.359 59 0.57 9 9 0 0 0 0 0 0 0 36 55 0 9 0 0 0 0 0 0 0 0 0 11 0 0 0.916 38 1.04 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 11 0 0 0.000 0 1.37 11 11 0 9 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 73 0 11 0 0 0.886 37 0.97 12 12 0 0 36 0 0 0 0 0 0 9 0 0 27 0 0 0 9 9 9 0 11 0 0 1.594 66 0.49 13 13 0 0 0 9 9 0 73 0 0 0 0 0 0 9 0 0 0 0 0 0 11 0 0 0.886 37 1.26 14 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 11 0 0 0.000 0 1.37 15 15 18 9 9 0 0 0 0 0 18 9 0 36 0 0 0 0 0 0 0 0 11 0 0 1.642 68 0.68 16 16 0 0 0 0 0 0 0 0 0 0 0 0 91 0 0 0 0 0 9 0 11 0 0 0.305 13 1.32 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 11 0 0 0.000 0 1.37 18 18 0 55 0 0 27 0 0 9 0 0 9 0 0 0 0 0 0 0 0 0 11 0 0 1.121 47 1.14 19 19 0 0 0 0 9 0 0 18 18 36 0 18 0 0 0 0 0 0 0 0 11 0 0 1.516 63 0.68 20 20 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 9 0 0 11 0 0 0.305 13 1.34 21 21 0 0 0 0 0 0 0 40 10 0 0 40 10 0 0 0 0 0 0 0 10 1 0 1.194 52 0.80 22 22 0 0 10 0 0 0 0 0 0 40 50 0 0 0 0 0 0 0 0 0 10 1 0 0.943 41 0.76 23 23 0 0 0 0 0 0 0 0 0 0 10 0 0 0 70 0 0 20 0 0 10 1 1 0.802 35 0.76 24 24 0 0 0 0 0 0 0 10 10 50 0 0 0 0 0 0 0 30 0 0 10 1 1 1.168 51 0.70 25 25 40 0 20 0 0 0 0 0 0 0 0 20 0 0 10 0 0 0 10 0 10 1 0 1.471 64 0.68 26 26 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 10 1 0 0.000 0 1.33 27 27 0 0 0 0 0 0 0 10 90 0 0 0 0 0 0 0 0 0 0 0 10 1 0 0.325 14 1.30 28 28 0 0 0 0 0 0 0 10 10 10 30 20 0 0 0 20 0 0 0 0 10 1 0 1.696 74 0.60 29 29 0 50 0 0 0 0 10 10 20 0 0 0 0 0 0 10 0 0 0 0 10 1 0 1.359 59 0.47 30 30 0 0 0 0 0 0 10 0 0 0 50 10 30 0 0 0 0 0 0 0 10 1 0 1.168 51 0.76 31 31 0 0 10 0 0 0 0 70 0 0 0 0 0 0 10 0 0 0 0 10 10 1 0 0.940 41 0.91 32 32 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 11 0 0 0.000 0 1.37 33 33 0 0 18 0 0 0 0 0 0 0 0 9 0 0 0 73 0 0 0 0 11 0 0 0.760 32 0.88 34 34 0 0 91 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 11 0 0 0.305 13 1.32 35 35 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.37 36 36 0 0 0 0 0 0 0 0 0 18 73 0 0 0 0 0 0 0 9 0 11 0 0 0.760 32 1.03 37 37 0 9 0 0 0 0 0 73 18 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.760 32 1.11 38 38 0 0 0 0 0 0 0 0 18 18 36 18 0 9 0 0 0 0 0 0 11 0 1 1.516 63 0.69 39 39 0 0 0 0 0 0 0 9 0 0 0 73 0 0 9 9 0 0 0 0 11 0 0 0.886 37 1.09 40 40 0 0 0 0 0 0 0 0 0 0 9 0 91 0 0 0 0 0 0 0 11 0 0 0.305 13 1.35 41 41 0 0 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 9 11 0 0 0.305 13 1.15 42 42 0 0 0 0 0 0 0 10 0 10 50 0 0 10 10 0 0 0 0 10 10 0 0 1.498 65 0.82 43 43 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 80 10 0 0 0.500 22 1.20 44 44 0 0 0 0 0 10 90 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.325 14 1.30 45 45 0 0 0 0 0 0 0 0 25 63 0 0 0 0 0 0 0 0 0 13 8 0 0 0.900 43 0.88 46 46 0 0 0 0 0 0 0 0 0 0 13 0 0 13 0 63 0 0 13 0 8 0 0 1.074 52 0.82 ## INSERTION LIST AliNo IPOS JPOS Len Sequence 2 23 24 1 sRe 9 24 250 31 gSHCEVLEKHPVCVRNHVPPHPPPPPQICGSVn 9 38 295 14 hPTCIRGDGYLCNQTr // profnet-1.0.22/src-phd/exa/1crn.phd0000644015075101507510000003063312021362702016224 0ustar lkajanlkajan******************************************************************************** * * * Publication to reference in reporting results: * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * * Rost, Burkhard; Sander, Chris: Prediction of protein structure * * at better than 70% accuracy. J. Mol. Biol., 1993, 232, 584-599. * * Rost, Burkhard; Sander, Chris: Combining evolutionary information * * and neural networks to predict protein secondary structure. * * Proteins, 1994, 19, 55-72. * * * ******************************************************************************** * * * Some statistics: * * ~~~~~~~~~~~~~~~~ * * * * Percentage of amino acids: * * * * +--------------+--------+--------+--------+--------+--------+ * | AA: | T | C | P | I | A | * | % of AA: | 13.0 | 13.0 | 10.9 | 10.9 | 10.9 | * +--------------+--------+--------+--------+--------+--------+ * | AA: | G | N | Y | V | S | * | % of AA: | 8.7 | 6.5 | 4.3 | 4.3 | 4.3 | * +--------------+--------+--------+--------+--------+--------+ * | AA: | R | L | F | E | D | * | % of AA: | 4.3 | 2.2 | 2.2 | 2.2 | 2.2 | * +--------------+--------+--------+--------+--------+--------+ * * * Percentage of secondary structure predicted/observed: * * * * +--------------+--------+--------+--------+ * | SecStr: | H | E | L | * | % Predicted: | 0.0 | 15.2 | 84.8 | * +--------------+--------+--------+--------+ * | SecStr: | H | E | L | * | % Observed: | 47.8 | 8.7 | 43.5 | * +--------------+--------+--------+--------+ * * * According to the following classes: * * all-alpha: %H>45 and %E< 5; all-beta : %H<5 and %E>45 * * alpha-beta : %H>30 and %E>20; mixed: rest, * * this means that the predicted class is: mixed class * * The class of the observed structure is: mixed class * * * ******************************************************************************** * * * * ******************************************************************************** * * * * * PHD output for your protein: * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * * * * Fri Sep 10 18:30:36 1999 * * * * Jury on: 10 different architectures (version 5.94_317 ). * * Note: differently trained architectures, i.e., different versions can * * result in different predictions. * * * * * ******************************************************************************** * * * * * * * About the protein: * * ------------------ * * * * * * HEADER PLANT SEED PROTEIN * * COMPND CRAMBIN * * SOURCE ABYSSINIAN CABBAGE (CRAMBE ABYSSINICA) SEED * * AUTHOR W.A.HENDRICKSON,M.M.TEETER * * SEQLENGTH 46 * * NCHAIN 1 chain(s) in 1crn data set * * NALIGN 11 * * (=number of aligned sequences in HSSP file) * * * * * ******************************************************************************** * * * * * * * Abbreviations: * * -------------- * * * * secondary structure : H=helix, E=extended (sheet), blank=rest (loop) * * * * AA: amino acid sequence * * PHD: Profile network prediction HeiDelberg * * Rel: Reliability index of prediction (0-9) * * * * detail: * * prH: 'probability' for assigning helix * * prE: 'probability' for assigning strand * * prL: 'probability' for assigning loop * * note: the 'probabilites' are scaled to the interval 0-9, * * i.e. prH=5 means, that the signal at the first * * output node is 0.5-0.6. * * * * subset: * * SUB: a subset of the prediction, for all residues with * * an expected accuracy > 82% (see tables in header) * * note: for this subset the following symbols are used: * * L: is loop (for which above " " is used) * * ".": means that no prediction is made for this residue, * * as the reliability is Rel < 5 * * * * * ******************************************************************************** * * * * * protein: 1crn length 46 * * * ....,....1....,....2....,....3....,....4....,....5....,....6 AA |TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN| Obs | EE HHHHHHHHHHH HHHHHHHH EE GGG | PHD | EEE EEEE | Rel |9768657886745421278999824316787389964899979999 detail: prH-|0000000000011221210000121000000000000000010000 prE-|0111121001122124300000026641101389973100000000 prL-|9878778887866544488999842347888610026889988989 subset: SUB |LLLLLLLLLLL.L....LLLLLL....LLLL.EEEE.LLLLLLLLL| * * ******************************************************************************** * * * * * * * Performance accuracy of the prediction * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * * * +-----------------+------------------------------------------------+-------------------+ | 1crn : 46 | method:jury | segments | +-----------------+------------------------------------------------+-------------------+ | number of residues with H,E,C | % of DSSP | % of Net | number |av length| +--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+ | |net H |net E |net C |sum DS| H | E | C | H | E | C |DSSP| Net|DSSP| Net| +--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+ | DSSP H | 0| 3| 19| 22| 0.0| 13.6| 86.4| 0| 42| 48| 2| 0| 9.5| 0.0| | DSSP E | 0| 2| 2| 4| 0.0| 50.0| 50.0| 0| 28| 5| 2| 2| 2.0| 3.5| | DSSP C | 0| 2| 18| 20| 0.0| 10.0| 90.0| 0| 28| 46| 7| 3| 1.6|13.0| +--------+------+------+------+------+-----+-----+-----+---+-+-+---+----+----+----+----+ | sum Net| 0| 7| 39| 46|corH |corE |corC | Q3 | SQ | 11| 5| 3.1| 9.2| | |0.00 |0.30 |0.13 | 43.5| 46.7| | +---------+--------------------------+++---+-----+-----++****+*****+-------------------+ | segments| % of observed || % of predicted | information | +---------+------+------+------+------++------+------+------+------+---------+---------+ | measure | % H | % E | % L | sum || % H | % E | % L | sum | I %obs | I %pred | +---------+------+------+------+------++------+------+------+------+---------+---------+ | SOV | 0.0 | 37.5 | 42.3 | 21.7 || 0.0 | 57.1 | 36.8 | 39.9 |-.01 -1%|-.03 -4%| +---------+------+------+------+------++------+------+------+------+---------+---------+ * * * * * * * * ******************************************************************************** * * * * END profnet-1.0.22/src-phd/exa/1crn.rdbPhd0000644015075101507510000000424212021362702016651 0ustar lkajanlkajan# Perl-RDB # # PHDsec: secondary structure prediction # # PDBID : 1crn # LENGTH : 46 # NOTATION No : residue number # NOTATION AA : amino acid one letter code # NOTATION OHEL : observed secondary structure # NOTATION PHEL : predicted secondary structure # NOTATION PHEL : H=helix, E=strand, L=non-regular (taken from DSSP) # NOTATION RI_S : reliability of secondary structure prediction , 0-9 # NOTATION pH : probability of predicting helix, 0-9 # NOTATION pE : probability of predicting strand # NOTATION pL : probability of predicting loop # NOTATION OtH : network output for helix, 0-100 # NOTATION OtE : network output for strand # NOTATION OtL : network output for loop # No AA OHEL PHEL RI_S pH pE pL OtH OtE OtL 4N 1 1 1 1N 1N 1N 1N 3N 3N 3N 1 T L L 9 0 0 9 1 1 96 2 T E L 7 0 1 8 1 14 82 3 C E L 6 0 1 7 1 19 78 4 C L L 8 0 1 8 1 12 85 5 P L L 6 0 1 7 4 14 71 6 S L L 5 0 2 7 3 23 65 7 I H L 7 0 1 8 4 12 78 8 V H L 8 0 0 8 5 6 85 9 A H L 8 0 0 8 4 7 85 10 R H L 6 0 1 7 4 17 75 11 S H L 7 0 1 8 6 11 80 12 N H L 4 1 2 6 10 22 61 13 F H L 5 1 2 6 15 20 61 14 N H L 4 2 1 5 22 19 58 15 V H L 2 2 2 4 21 28 45 16 C H L 1 1 4 4 9 40 42 17 R H L 2 2 3 4 20 28 40 18 L L L 7 1 0 8 9 9 77 19 P L L 8 0 0 8 7 4 86 20 G L L 9 0 0 9 3 2 87 21 T L L 9 0 0 9 4 2 93 22 P L L 9 0 0 9 3 1 95 23 E H L 8 1 0 8 10 3 84 24 A H L 2 2 2 4 27 23 42 25 I H E 4 1 6 2 9 61 24 26 C H E 3 0 6 3 6 59 30 27 A H E 1 0 4 4 4 47 45 28 T H L 6 0 1 7 4 17 76 29 Y H L 7 0 1 8 3 13 82 30 T H L 8 0 0 8 2 9 87 31 G L L 7 0 1 8 1 16 82 32 C L L 3 0 3 6 1 37 62 33 I E E 8 0 8 1 1 86 13 34 I E E 9 0 9 0 1 94 5 35 I L E 9 0 9 0 2 90 7 36 P L E 6 0 7 2 2 75 22 37 G L L 4 0 3 6 1 31 65 38 A L L 8 0 1 8 5 9 81 39 T L L 9 0 0 8 3 6 86 40 C L L 9 0 0 9 5 3 87 41 P L L 9 0 0 9 6 3 86 42 G H L 7 1 0 8 13 4 75 43 D H L 9 0 0 8 7 2 88 44 Y H L 9 0 0 9 3 4 90 45 A L L 9 0 0 8 2 8 91 46 N L L 9 0 0 9 3 1 96 profnet-1.0.22/src-phd/exa/1prcL.phd0000644015075101507510000006741212021362702016347 0ustar lkajanlkajan**************************************************************************** * * * PHD: Profile fed neural network systems from HeiDelberg * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * * Prediction of: * * secondary structure, by PHDsec * * solvent accessibility, by PHDacc * * and helical transmembrane regions, by PHDhtm * * * * Author: * * Burkhard Rost * * EMBL, 69012 Heidelberg, Germany * * Internet: Rost@EMBL-Heidelberg.DE * * * * All rights reserved. * * * **************************************************************************** * * * The network systems are described in: * * * * PHDsec: B Rost & C Sander: JMB, 1993, 232, 584-599. * * B Rost & C Sander: Proteins, 1994, 19, 55-72. * * PHDacc: B Rost & C Sander: Proteins, 1994, 20, 216-226. * * PHDhtm: B Rost et al.: Prot. Science, 1995, 4, 521-533. * * * **************************************************************************** * * * Some statistics * * ~~~~~~~~~~~~~~~ * * * * Percentage of amino acids: * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | G | L | F | A | V | * * | % of AA: | 12.8 | 11.7 | 9.5 | 7.3 | 6.6 | * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | S | I | W | P | Y | * * | % of AA: | 6.6 | 6.6 | 5.5 | 5.5 | 3.7 | * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | R | N | D | H | T | * * | % of AA: | 3.3 | 3.3 | 3.3 | 2.9 | 2.6 | * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | E | Q | K | M | C | * * | % of AA: | 2.6 | 1.8 | 1.8 | 1.5 | 1.1 | * * +--------------+--------+--------+--------+--------+--------+ * * * * Percentage of secondary structure predicted/observed: * * +--------------+--------+--------+--------+ * * | SecStr: | H | E | L | * * | % Predicted: | 50.9 | 11.7 | 37.4 | * * +--------------+--------+--------+--------+ * * | SecStr: | H | E | L | * * | % Observed: | 63.4 | 2.9 | 33.7 | * * +--------------+--------+--------+--------+ * * * * According to the following classes: * * all-alpha: %H>45 and %E< 5; all-beta : %H<5 and %E>45 * * alpha-beta : %H>30 and %E>20; mixed: rest, * * this means that the predicted class is: mixed class * * The class of the observed structure is: all-alpha * * * **************************************************************************** * * * PHD output for your protein * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * * Fri Sep 10 18:32:20 1999 * * Jury on: 10 different architectures (version 5.94_317 ). * * Note: differently trained architectures, i.e., different versions can * * result in different predictions. * * * **************************************************************************** * * * About the protein * * ~~~~~~~~~~~~~~~~~ * * * * HEADER PHOTOSYNTHETIC REACTION CENTER * * COMPND PHOTOSYNTHETIC REACTION CENTER * * SOURCE (RHODOPSEUDOMONAS $VIRIDIS) * * AUTHOR J.DEISENHOFER,O.EPP,K.MIKI,R.HUBER,H.MICHEL * * SEQLENGTH 1186 * * NCHAIN 4 chain(s) in 1prc data set * * KCHAIN 4 chain(s) used here ; chain(s) : C,L,M,H * * NALIGN 36 * * (=number of aligned sequences in HSSP file) * * * **************************************************************************** * * * Abbreviations: PHDsec * * ~~~~~~~~~~~~~~~~~~~~~ * * * * sequence: * * AA : amino acid sequence * * secondary structure: * * HEL: H=helix, E=extended (sheet), blank=other (loop) * * PHD: Profile network prediction HeiDelberg * * Rel: Reliability index of prediction (0-9) * * detail: * * prH: 'probability' for assigning helix * * prE: 'probability' for assigning strand * * prL: 'probability' for assigning loop * * note: the 'probabilites' are scaled to the interval 0-9, e.g.,* * prH=5 means, that the first output node is 0.5-0.6 * * subset: * * SUB: a subset of the prediction, for all residues with an expected * * average accuracy > 82% (tables in header) * * note: for this subset the following symbols are used: * * L: is loop (for which above " " is used) * * ".": means that no prediction is made for this residue, as the * * reliability is: Rel < 5 * * * * Abbreviations: PHDacc * * ~~~~~~~~~~~~~~~~~~~~~ * * * * SS : secondary structure * * HEL: H=helix, E=extended (sheet), blank=other (loop) * * solvent accessibility: * * 3st: relative solvent accessibility (acc) in 3 states: * * b = 0-9%, i = 9-36%, e = 36-100%. * * PHD: Profile network prediction HeiDelberg * * Rel: Reliability index of prediction (0-9) * * O_3: observed relative acc. in 3 states: B, I, E * * note: for convenience a blank is used intermediate (i). * * P_3: predicted relative accessibility in 3 states * * 10st:relative accessibility in 10 states: * * = n corresponds to a relative acc. of n*n % * * subset: * * SUB: a subset of the prediction, for all residues with an expected * * average correlation > 0.69 (tables in header) * * note: for this subset the following symbols are used: * * "I": is intermediate (for which above " " is used) * * ".": means that no prediction is made for this residue, as the * * reliability is: Rel < 4 * * * * * * Abbreviations: PHDhtm * * ~~~~~~~~~~~~~~~~~~~~~ * * * * secondary structure: * * HL: T=helical transmembrane region, blank=other (loop) * * PHD: Profile network prediction HeiDelberg * * PHDF:filtered prediction, i.e., too long transmembrane segments * * are split, too short ones are deleted * * Rel: Reliability index of prediction (0-9) * * detail: * * prH: 'probability' for assigning helical transmembrane region * * prL: 'probability' for assigning loop * * note: the 'probabilites' are scaled to the interval 0-9, e.g.,* * prH=5 means, that the first output node is 0.5-0.6 * * subset: * * SUB: a subset of the prediction, for all residues with an expected * * average accuracy > 82% (tables in header) * * note: for this subset the following symbols are used: * * L: is loop (for which above " " is used) * * ".": means that no prediction is made for this residue, as the * * reliability is: Rel < 5 * * * **************************************************************************** * * * protein: 1prc length 273 * * * ....,....1....,....2....,....3....,....4....,....5....,....6 AA |ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWD| OBS sec | HHH HHH EE EE HHHHHHHHHHHHHHHHHHHHH | PHD sec | EEE EEEEEHHHHHHHHHHHHHHHHHHHHHH | Rel sec |954323423357832422541332058368873236899999999999654664178654| detail: prH sec |012222111100000011111110100000002457899999999988776775410000| prE sec |011222233321135653224333420378875220000000000000122112110223| prL sec |965445545578853235664555468620012321100000000000000111378776| subset: SUB sec |LL........LLL.....L......LL.EEEE...HHHHHHHHHHHHHHH.HH..LLLL.| accessibility: 3st: O_3 acc |e b bbebbbb bbb e ee b bee eb be be bee eee ee eeebbeeee ee| P_3 acc |bbbebeeebeeebbbbbbbebbebebbbbbbbbbbbbbbbbbbbbbbbbbbbbeeeeebe| 10st: OBS acc |641410610203111356378515076471306326318756863865668226769586| PHD acc |000607670667000000060060600000000000000000000000000007677706| Rel acc |011141110201111031311000053333844233336584465547732010010110| subset: SUB acc |....b....................b....bbb.....bbbbbbbbbbb...........| ....,....7....,....8....,....9....,....10...,....11...,....12 AA |PFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLA| OBS sec | EE HHH HHH HHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHH| PHD sec |EEEEEE HHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHH| Rel sec |478874699955565568312063478889877887767899999999992575036999| detail: prH sec |000000000021100001345423678888877887777899999999984212457899| prE sec |688886200002112210000000011110011001111100000000000000010000| prL sec |311113799866676678654476210000000000000000000000005687431000| subset: SUB sec |.EEEE.LLLLLLLLLLLL....L..HHHHHHHHHHHHHHHHHHHHHHHHH.LLL..HHHH| accessibility: 3st: O_3 acc |ee bbb ee eee eeeebbbb ebbeb eeb bbbbbb bbbb e bbe | P_3 acc | bbbbbe eeeebbbbbbbbeebbbbbbbbbbbbbbbbbbbb bbebbeebbbb bbbbb| 10st: OBS acc |763453100338656693687612213622824533662535122000300224742083| PHD acc |500000747777000000007700000000000000000000500600670000500000| Rel acc |001612100203044023231313233775625243564544000206113131025548| subset: SUB acc |...b.........bb............bbbb.b.b.bbbbbb.....b........bbbb| ....,....13...,....14...,....15...,....16...,....17...,....18 AA |FCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFL| OBS sec |HHHHHHHHHHHH HHHHHH HHH EE HHHHHHHHHHH HHH HHHHHHHHHH| PHD sec |HHHHHHHHHHHHHHHEEEEE HHHHH E EEE E HHHHHHHHHH| Rel sec |999999999644311242322332354631224211122112233311491567656899| detail: prH sec |999999999766543222111223322124455433345322221111005777766899| prE sec |000000000012333454553210111122332232321234422244300000111000| prL sec |000000000121123223334455566753212333333432345544684211111000| subset: SUB sec |HHHHHHHHHH...............L.L.....................L.HHHHHHHHH| accessibility: 3st: O_3 acc | e ebe b b ebbee eb bbb b e be bbebbb bbbb bb e | P_3 acc |bbbbbbbbbbbbbbbbbbbbbbbebbbbbbbbbbebbbbbbbebbbbbbbbbbbbbbbbb| 10st: OBS acc |564626333140461077362422030447306401620233202145004454535744| PHD acc |000000000000000000000007000000000060000000600000000000000000| Rel acc |744886756572482656621221514067532504301221023031133115379578| subset: SUB acc |bbbbbbbbbbb.bb.bbbb.....b.b.bbb..b.b.................b.bbbbb| ....,....19...,....20...,....21...,....22...,....23...,....24 AA |FVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNI| OBS sec |HHHHHHHHHHHHHHHHHH HHHHHHHHHHHH HHHHHHHHHHHHHHH| PHD sec |HHHHHHHHHHHHHHHHEE HHHHHHHHHHHH HHHHHHHHHHHHHHH| Rel sec |999999999422755111368998677526997975564121334477899999999999| detail: prH sec |999999998655866443100000101257888876675321122677889999999999| prE sec |000000000000122444210001110000000011112223220010000000000000| prL sec |000000000344000012578888777731001012112344546211100000000000| subset: SUB sec |HHHHHHHHH...HHH....LLLLLLLLL.HHHHHHHHH........HHHHHHHHHHHHHH| accessibility: 3st: O_3 acc |eeb e bb bbbbbbbbb beeeeeb bbb bbbb bbbe b bbb b b e b b| P_3 acc |bbbbbbbbbbbbbbbbbbeeeeeeebebeeebbebb bbbbbbbbbbbbbbbbbbbbbb| 10st: OBS acc |860373115200211101426966613211322104101734243212403514732332| PHD acc |000000000000000000677777706077600600450000000000000000000000| Rel acc |522575954154476671112413302001000044002342042104621685679423| subset: SUB acc |b..bbbbbb.bbbbbbb....e............bb....b..b...bb..bbbbbbb..| ....,....25...,....26...,....27...,....28...,....29...,....30 AA |FLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS| OBS sec |HHHHHHHHH HHHH HHHH | PHD sec |HHHH EEEEEE HHHHHHHH | Rel sec |886126888873244569706899897547889| detail: prH sec |887421000000002220147888887621000| prE sec |000137888873321000000000000000000| prL sec |012441100015566779742100101268889| subset: SUB sec |HHH..EEEEEE....LLLL.HHHHHHHH.LLLL| accessibility: 3st: O_3 acc | e bbeb bbbbeb bb e b eeeb | P_3 acc |bbbbbbbbbbbbebbeee eebb bbbebeb e| 10st: OBS acc |564228134201162353004333650569924| PHD acc |000000000000600697366004000606039| Rel acc |140357676523000011001440331110003| subset: SUB acc |.b..bbbbbb...........bb..........| ************************************************************ * PHDhtm Helical transmembrane prediction * note: PHDacc and PHDsec are reliable for water- * soluble globular proteins, only. Thus, * please take the predictions above with * particular caution wherever transmembrane * helices are predicted by PHDhtm! ************************************************************ PHDhtm --- --- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION: SYMBOLS --- AA : amino acid in one-letter code --- OBS htm : HTM's observed (T=HTM, ' '=not HTM) --- PHD htm : HTM's predicted by the PHD neural network --- system (T=HTM, ' '=not HTM) --- Rel htm : Reliability index of prediction (0-9, 0 is low) --- detail : Neural network output in detail --- prH htm : 'Probability' for assigning a helical trans- --- membrane region (HTM) --- prL htm : 'Probability' for assigning a non-HTM region --- note: 'Probabilites' are scaled to the interval --- 0-9, e.g., prH=5 means, that the first --- output node is 0.5-0.6 --- subset : Subset of more reliable predictions --- SUB htm : All residues for which the expected average --- accuracy is > 82% (tables in header). --- note: for this subset the following symbols are used: --- L: is loop (for which above ' ' is used) --- '.': means that no prediction is made for this, --- residue as the reliability is: Rel < 5 --- other : predictions derived based on PHDhtm --- PHDFhtm : filtered prediction, i.e., too long HTM's are --- split, too short ones are deleted --- PHDRhtm : refinement of neural network output --- PHDThtm : topology prediction based on refined model --- symbols used: --- i: intra-cytoplasmic --- T: transmembrane region --- o: extra-cytoplasmic --- --- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION ....,....1....,....2....,....3....,....4....,....5....,....6 AA |ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWD| OBS htm | TTT TTT TTTTTTTTTTTTTTTTTTTTT | PHD htm | TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT| Rel htm |999999999999999999987653014677888877777777777777777777765310| detail: prH htm |000000000000000000001123457888999988888888888888888888887655| prL htm |999999999999999999998876542111000011111111111111111111112344| PHDRhtm | TTTTTTTTTTTTTTTTTTTTTTTTT | PHDThtm |iiiiiiiiiiiiiiiiiiiiiiiiiiiiTTTTTTTTTTTTTTTTTTTTTTTTTooooooo| subset: SUB htm |LLLLLLLLLLLLLLLLLLLLL.......HHHHHHHHHHHHHHHHHHHHHHHHHHH.....| ....,....7....,....8....,....9....,....10...,....11...,....12 AA |PFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLA| OBS htm | TTT TTT TTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTT| PHD htm | TTTTTTTTTTTTTTTTTTTTT TTTTTT| Rel htm |024567888889988887666403567778777777777765201344445442036777| detail: prH htm |432211000000000001111246788889888888888887654322222223568888| prL htm |567788999999999998888753211110111111111112345677777776431111| PHDRhtm | TTTTTTTTTTTTTTTTTT TTTT| PHDThtm |ooooooooooooooooooooooooTTTTTTTTTTTTTTTTTTiiiiiiiiiiiiiiTTTT| subset: SUB htm |.....LLLLLLLLLLLLL........HHHHHHHHHHHHHH.................HHH| ....,....13...,....14...,....15...,....16...,....17...,....18 AA |FCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFL| OBS htm |TTTTTTTTTTTT TTTTTT TTT TTTTTTTTTTT TTT TTTTTTTTTT| PHD htm |TTTTTTTTTTTTTTTTTTTTTTTT TTTTT TTTTTTTTTTT| Rel htm |788777777777777777665431000012211235665455643233213566777777| detail: prH htm |899888888888888888887765444556654332112222123333356788888888| prL htm |100111111111111111112234555443345667887777876666643211111111| PHDRhtm |TTTTTTTTTTTTTTTTTTT TTTTTTTT| PHDThtm |TTTTTTTTTTTTTTTTTTToooooooooooooooooooooooooooooooooTTTTTTTT| subset: SUB htm |HHHHHHHHHHHHHHHHHH....................................HHHHHH| ....,....19...,....20...,....21...,....22...,....23...,....24 AA |FVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNI| OBS htm |TTTTTTTTTTTTTTTTTT TTTTTTTTTTTT TTTTTTTTTTTTTTT| PHD htm |TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTT| Rel htm |777777777777653036789999999999999999988862034566766777777777| detail: prH htm |888888888888876531100000000000000000000013567788888888888888| prL htm |111111111111123468899999999999999999999986432211111111111111| PHDRhtm |TTTTTTTTTTTT TTTTTTTTTT| PHDThtm |TTTTTTTTTTTTiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiTTTTTTTTTT| subset: SUB htm |HHHHHHHHHHHH......LLLLLLLLLLLLLLLLLLLLLL........H..HHHHHHHHH| ....,....25...,....26...,....27...,....28...,....29...,....30 AA |FLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS| OBS htm |TTTTTTTTT TTTT TTTT | PHD htm |TTTTTTTTTTTTTT | Rel htm |777888888765420456788888899999888| detail: prH htm |888999999887764221100000000000000| prL htm |111000000112235778899999999999999| PHDRhtm |TTTTTTTTTT | PHDThtm |TTTTTTTTTTooooooooooooooooooooooo| subset: SUB htm |HHHHHHHHHH........LLLLLLLLLLLLLLL| --- --- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION END --- * * **************************************************************************** * * * Prediction accuracy for PHDsec * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * +-----------------+------------------------------------------------+-------------------+ | 1prc : 273 | method:jury | segments | +-----------------+------------------------------------------------+-------------------+ | number of residues with H,E,C | % of DSSP | % of Net | number |av length| +--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+ | |net H |net E |net C |sum DS| H | E | C | H | E | C |DSSP| Net|DSSP| Net| +--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+ | DSSP H | 131| 15| 27| 173| 75.7| 8.7| 15.6| 94| 46| 26| 10| 8|15.5|17.4| | DSSP E | 0| 4| 4| 8| 0.0| 50.0| 50.0| 0| 12| 3| 4| 9| 2.0| 3.6| | DSSP C | 8| 13| 71| 92| 8.7| 14.1| 77.2| 5| 40| 69| 22| 15| 2.0| 6.8| +--------+------+------+------+------+-----+-----+-----+---+-+-+---+----+----+----+----+ | sum Net| 139| 32| 102| 273|corH |corE |corC | Q3 | SQ | 36| 32| 5.7| 8.5| | |0.65 |0.21 |0.59 | 75.5| 67.6| | +---------+--------------------------+++---+-----+-----++****+*****+-------------------+ | segments| % of observed || % of predicted | information | +---------+------+------+------+------++------+------+------+------+---------+---------+ | measure | % H | % E | % L | sum || % H | % E | % L | sum | I %obs | I %pred | +---------+------+------+------+------++------+------+------+------+---------+---------+ | SOV | 81.3 | 27.5 | 70.2 | 76.0 || 94.3 | 25.0 | 63.9 | 74.8 |0.35 55%|0.27 43%| +---------+------+------+------+------++------+------+------+------+---------+---------+ +-------+----------------------+------------------------------+---------+-------+-------+ |name | Q2 b%o %p e%o %p | Q3 b%o %p i%o %p e%o %p |Q10o %p | c10 | N | +-------+----------------------+------------------------------+---------+-------+-------+ |1prc 9| 52.4 78 54 20 43 | 36.3 76 38 1 11 22 32 | 9 3 | 0.000 | 273 | ƒ˜ ‚À +-------+----------------------+------------------------------+---------+-------+-------+ +-----------------+------------------------------------------------+-------------------+ | 1prc : 273 | method:jury | segments | +-----------------+------------------------------------------------+-------------------+ | number of residues with H,E,C | % of DSSP | % of Net | number |av length| +--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+ | |net H |net E |net C |sum DS| H | E | C | H | E | C |DSSP| Net|DSSP| Net| +--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+ | DSSP H | 119| 0| 54| 173| 68.8| 0.0| 31.2| 79| 0| 43| 10| 6|15.5|25.0| | DSSP E | 5| 0| 3| 8| 62.5| 0.0| 37.5| 3| 0| 2| 4| 0| 2.0| 0.0| | DSSP C | 26| 0| 66| 92| 28.3| 0.0| 71.7| 17| 0| 53| 22| 7| 2.0|17.6| +--------+------+------+------+------+-----+-----+-----+---+-+-+---+----+----+----+----+ | sum Net| 150| 0| 123| 273|corH |corE |corC | Q3 | SQ | 36| 13| 5.7|21.0| | |0.37 |0.00 |0.38 | 67.8| 46.8| | +---------+--------------------------+++---+-----+-----++****+*****+-------------------+ | segments| % of observed || % of predicted | information | +---------+------+------+------+------++------+------+------+------+---------+---------+ | measure | % H | % E | % L | sum || % H | % E | % L | sum | I %obs | I %pred | +---------+------+------+------+------++------+------+------+------+---------+---------+ | SOV | 0.0 | 0.0 | 0.0 | 0.0 || 0.0 | 0.0 | 0.0 | 0.0 |0.09 15%|0.10 16%| +---------+------+------+------+------++------+------+------+------+---------+---------+ profnet-1.0.22/src-phd/exa/1prcL.rdbPhd0000644015075101507510000007611512021362702016777 0ustar lkajanlkajan# Perl-RDB # PHDsec+PHDacc+PHDhtm # Prediction of secondary structure, accessibility, and transmembrane helices # # # PDBID : 1prc # LENGTH : 273 # # NHTM_BEST : 5 (number of helices for best model) # NHTM_2ND_BEST : 4 (number of helices for second best model) # REL_BEST : 1.213 (reliability of best model =zscore) # REL_BEST_DIFF : 0.049 (reliability of best model =1st-2nd) # REL_BEST_DPROJ: 4 (reliability of best model projection of (1st-2nd) # # MODEL : iteratively adding transmembrane helices (HTM's) # MODEL_DAT : 1 , 0.5490 , 0.8922 , 29 - 53 # MODEL_DAT : 2 , 0.6063 , 0.8910 , 231 - 250 # MODEL_DAT : 3 , 0.6704 , 0.8810 , 117 - 139 # MODEL_DAT : 4 , 0.7262 , 0.8808 , 173 - 192 # MODEL_DAT : 5 , 0.7755 , 0.8737 , 85 - 102 # HTMTOP_OBS : unk (first loop region) # HTMTOP_PRD : in (first loop region, mode=top_fin) # HTMTOP_MODPRD : in (first loop region, mode=PRHL) # HTMTOP_RID : -9.771 (difference num(K+R), even-odd) # HTMTOP_RIP : 9 (reliability index =int(min{9,2*sqrt((DC)^2)}) ) # NOTATION No : residue number # NOTATION AA : amino acid one letter code # NOTATION OHEL : observed secondary structure # NOTATION PHEL : predicted secondary structure, H=helix, E=strand, L=non-regular (taken from DSSP) # NOTATION RI_S : reliability of secondary structure prediction , 0-9, (0 low, 9 high) # NOTATION OtH : network output for helix, 0-100, (0 low, 100 high) # NOTATION OtE : network output for strand, 0-100, (0 low, 100 high) # NOTATION OtL : network output for loop, 0-100, (0 low, 100 high) # NOTATION OACC : observed accessible surface area (from DSSP), 0-300 A**2 # NOTATION PACC : predicted accessible surface area, 0-300 A**2 # NOTATION OREL : observed relative accessible surface area, 0-100 # NOTATION PREL : predicted relative accessible surface area, 0-100 # NOTATION RI_A : reliability of accessibility prediction, 0-9, (0 low, 9 high) # NOTATION Obie : observed exposure state # NOTATION Pbie : predicted exposure state, b=buried, i=intermediate, e=exposed # NOTATION OTN : observed transmembrane helices # NOTATION PTN : predicted transmembrane helices, T=helical membrane, N=no helical transmembrane # NOTATION PFTN : filtered prediction of transmembrane helices # NOTATION PRTN : refined prediction (maximum score model) # NOTATION PiTo : predicted topology of transmembrane regions, i=loop inside, T=transmembrane, o=loop outside # NOTATION RI_H : reliability of secondary structure prediction , 0-9, (0 low, 9 high) # NOTATION OtT : network output for helix, 0-100, (0 low, 100 high) # NOTATION OtN : network output for loop, 0-100, (0 low, 100 high) # No AA OHEL PHEL RI_S OtH OtE OtL OACC PACC OREL PREL RI_A Obie Pbie Ot0 Ot1 Ot2 Ot3 Ot4 Ot5 Ot6 Ot7 Ot8 Ot9 OTN PTN PRTN PiTo RI_H OtT OtN 1 A L L 9 1 1 96 51 0 48 0 0 e b 14 11 6 6 5 4 4 4 9 12 L L L i 9 2 97 2 L L L 5 12 15 63 31 0 18 0 1 i b 14 12 9 8 7 6 5 4 3 2 L L L i 9 1 98 3 L L L 4 20 17 56 2 0 1 0 1 b b 11 10 8 8 8 8 7 5 3 2 L L L i 9 1 98 4 S L L 3 22 26 47 24 46 18 36 1 i e 7 7 6 7 8 11 13 13 9 5 L L L i 9 1 98 5 F L L 2 24 27 43 6 0 3 0 4 b b 24 20 11 9 7 6 4 3 2 2 L L L i 9 1 98 6 E L L 3 21 24 48 0 95 0 49 1 b e 4 5 6 7 8 10 12 12 9 7 L L L i 9 1 98 7 R H L 4 16 24 55 116 89 46 36 1 e e 4 5 7 8 10 12 12 11 7 6 H L L i 9 1 98 8 K H L 2 17 33 44 3 100 1 49 1 b e 3 3 5 6 8 11 13 14 11 8 H L L i 9 1 98 9 Y H L 3 13 30 52 2 0 0 0 0 b b 10 9 8 8 8 8 8 7 6 5 H L L i 9 1 98 10 R L L 3 11 32 55 13 89 5 36 2 b e 3 3 5 7 10 12 14 13 9 6 L L L i 9 1 98 11 V L L 5 6 22 70 0 51 0 36 0 b e 7 6 6 7 7 8 8 8 6 5 L L L i 9 1 98 12 R L L 7 6 13 80 28 121 11 49 1 i e 3 3 5 6 9 12 14 15 11 9 L L L i 9 1 98 13 G L L 8 5 10 84 1 0 1 0 1 b b 12 11 8 7 7 7 7 7 6 6 L L L i 9 1 98 14 G L L 3 9 35 56 1 0 1 0 1 b b 12 10 8 8 8 8 7 7 5 4 L L L i 9 1 98 15 T L E 2 8 54 40 4 0 2 0 1 b b 13 11 8 8 8 8 8 7 5 3 L L L i 9 1 98 16 L L E 4 9 63 30 17 0 10 0 0 i b 12 11 11 10 10 8 7 5 3 2 L L L i 9 1 98 17 I L E 2 11 53 37 59 0 34 0 3 i b 20 17 11 9 8 6 5 4 2 2 L L L i 9 1 98 18 G L L 2 10 35 53 33 0 39 0 1 e b 13 12 8 8 7 7 7 7 5 4 L L L i 9 2 97 19 G H L 5 10 23 65 9 0 10 0 3 i b 20 16 9 8 7 6 6 5 4 3 H L L i 9 3 96 20 D H L 4 10 25 64 87 58 53 36 1 e e 4 5 7 8 10 11 12 11 7 5 H L L i 8 5 94 21 L H L 1 10 40 48 125 0 76 0 1 e b 15 14 11 9 9 7 6 4 3 2 H L L i 7 11 88 22 F L L 3 12 32 53 53 0 26 0 0 i b 12 11 10 9 9 8 6 5 4 3 L L L i 6 15 84 23 D L L 3 14 31 52 2 58 1 36 0 b e 8 7 7 7 8 8 9 8 6 5 L L L i 5 23 76 24 F L L 2 8 37 52 50 0 25 0 0 i b 12 11 9 9 8 8 7 5 4 3 L L L i 3 34 65 25 W E L 0 11 45 45 0 81 0 36 0 b e 6 6 7 8 9 9 9 9 7 7 E L L i 0 46 53 26 V E L 5 8 24 67 70 0 49 0 5 e b 27 21 11 8 7 5 4 3 2 2 E H L i 1 59 40 27 G L L 8 4 9 86 41 0 48 0 3 e b 23 19 13 11 9 7 5 4 2 1 L H L i 4 71 28 28 P L L 3 4 34 61 30 0 22 0 3 i b 20 17 10 8 7 7 6 5 3 2 L H L i 6 80 19 29 Y E E 6 6 74 20 115 0 51 0 3 e b 22 18 12 10 8 6 5 3 2 1 E H H T 7 86 13 30 F E E 8 5 87 9 3 0 1 0 3 b b 26 23 17 14 11 7 4 2 1 1 E H H T 7 89 10 31 V L E 8 8 84 9 22 0 15 0 8 i b 36 28 13 9 7 5 3 2 1 1 L H H T 8 90 9 32 G L E 7 6 79 13 0 0 0 0 4 b b 25 20 12 10 9 7 6 4 2 2 L H H T 8 91 8 33 F H E 3 21 49 21 76 0 38 0 4 e b 25 21 13 10 8 6 4 3 2 2 H H H T 8 90 9 34 F H H 2 41 22 31 20 0 10 0 2 i b 17 15 10 8 7 6 5 4 3 3 H H H T 8 90 9 35 G H H 3 54 20 25 7 0 8 0 3 b b 21 18 12 9 8 7 6 5 3 2 H H H T 7 89 10 36 V H H 6 71 8 19 59 0 41 0 3 e b 20 17 10 9 8 7 5 4 2 2 H H H T 7 88 11 37 S H H 8 84 7 10 18 0 13 0 3 i b 20 17 10 9 9 8 7 5 3 2 H H H T 7 88 11 38 A H H 9 95 2 3 4 0 3 0 3 b b 21 17 9 8 8 8 8 6 4 2 H H H T 7 88 11 39 I H H 9 96 2 2 110 0 65 0 6 e b 31 24 12 9 7 5 4 3 2 1 H H H T 7 87 12 40 F H H 9 97 2 1 107 0 54 0 5 e b 29 24 13 10 8 6 4 3 1 1 H H H T 7 87 12 41 F H H 9 95 1 3 59 0 29 0 8 i b 36 28 14 10 7 5 4 2 1 1 H H H T 7 88 11 42 I H H 9 97 2 2 71 0 42 0 4 e b 22 18 9 8 7 7 7 6 4 2 H H H T 7 88 11 43 F H H 9 97 2 2 140 0 71 0 4 e b 23 19 11 9 8 7 5 4 2 1 H H H T 7 88 11 44 L H H 9 93 1 4 62 0 37 0 6 e b 33 26 14 10 8 5 3 2 1 1 H H H T 7 88 11 45 G H H 9 94 1 3 9 0 10 0 5 i b 28 22 10 8 7 6 5 4 3 2 H H H T 7 88 11 46 V H H 9 94 1 4 91 0 64 0 5 e b 28 22 11 9 7 6 5 4 2 1 H H H T 7 89 11 47 S H H 9 90 7 3 55 0 42 0 4 e b 24 19 10 9 8 7 6 5 3 2 H H H T 7 89 11 48 L H H 9 91 10 1 42 0 25 0 7 i b 35 28 15 10 8 5 3 2 1 1 H H H T 7 89 10 49 I H H 6 77 19 6 71 0 42 0 7 e b 34 27 13 9 7 5 3 2 1 1 H H H T 7 88 11 50 G H H 5 70 21 4 31 0 36 0 3 e b 21 17 9 8 7 7 6 5 4 3 H H H T 7 88 11 51 Y H H 4 66 28 8 144 0 64 0 2 e b 17 14 10 9 8 7 6 5 3 2 H H H T 7 88 11 52 A H H 6 72 16 12 8 0 7 0 0 b b 11 10 7 7 7 8 9 8 7 5 H H H T 7 88 11 53 A H H 6 71 16 12 8 0 7 0 1 b b 13 11 8 8 7 7 7 6 5 4 H H H T 7 88 11 54 S L H 4 60 23 16 51 63 39 49 0 e e 7 7 7 7 7 8 8 8 7 7 L H L o 7 86 13 55 Q L H 1 42 19 39 106 71 53 36 0 e e 7 7 7 7 8 9 9 8 7 6 L H L o 7 85 14 56 G L L 7 11 10 74 39 41 46 49 1 e e 4 4 5 7 8 10 12 12 10 9 L H L o 6 83 16 57 P L L 8 4 9 83 137 66 100 49 0 e e 7 6 6 6 7 7 8 9 9 8 L H L o 5 77 22 58 T L L 6 3 21 76 42 69 29 49 1 i e 4 4 5 7 8 11 13 13 11 9 L H L o 3 68 31 59 W L L 5 3 26 71 169 0 74 0 1 e b 13 12 11 10 8 7 5 4 3 3 L H L o 1 59 40 60 D L L 4 5 32 63 63 58 38 36 0 e e 6 6 6 7 9 10 11 10 6 5 L H L o 0 51 48 61 P L E 4 5 67 31 81 34 59 25 0 e i 7 7 8 9 10 10 10 8 6 4 L L L o 0 47 52 62 F L E 7 4 83 15 74 0 37 0 0 e b 11 10 9 9 9 8 7 5 4 3 L L L o 2 39 59 63 A L E 8 3 84 12 15 0 14 0 1 i b 13 12 10 10 9 9 7 5 3 2 L L L o 4 26 73 64 I L E 8 2 87 12 34 0 20 0 6 i b 29 23 12 9 7 5 4 3 2 2 L L L o 5 20 79 65 S E E 7 1 82 18 33 0 25 0 1 i b 12 10 8 8 8 7 7 7 5 5 E L L o 6 17 82 66 I E E 4 1 66 31 16 0 9 0 2 i b 17 14 9 7 6 5 4 4 4 4 E L L o 7 11 88 67 N L L 6 0 25 76 5 76 3 49 1 b e 3 4 5 6 8 10 12 12 10 9 L L L o 8 8 91 68 P L L 9 1 2 94 0 21 0 16 0 b i 8 8 9 9 9 9 8 7 5 4 L L L o 8 7 92 69 P L L 9 2 2 93 0 66 0 49 0 b e 5 5 6 7 8 8 9 9 8 8 L L L o 8 8 91 70 D L L 9 5 3 86 19 79 11 49 2 i e 3 4 5 6 8 11 14 15 13 12 L L L o 8 9 90 71 L H L 5 20 7 63 24 80 14 49 0 i e 5 5 6 7 8 9 10 10 9 8 H L L o 8 7 92 72 K H L 5 12 19 65 158 100 77 49 3 e e 2 3 4 5 7 10 15 18 16 14 H L L o 9 3 96 73 Y H L 5 10 18 67 83 0 37 0 0 e b 11 11 10 9 9 8 7 5 4 3 H L L o 9 3 96 74 G L L 6 6 17 74 23 0 27 0 4 i b 21 17 10 8 7 6 5 5 4 4 L L L o 8 5 94 75 L L L 5 4 26 66 73 0 44 0 4 e b 24 20 14 10 8 6 4 2 2 1 L L L o 8 6 93 76 G L L 5 6 26 66 36 0 42 0 0 e b 12 10 6 7 7 8 9 9 7 5 L L L o 8 7 92 77 A L L 6 9 16 72 97 0 91 0 2 e b 17 14 10 9 8 7 5 4 3 3 L L L o 8 7 92 78 A L L 8 12 6 82 14 0 13 0 3 i b 20 17 10 9 9 8 6 5 3 2 L L L o 7 10 89 79 P L L 3 35 4 64 51 0 37 0 2 e b 17 14 9 8 8 8 7 6 4 3 L L L o 6 15 84 80 L H L 1 46 3 55 106 0 64 0 3 e b 20 17 10 9 8 6 4 3 2 2 H L L o 6 17 82 81 L H L 2 56 3 46 83 80 50 49 1 e e 4 4 6 7 8 10 12 13 10 9 H L L o 6 19 80 82 E H L 0 51 3 50 81 95 41 49 3 e e 2 2 3 5 6 10 14 18 17 16 H L L o 4 25 74 83 G L L 6 23 1 79 1 0 1 0 1 b b 13 11 8 8 7 7 7 7 6 6 L L L o 0 48 51 84 G H L 3 36 2 61 5 0 5 0 3 b b 21 17 11 9 8 7 6 5 3 3 H H L o 3 68 31 85 F H H 4 62 7 27 13 0 6 0 2 b b 18 16 11 10 9 7 5 4 2 1 H H H T 5 78 21 86 W H H 7 80 12 11 4 0 1 0 3 b b 22 19 12 10 9 7 5 3 2 1 H H H T 6 83 16 87 Q H H 8 85 14 2 31 0 15 0 3 i b 21 17 11 9 9 8 6 5 2 1 H H H T 7 86 13 88 A H H 8 89 11 1 41 0 38 0 7 e b 34 27 13 9 7 5 4 3 2 1 H H H T 7 88 11 89 I H H 8 90 10 2 10 0 5 0 7 b b 34 26 12 9 7 6 5 3 2 1 H H H T 7 89 10 90 T H H 9 89 7 2 11 0 7 0 5 b b 25 19 9 8 8 7 7 6 4 2 H H H T 8 90 9 91 V H H 8 87 9 5 92 0 64 0 6 e b 30 24 12 9 7 6 4 3 2 1 H H H T 7 89 10 92 C H H 7 78 14 9 10 0 7 0 2 b b 18 15 10 9 8 7 6 5 3 2 H H H T 7 89 10 93 A H H 7 77 15 8 20 0 18 0 5 i b 27 21 11 9 8 6 4 3 2 2 H H H T 7 88 11 94 L H H 8 84 8 9 41 0 25 0 2 i b 17 14 9 8 8 7 7 6 4 3 H H H T 7 88 11 95 G H H 8 81 8 8 13 0 15 0 4 i b 22 18 10 8 7 6 6 5 3 3 H H H T 7 88 11 96 A H H 7 79 15 6 16 0 15 0 3 i b 19 16 9 8 8 7 7 6 4 3 H H H T 7 89 10 97 F H H 7 80 16 7 74 0 37 0 5 e b 27 22 12 9 8 6 4 3 2 1 H H H T 7 89 10 98 I H H 6 74 18 7 72 0 42 0 6 e b 32 25 13 10 7 5 4 2 1 1 H H H T 7 89 10 99 S H H 7 77 16 4 7 0 5 0 4 b b 24 19 11 10 9 7 6 4 3 2 H H H T 7 88 10 100 W H H 8 85 10 3 76 0 33 0 5 i b 29 24 14 11 8 6 4 2 2 1 H H H T 7 86 13 101 M H H 9 95 1 3 25 0 13 0 4 i b 22 17 9 8 7 7 6 5 4 3 H H H T 6 83 16 102 L H H 9 95 1 3 53 0 32 0 4 i b 25 21 13 10 8 6 4 3 2 2 H H H T 5 76 23 103 R H H 9 96 2 3 9 62 3 25 0 b i 8 9 9 9 10 10 9 7 4 3 H H L i 2 63 36 104 E H H 9 96 1 3 9 0 4 0 0 b b 10 9 6 6 7 8 10 10 7 5 H H L i 0 51 48 105 V H H 9 97 1 2 9 0 6 0 0 b b 12 11 10 10 10 9 7 5 3 2 H L L i 1 43 56 106 E H H 9 98 1 1 0 69 0 36 2 b e 5 5 5 7 9 11 14 13 9 6 H L L i 3 33 65 107 I H H 9 97 1 2 0 0 0 0 0 b b 11 10 7 8 8 8 8 7 5 3 H L L i 4 28 71 108 S H H 9 97 1 2 0 0 0 0 6 b b 29 22 10 8 7 6 5 4 3 2 H L L i 4 28 71 109 R H H 9 95 1 4 28 89 11 36 1 i e 6 6 7 8 9 10 11 10 6 4 H L L i 4 25 74 110 K H H 9 90 1 10 1 100 0 49 1 b e 5 5 5 5 7 8 11 12 10 8 H L L i 4 25 74 111 L H L 2 44 2 55 1 0 0 0 3 b b 19 16 10 9 7 6 5 4 3 2 H L L i 5 24 75 112 G L L 5 29 1 70 4 0 4 0 1 b b 13 11 8 7 7 7 7 7 6 5 L L L i 4 25 73 113 I L L 7 14 1 84 11 0 6 0 3 b b 19 16 10 9 7 6 5 4 3 2 L L L i 4 29 70 114 G L L 5 23 4 69 16 0 19 0 1 i b 13 11 8 7 7 8 8 8 6 5 L L L i 2 39 60 115 W L H 0 44 9 43 114 56 50 25 0 e i 6 6 7 9 10 10 10 9 6 5 L H L i 0 51 48 116 H H H 3 54 11 30 34 0 18 0 2 i b 19 16 11 10 9 7 6 4 2 2 H H L i 3 69 30 117 V H H 6 69 8 18 7 0 4 0 5 b b 32 26 16 12 9 6 4 2 1 1 H H H T 6 81 18 118 P H H 9 87 6 6 1 0 0 0 5 b b 25 20 9 8 8 7 7 6 4 2 H H H T 7 85 14 119 L H H 9 95 2 3 116 0 70 0 4 e b 22 18 11 9 7 6 5 4 2 2 H H H T 7 87 12 120 A H H 9 96 1 3 11 0 10 0 8 i b 36 28 12 9 7 5 4 3 2 1 H H H T 7 88 11 121 F H H 9 96 1 3 54 0 27 0 7 i b 35 28 15 11 8 5 3 2 1 1 H H H T 7 89 10 122 C H H 9 97 1 2 54 0 40 0 4 e b 22 18 9 8 8 7 7 6 4 3 H H H T 8 90 9 123 V H H 9 98 0 1 23 0 16 0 4 i b 23 18 9 8 8 7 7 6 4 2 H H H T 8 90 9 124 P H H 9 97 0 2 50 0 36 0 8 e b 37 28 12 9 7 5 4 3 2 1 H H H T 7 89 10 125 I H H 9 97 0 2 15 0 8 0 8 b b 38 30 15 10 7 5 3 2 1 1 H H H T 7 88 11 126 F H H 9 97 0 2 83 0 42 0 6 e b 30 24 12 9 7 6 5 3 2 2 H H H T 7 87 12 127 M H H 9 96 2 2 23 0 12 0 7 i b 35 26 11 8 7 5 4 4 2 2 H H H T 7 88 11 128 F H H 9 92 1 7 28 0 14 0 5 i b 30 25 14 11 8 6 4 3 1 1 H H H T 7 88 11 129 C H H 9 92 1 7 19 0 14 0 6 i b 33 26 13 9 7 6 4 3 2 1 H H H T 7 87 12 130 V H H 6 73 9 18 3 0 2 0 5 b b 28 22 11 9 8 7 6 4 2 1 H H H T 7 87 12 131 L H H 4 62 14 23 33 0 20 0 7 i b 37 29 15 10 7 5 3 2 1 1 H H H T 7 87 12 132 Q H H 4 58 19 16 0 0 0 0 2 b b 15 13 9 8 8 9 8 7 5 3 H H H T 7 88 11 133 V L H 3 50 30 15 30 0 21 0 4 i b 26 21 12 9 8 6 4 3 2 1 L H H T 7 88 11 134 F H H 1 38 32 25 89 0 45 0 8 e b 37 29 14 10 7 5 3 2 1 1 H H H T 7 87 12 135 R H H 1 34 29 30 3 0 1 0 2 b b 20 18 14 12 11 9 6 3 2 1 H H H T 7 88 11 136 P H E 2 27 46 22 0 0 0 0 6 b b 30 23 10 8 7 6 6 4 3 2 H H H T 7 87 12 137 L H E 4 23 55 20 85 0 51 0 5 e b 28 23 13 10 8 6 4 3 1 1 H H H T 7 87 12 138 L H E 2 20 46 31 81 0 49 0 6 e b 33 27 15 11 8 6 4 2 1 1 H H H T 7 86 13 139 L H E 3 16 52 29 17 0 10 0 6 i b 29 23 12 9 8 6 4 3 2 1 H H H T 6 84 15 140 G L E 2 10 50 38 36 0 42 0 2 e b 18 15 10 9 8 6 5 5 4 4 L H L o 6 80 19 141 S L L 2 13 36 49 7 0 5 0 1 b b 14 12 9 9 8 8 7 6 4 3 L H L o 5 77 22 142 W H L 3 24 25 49 51 0 22 0 2 i b 20 18 14 11 9 7 5 3 2 2 H H L o 4 72 27 143 G H L 3 28 16 53 7 0 8 0 2 b b 16 14 9 8 7 7 7 7 5 4 H H L o 3 65 34 144 H H L 2 40 9 54 14 90 7 49 1 b e 3 4 5 7 9 11 13 13 10 8 H H L o 1 55 44 145 A L L 3 30 13 54 0 0 0 0 5 b b 26 20 9 8 6 5 5 5 4 4 L L L o 0 47 52 146 F L L 5 20 14 64 31 0 15 0 1 i b 19 17 13 12 11 8 5 3 1 1 L L L o 0 48 51 147 P L L 4 21 15 59 0 0 0 0 4 b b 23 18 9 8 7 7 6 6 4 3 L L L o 0 49 50 148 Y E L 6 16 12 68 40 0 18 0 0 i b 11 11 10 9 9 8 7 5 3 3 E H L o 0 52 47 149 G E L 3 20 23 51 15 0 17 0 6 i b 29 23 11 9 7 6 5 4 3 3 E H L o 1 55 43 150 I L H 1 41 22 32 96 0 56 0 7 e b 35 29 16 12 8 5 3 1 1 1 L H L o 2 63 36 151 L L H 2 45 31 24 23 0 14 0 5 i b 28 23 14 11 9 6 4 2 1 1 L H L o 2 64 35 152 S H H 2 50 31 17 0 0 0 0 3 b b 19 15 9 9 8 8 8 7 4 3 H H L o 1 58 41 153 H H H 4 56 22 23 71 0 38 0 2 e b 18 16 11 11 10 8 6 4 2 2 H L L o 1 44 55 154 L H H 2 43 26 31 35 0 21 0 5 i b 31 26 18 12 8 5 3 2 1 1 H L L o 2 38 61 155 D H L 1 30 30 38 0 58 0 36 0 b e 7 7 8 8 9 10 10 8 6 5 H L L o 3 33 66 156 W H L 1 32 29 38 8 0 3 0 4 b b 24 20 13 10 8 6 4 3 2 2 H L L o 5 23 76 157 V H E 1 31 34 32 61 0 42 0 3 e b 22 18 10 9 8 7 7 5 3 2 H L L o 6 18 81 158 N H L 2 42 24 30 8 0 5 0 0 b b 11 10 8 8 8 9 8 7 5 4 H L L o 6 19 80 159 N H L 2 49 16 32 0 0 0 0 1 b b 12 10 8 7 7 8 8 8 6 5 H L L o 5 23 76 160 F H L 1 34 19 41 8 0 4 0 2 b b 19 16 11 10 9 7 6 4 2 2 H L L o 4 25 74 161 G H E 1 28 36 31 10 0 11 0 2 i b 17 14 8 8 8 8 8 7 5 4 H L L o 5 21 78 162 Y H E 2 29 42 26 27 0 12 0 1 i b 13 12 10 10 9 8 6 5 3 3 H L L o 5 21 78 163 Q L E 2 20 47 29 15 71 7 36 0 b e 7 7 7 8 9 10 10 9 6 4 L L L o 6 19 80 164 Y L L 3 23 25 47 0 0 0 0 2 b b 19 17 13 12 10 8 5 3 2 2 L L L o 4 26 73 165 L L L 3 16 27 54 7 0 4 0 3 b b 18 15 9 8 7 7 7 6 4 4 L L L o 3 31 68 166 N L L 3 12 28 55 2 0 1 0 0 b b 13 13 11 11 10 9 7 5 3 2 L L L o 2 36 63 167 W H L 1 11 39 46 39 0 17 0 3 i b 23 20 13 10 8 6 4 3 2 1 H L L o 3 34 65 168 H H E 1 12 47 42 52 0 28 0 1 i b 13 11 9 9 9 8 7 6 4 3 H L L o 3 31 68 169 Y H L 4 7 30 61 0 0 0 0 1 b b 16 15 13 12 10 7 5 3 2 2 H L L o 2 39 60 170 N L L 9 4 6 88 1 0 0 0 3 b b 23 20 14 12 10 8 5 3 1 1 L H L o 1 55 44 171 P H H 1 52 3 46 32 0 23 0 3 i b 21 17 10 9 8 7 5 4 3 2 H H L o 3 68 31 172 G H H 5 71 6 23 14 0 16 0 1 i b 13 11 7 6 6 6 6 6 6 6 H H L o 5 76 23 173 H H H 6 76 6 19 53 0 28 0 1 i b 15 14 11 11 10 9 7 5 3 2 H H H T 6 80 19 174 M H H 7 80 8 14 46 0 24 0 5 i b 29 23 13 10 8 6 5 3 2 1 H H H T 6 82 17 175 S H H 6 73 14 14 43 0 33 0 3 i b 22 18 12 9 8 6 5 4 2 2 H H H T 7 86 13 176 S H H 5 63 19 16 19 0 14 0 7 i b 32 25 11 8 7 6 5 4 3 2 H H H T 7 87 12 177 V H H 6 69 17 14 36 0 25 0 9 i b 43 33 15 10 7 5 3 2 1 0 H H H T 7 89 10 178 S H H 8 84 8 7 68 0 52 0 5 e b 27 21 9 8 8 8 8 7 4 2 H H H T 7 89 10 179 F H H 9 95 2 3 38 0 19 0 7 i b 34 27 14 10 8 6 4 3 1 1 H H H T 7 88 11 180 L H H 9 95 2 3 28 0 17 0 8 i b 37 29 14 10 7 5 3 2 1 1 H H H T 7 87 12 181 F H H 9 96 1 3 138 0 70 0 5 e b 28 23 15 11 9 6 4 2 1 1 H H H T 7 88 11 182 V H H 9 95 1 4 60 0 42 0 2 e b 16 13 9 8 8 8 8 7 5 4 H H H T 7 88 11 183 N H H 9 96 1 2 1 0 0 0 2 b b 17 14 9 8 8 8 8 7 5 3 H H H T 7 88 11 184 A H H 9 98 0 1 13 0 12 0 5 i b 26 20 11 9 8 7 6 4 3 2 H H H T 7 88 11 185 M H H 9 98 0 1 116 0 61 0 7 e b 35 27 13 9 7 5 3 2 1 1 H H H T 7 87 12 186 A H H 9 98 1 1 13 0 12 0 5 i b 27 21 12 9 8 7 5 4 2 1 H H H T 7 87 12 187 L H H 9 97 1 2 5 0 3 0 9 b b 43 32 12 9 6 4 3 2 1 1 H H H T 7 89 10 188 G H H 9 96 1 3 1 0 1 0 5 b b 28 21 9 8 7 6 6 5 3 2 H H H T 7 89 10 189 L H H 9 90 1 9 50 0 30 0 4 i b 26 21 12 10 8 6 4 3 2 2 H H H T 7 89 10 190 H H H 4 71 0 34 11 0 5 0 1 b b 15 14 11 10 9 8 6 5 3 2 H H H T 7 89 10 191 G H H 2 61 0 46 0 0 0 0 5 b b 27 21 10 8 7 6 5 5 4 3 H H H T 7 88 11 192 G H H 2 58 1 42 0 0 0 0 4 b b 24 19 9 8 7 7 6 6 4 3 H H H T 7 86 13 193 L H H 7 79 9 8 9 0 5 0 4 b b 24 19 10 8 8 7 6 5 3 2 H H L i 6 83 16 194 I H H 5 69 24 9 2 0 1 0 7 b b 35 27 13 10 8 6 4 2 1 1 H H L i 5 77 22 195 L H H 5 71 26 5 2 0 1 0 6 b b 34 27 15 11 8 5 4 2 1 1 H H L i 3 68 31 196 S H H 1 49 44 6 2 0 1 0 6 b b 28 21 9 8 7 6 6 5 4 3 H H L i 0 54 45 197 V H E 1 39 43 11 0 0 0 0 7 b b 33 25 11 8 7 5 4 3 2 2 H L L i 3 34 64 198 A H E 1 34 41 18 2 0 1 0 1 b b 12 11 7 7 8 8 8 8 6 4 H L L i 6 18 80 199 N L L 3 15 25 53 30 56 19 36 1 i e 3 4 6 7 9 12 13 13 10 8 L L L i 7 10 89 200 P L L 6 8 14 72 12 66 8 49 1 b e 3 4 5 6 7 9 11 13 13 12 L L L i 8 6 93 201 G L L 8 7 3 85 38 41 45 49 2 e e 2 3 4 6 8 10 12 15 14 14 L L L i 9 4 94 202 D L L 9 6 4 86 162 79 99 49 4 e e 1 2 3 4 7 11 17 22 21 20 L L L i 9 3 96 203 G L L 9 6 5 87 36 41 42 49 1 e e 3 3 5 6 8 10 12 14 13 13 L L L i 9 2 97 204 D L L 8 8 10 82 61 79 37 49 3 e e 1 2 3 5 7 11 16 20 19 19 L L L i 9 1 98 205 K L L 6 11 16 71 100 100 48 49 3 e e 1 2 3 5 8 12 18 21 18 15 L L L i 9 1 98 206 V L L 7 9 14 75 3 0 2 0 0 b b 8 8 7 8 8 8 8 8 6 6 L L L i 9 0 99 207 K L L 7 14 7 76 28 73 13 36 2 i e 2 3 4 7 10 14 17 17 12 8 L L L i 9 0 99 208 T L L 5 20 5 69 8 0 5 0 0 b b 10 9 6 7 7 8 9 9 7 6 L L L i 9 0 99 209 A H H 2 50 5 35 3 51 2 49 0 b e 5 5 6 7 8 10 11 11 9 8 H L L i 9 0 99 210 E H H 6 77 3 19 7 95 3 49 1 b e 2 3 4 6 7 10 12 14 12 10 H L L i 9 0 99 211 H H H 9 89 2 8 19 66 10 36 0 i e 6 6 8 9 10 11 12 10 7 5 H L L i 9 0 99 212 E H H 9 90 2 8 16 0 8 0 0 b b 9 8 7 7 8 8 9 9 7 5 H L L i 9 1 98 213 N H H 7 84 1 15 8 0 5 0 0 b b 10 9 7 8 8 9 9 9 7 5 H L L i 9 1 98 214 Q H H 9 88 3 7 2 71 1 36 0 b e 8 8 8 8 9 10 10 8 5 3 H L L i 9 1 98 215 Y H H 7 76 10 12 2 0 0 0 4 b b 24 20 12 10 8 6 5 3 2 1 H L L i 9 1 98 216 F H H 5 68 11 21 33 0 16 0 4 i b 27 22 14 11 8 6 4 2 1 1 H L L i 9 2 97 217 R H H 5 68 14 19 9 39 3 16 0 b i 10 10 9 10 10 10 9 6 4 3 H L L i 9 3 96 218 D H H 6 71 16 13 0 40 0 25 0 b i 10 9 8 8 9 10 10 8 5 3 H L L i 8 5 94 219 V H H 4 56 21 22 4 0 2 0 2 b b 19 16 11 10 9 8 6 5 3 2 H L L i 8 7 92 220 V H H 1 39 26 32 86 0 60 0 3 e b 22 18 11 8 7 6 5 4 3 2 H L L i 8 8 91 221 G L L 2 24 27 45 8 0 9 0 4 i b 22 17 9 7 7 7 7 6 4 3 L L L i 6 16 83 222 Y L L 1 18 37 41 53 0 23 0 2 i b 19 17 13 12 10 7 5 3 2 1 L L L i 2 38 61 223 S L L 3 19 29 50 10 0 7 0 0 b b 11 10 8 8 8 8 9 7 5 4 L H L i 0 53 46 224 I L L 3 26 27 47 40 0 23 0 4 i b 24 19 10 8 7 6 5 4 3 2 L H L i 3 67 32 225 G L L 4 28 8 62 10 0 11 0 2 i b 18 14 8 8 7 8 8 7 6 4 L H L i 4 73 25 226 A H H 4 64 9 27 6 0 5 0 1 b b 14 12 9 9 9 9 8 7 5 4 H H L i 5 78 21 227 L H H 7 76 11 16 6 0 3 0 0 b b 11 10 8 8 8 8 8 7 4 4 H H L i 6 81 18 228 S H H 7 81 7 13 10 0 7 0 4 b b 24 19 11 9 8 6 5 4 3 3 H H L i 6 84 15 229 I H H 8 86 5 11 31 0 18 0 6 i b 32 26 13 10 7 5 3 2 1 1 H H L i 7 85 14 230 H H H 9 89 3 8 0 0 0 0 2 b b 18 16 11 10 9 8 7 4 2 1 H H L i 6 84 15 231 R H H 9 93 2 5 30 0 12 0 1 i b 14 13 12 11 11 9 8 5 3 2 H H H T 6 84 15 232 L H H 9 93 2 7 56 0 34 0 6 i b 32 25 14 10 8 5 4 3 2 1 H H H T 7 85 14 233 G H H 9 95 2 3 1 0 1 0 8 b b 38 29 12 9 7 6 5 4 2 2 H H H T 7 87 13 234 L H H 9 96 2 3 30 0 18 0 5 i b 27 22 12 10 8 7 5 3 2 1 H H H T 7 87 12 235 F H H 9 95 2 3 116 0 58 0 6 e b 31 25 14 10 8 6 4 3 1 1 H H H T 7 87 12 236 L H H 9 96 1 3 17 0 10 0 7 i b 36 29 15 11 8 5 3 2 1 1 H H H T 7 87 12 237 A H H 9 98 0 1 7 0 6 0 9 b b 39 29 11 8 6 5 4 3 2 2 H H H T 7 88 11 238 S H H 9 97 1 3 17 0 13 0 4 i b 24 20 11 9 8 6 5 4 2 2 H H H T 7 88 11 239 N H H 9 95 1 4 24 0 15 0 2 i b 17 14 8 8 8 8 8 7 5 3 H H H T 7 88 11 240 I H H 9 95 2 3 10 0 5 0 3 b b 21 16 8 7 7 7 7 7 5 3 H H H T 7 88 11 241 F H H 8 89 2 10 65 0 32 0 1 i b 12 10 7 6 7 7 8 8 6 5 H H H T 7 88 11 242 L H H 8 87 3 10 67 0 40 0 4 e b 26 22 14 11 8 6 4 2 1 1 H H H T 7 88 11 243 T H H 6 72 6 21 32 0 22 0 0 i b 12 11 8 7 8 9 9 8 6 4 H H H T 7 89 10 244 G H H 1 43 13 38 6 0 7 0 3 b b 19 15 8 7 6 6 7 7 5 4 H H H T 8 90 9 245 A H L 2 21 28 42 7 0 6 0 5 b b 28 22 11 9 7 6 4 3 3 2 H H H T 8 90 9 246 F H E 6 9 71 15 158 0 80 0 7 e b 33 26 12 9 7 6 4 3 2 1 H H H T 8 91 8 247 G H E 8 6 81 10 3 0 3 0 6 b b 33 25 12 10 8 6 5 4 2 1 H H H T 8 91 8 248 T H E 8 8 84 7 13 0 9 0 7 i b 35 27 12 9 7 5 4 3 1 1 H H H T 8 91 8 249 I H E 8 8 81 7 38 0 22 0 6 i b 31 24 12 9 7 5 4 2 2 1 H H H T 8 90 9 250 A L E 8 6 80 9 9 0 8 0 5 b b 27 22 13 9 7 6 4 3 2 2 L H H T 7 88 11 251 S L E 7 4 80 17 0 0 0 0 2 b b 17 13 7 7 6 7 8 8 6 6 L H L o 6 84 15 252 G L L 3 3 37 58 1 0 1 0 3 b b 20 17 11 9 8 6 5 4 3 3 L H L o 5 79 20 253 P L L 2 3 40 57 3 48 2 36 0 b e 6 7 7 8 9 10 10 9 7 5 L H L o 4 71 28 254 F L L 4 8 27 59 79 0 40 0 0 e b 10 10 9 9 9 8 7 5 4 3 L H L o 2 61 38 255 W L L 4 19 13 57 19 0 8 0 0 b b 10 10 9 10 10 9 7 6 4 3 L L L o 0 47 51 256 T L L 5 23 5 72 21 51 14 36 0 i e 6 6 7 7 8 9 9 9 7 6 L L L o 4 29 70 257 R L L 6 24 1 79 88 200 35 81 1 i e 2 2 4 6 8 11 14 17 18 19 L L L o 5 20 79 258 G L L 9 6 3 90 8 41 9 49 1 i e 4 5 6 7 8 9 11 13 12 12 L L L o 6 16 83 259 W H L 7 16 4 79 1 20 0 9 0 b i 10 11 12 13 12 10 6 4 2 2 H L L o 7 12 87 260 P H L 0 51 2 51 0 48 0 36 0 b e 6 6 6 7 8 9 10 10 7 6 H L L o 8 7 92 261 E H H 6 76 2 22 41 69 21 36 1 i e 4 4 6 7 9 11 11 11 8 7 H L L o 8 5 94 262 W H H 8 87 3 11 28 0 12 0 4 i b 27 23 16 13 10 7 4 2 1 1 H L L o 8 6 93 263 W L H 9 90 4 8 32 0 14 0 4 i b 27 23 15 12 9 6 3 2 1 1 L L L o 8 7 92 264 G H H 9 90 3 7 8 13 9 16 0 i i 9 9 9 9 9 9 8 7 5 4 H L L o 8 8 92 265 W H H 8 86 4 11 111 0 48 0 3 e b 24 21 14 11 9 6 4 2 2 1 H L L o 8 5 94 266 W H H 9 90 3 7 59 0 25 0 3 i b 20 17 11 10 8 7 5 4 2 2 H L L o 9 3 96 267 L H H 7 80 6 16 1 0 0 0 1 b b 13 12 10 9 8 7 6 5 4 3 H L L o 9 4 95 268 D L H 5 68 7 27 51 58 31 36 1 i e 4 4 5 7 9 11 13 12 9 7 L L L o 9 3 96 269 I L L 4 26 6 66 63 0 37 0 1 e b 14 13 11 10 10 8 6 4 2 2 L L L o 9 4 95 270 P L L 7 13 3 82 115 48 84 36 0 e e 7 7 7 7 8 9 9 8 6 5 L L L o 9 4 96 271 F L L 8 8 5 84 171 0 86 0 0 e b 9 9 9 9 8 7 6 4 3 3 L L L o 8 5 94 272 W L L 8 6 5 86 19 20 8 9 0 b i 8 8 8 9 8 7 5 4 4 4 L L L o 8 8 91 273 S L L 9 2 1 96 26 105 20 81 3 i e 3 3 4 5 5 6 7 9 15 19 L L L o 8 6 93 profnet-1.0.22/src-phd/exa/1prcL_phd.html0000644015075101507510000045114512021362702017373 0ustar lkajanlkajan

PHD predictions for 1prcL

Different levels of data:
  1. PHD brief
  2. PHD normal
  3. PHD detail








AA : amino acid sequence
OBS_sec: observed secondary structure: H=helix, E=extended (sheet), blank=other (loop)
PHD_sec: PHD predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop)
PHD = PHD: Profile network prediction HeiDelberg
Rel_sec: reliability index for PHDsec prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'
SUB_sec: subset of the PHDsec prediction, for all residues with an expected average accuracy > 82% (tables in header)
NOTE: for this subset the following symbols are used:
L: is loop (for which above ' ' is used)
.: means that no prediction is made for this residue, as the reliability is: Rel < 5
pH_sec: 'probability' for assigning helix (1=high, 0=low)
pE_sec: 'probability' for assigning strand (1=high, 0=low)
pL_sec: 'probability' for assigning neither helix, nor strand (1=high, 0=low)
O_3_acc: observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
P_3_acc: PHD predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
Rel_acc: reliability index for PHDacc prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'
SUB_acc: subset of the PHDacc prediction, for all residues with an expected average correlation > 0.69 (tables in header)
NOTE: for this subset the following symbols are used:
I: is intermediate (for which above ' ' is used)
.: means that no prediction is made for this residue, as the reliability is: Rel < 4
OBS_acc: observerd relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%).
PHD_acc: PHD predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%).
PHD_htm: PHD predicted membrane helix: M=helical transmembrane region, blank=non-membrane
PHD = PHD: Profile network prediction HeiDelberg
Rel_htm: reliability index for PHDhtm prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'
SUB_htm: subset of the PHDhtm prediction, for all residues with an expected average accuracy > 98% (tables in header)
NOTE: for this subset the following symbols are used:
N: is non-membrane region (for which above ' ' is used)
.: means that no prediction is made for this residue, as the reliability is: Rel < 5
PiMohtm: PHD prediction of membrane topology: T=helical transmembrane region, i=inside of membrane, o=outside of membrane
pT_htm: 'probability' for assigning transmembrane helix
pN_htm: 'probability' for assigning globular region



PHD results (brief)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10...,....11...,....12...,....13...,....14...,....15...,....16...,....17...,....18...,....19...,....20...,....21...,....22...,....23...,....24...,....25...,....26...,....27...,....28
AA         ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS
OBS_sec          HHH         HHH   EE  EE  HHHHHHHHHHHHHHHHHHHHH           EE    HHH      HHH HHHHHHHHHHHHHHHHHHHHHHHHHHHH    HHHHHHHHHHHHHHHHH HHHHHH  HHH   EE  HHHHHHHHHHH    HHH HHHHHHHHHHHHHHHHHHHHHHHHHHHH          HHHHHHHHHHHH     HHHHHHHHHHHHHHHHHHHHHHHH         HHHH HHHH      
PHD_sec                  EEE           EEEEEHHHHHHHHHHHHHHHHHHHHHH     EEEEEE                  HHHHHHHHHHHHHHHHHHHHHHHHHH    HHHHHHHHHHHHHHHHHHHHHEEEEE         HHHHH  E   EEE    E  HHHHHHHHHHHHHHHHHHHHHHHHHHEE          HHHHHHHHHHHH     HHHHHHHHHHHHHHHHHHH EEEEEE         HHHHHHHH     
Rel_sec    **        ***     *      ** ****   *************** **  ****  **** ************    *  ************************* ***  **************               * *                     * ******************   ***    ********* *********        *****************  ******    **** ******** ****

O_3_acc    e b bbebbbb bbb  e ee b bee eb be be bee eee ee eeebbeeee eeee    bbb  ee eee eeeebbbb ebbeb    eeb   bbbbbb bbbb e bbe  e ebe   b b ebbee eb bbb b  e be bbebbb  bbbb  bb       e  eeb e bb bbbbbbbbb beeeeeb bbb bbbb bbbe  b  bbb b  b e b  b e bbeb  bbbbeb   bb    e b eeeb 
P_3_acc    bbbebeeebeeebbbbbbbebbebebbbbbbbbbbbbbbbbbbbbbbbbbbbbeeeeebe bbbbbe eeeebbbbbbbbeebbbbbbbbbbbbbbbbbbbb bbebbeebbbb bbbbbbbbbbbbbbbbbbbbbbbbbbbbebbbbbbbbbbebbbbbbbebbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbeeeeeeebebeeebbebb  bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbebbeee eebb bbbebeb e
Rel_acc        *                    *    ***     ***********              *         **            **** * * ******     *        *************** ** ****     * * ***  * *                 * ******  ****** *******    *            **    *  *   **  *******   *  ******           **          

PHD_htm                             MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM                       MMMMMMMMMMMMMMMMMMMMM          MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM   MMMMM                 MMMMMMMMMMMMMMMMMMMMMMMMMMM                          MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM                   
Rel_htm    *          **             *  ***    ************       **    ****  ***       *       ************ ************  *    ************                                        *   *   ************   *       **** **   *****           ****************    *****      **  ******  ****

PiMohtm    iiiiiiiiiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMMMoooooooooooooooooooooooooooooooMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMoooooooooooooooooooooooooooooooooMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMooooooooooooooooooooooo





PHD results (normal)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10...,....11...,....12...,....13...,....14...,....15...,....16...,....17...,....18...,....19...,....20...,....21...,....22...,....23...,....24...,....25...,....26...,....27...,....28
AA         ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS
OBS_sec          HHH         HHH   EE  EE  HHHHHHHHHHHHHHHHHHHHH           EE    HHH      HHH HHHHHHHHHHHHHHHHHHHHHHHHHHHH    HHHHHHHHHHHHHHHHH HHHHHH  HHH   EE  HHHHHHHHHHH    HHH HHHHHHHHHHHHHHHHHHHHHHHHHHHH          HHHHHHHHHHHH     HHHHHHHHHHHHHHHHHHHHHHHH         HHHH HHHH      
PHD_sec                  EEE           EEEEEHHHHHHHHHHHHHHHHHHHHHH     EEEEEE                  HHHHHHHHHHHHHHHHHHHHHHHHHH    HHHHHHHHHHHHHHHHHHHHHEEEEE         HHHHH  E   EEE    E  HHHHHHHHHHHHHHHHHHHHHHHHHHEE          HHHHHHHHHHHH     HHHHHHHHHHHHHHHHHHH EEEEEE         HHHHHHHH     
Rel_sec    954323423357832422541332058368873236899999999999654664178654478874699955565568312063478889877887767899999999992575036999999999999644311242322332354631224211122112233311491567656899999999999422755111368998677526997975564121334477899999999999886126888873244569706899897547889
SUB_sec    LL........LLL.....L......LL.EEEE...HHHHHHHHHHHHHHH.HH..LLLL..EEEE.LLLLLLLLLLLL....L..HHHHHHHHHHHHHHHHHHHHHHHHH.LLL..HHHHHHHHHHHHHH...............L.L.....................L.HHHHHHHHHHHHHHHHHH...HHH....LLLLLLLLL.HHHHHHHHH........HHHHHHHHHHHHHHHHH..EEEEEE....LLLL.HHHHHHHH.LLLL

O_3_acc    e b bbebbbb bbb  e ee b bee eb be be bee eee ee eeebbeeee eeee    bbb  ee eee eeeebbbb ebbeb    eeb   bbbbbb bbbb e bbe  e ebe   b b ebbee eb bbb b  e be bbebbb  bbbb  bb       e  eeb e bb bbbbbbbbb beeeeeb bbb bbbb bbbe  b  bbb b  b e b  b e bbeb  bbbbeb   bb    e b eeeb 
P_3_acc    bbbebeeebeeebbbbbbbebbebebbbbbbbbbbbbbbbbbbbbbbbbbbbbeeeeebe bbbbbe eeeebbbbbbbbeebbbbbbbbbbbbbbbbbbbb bbebbeebbbb bbbbbbbbbbbbbbbbbbbbbbbbbbbbebbbbbbbbbbebbbbbbbebbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbeeeeeeebebeeebbebb  bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbebbeee eebb bbbebeb e
Rel_acc    011141110201111031311000053333844233336584465547732010010110001612100203044023231313233775625243564544000206113131025548744886756572482656621221514067532504301221023031133115379578522575954154476671112413302001000044002342042104621685679423140357676523000011001440331110003
SUB_acc    ....b....................b....bbb.....bbbbbbbbbbb..............b.........bb............bbbb.b.b.bbbbbb.....b........bbbbbbbbbbbbbbb.bb.bbbb.....b.b.bbb..b.b.................b.bbbbbb..bbbbbb.bbbbbbb....e............bb....b..b...bb..bbbbbbb...b..bbbbbb...........bb..........

PHD_htm                             MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM                       MMMMMMMMMMMMMMMMMMMMM          MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM   MMMMM                 MMMMMMMMMMMMMMMMMMMMMMMMMMM                          MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM                   
Rel_htm    954323423357832422541332058368873236899999999999654664178654478874699955565568312063478889877887767899999999992575036999999999999644311242322332354631224211122112233311491567656899999999999422755111368998677526997975564121334477899999999999886126888873244569706899897547889
SUB_htm    N..........NN.............M..MMM....MMMMMMMMMMMM.......MM....NNNN..NNN.......N.......MMMMMMMMMMMM.MMMMMMNNNNNN..N....MMMMMMMMMMMM........................................M...M...MMMMMMMMMMMM...M.......NNNN.NN...NNNNN...........MMMMMMMMMMMMMMMM....MMMMM......NN..NNNNNN..NNNN

PiMohtm    iiiiiiiiiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMMMoooooooooooooooooooooooooooooooMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMoooooooooooooooooooooooooooooooooMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMooooooooooooooooooooooo





PHD results (detail)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10...,....11...,....12...,....13...,....14...,....15...,....16...,....17...,....18...,....19...,....20...,....21...,....22...,....23...,....24...,....25...,....26...,....27...,....28
AA         ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS
P_3_acc    bbbebeeebeeebbbbbbbebbebebbbbbbbbbbbbbbbbbbbbbbbbbbbbeeeeebe bbbbbe eeeebbbbbbbbeebbbbbbbbbbbbbbbbbbbb bbebbeebbbb bbbbbbbbbbbbbbbbbbbbbbbbbbbbebbbbbbbbbbebbbbbbbebbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbeeeeeeebebeeebbebb  bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbebbeee eebb bbbebeb e
OBS_acc                                                           .                   .                                                                                                                            .                                                                   ..    100% OBS_acc   
OBS_acc                       .                 .   .  .    .     . .            .    .  .          .                           .                                                             .                    .                                           .                       ..     81% OBS_acc   
OBS_acc                      ..    .  .         ..  .  .    .   . . . .          .    .  ..         .                       .   .                 ..           .                           .  .   .                .                 .              .          .                       ..     64% OBS_acc   
OBS_acc   .     .          . ..    .. .   .  .  .. ... .. ...  .... ....         .. ... ....     .  .     ..                .   .  . . .       .  .. .         .  .   .                    .  ..  .               .....              .              .      .   .       .          .   ...     49% OBS_acc   
OBS_acc   .     .         .. ... . .. .   .  .  ...... ......  .........  .      ...... ....     .  .  .  .. . .            .   . .. . .       .  .. .         .  .   .          .    . . ..  ..  .   .           .....              .           .  .     ..   .       .  .       .. ....     36% OBS_acc   
OBS_acc   .. .  .         .. ... . ....   .  .  ...... ......  ......... ..      ...... ....     .  . ..  .. . .           ...  . .... .    . ..  .. . .     ...  ..  .         ..  ..... ......  .   .         . .....          .   . . .    .  . ..     ...  .  .    .  .   .   .. .... .   25% OBS_acc   
OBS_acc   .. .  .    .   ....... . .... . .. .. .............  .............   .............    ..  . ...... ...      .    ...  ...... .... . ..  .... .   . .... ..  .   ..    ..  ............ ...  .         . ..... .   .    .   ... ..   . .. ... .. ...  . ..    . ...  ...... .... .   16% OBS_acc   
OBS_acc   .. .  .  . .   ....... . .... . ..... ............................   ............. .. ................ ..   .  ...... ........... . ..  ........ . .... ..  .. .... . ..  ............ ...  ..  .     ....... ..  ...  .   ....... .. .. ............. ...   .....  ...... ......    9% OBS_acc   
OBS_acc   ..... .. . ............. ...... ...................................  ....................................   .  ...... ............. ... ........ . .... .. ... .... ....  ............ .......  .... ................. .. ........... .................... .......  ...... ......    4% OBS_acc   
          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
PHD_acc                                                                                                                                                                                                                                                                   .               .  100% PHD_acc   
PHD_acc                                                                                                                                                                                                                                                                   .               .   81% PHD_acc   
PHD_acc        . .   .                                         . ...        . ....        ..                           .                                 .                                                       ......   ..                                              ..              .   64% PHD_acc   
PHD_acc      . ... ...       .  . .                            ..... .      . ....        ..                       .  ..                                 .          .       .                                   ....... . ...  .                                      .  ... ..      . .  .   49% PHD_acc   
PHD_acc      . ... ...       .  . .                            ..... ..     . ....        ..                    .  .  ..    .                            .          .       .                                   ....... . ...  .   .                                  .  ... ..      . .  .   36% PHD_acc   
PHD_acc      . ... ...       .  . .                            ..... ..     ......        ..                    .  .  ..    .                            .          .       .                                   ....... . ...  .  ..                                  .  ... ..  .   . .  .   25% PHD_acc   
PHD_acc      . ... ...       .  . .                            ..... ..     ......        ..                    .  .  ..    .                            .          .       .                                   ....... . ...  .  ..                                  .  ......  .   . . ..   16% PHD_acc   
PHD_acc      . ... ...       .  . .                            ..... ..     ......        ..                    .  .  ..    .                            .          .       .                                   ....... . ...  .  ..                                  .  ......  .   . . ..    9% PHD_acc   
PHD_acc      . ... ...       .  . .                            ..... ..     ......        ..                    .  .  ..    .                            .          .       .                                   ....... . ...  .  ..                                  .  ......  .   . . ..    4% PHD_acc   
          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 pT_htm                                        .............                                    ..... ..................       ............                                                ............   . .               .. .               ...........                      .. .         1.0  pT_htm   
 pT_htm                                       .................                                .........................       .............                                          ... .............   ....             ......  .        ................                   ......        0.9  pT_htm   
 pT_htm                                      ...................                               .........................      .................                  ..                  ..................   .....            ..........      ..................                 ........       0.8  pT_htm   
 pT_htm                                     ....................                              ..........................     ...................                ...     .            ...................  ......           ..........      ..................                 ........       0.7  pT_htm   
 pT_htm                                   .......................                         ..  ..........................    .......................            .....   ..  .        ............................          ............     ...................   ..          .........       0.6  pT_htm   
 pT_htm                                 . .......................                        ...  ...........................   .......................      .     ..............       ............................          ............     ...................   ...         .........       0.5  pT_htm   
 pT_htm      ...                       ..........................                       .... ............................   .........................  ....    ...............      ............................          .............. ...........................         .........       0.4  pT_htm   
 pT_htm     .......      ..     .     ...........................      ..       .       .................................. .................................. .................  .  .............................        ...........................................    ...  ..........      0.3  pT_htm   
 pT_htm    .........   .............  ............................    ....      ...   ............................................................................................. ..............................    ...............................................  .... ............     0.2  pT_htm   
          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 pN_htm   .         ...             ..                            ....    ......   ...                                                                                             .                             .....                                               ..    .            ...  1.0  pN_htm   
 pN_htm   ..      .......  ..... .....                           ...... ........ .......                                  .                                  .                 .. ..                             ........                                           ....   ..          ....  0.9  pN_htm   
 pN_htm   ...   .......................                          .......................    .                            ...                         ..    ....               ......                            ..........              .                           .........         .....  0.8  pN_htm   
 pN_htm   .............................. .                       ........................   ..                           ...                       ...... .....              .......                            ..........            .....                   ...  ..........         .....  0.7  pN_htm   
 pN_htm   .................................                      .........................  ..                          ....                       ............     ...  .. ........                            ..........            .....                   ...  ...........        .....  0.6  pN_htm   
 pN_htm   ..................................                    ..............................                          .....                   ................   ..... ............                   ..      ...........          ......                  .................        .....  0.5  pN_htm   
 pN_htm   ...................................                   ...............................                         ......                 ..................  ..................                  ...     ............          ......                  .................        .....  0.4  pN_htm   
 pN_htm   ....................................                 ................................                         .......             ...........................................  .             ...    .............      .. ........                ...................      ......  0.3  pN_htm   
 pN_htm   .....................................             ....................................     .                 ........            ................................................            ... . ...............  . ...............           ......................  . .......  0.2  pN_htm   
          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
profnet-1.0.22/src-phd/.HSancillary0000644015075101507510000000406412021362704016322 0ustar lkajanlkajanDATAuxttÇ’¼€Ëmatphd.fhd.txtMATTEXTuxttÇ’¼€Ëphd.fd.fhd.txtPHD.FTEXTuxexÇ’¼€Ëcompile.pld.txtCOMPILE.PLTEXTuxttÇ’¼€ËphdParameter.ftPHDPARAM.ETETEXTuxttÇ’¼€ËDoc-code-phd.txtDOC-CODE.-PHTEXTuxttÇ’¼€ËReadMee-phd.txtREADME..CT8BIMÇ’¼€Ëlib-phd.fhd.txtLIB-PHD.Fprofnet-1.0.22/src-phd/1crn.hssp0000644015075101507510000003325612021362704015657 0ustar lkajanlkajanHSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 1.0 1991 PDBID 1crn DATE file generated on 9-Aug-98 SEQBASE RELEASE 36.0 OF EMBL/SWISS-PROT WITH 74019 SEQUENCES PARAMETER SMIN: -0.5 SMAX: 1.0 PARAMETER gap-open: 3.0 gap-elongation: 0.1 PARAMETER conservation weights: YES PARAMETER InDels in secondary structure allowed: YES PARAMETER alignments sorted according to :DISTANCE THRESHOLD according to: t(L)=(290.15 * L ** -0.562) + 5 REFERENCE Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991). CONTACT e-mail (INTERNET) Schneider@EMBL-Heidelberg.DE or Sander@EMBL-Heidelberg.DE / fax +49-6221-387306 AVAILABLE Free academic use. Commercial users must apply for license. AVAILABLE No inclusion in other databanks without permission. HEADER PLANT SEED PROTEIN COMPND CRAMBIN SOURCE ABYSSINIAN CABBAGE (CRAMBE ABYSSINICA) SEED AUTHOR W.A.HENDRICKSON,M.M.TEETER SEQLENGTH 46 NCHAIN 1 chain(s) in 1crn data set NALIGN 11 NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry NOTATION : %IDE: percentage of residue identity of the alignment NOTATION : %SIM (%WSIM): (weighted) similarity of the alignment NOTATION : IFIR/ILAS: first and last residue of the alignment in the test sequence NOTATION : JFIR/JLAS: first and last residue of the alignment in the alignend protein NOTATION : LALI: length of the alignment excluding insertions and deletions NOTATION : NGAP: number of insertions and deletions in the alignment NOTATION : LGAP: total length of all insertions and deletions NOTATION : LSEQ2: length of the entire sequence of the aligned protein NOTATION : ACCNUM: SwissProt accession number NOTATION : PROTEIN: one-line description of aligned protein NOTATION : SeqNo,PDBNo,AA,STRUCTURE,BP1,BP2,ACC: sequential and PDB residue numbers, amino acid (lower case = Cys), secondary NOTATION : structure, bridge partners, solvent exposure as in DSSP (Kabsch and Sander, Biopolymers 22, 2577-2637(1983) NOTATION : VAR: sequence variability on a scale of 0-100 as derived from the NALIGN alignments NOTATION : pair of lower case characters (AvaK) in the alignend sequence bracket a point of insertion in this sequence NOTATION : dots (....) in the alignend sequence indicate points of deletion in this sequence NOTATION : SEQUENCE PROFILE: relative frequency of an amino acid type at each position. Asx and Glx are in their NOTATION : acid/amide form in proportion to their database frequencies NOTATION : NOCC: number of aligned sequences spanning this position (including the test sequence) NOTATION : NDEL: number of sequences with a deletion in the test protein at this position NOTATION : NINS: number of sequences with an insertion in the test protein at this position NOTATION : ENTROPY: entropy measure of sequence variability at this position NOTATION : RELENT: relative entropy, i.e. entropy normalized to the range 0-100 NOTATION : WEIGHT: conservation weight ## PROTEINS : EMBL/SWISSPROT identifier and alignment statistics NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN 1 : cram_craab 1AB1 1.00 1.00 1 46 1 46 46 0 0 46 P01542 CRAMBIN. 2 : thn_pyrpu 0.53 0.60 2 46 2 47 45 1 1 47 P07504 THIONIN. 3 : thn_dencl 0.53 0.69 2 44 2 44 43 0 0 46 P01541 DENCLATOXIN B. 4 : thn3_visal 0.49 0.65 2 46 28 72 45 0 0 111 P01538 VISCOTOXIN A3 PRECURSOR. 5 : thn_pholi 0.47 0.61 2 46 2 46 45 0 0 46 P01540 LIGATOXIN A. 6 : thnb_visal 0.44 0.61 2 46 8 52 45 0 0 103 P08943 VISCOTOXIN B PRECURSOR (FRAGMENT). 7 : thn5_horvu 0.44 0.61 2 46 30 74 45 0 0 137 P09617 DG3). 8 : y4ik_rhisn 0.54 0.37 8 46 180 207 28 1 11 232 P55494 HYPOTHETICAL 26.8 KD PROTEIN Y4IK. 9 : dp87_dicdi 0.47 0.26 9 44 234 314 36 2 45 555 Q04503 PRESPORE PROTEIN DP87 PRECURSOR. 10 : thn2_visal 0.43 0.61 2 41 2 41 40 0 0 46 P32880 VISCOTOXIN A2. 11 : thn6_horvu 0.40 0.57 2 46 30 74 45 0 0 137 P09618 LEAF-SPECIFIC THIONIN PRECURSOR (CLONE BT ## ALIGNMENTS 1 - 11 SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7 1 1 T 0 0 77 1 0 T 2 2 T E -A 34 0A 21 9 22 TSSSSSS SS 3 3 C E -A 33 0A 0 9 0 CCCCCCC CC 4 4 C - 0 0 0 9 0 CCCCCCC CC 5 5 P S S+ 0 0 52 9 26 PRPPPPK PK 6 6 S S > S- 0 0 48 9 34 SNTNSNN ND 7 7 I H > S+ 0 0 123 9 24 ITTTTTT TT 8 8 V H > S+ 0 0 98 10 45 VWATTTTV TL 9 9 A H > S+ 0 0 6 11 21 AAAGAGGSAGA 10 10 R H X S+ 0 0 55 11 0 RRRRRRRRRRR 11 11 S H X S+ 0 0 63 11 39 SNNNNNNLPNN 12 12 N H X S+ 0 0 82 11 56 NCQIIICEPIC 13 13 F H X S+ 0 0 5 11 24 FYYYYYYMHYY 14 14 N H X S+ 0 0 87 11 0 NNNNNNNNNNN 15 15 V H >< S+ 0 0 99 11 42 VVIATTAPLTT 16 16 C H 3<>S+ 0 0 18 11 16 CCCCCCCNCCC 17 17 R H ><5S+ 0 0 94 11 0 RRRRRRRRRRR 18 18 L T <<5S+ 0 0 144 11 33 LLLLLLFSGFF 19 19 P T 3 5S- 0 0 107 11 42 PPPTTGAPFGA 20 20 G T < 5 + 0 0 53 11 9 GGGGGGGEGGG 21 21 T < - 0 0 37 10 32 TTTATGG.CGG 22 22 P >> - 0 0 81 10 32 PIPPSSS.PSS 23 23 E H 3> S+ 0 0 70 10 37 EsRRRRR.ERR 24 24 A H 3> S+ 0 0 63 10 35 AePPPEP.gEP 25 25 I H <> S+ 0 0 99 10 39 IIVTTRV.nVV 26 26 C H X S+ 0 0 0 10 0 CCCCCCC.CCC 27 27 A H X S+ 0 0 12 10 8 AAAAAAA.GAA 28 28 T H < S+ 0 0 120 10 41 TKAKSST.PSG 29 29 Y H < S+ 0 0 176 10 53 YKLLLLA.GLA 30 30 T H < S- 0 0 24 10 38 TCSSSSC.YSC 31 31 G S < S+ 0 0 35 10 31 GDGGGGG.IGR 32 32 C - 0 0 5 11 0 CCCCCCCCCCC 33 33 I E -A 3 0A 51 11 40 IKKKKKKITKK 34 34 I E -A 2 0A 78 11 16 IIIIIIIRIII 35 35 I - 0 0 34 11 0 IIIIIIIIIII 36 36 P S S+ 0 0 143 11 29 PSSSSSSPNSS 37 37 G S S- 0 0 41 11 24 GGGGGAGLGAG 38 38 A S S+ 0 0 80 11 41 ATTSSSPAhSP 39 39 T - 0 0 127 11 24 TTGTTTTTrTK 40 40 C - 0 0 46 11 7 CCCCCCCSCCC 41 41 P > - 0 0 53 11 8 PPPPBPPPPPP 42 42 G G > S+ 0 0 75 10 41 GSPSSSRDH S 43 43 D G 3 S+ 0 0 116 10 9 DDGDGDDDD D 44 44 Y G < S+ 0 0 66 10 3 YYYYWYYYY Y 45 45 A < 0 0 70 8 31 AP PBPPA P 46 46 N 0 0 76 8 37 NK KHKKS K ## SEQUENCE PROFILE AND ENTROPY SeqNo PDBNo V L I M F W Y G A P S T C H R K Q E N D NOCC NDEL NINS ENTROPY RELENT WEIGHT 1 1 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00 2 2 0 0 0 0 0 0 0 0 0 0 89 11 0 0 0 0 0 0 0 0 9 0 0 0.349 16 1.00 3 3 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.34 4 4 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.34 5 5 0 0 0 0 0 0 0 0 0 67 0 0 0 0 11 22 0 0 0 0 9 0 0 0.849 39 0.82 6 6 0 0 0 0 0 0 0 0 0 0 22 11 0 0 0 0 0 0 56 11 9 0 0 1.149 52 0.78 7 7 0 0 11 0 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 0 9 0 0 0.349 16 0.97 8 8 20 10 0 0 0 10 0 0 10 0 0 50 0 0 0 0 0 0 0 0 10 0 0 1.359 59 0.57 9 9 0 0 0 0 0 0 0 36 55 0 9 0 0 0 0 0 0 0 0 0 11 0 0 0.916 38 1.04 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 11 0 0 0.000 0 1.37 11 11 0 9 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 73 0 11 0 0 0.886 37 0.97 12 12 0 0 36 0 0 0 0 0 0 9 0 0 27 0 0 0 9 9 9 0 11 0 0 1.594 66 0.49 13 13 0 0 0 9 9 0 73 0 0 0 0 0 0 9 0 0 0 0 0 0 11 0 0 0.886 37 1.26 14 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 11 0 0 0.000 0 1.37 15 15 18 9 9 0 0 0 0 0 18 9 0 36 0 0 0 0 0 0 0 0 11 0 0 1.642 68 0.68 16 16 0 0 0 0 0 0 0 0 0 0 0 0 91 0 0 0 0 0 9 0 11 0 0 0.305 13 1.32 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 11 0 0 0.000 0 1.37 18 18 0 55 0 0 27 0 0 9 0 0 9 0 0 0 0 0 0 0 0 0 11 0 0 1.121 47 1.14 19 19 0 0 0 0 9 0 0 18 18 36 0 18 0 0 0 0 0 0 0 0 11 0 0 1.516 63 0.68 20 20 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 9 0 0 11 0 0 0.305 13 1.34 21 21 0 0 0 0 0 0 0 40 10 0 0 40 10 0 0 0 0 0 0 0 10 1 0 1.194 52 0.80 22 22 0 0 10 0 0 0 0 0 0 40 50 0 0 0 0 0 0 0 0 0 10 1 0 0.943 41 0.76 23 23 0 0 0 0 0 0 0 0 0 0 10 0 0 0 70 0 0 20 0 0 10 1 1 0.802 35 0.76 24 24 0 0 0 0 0 0 0 10 10 50 0 0 0 0 0 0 0 30 0 0 10 1 1 1.168 51 0.70 25 25 40 0 20 0 0 0 0 0 0 0 0 20 0 0 10 0 0 0 10 0 10 1 0 1.471 64 0.68 26 26 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 10 1 0 0.000 0 1.33 27 27 0 0 0 0 0 0 0 10 90 0 0 0 0 0 0 0 0 0 0 0 10 1 0 0.325 14 1.30 28 28 0 0 0 0 0 0 0 10 10 10 30 20 0 0 0 20 0 0 0 0 10 1 0 1.696 74 0.60 29 29 0 50 0 0 0 0 10 10 20 0 0 0 0 0 0 10 0 0 0 0 10 1 0 1.359 59 0.47 30 30 0 0 0 0 0 0 10 0 0 0 50 10 30 0 0 0 0 0 0 0 10 1 0 1.168 51 0.76 31 31 0 0 10 0 0 0 0 70 0 0 0 0 0 0 10 0 0 0 0 10 10 1 0 0.940 41 0.91 32 32 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 11 0 0 0.000 0 1.37 33 33 0 0 18 0 0 0 0 0 0 0 0 9 0 0 0 73 0 0 0 0 11 0 0 0.760 32 0.88 34 34 0 0 91 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 11 0 0 0.305 13 1.32 35 35 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.37 36 36 0 0 0 0 0 0 0 0 0 18 73 0 0 0 0 0 0 0 9 0 11 0 0 0.760 32 1.03 37 37 0 9 0 0 0 0 0 73 18 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.760 32 1.11 38 38 0 0 0 0 0 0 0 0 18 18 36 18 0 9 0 0 0 0 0 0 11 0 1 1.516 63 0.69 39 39 0 0 0 0 0 0 0 9 0 0 0 73 0 0 9 9 0 0 0 0 11 0 0 0.886 37 1.09 40 40 0 0 0 0 0 0 0 0 0 0 9 0 91 0 0 0 0 0 0 0 11 0 0 0.305 13 1.35 41 41 0 0 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 9 11 0 0 0.305 13 1.15 42 42 0 0 0 0 0 0 0 10 0 10 50 0 0 10 10 0 0 0 0 10 10 0 0 1.498 65 0.82 43 43 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 80 10 0 0 0.500 22 1.20 44 44 0 0 0 0 0 10 90 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.325 14 1.30 45 45 0 0 0 0 0 0 0 0 25 63 0 0 0 0 0 0 0 0 0 13 8 0 0 0.900 43 0.88 46 46 0 0 0 0 0 0 0 0 0 0 13 0 0 13 0 63 0 0 13 0 8 0 0 1.074 52 0.82 ## INSERTION LIST AliNo IPOS JPOS Len Sequence 2 23 24 1 sRe 9 24 250 31 gSHCEVLEKHPVCVRNHVPPHPPPPPQICGSVn 9 38 295 14 hPTCIRGDGYLCNQTr // profnet-1.0.22/src-phd/1crn.phd0000644015075101507510000003063312021362702015447 0ustar lkajanlkajan******************************************************************************** * * * Publication to reference in reporting results: * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * * Rost, Burkhard; Sander, Chris: Prediction of protein structure * * at better than 70% accuracy. J. Mol. Biol., 1993, 232, 584-599. * * Rost, Burkhard; Sander, Chris: Combining evolutionary information * * and neural networks to predict protein secondary structure. * * Proteins, 1994, 19, 55-72. * * * ******************************************************************************** * * * Some statistics: * * ~~~~~~~~~~~~~~~~ * * * * Percentage of amino acids: * * * * +--------------+--------+--------+--------+--------+--------+ * | AA: | T | C | P | I | A | * | % of AA: | 13.0 | 13.0 | 10.9 | 10.9 | 10.9 | * +--------------+--------+--------+--------+--------+--------+ * | AA: | G | N | Y | V | S | * | % of AA: | 8.7 | 6.5 | 4.3 | 4.3 | 4.3 | * +--------------+--------+--------+--------+--------+--------+ * | AA: | R | L | F | E | D | * | % of AA: | 4.3 | 2.2 | 2.2 | 2.2 | 2.2 | * +--------------+--------+--------+--------+--------+--------+ * * * Percentage of secondary structure predicted/observed: * * * * +--------------+--------+--------+--------+ * | SecStr: | H | E | L | * | % Predicted: | 0.0 | 6.5 | 93.5 | * +--------------+--------+--------+--------+ * | SecStr: | H | E | L | * | % Observed: | 47.8 | 8.7 | 43.5 | * +--------------+--------+--------+--------+ * * * According to the following classes: * * all-alpha: %H>45 and %E< 5; all-beta : %H<5 and %E>45 * * alpha-beta : %H>30 and %E>20; mixed: rest, * * this means that the predicted class is: mixed class * * The class of the observed structure is: mixed class * * * ******************************************************************************** * * * * ******************************************************************************** * * * * * PHD output for your protein: * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * * * * Thu Mar 1 21:40:00 2001 * * * * Jury on: 1 different architectures (version 5.94_317 ). * * Note: differently trained architectures, i.e., different versions can * * result in different predictions. * * * * * ******************************************************************************** * * * * * * * About the protein: * * ------------------ * * * * * * HEADER PLANT SEED PROTEIN * * COMPND CRAMBIN * * SOURCE ABYSSINIAN CABBAGE (CRAMBE ABYSSINICA) SEED * * AUTHOR W.A.HENDRICKSON,M.M.TEETER * * SEQLENGTH 46 * * NCHAIN 1 chain(s) in 1crn data set * * NALIGN 11 * * (=number of aligned sequences in HSSP file) * * * * * ******************************************************************************** * * * * * * * Abbreviations: * * -------------- * * * * secondary structure : H=helix, E=extended (sheet), blank=rest (loop) * * * * AA: amino acid sequence * * PHD: Profile network prediction HeiDelberg * * Rel: Reliability index of prediction (0-9) * * * * detail: * * prH: 'probability' for assigning helix * * prE: 'probability' for assigning strand * * prL: 'probability' for assigning loop * * note: the 'probabilites' are scaled to the interval 0-9, * * i.e. prH=5 means, that the signal at the first * * output node is 0.5-0.6. * * * * subset: * * SUB: a subset of the prediction, for all residues with * * an expected accuracy > 82% (see tables in header) * * note: for this subset the following symbols are used: * * L: is loop (for which above " " is used) * * ".": means that no prediction is made for this residue, * * as the reliability is Rel < 5 * * * * * ******************************************************************************** * * * * * protein: 1crn length 46 * * * ....,....1....,....2....,....3....,....4....,....5....,....6 AA |TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN| Obs | EE HHHHHHHHHHH HHHHHHHH EE GGG | PHD | EEE | Rel |9999999998433445789999962233599743337799999999 detail: prH-|0000000001211121100000011101100000000100000000 prE-|0000000000122211000000013322100166630000000000 prL-|9999999998656657789999974565799823368899999999 subset: SUB |LLLLLLLLLL.....LLLLLLLLL....LLLL....LLLLLLLLLL| * * ******************************************************************************** * * * * * * * Performance accuracy of the prediction * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * * * +-----------------+------------------------------------------------+-------------------+ | 1crn : 46 | method:jury | segments | +-----------------+------------------------------------------------+-------------------+ | number of residues with H,E,C | % of DSSP | % of Net | number |av length| +--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+ | |net H |net E |net C |sum DS| H | E | C | H | E | C |DSSP| Net|DSSP| Net| +--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+ | DSSP H | 0| 0| 22| 22| 0.0| 0.0|100.0| 0| 0| 51| 2| 0| 9.5| 0.0| | DSSP E | 0| 2| 2| 4| 0.0| 50.0| 50.0| 0| 66| 4| 2| 1| 2.0| 3.0| | DSSP C | 0| 1| 19| 20| 0.0| 5.0| 95.0| 0| 33| 44| 7| 2| 1.6|21.5| +--------+------+------+------+------+-----+-----+-----+---+-+-+---+----+----+----+----+ | sum Net| 0| 3| 43| 46|corH |corE |corC | Q3 | SQ | 11| 3| 3.1|15.3| | |0.00 |0.54 |0.05 | 45.7| 48.3| | +---------+--------------------------+++---+-----+-----++****+*****+-------------------+ | segments| % of observed || % of predicted | information | +---------+------+------+------+------++------+------+------+------+---------+---------+ | measure | % H | % E | % L | sum || % H | % E | % L | sum | I %obs | I %pred | +---------+------+------+------+------++------+------+------+------+---------+---------+ | SOV | 0.0 | 50.0 | 37.4 | 20.6 || 0.0 |100.0 | 28.1 | 32.8 |0.05 7%|0.22 35%| +---------+------+------+------+------++------+------+------+------+---------+---------+ * * * * * * * * ******************************************************************************** * * * * END profnet-1.0.22/src-phd/1crn.rdbPhd0000644015075101507510000000424212021362705016077 0ustar lkajanlkajan# Perl-RDB # # PHDsec: secondary structure prediction # # PDBID : 1crn # LENGTH : 46 # NOTATION No : residue number # NOTATION AA : amino acid one letter code # NOTATION OHEL : observed secondary structure # NOTATION PHEL : predicted secondary structure # NOTATION PHEL : H=helix, E=strand, L=non-regular (taken from DSSP) # NOTATION RI_S : reliability of secondary structure prediction , 0-9 # NOTATION pH : probability of predicting helix, 0-9 # NOTATION pE : probability of predicting strand # NOTATION pL : probability of predicting loop # NOTATION OtH : network output for helix, 0-100 # NOTATION OtE : network output for strand # NOTATION OtL : network output for loop # No AA OHEL PHEL RI_S pH pE pL OtH OtE OtL 4N 1 1 1 1N 1N 1N 1N 3N 3N 3N 1 T L L 9 0 0 9 2 0 94 2 T E L 9 0 0 9 1 1 91 3 C E L 9 0 0 9 1 1 89 4 C L L 9 0 0 9 2 0 90 5 P L L 9 0 0 9 3 0 93 6 S L L 9 0 0 9 4 0 93 7 I H L 9 0 0 9 3 0 95 8 V H L 9 0 0 9 4 0 95 9 A H L 9 0 0 9 3 0 94 10 R H L 8 1 0 8 9 2 85 11 S H L 4 2 1 6 20 10 60 12 N H L 3 1 2 5 13 19 46 13 F H L 3 1 2 6 8 21 50 14 N H L 4 1 2 6 14 16 49 15 V H L 4 2 1 5 18 16 48 16 C H L 5 1 1 7 17 9 65 17 R H L 7 1 0 7 11 7 71 18 L L L 8 0 0 8 5 5 78 19 P L L 9 0 0 9 3 1 92 20 G L L 9 0 0 9 3 0 92 21 T L L 9 0 0 9 3 0 94 22 P L L 9 0 0 9 2 0 93 23 E H L 9 0 0 9 2 1 92 24 A H L 6 1 1 7 13 9 65 25 I H L 2 1 3 4 12 26 37 26 C H L 2 1 3 5 11 27 41 27 A H L 3 0 2 6 6 21 48 28 T H L 3 1 2 5 11 23 44 29 Y H L 5 1 1 7 8 12 58 30 T H L 9 0 0 9 2 1 95 31 G L L 9 0 0 9 1 3 94 32 C L L 7 0 1 8 1 13 80 33 I E E 4 0 6 2 2 64 28 34 I E E 3 0 6 3 2 63 33 35 I L E 3 0 6 3 5 51 26 36 P L L 3 0 3 6 5 25 47 37 G L L 7 0 0 8 6 7 70 38 A L L 7 1 0 8 13 2 82 39 T L L 9 0 0 9 7 1 87 40 C L L 9 0 0 9 3 0 93 41 P L L 9 0 0 9 3 0 96 42 G H L 9 0 0 9 2 0 97 43 D H L 9 0 0 9 4 0 94 44 Y H L 9 0 0 9 3 0 96 45 A L L 9 0 0 9 3 0 93 46 N L L 9 0 0 9 3 0 94 profnet-1.0.22/src-phd/Makefile0000644015075101507510000001426112021362702015546 0ustar lkajanlkajanARCH = LINUX F77 = gfortran # gfortran does not compile usable code with anything other than -O0 or without -O. It fails like this: #5..4..3..2..*** ERROR prof: line number of error=106 #*** ERROR failed prof:full:doOne dbfile=../testhome/usr/share/profphd/prof/exa/1ppt.f, chain=*! #*** ERROR msg from where it failed: #*** ERROR doOne: assHack1994 failed #*** ERROR assHack1994: SYSTEM call: # /tmp/testhome/usr/share/profphd/prof/embl/phd.pl ../testhome/usr/share/profphd/prof/exa/1ppt.f exePhd=/tmp/testhome/usr/share/profphd/prof/bin/phd1994.LINUX exeHsspFilter=/tmp/testhome/usr/share/profphd/prof/bin/filter_hssp.LINUX exeHsspFilterPl=/tmp/testhome/usr/share/profphd/prof/scr/hssp_filter.pl exeHsspFilterPack=/tmp/testhome/usr/share/profphd/prof/scr/pack/hssp_filter.pm exeConvertSeq=/tmp/testhome/usr/share/profphd/prof/bin/convert_seq.LINUX exeCopf=/tmp/testhome/usr/share/profphd/prof/scr/copf.pl exeCopfPack=/tmp/testhome/usr/share/profphd/prof/scr/pack/copf.pm exeConvHssp2saf=/tmp/testhome/usr/share/profphd/prof/embl/scr/conv_hssp2saf.pl ARCH=LINUX filePhd=PROF8406_9zqqcndm7996nsqosopo.phdEMBL fileRdb=PROF8406_9zqqcndm7996nsqosopo.rdbPhdEMBL fileNotHtm=PROF8406_9zqqcndm7996nsqosopo.notHtm # failed producing output file=PROF8406_9zqqcndm7996nsqosopo.rdbPhdEMBL # # phd.pl fails like this: # /usr/share/profphd/prof/embl/phd.pl 1ppt.f exePhd=/usr/bin/phd1994.LINUX exeHsspFilter=/usr/bin/filter_hssp.LINUX exeHsspFilterPl=/usr/share/profphd/prof/scr/hssp_filter.pl exeHsspFilterPack=/usr/share/profphd/prof/scr/pack/hssp_filter.pm exeConvertSeq=/usr/bin/convert_seq.LINUX exeCopf=/usr/share/profphd/prof/scr/copf.pl exeCopfPack=/usr/share/profphd/prof/scr/pack/copf.pm exeConvHssp2saf=/usr/share/profphd/prof/embl/scr/conv_hssp2saf.pl ARCH=LINUX filePhd=PROF14055_49jmm2bo3981bmu3c3al.phdEMBL fileRdb=PROF14055_49jmm2bo3981bmu3c3al.rdbPhdEMBL fileNotHtm=PROF14055_49jmm2bo3981bmu3c3al.notHtm dbg # /usr/bin/phd1994.LINUX 1ppt.hssp no no sec phd Para_14322-sec317-may94.com rdb 0 /tmp/proftest XPHD14322.phdSec XPHD14322.rdbSec # --- # --- Arguments given for calling FORTRAN program phd: # --- Arg 1 |1ppt.hssp| # --- Arg 2 |no| # --- Arg 3 |no| # --- Arg 4 |sec| # --- Arg 5 |phd| # --- Arg 6 |Para_14322-sec317-may94.com| # --- Arg 7 |rdb| # --- Arg 8 |0| # --- Arg 9 |/tmp/proftest| # --- Arg 10 |XPHD14322.phdSec| # --- Arg 11 |XPHD14322.rdbSec| # --- working directory "/tmp/proftest" # --- FILEPRED "XPHD14322.phdSec" # --- FILE_RDB "XPHD14322.rdbSec" # ---------------------------------------------------------------------- # --- Protein from HSSP: 1ppt.hssp # ---------------------------------------------------------------------- # --- # --- HSSP file 1ppt.hssp # --- RS_READHSSP PROTEINS-block done # --- RS_READHSSP ALIGNMENTS-block done # --- RS_READHSSP PROFILE-block done # --- RS_READHSSP ok(cut 50): 1ppt.hssp # xx LERROR after read hssp: F # --- RS_GETHSSP(final words) got: # --- protname(50) 1pptPANCREAT # --- length: 36 N alis: 0 # --- sequence GPSQPTYPGDDAPVEDLIRFYDNLQQYLNVVTRHRY # --- structure LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL # --- OFFSET 1 # --- RS_GETHSSP END(really) # *** ************************************************************ # *** ERROR in reading HSSP (?), claimed to be empty (main PHD) # *** ************************************************************ #*** ERROR lib-ut:sysRunProg: failed on system call to FORTRAN (/usr/bin/phd1994.LINUX): #*** no pred file ',XPHD14322.phdSec' #*** no RDB file ',XPHD14322.rdbSec' # # /usr/bin/phd1994.LINUX 1ppt.hssp no no sec phd Para_14202-sec317-may94.com rdb 0 /tmp/proftest XPHD14202.phdSec XPHD14202.rdbSec | fails like this: # --- # --- Arguments given for calling FORTRAN program phd: # --- Arg 1 |1ppt.hssp| # --- Arg 2 |no| # --- Arg 3 |no| # --- Arg 4 |sec| # --- Arg 5 |phd| # --- Arg 6 |Para_14202-sec317-may94.com| # --- Arg 7 |rdb| # --- Arg 8 |0| # --- Arg 9 |/tmp/proftest| # --- Arg 10 |XPHD14202.phdSec| # --- Arg 11 |XPHD14202.rdbSec| # --- working directory "/tmp/proftest" # --- FILEPRED "XPHD14202.phdSec" # --- FILE_RDB "XPHD14202.rdbSec" # ---------------------------------------------------------------------- # --- Protein from HSSP: 1ppt.hssp # ---------------------------------------------------------------------- # --- # --- HSSP file 1ppt.hssp # --- RS_READHSSP PROTEINS-block done # --- RS_READHSSP ALIGNMENTS-block done # --- RS_READHSSP PROFILE-block done # --- RS_READHSSP ok(cut 50): 1ppt.hssp # xx LERROR after read hssp: F # --- RS_GETHSSP(final words) got: # --- protname(50) 1pptPANCREAT # --- length: 36 N alis: 0 # --- sequence GPSQPTYPGDDAPVEDLIRFYDNLQQYLNVVTRHRY # --- structure LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL # --- OFFSET 1 # --- RS_GETHSSP END(really) # *** ************************************************************ # *** ERROR in reading HSSP (?), claimed to be empty (main PHD) # *** ************************************************************ # # NOTE that N alis above is 1 in the correct version working with the same input. # # -finit-local-zero - initializing variables - solves all of the above but not all compilers support it. Solution: initialize all variables properly. FFLAGS := -O3 -fbounds-check FFLAGS := $(FFLAGS) -Wall profphd_net : phd.f lib-phd.f phdParameter.f $(F77) $(FFLAGS) -o $@ phd.f lib-phd.f #phd.o : phdParameter.f clean: rm -f *.o profphd_net install: mkdir -p $(DESTDIR)$(prefix)/bin && \ cp profphd_net $(DESTDIR)$(prefix)/bin/ rm -f $(DESTDIR)$(prefix)/bin/phd1994 && ln -s profphd_net $(DESTDIR)$(prefix)/bin/phd1994 .PHONY: clean install profnet-1.0.22/src-phd/Para-test.com0000755015075101507510000000347612021362702016457 0ustar lkajanlkajan************************************************************************************* ***** ***** ***** Secondary Structure Prediction by a Layered Network ***** ***** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ***** ***** ***** ***** Burkhard Rost, EMBL, Heidelberg, FRG ***** ***** (Internet: rost@EMBL-Heidelberg.DE) ***** ***** ***** ***** Wed Oct 14 13:57:04 1992 ***** ***** ***** ***** This file contains the required parameters. ***** ***** ***** ************************************************************************************* ***** ***** ***** PATH_ARCH /home/rost/pub/phd/net/ ***** MAXVAR= 150 MAXACC= 150 PROFACC= 4 CASCACC= 8 NBIOLOBJ 21 ***** NUMNETFST= 1 NUMNETSND= 1 NUMNETJURY= 1 ***** TRANS2FROM1(1:NUMNETSND) (20I4) 1 ***** MODEASSCAS(1:NUMNETFST) (row: no. A25) 1 P-REAL-CICLD ***** MODEASSSTR(1:NUMNETSND) (row: no. A25) 1 REAL-CCLD ***** FILEARCHFST(1:NUMNETFST) (row: no. A50) 1 F252x-15pcicld.DAT FILEASND(1:NUMNETSND) (row: no. A50) 1 S252x-rccld-15pcicld.DAT END profnet-1.0.22/src-phd/Para_23930036-test.com0000644015075101507510000000347612021362705017450 0ustar lkajanlkajan************************************************************************************* ***** ***** ***** Secondary Structure Prediction by a Layered Network ***** ***** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ***** ***** ***** ***** Burkhard Rost, EMBL, Heidelberg, FRG ***** ***** (Internet: rost@EMBL-Heidelberg.DE) ***** ***** ***** ***** Wed Oct 14 13:57:04 1992 ***** ***** ***** ***** This file contains the required parameters. ***** ***** ***** ************************************************************************************* ***** ***** ***** PATH_ARCH /home/rost/pub/phd/net/ ***** MAXVAR= 150 MAXACC= 150 PROFACC= 4 CASCACC= 8 NBIOLOBJ 21 ***** NUMNETFST= 1 NUMNETSND= 1 NUMNETJURY= 1 ***** TRANS2FROM1(1:NUMNETSND) (20I4) 1 ***** MODEASSCAS(1:NUMNETFST) (row: no. A25) 1 P-REAL-CICLD ***** MODEASSSTR(1:NUMNETSND) (row: no. A25) 1 REAL-CCLD ***** FILEARCHFST(1:NUMNETFST) (row: no. A50) 1 F252x-15pcicld.DAT FILEASND(1:NUMNETSND) (row: no. A50) 1 S252x-rccld-15pcicld.DAT END profnet-1.0.22/src-phd/ReadMe0000644015075101507510000001150412021362704015165 0ustar lkajanlkajan*----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * *----------------------------------------------------------------------* * ------------------------------ * * This directory contains: * * ------------------------------ * * * * - all PHD FORTRAN files : (phd.f + lib-phd.f) * * - PHD include files : (phdParameter.f) * * - documentation : (Doc-code-phd.txt) * * - general perl make script : (compile.pl) * * - make-files : (mat/makePhd*) * * * * ------------------------------ * * to DO for compile: * * ------------------------------ * * * * compile.pl -> gives help * * compile.pl auto -> DOES it.. * * * * * *----------------------------------------------------------------------* * * * * * Short explanations about the FORTRAN code in the following * * * * * * ------------- * * General notes * * ------------- * * * * FILES NEEDED: * * ~~~~~~~~~~~~~ * * - phd.f FORTRAN code * * - phdParameter.f parameter files (INCLUDE) * * - lib-phd.f FORTRAN library * * * * COMPILATION: * * ~~~~~~~~~~~~ * * - make -f makePhd.$ARCH * * OR: * * - f77 -O2 phd.f lib-phd.f * * * * DOCUMENTATION: * * ~~~~~~~~~~~~~~ * * - Doc-code-phd.txt * * * * ------------- * * Porting notes * * ------------- * * * * To port it: hard coded is only the path for the *.com file * * currently: /home/rost/pub * * or: /home/phd/net (if arg5=server) * * or: explicitly given in arg6 * * NOTE: defined in 'iniphd.f', * * --> grep 'change to port' * * * * * * ----------------- * * Other questions ? * * ----------------- * * * * --> see Doc-code-phd.txt, or code... * * * *----------------------------------------------------------------------* profnet-1.0.22/src-phd/ReadMe-mac0000644015075101507510000000040712021362704015723 0ustar lkajanlkajan# gnue g77 -o phd.MAC -O3 phd.f lib-phd.f lib-sys.f lib-sys.f g77 -o phdx.MAC -g0 -pedantic phd.f lib-phd.f lib-sys.f /usr/local/bin/gfortran -o phd.MACINTEL -O3 phd.f lib-phd.f lib-sys.f # ibm /opt/ibmcmp/xlf/8.1/bin/f77 -o phd.IBM -O3 phd.f lib-phd-MACIBM.f profnet-1.0.22/src-phd/ReadMe-sgiShit0000644015075101507510000000045112021362705016575 0ustar lkajanlkajanSGI has the following problem if (logical) then DOES NOT work rather you want to use if (logical .eq. .true.) then ... perl -ne '++$ct; if ($_=~/^[cC\*]/ || $_!~/[\s\t]+if\s+\(\s*[a-z\-\_]*\s*\)/i) {print; } else { $_=~s/IF (\(\S+*)\)/$1 \.EQ\. \.TRUE\./)/; print "$_"; ' phd.f >> new-phd.fprofnet-1.0.22/src-phd/ReadMe_sgi640000644015075101507510000000015512021362702016177 0ustar lkajanlkajanNOTE the new SGI compiler is messed!!! please use the version without optimisation mat/makePhd.SGI64_no64_O1profnet-1.0.22/src-phd/compile.pl0000755015075101507510000001576012021362705016106 0ustar lkajanlkajan#!/bin/env perl ##!/usr/local/bin/perl -w # # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="compile PHD FORTRAN tools programs (convert_seq, filter_hssp)"; #$scrGoal="compile PHD FORTRAN tools programs (convert_seq, filter_hssp, maxhom ?)"; # # $[ =1 ; $dirMake= "mat/"; # for PHD $fileMake{"convert"}="make_convert_seq.ARCH"; $fileMake{"filter"}= "make_filter_hssp.ARCH"; $fileMake{"phd"}= "makePhd.ARCH"; # for TOPITS $fileMake{"metr2st"}="make_metr2st_make.ARCH"; # for MaxHom $fileMake{"maxhom"}= "make_maxhom.ARCH"; $fileMake{"profile"}="make_profile_make.ARCH"; $exe{"convert"}= "convert_seq.". "ARCH"; $exe{"filter"}= "filter_hssp.". "ARCH"; $exe{"phd"}= "phd.". "ARCH"; $exe{"metr2st"}= "metr2st_make.". "ARCH"; $exe{"maxhom"}= "maxhom.". "ARCH"; $exe{"profile"}= "profile_make.". "ARCH"; $LnotMaxhome= 1; #$LnotMaxhome= 0; @all=("convert","filter","metr2st","maxhom","profile","phd"); # ------------------------------ if ($#ARGV<1){ # help print "goal: $scrGoal\n"; print "use: '$scrName '\n"; print "opt: (pass the following arguments like '$scrName arg=val')\n"; # 'keyword' 'value' 'description' printf " %-12s=%-10s %-22s %-s\n","." x 10, "." x 10, "." x 15, "." x 20; printf " %-12s=%-10s %-22s %-s\n","keyword", "value", "default", "explanation"; printf " %-12s=%-10s %-22s %-s\n","." x 10, "." x 10, "." x 15, "." x 20; printf " %-12s=%-10s %-22s %-s\n","ARCH", "ALPHA", "", "system arch: SGI64|SGI32|SGI5|ALPHA|SUNMP|LINUX"; printf " %-12s=%-10s %-22s %-s\n","dir", "mat",$dirMake, "directory with make file"; foreach $kwd (@all){ next if ($LnotMaxhom && $kwd eq "maxhom"); printf " %-12s=%-10s %-22s %-s\n","exe_".$kwd,"x", $exe{$kwd}, "name of executable"; } foreach $kwd (@all){ next if ($LnotMaxhom && $kwd eq "maxhom"); printf " %-12s=%-10s %-22s %-s\n","make_".$kwd,"x", $fileMake{$kwd},"make file";} foreach $kwd (@all){ next if ($LnotMaxhom && $kwd eq "maxhom"); printf " %-12s %-10s %-22s %-s\n",$kwd, "no value", "1","compiles $kwd";} exit; } foreach $kwd (@all) { $do{$kwd}=0;} $Lopted=0; # ------------------------------ # read command line foreach $arg (@ARGV){ next if ($arg eq $ARGV[1] && $arg =~ /^(auto|do)$/); if ($arg=~/^ARCH=(.*)$/i) { $ARCH=$1;} elsif ($arg=~/^make_(.*)=(.*)$/) { $fileMake{$1}=$2;} elsif ($arg=~/^exe_(.*)=(.*)$/) { $exe{$1}=$2;} elsif ($arg=~/^conv(ert)?$/) { $do{"convert"}=1; $Lopted=1;} elsif ($arg=~/^fil(ter)?$/) { $do{"filter"}= 1; $Lopted=1;} elsif ($arg=~/^metr(2st)?$/) { $do{"metr2st"}=1; $Lopted=1;} elsif ($arg=~/^max(hom)?$/) { $do{"maxhom"}= 1; $Lopted=1;} elsif ($arg=~/^prof(ile)?$/) { $do{"profile"}=1; $Lopted=1;} elsif ($arg=~/^phd?$/) { $do{"phd"}=1; $Lopted=1;} elsif ($arg=~/^dir=(.*)$/) { $dirMake=$1;} # elsif ($arg=~/^=(.*)$/){ $=$1;} else { print "*** ERROR $scrName: wrong command line arg '$arg'\n"; die;}} $ARCH= $ARCH || $ENV{'ARCH'}; $dirMake.="/" if ($dirMake !~/\// && length($dirMake)>=1); if (! defined $ARCH) { $ansr= &get_in_keyboardLoc("ARCH","",$scrName); $ARCH=$ansr; } if ($ARCH !~ /ALPHA|SGI(64|32|5)|SUNMP|SUN4SOL|LINUX/){ print "--- $scrName: ARCH must be either of the following :\n"; print "--- "." " x length($scrName)." ALPHA|SGI64|SGI32|SGI5|SUNMP|SUN4SOL\n"; $ansr= &get_in_keyboardLoc("ARCH","",$scrName); $ARCH=$ansr; } if ($ARCH !~ /ALPHA|SGI(64|32|5)|SUNMP|SUN4SOL|LINUX/){ print "*** ERROR $scrName: ARCH really must be either of the following :\n"; print "*** "." " x length($scrName)." ALPHA|SGI64|SGI32|SGI5|SUNMP|SUN4SOL\n"; die; } # default: do all 3 compilations if (! $Lopted){ foreach $kwd (@all){ next if ($LnotMaxhom && $kwd eq "maxhom"); $do{$kwd}=1;}} foreach $kwd (@all) { next if (! $do{$kwd}); $fileMake{$kwd}=~s/ARCH/$ARCH/ if ($fileMake{$kwd} =~ /ARCH/); $fileMake{$kwd}=$dirMake.$fileMake{$kwd} if ($fileMake{$kwd} !~ /$dirMake/); $fileMake=$fileMake{$kwd}; undef $exeOut; if (defined $exe{$kwd}) { $exeOut= $exe{$kwd}; $exeOut=~s/ARCH/$ARCH/ if ($exeOut=~/ARCH/);} $exeDef= "convert_seq.".$ARCH if ($kwd eq "convert"); $exeDef= "filter_hssp.".$ARCH if ($kwd eq "filter"); $exeDef= "maxhom." .$ARCH if ($kwd eq "maxhom"); $exeDef= "phd." .$ARCH if ($kwd eq "phd"); # local copy of make file $fileMakeTmp="make_".$kwd."_tmp_".$$.".".$ARCH; print "--- $scrName: system '\\cp $fileMake $fileMakeTmp '\n"; system("\\cp $fileMake $fileMakeTmp"); # compile print "--- $scrName: system 'make -f $fileMakeTmp'\n"; system("make -f $fileMakeTmp"); if (-e $exeDef && defined $exeOut && ($exeDef ne $exeOut)) { print "--- $scrName: system '\\mv $exeDef $exeOut'\n"; system("\\mv $exeDef $exeOut"); $exeDef=$exeOut; } print "--- $scrName: expected executable: $exeDef\n" if (-e $exeDef); print "*** ERROR $scrName: never made '$exeDef'\n" if (! -e $exeDef); unlink($fileMakeTmp); } exit; #=============================================================================== sub get_in_keyboardLoc { local($des,$def,$pre,$Lmirror)=@_;local($txt); #-------------------------------------------------------------------------------- # get_in_keyboardLoc gets info from keyboard # in: $des : keyword to get # in: $def : default settings # in: $pre : text string beginning screen output # default '--- ' # in: $Lmirror: if true, the default is mirrored # out: $val : value obtained #-------------------------------------------------------------------------------- $pre= "---" if (! defined $pre); $Lmirror=0 if (! defined $Lmirror || ! $Lmirror); $txt=""; # ini printf "%-s %-s\n", $pre,"-" x (79 - length($pre)); printf "%-s %-15s:%-s\n", $pre,"type value for",$des; if (defined $def){ printf "%-s %-15s:%-s\n",$pre,"type RETURN to enter value, or to keep default"; printf "%-s %-15s>%-s\n",$pre,"default value",$def;} else { printf "%-s %-15s>%-s\n",$pre,"type RETURN to enter value"; } $txt=$def if ($Lmirror); # mirror it printf "%-s %-15s>%-s", $pre,"type",$txt; while(){ $txt.=$_; last if ($_=~/\n/);} $txt=~s/^\s+|\s+$//g; $txt=$def if (length($txt) < 1); printf "%-s %-15s>%-s\n", $pre,"--> you chose",$txt; return ($txt); } # end of get_in_keyboardLoc profnet-1.0.22/src-phd/compile_macintel.csh0000755015075101507510000000033212021362704020110 0ustar lkajanlkajan# gnu gfortran compiler - only on INTEL MAC echo "--- now PHD: " echo "/usr/local/bin/gfortran -o phd.MACINTEL -O3 phd.f lib-phd.f lib-sys.f " /usr/local/bin/gfortran -o phd.MACINTEL -O3 phd.f lib-phd.f lib-sys.f profnet-1.0.22/src-phd/lib-phd.f0000644015075101507510000103052412021362705015600 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** FCT EMPTYSTRING ***** ------------------------------------------------------------------ C---- C---- NAME : EMPTYSTRING C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* FUNCTION EMPTYSTRING(STRING) LOGICAL EMPTYSTRING CHARACTER*222 STRING EMPTYSTRING=.TRUE. DO I=1,LEN(STRING) IF(STRING(I:I).NE.' ') THEN EMPTYSTRING=.FALSE. RETURN ENDIF ENDDO RETURN END ***** end of EMPTYSTRING ***** ------------------------------------------------------------------ ***** FCT FC_REXP_TO_3STCHAR ***** ------------------------------------------------------------------ C---- C---- NAME : FC_REXP_TO_3STCHAR C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Returns 'b', 'i', or 'e' for the exposure state. * * input: REXP (real 0-1), T3A (real 0-1), T3B (real 0-1) * * output: B, if REXP < T3A * * ------- I, if T3A <= REXP < T3B * * I, if REXP >= T3B * *----------------------------------------------------------------------* CHARACTER*1 FUNCTION FC_REXP_TO_3STCHAR(REXP,T3A,T3B) IMPLICIT NONE C---- variables passed REAL REXP,T3A,T3B ******------------------------------*-----------------------------****** IF (REXP.LT.T3A) THEN FC_REXP_TO_3STCHAR='b' ELSEIF (REXP.GE.T3B) THEN FC_REXP_TO_3STCHAR='e' ELSE FC_REXP_TO_3STCHAR='i' END IF END ***** end of FC_REXP_TO_3STCHAR ***** ------------------------------------------------------------------ ***** FCT FC_REXPI_TO_3STCHAR ***** ------------------------------------------------------------------ C---- C---- NAME : FC_REXPI_TO_3STCHAR C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Returns 'b', 'i', or 'e' for the exposure state. * * note: in contrast to FC_REXP_TO_3STCHAR this works on * * integer values * * input: REXP (real 0-1), T3A (real 0-1), T3B (real 0-1) * * output: B, if REXP < T3A * * ------- I, if T3A <= REXP < T3B * * I, if REXP >= T3B * *----------------------------------------------------------------------* CHARACTER*1 FUNCTION FC_REXPI_TO_3STCHAR(IREXP,IT3A,IT3B) IMPLICIT NONE C---- variables passed INTEGER IREXP,IT3A,IT3B ******------------------------------*-----------------------------****** IF (IREXP.LT.IT3A) THEN FC_REXPI_TO_3STCHAR='b' ELSEIF (IREXP.GE.IT3B) THEN FC_REXPI_TO_3STCHAR='e' ELSE FC_REXPI_TO_3STCHAR='i' END IF END ***** end of FC_REXP_TO_3STCHAR ***** ------------------------------------------------------------------ ***** FCT FCCONV_LOWCASE_AA_TO_CYS ***** ------------------------------------------------------------------ C---- C---- NAME : FCCONV_LOWCASE_AA_TO_CYS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: [a-z] -> C * *----------------------------------------------------------------------* CHARACTER*1 FUNCTION FCCONV_LOWCASE_AA_TO_CYS(AA) IMPLICIT NONE CHARACTER*1 AA ******------------------------------*-----------------------------****** IF ( (AA.EQ.'a').OR.(AA.EQ.'b').OR. + (AA.EQ.'c').OR.(AA.EQ.'d').OR. + (AA.EQ.'e').OR.(AA.EQ.'f').OR. + (AA.EQ.'g').OR.(AA.EQ.'h').OR. + (AA.EQ.'i').OR.(AA.EQ.'j').OR. + (AA.EQ.'k').OR.(AA.EQ.'l').OR. + (AA.EQ.'m').OR.(AA.EQ.'n').OR. + (AA.EQ.'o').OR.(AA.EQ.'p').OR. + (AA.EQ.'q').OR.(AA.EQ.'r').OR. + (AA.EQ.'s').OR.(AA.EQ.'t').OR. + (AA.EQ.'u').OR.(AA.EQ.'v').OR. + (AA.EQ.'w').OR.(AA.EQ.'x').OR. + (AA.EQ.'y').OR.(AA.EQ.'z')) THEN FCCONV_LOWCASE_AA_TO_CYS='C' ELSE FCCONV_LOWCASE_AA_TO_CYS=AA END IF END ***** end of FCCONV_LOWCASE_AA_TO_CYS ***** ------------------------------------------------------------------ ***** FCT FCUT_SPACES ***** ------------------------------------------------------------------ C---- C---- NAME : FCUT_SPACES C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: cuts off spaces from string of *80 * * ext. library: FILEN_STRING, * *----------------------------------------------------------------------* FUNCTION FCUT_SPACES(STRING) IMPLICIT NONE C---- variables passed CHARACTER*222 FCUT_SPACES CHARACTER*(*) STRING C---- local variables INTEGER ITER,ITER2,COUNT CHARACTER*222 ABCUP,ABCLOW,NUMSIG LOGICAL LHELP ******------------------------------*-----------------------------****** C---- defaults ABCUP ='ABCDEFGHIJKLMNOPQRSTUVWXYZ' ABCLOW='abcdefghijklmnopqrstuvwxyz' NUMSIG='1234567890-._/=+' FCUT_SPACES='x' COUNT=0 DO ITER=1,222 LHELP=.TRUE. DO ITER2=1,26 IF (LHELP.EQV. .TRUE. + .AND.STRING(ITER:ITER).EQ.ABCUP(ITER2:ITER2)) THEN LHELP=.FALSE. END IF IF (LHELP.EQV. .TRUE. .AND. + (STRING(ITER:ITER).EQ.ABCLOW(ITER2:ITER2))) THEN LHELP=.FALSE. END IF END DO IF (LHELP .EQV. .TRUE.) THEN DO ITER2=1,16 IF (LHELP.EQV. .TRUE. .AND. + (STRING(ITER:ITER).EQ.NUMSIG(ITER2:ITER2))) THEN LHELP=.FALSE. END IF END DO END IF IF (LHELP.EQV. .FALSE.) THEN COUNT=COUNT+1 FCUT_SPACES(COUNT:COUNT)=STRING(ITER:ITER) END IF END DO END ***** end of FCUT_SPACES ***** ------------------------------------------------------------------ ***** FCT FIEXP_NOINBIN_SUM ***** ------------------------------------------------------------------ C---- C---- NAME : FIEXP_NOINBIN_SUM C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: All values of the matrix EXP_NOINBIN are summed * * -------- which fulfill: TL <= i < TU. * * MODE='obs' -> sum M(i,j) over i * * MODE='pred' -> sum M(i,j) over j * * input : EXP_NOINBIN, TL, TU, MODE * * output : number of occurences * *----------------------------------------------------------------------* INTEGER FUNCTION FIEXP_NOINBIN_SUM(EXP_NOINBIN,TL,TU,MODE) IMPLICIT NONE C---- variables passed from/to SBR calling INTEGER EXP_NOINBIN(0:9,0:9),TL,TU,SUM CHARACTER*(*) MODE C---- local variables INTEGER ITOBS,ITPRED ******------------------------------*-----------------------------****** * EXP_NOINBIN(i,j)=n means n residues observed in state i and * * predicted in state j. Where the relative * * solvent accessibility is (i*i), or (j*j). * * Mode = * * "obs" all occurences observed with TL <= i < TU * * are counted. * * "pred" all occurences predicted with TL <= i < TU * * are counted. * * TL,TU Counted are all cases with TL <= i < TU * ******------------------------------*-----------------------------****** C---- parameter check IF ( (TL.LT.0).OR.(TU.GT.10) ) THEN WRITE(6,'(T2,A,T10,A)')'***','FIEXP_NOINBIN_SUM: '// + 'thresholds wrong! ' WRITE(6,'(T2,A,T10,A,T20,i2,a,t30,i2)') + '***','TL= ',TL,' TU = ',TU STOP END IF C---- summing up SUM=0 IF (MODE.EQ.'obs') THEN DO ITOBS=TL,(TU-1) DO ITPRED=0,9 SUM=SUM+EXP_NOINBIN(ITOBS,ITPRED) END DO END DO ELSEIF (MODE.EQ.'pred') THEN DO ITPRED=TL,(TU-1) DO ITOBS=0,9 SUM=SUM+EXP_NOINBIN(ITOBS,ITPRED) END DO END DO ELSE WRITE(6,'(T2,A,T10,A)')'***','FIEXP_NOINBIN_SUM: '// + 'mode should be either "observed" or "predicted".' WRITE(6,'(T2,A,T10,A,T40,A)')'***','However, it is:',MODE END IF FIEXP_NOINBIN_SUM=SUM END ***** end of FIEXP_NOINBIN_SUM ***** ------------------------------------------------------------------ ***** FCT FILEN_STRING ***** ------------------------------------------------------------------ C---- C---- NAME : FILEN_STRING C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1993 version 0.1 * * changed: Oct, 1994 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The length of a given character string is returned * input: STRING string of CHARACTER*222 * * output: LEN length of string without blanks * *----------------------------------------------------------------------* INTEGER FUNCTION FILEN_STRING(STRING) C---- variables passing CHARACTER STRING*(*) C---- local variables INTEGER ITER,ITER2,COUNT,LEADSPCCNT,NCHAR CHARACTER*222 CHECK LOGICAL LHELP,LHELP2 ******------------------------------*-----------------------------****** C---- defaults FILEN_STRING= 0 CHECK(1:52)= + 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz' CHECK(53:67)='1234567890-._/+' NCHAR=67 LHELP=.TRUE. COUNT=0 LEADSPCCNT=0 DO ITER=1,len(STRING) IF (LHELP .EQV. .TRUE.) THEN LHELP2=.FALSE. DO ITER2=1,NCHAR IF ((LHELP2.EQV. .FALSE.).AND. + STRING(ITER:ITER).EQ.CHECK(ITER2:ITER2)) THEN LHELP2=.TRUE. COUNT=COUNT+1 END IF END DO IF (LHELP2.EQV. .FALSE.) THEN IF ( (COUNT.EQ.0).AND.(STRING(ITER:ITER).eq.' ') ) THEN LEADSPCCNT=LEADSPCCNT+1 ELSE LHELP=.FALSE. FILEN_STRING=ITER-1-LEADSPCCNT END IF ELSE FILEN_STRING=ITER-LEADSPCCNT END IF END IF END DO IF (COUNT.NE.FILEN_STRING) THEN WRITE(6,'(T2,A)')'-!-' WRITE(6,'(T2,A,T10,A)')'-!-','WARNING FILEN_STRING:'// + 'two different results.' WRITE(6,'(T2,A,T10,A,T20,I5,T30,A,T40,I5,T50,A,T60,A1,A,A1)') + '-!-','first = ',FILEN_STRING, + 'count: ',COUNT,'for: ','|',STRING,'|' WRITE(6,'(T2,A)')'-!-' END IF FILEN_STRING=COUNT END ***** end of FILEN_STRING ***** ------------------------------------------------------------------ ***** FCT FILENSTRING ***** ------------------------------------------------------------------ C---- C---- NAME : FILENSTRING C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The length of a given character string is returned * input: STRING string of CHARACTER*222 * * output: LEN length of string without blanks * *----------------------------------------------------------------------* INTEGER FUNCTION FILENSTRING(STRING) C---- variables passing CHARACTER STRING*(*) C---- local variables INTEGER ICOUNT,ITER LOGICAL LHELP ******------------------------------*-----------------------------****** C---- defaults ICOUNT=0 LHELP=.TRUE. DO ITER=1,80 IF (LHELP.EQV. .TRUE. .AND.(STRING(ITER:ITER).NE.' ')) THEN ICOUNT=ICOUNT+1 ELSE LHELP=.FALSE. END IF END DO FILENSTRING=ICOUNT END ***** end of FILENSTRING ***** ------------------------------------------------------------------ ***** FCT FIRELIND_2ND ***** ------------------------------------------------------------------ C---- C---- NAME : FIRELIND_2ND C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Returns the difference between largest and 2nd * * -------- largest component of a vector, projected onto a * * grid 0-9. Note: SCALE gives the maxima of RVEC * * input: RVEC, NCOLMAX, NCOL, SCALE * * output: 0-9 * *----------------------------------------------------------------------* INTEGER FUNCTION FIRELIND_2ND(NCOLMAX,NCOL,RVEC,SCALE) IMPLICIT NONE C---- variables passed INTEGER NCOLMAX,NCOL REAL RVEC(1:NCOLMAX),SCALE C---- local variables INTEGER ITCOL,IMAX REAL MAX,MAX2,DIFF,SCALE_LOC ******------------------------------*-----------------------------****** IMAX= 0 C---- check limits IF (NCOL.EQ.0) THEN WRITE(6,'(T2,A,T10,A,T20,I5,T30,A,T40,I5)')'***', + 'ERROR in lib-prot.f Function FIRELIND_2nd: NROW OR NCOL=0' WRITE(6,'(T2,A,T10,A)')'***','ncol=',ncol STOP END IF C---- for security IF (SCALE.LT.1) THEN SCALE_LOC=1. ELSE SCALE_LOC=SCALE END IF C---- compute maximum and 2nd largest MAX=0 DO ITCOL=1,NCOL IF (RVEC(ITCOL).GT.MAX) THEN MAX=RVEC(ITCOL) IMAX=ITCOL END IF END DO MAX2=0 DO ITCOL=1,NCOL IF ( (RVEC(ITCOL).GT.MAX2).AND.(ITCOL.NE.IMAX) ) THEN MAX2=RVEC(ITCOL) END IF END DO C---- difference onto grid IF (SCALE_LOC.GT.0) THEN DIFF=(MAX-MAX2)*10./SCALE_LOC ELSE DIFF=0 END IF FIRELIND_2ND=MIN(9,INT(DIFF)) END ***** end of FIRELIND_2ND ***** ------------------------------------------------------------------ ***** FCT FIRELIND_2ND3OFF ***** ------------------------------------------------------------------ C---- C---- NAME : FIRELIND_2ND3OFF C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Returns the difference between largest and 2nd * * -------- largest component of a vector, projected onto a * * grid 0-9. The 2nd largest value has to be 3 * * units off the maximum * * input: RVEC, NCOLMAX, NCOL * * output: 0-9 * *----------------------------------------------------------------------* INTEGER FUNCTION FIRELIND_2ND3OFF(NCOLMAX,NCOL,RVEC) IMPLICIT NONE C---- variables passed INTEGER NCOLMAX,NCOL,IMAX REAL RVEC(1:NCOLMAX) C---- local variables INTEGER ITCOL REAL MAX,MAX2,DIFF ******------------------------------*-----------------------------****** IMAX= 0 C---- check limits IF (NCOL.EQ.0) THEN WRITE(6,'(T2,A,T10,A,T20,I5,T30,A,T40,I5)')'***', + 'ERROR in lib-prot.f Function FIRELIND_2nd3off: NROW OR NCOL=0' WRITE(6,'(T2,A,T10,A)')'***','ncol=',ncol STOP END IF C---- compute maximum and 2nd3off largest MAX=0 DO ITCOL=1,NCOL IF (RVEC(ITCOL).GT.MAX) THEN MAX=RVEC(ITCOL) IMAX=ITCOL END IF END DO MAX2=0 DO ITCOL=1,NCOL IF ((ITCOL.GT.(IMAX+2)).OR.(ITCOL.LT.(IMAX-2))) THEN IF (RVEC(ITCOL).GT.MAX2) THEN MAX2=RVEC(ITCOL) END IF END IF END DO C---- difference onto grid C !SCALE! DIFF=(MAX-MAX2)*30. C DIFF=(MAX-MAX2)*10. FIRELIND_2ND3OFF=MIN(9,INT(DIFF)) C write(6,'(a,t20,f6.2,i3,t30,10i4)') C + 'x.x firelind: ',diff,FIRELIND_2nd3off, C + (int(100*rvec(itcol)),itcol=1,10) END ***** end of FIRELIND_2ND3OFF ***** ------------------------------------------------------------------ ***** FCT FL_OTHER ***** ------------------------------------------------------------------ C---- C---- NAME : FL_OTHER C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1995 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* LOGICAL FUNCTION FL_OTHER(INPUT) IMPLICIT NONE CHARACTER*24 INPUT ******------------------------------*-----------------------------****** IF ((INPUT(24:24).EQ.'7').OR.(INPUT(24:24).EQ.'8').OR. + (INPUT(24:24).EQ.'9').OR.(INPUT(24:24).EQ.'0')) THEN FL_OTHER=.TRUE. ELSE C FL_OTHER=.TRUE. FL_OTHER=.FALSE. END IF END ***** end of FL_OTHER ***** ------------------------------------------------------------------ ***** FCT FR_EXP_TO_REXP ***** ------------------------------------------------------------------ C---- C---- NAME : FR_EXP_TO_REXP C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The passed accessibility is normalised according * * -------- to the amino acid type passed. * * input : EXPIN accessibility from DSSP * * ------- AAIN 1 letter symbol for amino acid * * output : FR_EXP_TO_REXP accessibility normalised * * SBRs calling: from lib-prot.f: * * -------------- FCCONV_LOWCASE_AA_TO_CYS * *----------------------------------------------------------------------* REAL FUNCTION FR_EXP_TO_REXP(EXPIN,AAIN) IMPLICIT NONE C---- variables passed from/to SBR calling INTEGER EXPIN CHARACTER*1 AAIN C---- local function CHARACTER*1 FCCONV_LOWCASE_AA_TO_CYS C---- local variables INTEGER ITER,THRESHR(1:26),ITFOUND CHARACTER*1 AA(1:26),AAX LOGICAL LFOUND ******------------------------------*-----------------------------****** C---- defaults ITFOUND= 0 AA(1)= 'A' C D or N AA(2)= 'B' AA(3)= 'C' AA(4)= 'D' AA(5)= 'E' AA(6)= 'F' AA(7)= 'G' AA(8)= 'H' AA(9)= 'I' AA(10)='K' AA(11)='L' AA(12)='M' AA(13)='N' AA(14)='P' AA(15)='Q' AA(16)='R' AA(17)='S' AA(18)='T' AA(19)='V' AA(20)='W' C undetermined AA(21)='X' AA(22)='Y' C E or Q AA(23)='Z' C---- from FADENUDEL (Reinhard) THRESHR(1) =106 THRESHR(2) =160 THRESHR(3) =135 THRESHR(4) =163 THRESHR(5) =194 THRESHR(6) =197 THRESHR(7) = 84 THRESHR(8) =184 THRESHR(9) =169 THRESHR(10)=205 THRESHR(11)=164 THRESHR(12)=188 THRESHR(13)=157 THRESHR(14)=136 THRESHR(15)=198 THRESHR(16)=248 THRESHR(17)=130 THRESHR(18)=142 THRESHR(19)=142 THRESHR(20)=227 C---- without real reason! THRESHR(21)=180 THRESHR(22)=222 THRESHR(23)=196 C-------------------------------------------------- C---- C-------------------------------------------------- C---- convert [a-z] to C C ------------------------ AAX=FCCONV_LOWCASE_AA_TO_CYS(AAIN) C ------------------------ LFOUND=.FALSE. DO ITER=1,23 IF ((LFOUND.EQV. .FALSE.).AND.(AA(ITER).EQ.AAX)) THEN LFOUND=.TRUE. ITFOUND=ITER END IF END DO FR_EXP_TO_REXP=1. IF (LFOUND.EQV. .TRUE.) THEN IF (THRESHR(ITFOUND).GT.0) THEN FR_EXP_TO_REXP=MIN(1.,EXPIN/REAL(THRESHR(ITFOUND))) END IF END IF END ***** end of FR_EXP_TO_REXP ***** ------------------------------------------------------------------ ***** FCT FR_REXP_TO_EXP ***** ------------------------------------------------------------------ C---- C---- NAME : FR_REXP_TO_EXP C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The passed relative exposure is multiplied by the* * -------- maximal exposure of the amino acid passed. * * input : REXPIN accessibility from DSSP * * ------- AAIN 1 letter symbol for amino acid * * output : FR_REXP_TO_EXP accessibility normalised * * SBRs calling: from lib-prot.f: * * -------------- FCCONV_LOWCASE_AA_TO_CYS * *----------------------------------------------------------------------* REAL FUNCTION FR_REXP_TO_EXP(REXPIN,AAIN) IMPLICIT NONE C---- variables passed from/to SBR calling REAL REXPIN CHARACTER*1 AAIN C---- local function CHARACTER*1 FCCONV_LOWCASE_AA_TO_CYS C---- local variables INTEGER ITER,THRESHR(1:26),ITFOUND CHARACTER*1 AA(1:26),AAX LOGICAL LFOUND ******------------------------------*-----------------------------****** * execution of function * C---- defaults ITFOUND= 0 AA(1)= 'A' C D or N AA(2)= 'B' AA(3)= 'C' AA(4)= 'D' AA(5)= 'E' AA(6)= 'F' AA(7)= 'G' AA(8)= 'H' AA(9)= 'I' AA(10)='K' AA(11)='L' AA(12)='M' AA(13)='N' AA(14)='P' AA(15)='Q' AA(16)='R' AA(17)='S' AA(18)='T' AA(19)='V' AA(20)='W' C undetermined AA(21)='X' AA(22)='Y' C E or Q AA(23)='Z' C---- from FADENUDEL (Reinhard) THRESHR(1) =106 THRESHR(2) =160 THRESHR(3) =135 THRESHR(4) =163 THRESHR(5) =194 THRESHR(6) =197 THRESHR(7) = 84 THRESHR(8) =184 THRESHR(9) =169 THRESHR(10)=205 THRESHR(11)=164 THRESHR(12)=188 THRESHR(13)=157 THRESHR(14)=136 THRESHR(15)=198 THRESHR(16)=248 THRESHR(17)=130 THRESHR(18)=142 THRESHR(19)=142 THRESHR(20)=227 C---- without real reason! THRESHR(21)=180 THRESHR(22)=222 THRESHR(23)=196 C-------------------------------------------------- C---- C-------------------------------------------------- C---- convert [a-z] to C C ------------------------ AAX=FCCONV_LOWCASE_AA_TO_CYS(AAIN) C ------------------------ LFOUND=.FALSE. DO ITER=1,23 IF ((LFOUND.EQV. .FALSE.).AND.(AA(ITER).EQ.AAX)) THEN LFOUND=.TRUE. ITFOUND=ITER END IF END DO IF (LFOUND .EQV. .TRUE.) THEN FR_REXP_TO_EXP=REXPIN*THRESHR(ITFOUND) ELSE FR_REXP_TO_EXP=100. END IF END ***** end of FR_REXP_TO_EXP ***** ------------------------------------------------------------------ ***** FCT FRCORRVEC ***** ------------------------------------------------------------------ C---- C---- NAME : FRCORRVEC C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Computes the correlation coefficient between all * * -------- elemnts of the two real vectors RVEC1, RVEC2: * * - * * FRCORRVEC= ---------------------------------------- * * sqrt{-**2} sqrt {-**2} * * input: VEC1, VEC2, MAXCOL, ICOL * * output: correlation between VEC1 and VEC2 * * ext. library: SISTZ1: setting zero all elements of an integer * * ------------- vector * *----------------------------------------------------------------------* REAL FUNCTION FRCORRVEC(NCOLMAX,NCOL,RVECX,RVECY,NORM) IMPLICIT NONE C---- variables passed INTEGER NCOLMAX,NCOL REAL NORM,RVECX(1:NCOLMAX),RVECY(1:NCOLMAX) C---- local variables INTEGER ITCOL REAL R_1,R_2,R_12,R_11,R_22,NOMINATOR,DENOMINATOR ******------------------------------*-----------------------------****** * NORM normalisation of components of the vectors to * * yield values < 1. * ******------------------------------*-----------------------------****** C---- check limits IF (NCOL.EQ.0) THEN WRITE(6,'(T2,A,T10,A,T20,I5,T30,A,T40,I5)')'***', + 'ERROR in lib-comp.f Function FRCORRVEC: NROW OR NCOL=0' WRITE(6,'(T2,A,T10,A)')'***','ncol=',ncol STOP END IF R_12=0 R_1=0 R_2=0 R_11=0 R_22=0 DO ITCOL=1,NCOL R_12=R_12+(RVECX(ITCOL)*RVECY(ITCOL)) R_1 =R_1 +RVECX(ITCOL) R_2 =R_2 +RVECY(ITCOL) R_11=R_11+(RVECX(ITCOL)*RVECX(ITCOL)) R_22=R_22+(RVECY(ITCOL)*RVECY(ITCOL)) END DO C---- normalise with the passed quantity NORM R_12=R_12/(NORM*NORM*NCOL) R_11=R_11/(NORM*NORM*NCOL) R_22=R_22/(NORM*NORM*NCOL) R_1=R_1/(NORM*NCOL) R_2=R_2/(NORM*NCOL) C---- normalise with dimension to obtain proper averages R_1 =R_1 /REAL(NCOL) R_2 =R_2 /REAL(NCOL) R_12=R_12/REAL(NCOL) R_11=R_11/REAL(NCOL) R_22=R_22/REAL(NCOL) C---- nominator: - NOMINATOR=R_12 - ( R_1*R_2 ) C---- denominator: - DENOMINATOR=SQRT( R_11 - (R_1*R_1) )*SQRT( R_22 - (R_2*R_2) ) IF (ABS(DENOMINATOR).GT.10E-15) THEN FRCORRVEC=NOMINATOR/DENOMINATOR ELSE FRCORRVEC=0. END IF END ***** end of FRCORRVEC ***** ------------------------------------------------------------------ ***** FCT FRCORRVEC_REAL4 ***** ------------------------------------------------------------------ C---- C---- NAME : FRCORRVEC_REAL4 C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Computes the correlation coefficient between all * * -------- elemnts of the two real vectors RVEC1, RVEC2: * * - * * FRCORRVEC= ---------------------------------------- * * sqrt{-**2} sqrt {-**2} * * input: VEC1, VEC2, MAXCOL, ICOL * * output: correlation between VEC1 and VEC2 * * ext. library: SISTZ1: setting zero all elements of an integer * * ------------- vector * *----------------------------------------------------------------------* REAL FUNCTION FRCORRVEC_REAL4(NCOLMAX,NCOL,RVECX,RVECY,NORM) IMPLICIT NONE C---- variables passed INTEGER NCOLMAX,NCOL REAL*4 RVECX(1:NCOLMAX),RVECY(1:NCOLMAX) REAL NORM C---- local variables INTEGER ITCOL REAL R_1,R_2,R_12,R_11,R_22,NOMINATOR,DENOMINATOR, + NORM_NCOL ******------------------------------*-----------------------------****** * NORM normalisation of components of the vectors to * * yield values < 1. * ******------------------------------*-----------------------------****** C---- check limits IF (NCOL.EQ.0) THEN WRITE(6,'(T2,A,T10,A,T20,I5,T30,A,T40,I5)')'***', + 'ERROR in lib-comp.f Function FRCORRVEC_REAL4: NCOL=0' WRITE(6,'(T2,A,T10,A)')'***','ncol=',ncol STOP END IF C---- R_12= < m1(i,j) * m2(i,j) > C---- R_1= C---- R_2= C---- R_11= C---- R_22= R_12=0 R_1=0 R_2=0 R_11=0 R_22=0 DO ITCOL=1,NCOL R_12=R_12+(RVECX(ITCOL)*RVECY(ITCOL)) R_1 =R_1 +RVECX(ITCOL) R_2 =R_2 +RVECY(ITCOL) R_11=R_11+(RVECX(ITCOL)*RVECX(ITCOL)) R_22=R_22+(RVECY(ITCOL)*RVECY(ITCOL)) END DO C---- normalise with the passed quantity NORM NORM_NCOL=NORM*NCOL IF ((NORM.NE.1).AND.(ABS(NORM_NCOL).GT.10E-15)) THEN R_12=R_12/(NORM*NORM*NCOL) R_11=R_11/(NORM*NORM*NCOL) R_22=R_22/(NORM*NORM*NCOL) R_1=R_1/(NORM*NCOL) R_2=R_2/(NORM*NCOL) ELSEIF ((ABS(NORM_NCOL).LE.10E-15)) THEN R_12=0 R_11=0 R_22=0 R_1=0 R_2=0 END IF C---- normalise with dimension to obtain proper averages IF (NCOL.EQ.0) THEN R_1 =R_1 /REAL(NCOL) R_2 =R_2 /REAL(NCOL) R_12=R_12/REAL(NCOL) R_11=R_11/REAL(NCOL) R_22=R_22/REAL(NCOL) ELSE R_12=0 R_11=0 R_22=0 R_1=0 R_2=0 END IF C---- nominator: - C NOMINATOR=R_XY - ( R_X*R_Y ) NOMINATOR=R_12 - ( R_1*R_2 ) C---- denominator: - C DENOMINATOR=SQRT( (R_XX-(R_X*R_X))*(R_YY-(R_Y*R_Y)) ) DENOMINATOR=SQRT( (R_11-(R_1*R_1))*(R_22-(R_2*R_2)) ) C write(6,'(t2,a,t30,f6.3,t40,a,t50,f6.3)') C + 'x.x frcorrvec_real4: nom=',nominator,'den ',denominator C write(6,'(t2,a,t30,5f8.3)')'x.x sq

sq

', C + R_1,R_11,R_2,R_22,R_12 IF (ABS(DENOMINATOR).GT.10E-15) THEN FRCORRVEC_REAL4=NOMINATOR/DENOMINATOR ELSE FRCORRVEC_REAL4=0. END IF END ***** end of FRCORRVEC_REAL4 ***** ------------------------------------------------------------------ ***** FCT FRDIVIDE_SAFE ***** ------------------------------------------------------------------ C---- C---- NAME : FRDIVIDE_SAFE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Divides NOM/DEN, returns 0 if ABS(DEN)<10E-15. * * input : NOM, DEN * *----------------------------------------------------------------------* REAL FUNCTION FRDIVIDE_SAFE(NOM,DEN) IMPLICIT NONE C---- variables passed from/to SBR calling REAL NOM,DEN ******------------------------------*-----------------------------****** * execution of function * IF (ABS(DEN).LT.10E-15) THEN FRDIVIDE_SAFE=0 ELSE FRDIVIDE_SAFE=NOM/DEN END IF END ***** end of FRDIVIDE_SAFE ***** ------------------------------------------------------------------ ***** FCT FWRITE_STRING_NUMBERS ***** ------------------------------------------------------------------ C---- C---- NAME : FWRITE_STRING_NUMBERS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Apr, 1993 version 0.1 * * changed: Apr, 1993 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* CHARACTER*222 FUNCTION FWRITE_STRING_NUMBERS(L80,ILINE) IMPLICIT NONE C---- local variables * INTEGER ILINE CHARACTER*222 CHARLINE LOGICAL L80 ******------------------------------*-----------------------------****** C---- write for 80 characters per line IF (L80.EQV. .TRUE.) THEN IF ((ILINE.EQ.1).OR.(ILINE.GT.13)) THEN CHARLINE(1:40) ='....,....1....,....2....,....3....,....4' CHARLINE(41:80)='....,....5....,....6....,....7....,....8' ELSEIF (ILINE.EQ.2) THEN CHARLINE(1:40) ='....,....9....,....10...,....11...,....1' CHARLINE(41:80)='2...,....13...,....14...,....15...,....1' ELSEIF (ILINE.EQ.3) THEN CHARLINE(1:40) ='6...,....17...,....18...,....19...,....2' CHARLINE(41:80)='0...,....21...,....22...,....23...,....2' ELSEIF (ILINE.EQ.4) THEN CHARLINE(1:40) ='4...,....25...,....26...,....27...,....2' CHARLINE(41:80)='8...,....29...,....30...,....31...,....3' ELSEIF (ILINE.EQ.5) THEN CHARLINE(1:40) ='2...,....33...,....34...,....35...,....3' CHARLINE(41:80)='6...,....37...,....38...,....39...,....4' ELSEIF (ILINE.EQ.6) THEN CHARLINE(1:40) ='0...,....41...,....42...,....43...,....4' CHARLINE(41:80)='4...,....45...,....46...,....47...,....4' ELSEIF (ILINE.EQ.7) THEN CHARLINE(1:40) ='8...,....49...,....50...,....51...,....5' CHARLINE(41:80)='2...,....53...,....54...,....55...,....5' ELSEIF (ILINE.EQ.8) THEN CHARLINE(1:40) ='6...,....57...,....58...,....59...,....6' CHARLINE(41:80)='0...,....61...,....62...,....63...,....6' ELSEIF (ILINE.EQ.9) THEN CHARLINE(1:40) ='4...,....65...,....66...,....67...,....6' CHARLINE(41:80)='8...,....69...,....70...,....71...,....7' ELSEIF (ILINE.EQ.10) THEN CHARLINE(1:40) ='2...,....73...,....74...,....75...,....7' CHARLINE(41:80)='6...,....77...,....78...,....79...,....8' ELSEIF (ILINE.EQ.11) THEN CHARLINE(1:40) ='0...,....81...,....82...,....83...,....8' CHARLINE(41:80)='4...,....85...,....86...,....87...,....8' ELSEIF (ILINE.EQ.12) THEN CHARLINE(1:40) ='8...,....89...,....90...,....91...,....9' CHARLINE(41:80)='2...,....93...,....94...,....95...,....9' ELSEIF (ILINE.EQ.13) THEN CHARLINE(1:40) ='6...,....97...,....98...,....99...,....1' CHARLINE(41:80)='00..,....110..,....120..,....130..,....1' ELSEIF (ILINE.EQ.14) THEN CHARLINE(1:40) ='140.,....150..,....160..,....170..,....1' CHARLINE(41:80)='80..,....190..,....200..,....210..,....2' ELSEIF (ILINE.EQ.15) THEN CHARLINE(1:40) ='230.,....240..,....250..,....260..,....2' CHARLINE(41:80)='70..,....280..,....290..,....300..,....2' ELSEIF (ILINE.EQ.16) THEN CHARLINE(1:40) ='310.,....320..,....330..,....340..,....3' CHARLINE(41:80)='50..,....360..,....370..,....380..,....3' ELSEIF (ILINE.EQ.17) THEN CHARLINE(1:40) ='390.,....400..,....410..,....420..,....4' CHARLINE(41:80)='30..,....440..,....450..,....460..,....4' ELSEIF (ILINE.EQ.18) THEN CHARLINE(1:40) ='470.,....480..,....490..,....500..,....5' CHARLINE(41:80)='10..,....520..,....530..,....540..,....5' ELSEIF (ILINE.EQ.19) THEN CHARLINE(1:40) ='550.,....560..,....570..,....580..,....5' CHARLINE(41:80)='90..,....600..,....610..,....620..,....5' ELSE CHARLINE(1:40) ='x0..,....x1...,....x2...,....x3...,....x' CHARLINE(41:80)='4...,....x5...,....x6...,....x7...,....8' END IF C---- write for 60 characters per line ELSE IF ((ILINE.EQ.1).OR.(ILINE.GT.18)) THEN CHARLINE(1:40) ='....,....1....,....2....,....3....,....4' CHARLINE(41:60)='....,....5....,....6' ELSEIF (ILINE.EQ.2) THEN CHARLINE(1:40) ='....,....7....,....8....,....9....,....1' CHARLINE(41:60)='0...,....11...,....1' ELSEIF (ILINE.EQ.3) THEN CHARLINE(1:40) ='2...,....13...,....14...,....15...,....1' CHARLINE(41:60)='6...,....17...,....1' ELSEIF (ILINE.EQ.4) THEN CHARLINE(1:40) ='8...,....19...,....20...,....21...,....2' CHARLINE(41:60)='2...,....23...,....2' ELSEIF (ILINE.EQ.5) THEN CHARLINE(1:40) ='4...,....25...,....26...,....27...,....2' CHARLINE(41:60)='8...,....29...,....3' ELSEIF (ILINE.EQ.6) THEN CHARLINE(1:40) ='0...,....31...,....32...,....33...,....3' CHARLINE(41:60)='4...,....35...,....3' ELSEIF (ILINE.EQ.7) THEN CHARLINE(1:40) ='6...,....37...,....38...,....39...,....4' CHARLINE(41:60)='0...,....41...,....4' ELSEIF (ILINE.EQ.8) THEN CHARLINE(1:40) ='2...,....43...,....44...,....45...,....4' CHARLINE(41:60)='6...,....47...,....4' ELSEIF (ILINE.EQ.9) THEN CHARLINE(1:40) ='8...,....49...,....50...,....51...,....5' CHARLINE(41:60)='2...,....53...,....5' ELSEIF (ILINE.EQ.10) THEN CHARLINE(1:40) ='4...,....55...,....56...,....57...,....5' CHARLINE(41:60)='8...,....59...,....6' ELSEIF (ILINE.EQ.11) THEN CHARLINE(1:40) ='0...,....61...,....62...,....63...,....6' CHARLINE(41:60)='4...,....65...,....6' ELSEIF (ILINE.EQ.12) THEN CHARLINE(1:40) ='6...,....67...,....68...,....69...,....7' CHARLINE(41:60)='0...,....71...,....7' ELSEIF (ILINE.EQ.13) THEN CHARLINE(1:40) ='2...,....73...,....74...,....75...,....7' CHARLINE(41:60)='6...,....77...,....7' ELSEIF (ILINE.EQ.14) THEN CHARLINE(1:40) ='8...,....79...,....80...,....81...,....8' CHARLINE(41:60)='2...,....83...,....8' ELSEIF (ILINE.EQ.15) THEN CHARLINE(1:40) ='4...,....85...,....86...,....87...,....8' CHARLINE(41:60)='8...,....89...,....9' ELSEIF (ILINE.EQ.16) THEN CHARLINE(1:40) ='0...,....91...,....92...,....93...,....9' CHARLINE(41:60)='4...,....95...,....9' ELSEIF (ILINE.EQ.17) THEN CHARLINE(1:40) ='6...,....97...,....98...,....99...,....1' CHARLINE(41:60)='00..,....110..,....2' ELSEIF (ILINE.EQ.18) THEN CHARLINE(1:40) ='120.,....130..,....140..,....150..,....1' CHARLINE(41:60)='60..,....170..,....8' ELSEIF (ILINE.EQ.19) THEN CHARLINE(1:40) ='180.,....190..,....200..,....210..,....2' CHARLINE(41:60)='20..,....230..,....4' ELSEIF (ILINE.EQ.20) THEN CHARLINE(1:40) ='240.,....250..,....260..,....270..,....2' CHARLINE(41:60)='80..,....290..,....3' ELSEIF (ILINE.EQ.21) THEN CHARLINE(1:40) ='300.,....310..,....320..,....330..,....3' CHARLINE(41:60)='40..,....350..,....6' ELSEIF (ILINE.EQ.22) THEN CHARLINE(1:40) ='360.,....370..,....380..,....390..,....4' CHARLINE(41:60)='00..,....410..,....2' ELSEIF (ILINE.EQ.23) THEN CHARLINE(1:40) ='420.,....430..,....440..,....450..,....4' CHARLINE(41:60)='60..,....470..,....8' ELSEIF (ILINE.EQ.24) THEN CHARLINE(1:40) ='480.,....490..,....500..,....510..,....5' CHARLINE(41:60)='20..,....530..,....4' ELSEIF (ILINE.EQ.25) THEN CHARLINE(1:40) ='540.,....550..,....560..,....570..,....5' CHARLINE(41:60)='80..,....590..,....6' ELSE CHARLINE(1:40) ='x0..,....x1...,....x2...,....x3...,....x' CHARLINE(41:60)='4...,....x5...,....6' END IF END IF FWRITE_STRING_NUMBERS=CHARLINE END ***** end of FWRITE_STRING_NUMBERS ***** ------------------------------------------------------------------ ***** SUB GETCHAR ***** ------------------------------------------------------------------ C---- C---- NAME : GETCHAR C---- ARG : C---- DES : prompts for printable (keyboard) characters C---- DES : Caution: line with '$!' is truncated as comment C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE GETCHAR(KCHAR,CHARARR,CTEXT) LOGICAL EMPTYSTRING CHARACTER*222 LINE CHARACTER*222 CTEXT CHARACTER CHARARR*(*) WRITE(*,*) WRITE(*,*)'================================================='// + '==============================' CALL WRITELINES(CTEXT) IF(KCHAR.LT.1)THEN WRITE(*,*)'*** CHARPROMPT: illegal KCHAR',KCHAR RETURN ENDIF 10 CONTINUE WRITE(*,*) IF(KCHAR.GT.1) THEN WRITE(*,'(2X,''Enter letter string of length <'',I3)')KCHAR ELSE WRITE(*,'(2X,''Enter one letter !'')') ENDIF WRITE(*,'(2X,''[CR=default]: '')') WRITE(*, '(2X,''Default: '',80A1)' ) (CHARARR(K:K),K=1,KCHAR) LINE=' ' READ(*,'(A80)',ERR=10,END=11) LINE IF(.NOT.EMPTYSTRING(LINE)) THEN C ! assuming default values were set outside .... C...remove comments ( 34535345 !$ comment ) KCOMMENT=INDEX(LINE,'!$') IF(KCOMMENT.NE.0) LINE(KCOMMENT:80)=' ' DO I=1,80 IF (INDEX(' ABCDEFGHIJKLMNOPQRSTUVWXYZ',LINE(I:I)) + .EQ.0) THEN IF (INDEX(' abcdefghijklmnopqrstuvwxyz',LINE(I:I)) + .EQ.0) THEN C IF (INDEX('~!@#$%^&*()_+=-{}[]:""|\;,' ,LINE(I:I)) IF (INDEX('~!@#$%^&*()_+=-{}[]:""|;,' ,LINE(I:I)) + .EQ.0) THEN IF (INDEX('.?/><1234567890 ',LINE(I:I)) + .EQ.0) THEN WRITE(*, + '(2X,''*** characters only, not: '',A40)') + LINE(1:40) GO TO 10 ENDIF ENDIF ENDIF ENDIF ENDDO READ(LINE,'(80A1)',ERR=10,END=99) (CHARARR(K:K),K=1,KCHAR) ENDIF 11 WRITE(*,'(2X,A7,60A1)') ' echo: ', (CHARARR(K:K),K=1,KCHAR) RETURN 99 WRITE(*,*)' CHARPROMPT: END OF LINE DURING READ - check format!' END ***** end of GETCHAR ***** ------------------------------------------------------------------ ***** SUB GET_ARGUMENT ***** ------------------------------------------------------------------ C---- C---- NAME : GET_ARGUMENT C---- ARG : NUMBER,ARGUMENT C---- DES : returns the content of x-th argument C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE GET_ARGUMENT(INUMBER,ARGUMENT) CHARACTER*222 ARGUMENT INTEGER INUMBER CALL GETARG(INUMBER,ARGUMENT) RETURN END ***** end of GET_ARGUMENT ***** ------------------------------------------------------------------ ***** SUB GET_ARG_NUMBER ***** ------------------------------------------------------------------ C---- C---- NAME : GET_ARG_NUMBER C---- ARG : INUMBER C---- DES : returns number of arguments C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE GET_ARG_NUMBER(INUMBER) INTEGER INUMBER,IARGC INUMBER=0 INUMBER=IARGC() RETURN END ***** end of GET_ARG_NUMBER ***** ------------------------------------------------------------------ ***** SUB SCHECKPASS ***** ------------------------------------------------------------------ C---- C---- NAME : SCHECKPASS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Sep, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: Check whether arrays passed between SBRs are cor-* C -------- rectly passed or not * C input variables:CHVP1-N,CHVPL * C output variab.: LERRCHVP,POSERRCHVP * C----------------------------------------------------------------------- SUBROUTINE SCHECKPASS(CHVPM,CHVPL,LERRCHVP) IMPLICIT NONE C---- local variables * INTEGER ITER,CHVPM(*),CHVPL LOGICAL LERRCHVP,LPOSERRCHVP(1:50) ******------------------------------*-----------------------------****** C---- initial check of maximal dimension IF (CHVPL.GT.10) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'WARNING: SCHECKPASS:number of passed variables not fitting' END IF LERRCHVP=.FALSE. DO ITER=1,CHVPL LPOSERRCHVP(ITER)=.FALSE. END DO DO ITER=1,CHVPL IF (CHVPM(ITER).NE.ITER) THEN LPOSERRCHVP(ITER)=.TRUE. LERRCHVP=.TRUE. WRITE(6,*)'x.x',iter,' - chvpm=',chvpm(iter) END IF END DO IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for SCHECKPASS: variables passed not correct !' DO ITER=1,CHVPL IF (LPOSERRCHVP(ITER).EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A,T60,I4)')'***', + 'The check detected a fault for variable:',ITER END IF END DO END IF END ***** end of SCHECKPASS ***** ------------------------------------------------------------------ ***** SUB SEVALINFOFILE ***** ------------------------------------------------------------------ C---- C---- NAME : SEVALINFOFILE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The information (entropy) for the current output * * -------- is computed). * * input variables:NSECELLIB, MATNUMALL * * output variab.: INFO, NORMINFO * * called by: SEVALSEC (in lib-prot.f) * * SBRs calling: functions from lib-comp.f: * * FRMEAN1,FRVAR1 * * procedure: Sinfo= ln [ (n!) / prod/s {n(s)!} ] + * * ---------- - sum /[s] * * ln [ (m(s)!) / prod/s {m(s,s')!} ] * * normalization: by: n*ln(3) - ln(n) -ln(2*pi) + * * + 1.5 ln(3) * * new formulation according to JuMBo: * * a(i): number of predicted in structure i * * b(i): number of observed in structure i * * A(ij):predicted in j, observed in i * * sum/i {a(i)ln a(i)} - sum/ij {A(ij)ln A(ij)} * * I = 1 - -------------------------------------------- * * N ln N - sum/i {b(i) ln b(i) } * *----------------------------------------------------------------------* SUBROUTINE SEVALINFOFILE(KUNIT,NSECELLIB,MAXNSECEL, + MATNUMALL,INFO,INFO_INV,LWRITE) IMPLICIT NONE C---- passed variables INTEGER NSECELLIB,KUNIT,MAXNSECEL, + MATNUMALL(1:(MAXNSECEL+1),1:(MAXNSECEL+1)) REAL INFO,INFO_INV C---- local variables * INTEGER ITSEC,ITSEC2 REAL INTER,SUM,N,NOMINATOR,DENOMINATOR, + TERM_AIJ,TERM_PRED,TERM_DSSP,TERM_N LOGICAL LWRITE ******------------------------------*-----------------------------****** *--------------------- * * passed variables * * INFO information as defined in procedure above * * INFO_INV same as info but now as %of predicted so to speak* * KUNIT number of unit to write the files upon * * LWRITE if true the results are written onto the KUNIT * * MAXNSECEL maximal number of secondary structures for array * * boundaries * * MATNUM(i,j) the number of residues in a certain secondary * * structure, i labels DSSP assignment, i.e. all * * numbers with i=1 are according to DSSP helices, * * j labels the prediction. That means, e.g.: * * MATNUM(1,1) are all DSSP helices predicted to be * * a helix, MATNUM(1,2) those DSSP helices predicted* * as strands and MATNUM(1,4) all DSSP helices, resp. * MATNUM(4,4) all residues predicted. * * N total number of residues * * NOMINATOR = TERM_PRED - TERM_AIJ * * NSECEL number of secondary structure types used * *--------------------- * * local variables * * MUE,NUE,ITSEC,ITSEC2,ITER,ITHISTO,ITFILES iteration variables * * NOMINATOR = TERM_PRED - TERM_AIJ * * TERM_AIJ sum/ij of A(ij): number of residues predicted in * * structure j, observed in i * * TERM_DSSP sum over residues observed in: H + E + L * * TERM_N N * ln (N) * * TERM_PRED sum over residues predicted in: H + E + L * ******------------------------------*-----------------------------****** TERM_N= 0 C---- compute the mixed term: m(s,s2) A(ij) SUM=0. DO ITSEC2=1,NSECELLIB DO ITSEC=1,NSECELLIB INTER=REAL(MATNUMALL(ITSEC,ITSEC2)) IF (INTER.GT.0) THEN SUM=SUM+( (INTER+0.5) * LOG(INTER) ) END IF END DO END DO TERM_AIJ=SUM C---- compute the term of sum over prediction m(s) = pred(i) SUM=0. DO ITSEC=1,NSECELLIB INTER=REAL(MATNUMALL((NSECELLIB+1),ITSEC)) IF (INTER.GT.0) THEN SUM=SUM+( (INTER+0.5) * LOG(INTER) ) END IF END DO TERM_PRED=SUM C---- compute the term stemming from the data bank n(s) = DSSP(i) SUM=0. DO ITSEC=1,NSECELLIB INTER=REAL(MATNUMALL(ITSEC,(NSECELLIB+1))) IF (INTER.GT.0) THEN SUM=SUM+( (INTER+0.5) * LOG(INTER) ) END IF END DO TERM_DSSP=SUM C---- compute the term for all residues N=REAL(MATNUMALL((NSECELLIB+1),(NSECELLIB+1))) IF (N.LT.10E15) THEN TERM_N=N * LOG (N) ELSE WRITE(6,'(T2,A,T10,A,T70,F12.1)')'***', + 'ERROR for computation of information: N too big=',N END IF C-------------------------------------------------- C---- add up all terms ----- C-------------------------------------------------- C---- %observed NOMINATOR =TERM_PRED - TERM_AIJ DENOMINATOR=TERM_N - TERM_DSSP IF (ABS(DENOMINATOR).GT.10E-15) THEN INFO=1-(NOMINATOR/DENOMINATOR) ELSE IF (NOMINATOR.GE.10E15) THEN INFO=0 ELSE INFO=10 END IF END IF C---- %predicted NOMINATOR =TERM_DSSP - TERM_AIJ DENOMINATOR=TERM_N - TERM_PRED IF (ABS(DENOMINATOR).GT.10E-15) THEN INFO_INV=1-(NOMINATOR/DENOMINATOR) ELSE IF (NOMINATOR.GE.10E15) THEN INFO_INV=0 ELSE INFO_INV=10 END IF END IF C---- write results onto printer IF (LWRITE .EQV. .TRUE.) THEN WRITE(KUNIT,'(T57,A10,F6.3,A9,F6.3,A2)') + '| I %obs= ',INFO,', %pred= ',INFO_INV,' |' WRITE(KUNIT,'(T57,A)') + '+-------------------------------+' WRITE(KUNIT,'(T2,A)')'---' END IF END ***** end of SEVALINFOFILE ***** ------------------------------------------------------------------ ***** SUB SEVALLEN ***** ------------------------------------------------------------------ C---- C---- NAME : SEVALLEN C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Apr, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The lengths and number of the secondary structure* * -------- elements for a given protein are evaluated. * * input variables:NSECELLIB,LENGTHLIB,NHISTOLIB,DSSPCHAR,PREDCHAR * * output variab.: MATLEN,MATLENDIS * * called by: SEVALSEC (in lib-prot.f) * * procedure: straightforward * *----------------------------------------------------------------------* SUBROUTINE SEVALLEN(NSECELLIB,MAXNSECEL,LENGTHLIB,MAXLENGTH, + NHISTOLIB,MAXNHISTO,DSSPCHAR,PREDCHAR,MATLEN,MATLENDIS) IMPLICIT NONE C---- local parameter * LOGICAL LWRT PARAMETER (LWRT=.FALSE.) C PARAMETER (LWRT=.TRUE.) C---- * C---- variables passed INTEGER MAXNSECEL,MAXLENGTH,MAXNHISTO,NSECELLIB, + LENGTHLIB,NHISTOLIB,MATLEN(1:(MAXNSECEL+1),1:4), + MATLENDIS(1:MAXNHISTO,1:(2*MAXNSECEL)) CHARACTER*1 DSSPCHAR(1:MAXLENGTH),PREDCHAR(1:MAXLENGTH) C---- local variables INTEGER ITSEC,ITEL,ITHISTO,MUE,IHELP INTEGER COUNTMUE,COUNTSTR,ELNO,ELLEN(1:2000), + ELNOTOT(1:9),ELLENTOT(1:9) LOGICAL NEWSTR,LHELP CHARACTER*1 SSCHAR(1:8),CURSTR,ELCHAR(1:2000) ******------------------------------*-----------------------------****** * MUE,NUE,ITSEC,ITSEC2,ITER,ITHISTO,ITFILES iteration variables * * COUNTMUE counts the number of samples * * =sum(nue=1,numprottest){numrestest(nue)} * * COUNTSTR counts the number of secondary elements within * * each protein, resp. the sum over all proteins * * CURSTR stores intermediately the name of the currently * * treate secondary element * * DSSPCHAR(i) secondary structure according to DSSP for a par- * * ticular protein * * ELCHAR(i) one-letter symbol of secondary structure for * * the i-th element * * ELDIS(c,h) number of elements of class c with length h * * ELNO number of secondary elements * * ELNOTOT(c) distinct number of all elements of class * * * ELLEN(i) length (number of residues) for element i * * ELLENTOT(c) summed length of all elements of class * * * LENGTHLIB current length of protein * * LWRT if true certain information is written onto prin-* * ter, e.g. the length distribution * * MATLEN(i,j) matrix with the lengths of the elements: * * i=1,4 => H,E,C,all * * j=1 => number of elements DSSP * * j=2 => number of elements PRED * * j=2 => summed length of all elements for DSSP * * j=2 => summed length of all elements for PRED * * MATLENDIS(i,j) gives the distribution of the elements * * i=1,50=> for histogram (lengths 1-50) * * j=1,3 => H,E,C for DSSP * * j=4,6 => H,E,C for PRED * * MAXLENGTH maximal length of current protein allowed * * MAXNHISTO maximal number of columns for histogram * * MAXNSECEL maximal number of secondary structures allowed * * NEWSTR required for ending the summing up of the length * * of a particular structure * * NHISTOLIB number of columns for histogram of lenght distri-* * bution * * NSECELLIB currently read number of secondary structures * * NUMFILESREAD number of files to be read * * NUMPROTLIB number of proteins of particular file read * * PREDCHAR(i) secondary structure according to prediction for a* * particular protein * * SSCHAR(i) character giving the one-letter symbol for i-th * * secondary structure class * ******------------------------------*-----------------------------****** IF (LWRT .EQV. .TRUE.) THEN WRITE(6,'(T2,A3,T5,A50,T56,A)')'---', + 'computing the lengths of DSSP and PRED elements by', + ' SBR SEVALLEN form lib-prot.f' END IF C---- check variables passed IF (LENGTHLIB.GT.MAXLENGTH) THEN WRITE(6,'(T5,A)') + ' The length of the protein passed to SBR SEVALLEN' WRITE(6,'(T5,A)') + ' exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current length: ',LENGTHLIB,' allocated:',MAXLENGTH WRITE(6,'(T5,A)')' Stopped in SEVALLEN 12-2-92:1' STOP END IF IF (NSECELLIB.GT.MAXNSECEL) THEN WRITE(6,'(T5,A)') + 'The number of secondary structures passed to SBR SEVALLEN' WRITE(6,'(T5,A)') + 'exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current number: ',NSECELLIB,' allocated:',MAXNSECEL WRITE(6,'(T5,A)')' Stopped in SEVALLEN 12-2-92:2' STOP END IF C---- assign secondary characters SSCHAR(1)='H' SSCHAR(2)='E' SSCHAR(NSECELLIB)='L' IF (NSECELLIB.EQ.4) THEN SSCHAR(3)='T' ELSEIF (NSECELLIB.EQ.5) THEN SSCHAR(3)='T' SSCHAR(4)='S' ELSEIF (NSECELLIB.GT.5) THEN WRITE(6,'(T5,A)') + 'Caution: current version of SEVALLEN distinguishes' WRITE(6,'(T5,A)')'only five different secondary structures!' WRITE(6,'(T5,A)')'Stopped in SBR SEVALLEN: 12-2-92:3' STOP END IF C---- to be on the save side: substitute potential blanks by 'L' DO MUE=1,LENGTHLIB LHELP=.TRUE. DO ITSEC=1,(NSECELLIB-1) IF (LHELP.EQV. .TRUE. + .AND.(PREDCHAR(MUE).EQ.SSCHAR(ITSEC))) THEN LHELP=.FALSE. END IF END DO IF (LHELP .EQV. .TRUE.) THEN PREDCHAR(MUE)='L' END IF END DO C---- setting initially to zero (explicit as INTEGER*2) ELNO=0 CALL SISTZ1(ELLEN,2000) CALL SISTZ1(ELNOTOT,9) CALL SISTZ1(ELLENTOT,9) CALL SISTZ2(MATLENDIS,MAXNHISTO,(2*MAXNSECEL)) C-------------------------------------------------- C---- discriminate elements for DSSP ----- C-------------------------------------------------- C---- counting elements and summing up their lengths COUNTMUE=0 MUE=0 COUNTSTR=0 DO WHILE (MUE.LT.LENGTHLIB) COUNTSTR=COUNTSTR+1 NEWSTR=.FALSE. DO WHILE ((MUE.LT.(LENGTHLIB-1)).AND.(.NOT.NEWSTR)) MUE=MUE+1 COUNTMUE=COUNTMUE+1 CURSTR=DSSPCHAR(COUNTMUE) ELCHAR(COUNTSTR)=CURSTR ELLEN(COUNTSTR)=ELLEN(COUNTSTR)+1 IF (DSSPCHAR(COUNTMUE+1).NE.CURSTR) THEN NEWSTR=.TRUE. END IF END DO IF ((NEWSTR.EQV. .FALSE.).AND.(MUE.EQ.(LENGTHLIB-1))) THEN MUE=MUE+1 COUNTMUE=COUNTMUE+1 CURSTR=DSSPCHAR(COUNTMUE) ELCHAR(COUNTSTR)=CURSTR ELLEN(COUNTSTR)=ELLEN(COUNTSTR)+1 ELSEIF (NEWSTR.EQV. .TRUE. .AND.(MUE.EQ.(LENGTHLIB-1))) THEN MUE=MUE+1 COUNTMUE=COUNTMUE+1 COUNTSTR=COUNTSTR+1 CURSTR=DSSPCHAR(COUNTMUE) ELCHAR(COUNTSTR)=CURSTR ELLEN(COUNTSTR)=ELLEN(COUNTSTR)+1 END IF END DO ELNO=COUNTSTR C-------------------------------------------------- C---- compute total number of elements and ----- C---- averaged length for each secondary class ---- C-------------------------------------------------- DO ITEL=1,ELNO LHELP=.TRUE. DO ITSEC=1,NSECELLIB IF ((ELCHAR(ITEL).EQ.SSCHAR(ITSEC)).AND.LHELP) THEN ELNOTOT(ITSEC)=ELNOTOT(ITSEC)+1 ELLENTOT(ITSEC)=ELLENTOT(ITSEC)+ELLEN(ITEL) LHELP=.FALSE. END IF END DO END DO DO ITSEC=1,NSECELLIB ELNOTOT(NSECELLIB+1)=ELNOTOT(NSECELLIB+1)+ELNOTOT(ITSEC) ELLENTOT(NSECELLIB+1)= + ELLENTOT(NSECELLIB+1)+ELLENTOT(ITSEC) END DO DO ITSEC=1,(NSECELLIB+1) MATLEN(ITSEC,1)=ELNOTOT(ITSEC) MATLEN(ITSEC,3)=ELLENTOT(ITSEC) END DO C-------------------------------------------------- C---- evaluate desired distribution of elements --- C-------------------------------------------------- DO ITEL=1,ELNO IF (ELLEN(ITEL).LE.NHISTOLIB) THEN IHELP=ELLEN(ITEL) ELSE IHELP=NHISTOLIB END IF LHELP=.TRUE. DO ITSEC=1,(NSECELLIB-1) IF (LHELP.EQV. .TRUE. .AND. + (ELCHAR(ITEL).EQ.SSCHAR(ITSEC))) THEN MATLENDIS(IHELP,ITSEC)=MATLENDIS(IHELP,ITSEC)+1 LHELP=.FALSE. END IF END DO IF (LHELP .EQV. .TRUE.) THEN MATLENDIS(IHELP,NSECELLIB)=MATLENDIS(IHELP,NSECELLIB)+1 END IF END DO C---- write desired quantities seperately onto the printer C---- NOTE: INTERWRTDES is a local parameter, see above IF (LWRT .EQV. .TRUE.) THEN WRITE(6,'(T5,A,T20,A,T65,A)')' SEVALLEN:', + 'number of DSSP elements for each prot', + 'class: length' WRITE(6,'(T2,A,T15,30I3)')'X.X: LEN ', + (ELLEN(ITEL),ITEL=1,ELNO) IF (NSECELLIB.EQ.3) THEN WRITE(6,'(T2,A,T15,4I5)')'X.X: NOTOT:', + (ELNOTOT(ITSEC),ITSEC=1,NSECELLIB+1) WRITE(6,'(T2,A,T15,4I5)')' LENTOT:', + (ELLENTOT(ITSEC),ITSEC=1,NSECELLIB+1) ELSEIF (NSECELLIB.EQ.2) THEN WRITE(6,'(T2,A,T15,2I5)')'X.X: NOTOT:', + (ELNOTOT(ITSEC),ITSEC=1,NSECELLIB+1) WRITE(6,'(T2,A,T15,2I5)')' LENTOT:', + (ELLENTOT(ITSEC),ITSEC=1,NSECELLIB+1) ELSEIF (NSECELLIB.EQ.4) THEN WRITE(6,'(T2,A,T15,5I5)')'X.X: NOTOT:', + (ELNOTOT(ITSEC),ITSEC=1,NSECELLIB+1) WRITE(6,'(T2,A,T15,5I5)')' LENTOT:', + (ELLENTOT(ITSEC),ITSEC=1,NSECELLIB+1) END IF WRITE(6,*) WRITE(6,'(T5,A)')'distribution of DSSP elements' WRITE(6,'(T2,A2,T5,30I3)') + 'H:',(MATLENDIS(ITHISTO,3),ITHISTO=1,30) IF (NSECELLIB.GT.2) THEN WRITE(6,'(T2,A2,T5,30I3)') + 'E:',(MATLENDIS(ITHISTO,2),ITHISTO=1,30) END IF IF (NSECELLIB.GT.3) THEN WRITE(6,'(T2,A2,T5,30I3)') + 'T:',(MATLENDIS(ITHISTO,3),ITHISTO=1,30) END IF WRITE(6,'(T2,A2,T5,30I3)') + 'C:',(MATLENDIS(ITHISTO,NSECELLIB),ITHISTO=1,30) END IF C-------------------------------------------------- C---- discriminate elements for PRED ----- C-------------------------------------------------- C---- setting initially to zero ELNO=0 CALL SISTZ1(ELLEN,2000) CALL SISTZ1(ELNOTOT,9) CALL SISTZ1(ELLENTOT,9) C---- counting elements and summing up their lengths COUNTMUE=0 MUE=0 COUNTSTR=0 DO WHILE (MUE.LT.LENGTHLIB) COUNTSTR=COUNTSTR+1 NEWSTR=.FALSE. DO WHILE ((MUE.LT.(LENGTHLIB-1)).AND.(NEWSTR.EQV. .FALSE.)) MUE=MUE+1 COUNTMUE=COUNTMUE+1 CURSTR=PREDCHAR(COUNTMUE) ELCHAR(COUNTSTR)=CURSTR ELLEN(COUNTSTR)=ELLEN(COUNTSTR)+1 IF (PREDCHAR(COUNTMUE+1).NE.CURSTR) THEN NEWSTR=.TRUE. END IF END DO IF ((NEWSTR.EQV. .FALSE.).AND.(MUE.EQ.(LENGTHLIB-1))) THEN MUE=MUE+1 COUNTMUE=COUNTMUE+1 CURSTR=PREDCHAR(COUNTMUE) ELCHAR(COUNTSTR)=CURSTR ELLEN(COUNTSTR)=ELLEN(COUNTSTR)+1 ELSEIF (NEWSTR.EQV. .TRUE. .AND.(MUE.EQ.(LENGTHLIB-1))) THEN MUE=MUE+1 COUNTMUE=COUNTMUE+1 COUNTSTR=COUNTSTR+1 CURSTR=PREDCHAR(COUNTMUE) ELCHAR(COUNTSTR)=CURSTR ELLEN(COUNTSTR)=ELLEN(COUNTSTR)+1 END IF END DO ELNO=COUNTSTR C-------------------------------------------------- C---- compute total number of elements and ----- C---- averaged length for each secondary class ---- C-------------------------------------------------- DO ITEL=1,ELNO LHELP=.TRUE. DO ITSEC=1,NSECELLIB IF ((ELCHAR(ITEL).EQ.SSCHAR(ITSEC)).AND.LHELP) THEN ELNOTOT(ITSEC)=ELNOTOT(ITSEC)+1 ELLENTOT(ITSEC)=ELLENTOT(ITSEC)+ELLEN(ITEL) LHELP=.FALSE. END IF END DO END DO DO ITSEC=1,NSECELLIB ELNOTOT(NSECELLIB+1)=ELNOTOT(NSECELLIB+1)+ELNOTOT(ITSEC) ELLENTOT(NSECELLIB+1)= + ELLENTOT(NSECELLIB+1)+ELLENTOT(ITSEC) END DO DO ITSEC=1,(NSECELLIB+1) MATLEN(ITSEC,2)=ELNOTOT(ITSEC) MATLEN(ITSEC,4)=ELLENTOT(ITSEC) END DO C-------------------------------------------------- C---- evaluate desired distribution of elements --- C-------------------------------------------------- DO ITEL=1,ELNO IF (ELLEN(ITEL).LE.NHISTOLIB) THEN IHELP=ELLEN(ITEL) ELSE IHELP=NHISTOLIB END IF LHELP=.TRUE. DO ITSEC=1,(NSECELLIB-1) IF (LHELP.EQV. .TRUE. .AND. + (ELCHAR(ITEL).EQ.SSCHAR(ITSEC))) THEN MATLENDIS(IHELP,(NSECELLIB+ITSEC))= + MATLENDIS(IHELP,(NSECELLIB+ITSEC))+1 LHELP=.FALSE. END IF END DO IF (LHELP .EQV. .TRUE.) THEN MATLENDIS(IHELP,2*NSECELLIB)=MATLENDIS(IHELP,2*NSECELLIB)+1 END IF END DO C---- write desired quantities seperately onto the printer C---- NOTE: INTERWRTDES is a local parameter, see above IF (LWRT .EQV. .TRUE.) THEN WRITE(6,'(T5,A,T20,A,T65,A)')' SEVALLEN:', + 'number of predicted elements for each prot', + 'class: length' WRITE(6,'(T2,A,T15,30I3)')'X.X: LEN ', + (ELLEN(ITEL),ITEL=1,ELNO) IF (NSECELLIB.EQ.3) THEN WRITE(6,'(T2,A,T15,4I5)')'X.X: NOTOT:', + (ELNOTOT(ITSEC),ITSEC=1,NSECELLIB+1) WRITE(6,'(T2,A,T15,4I5)')' LENTOT:', + (ELLENTOT(ITSEC),ITSEC=1,NSECELLIB+1) ELSEIF (NSECELLIB.EQ.2) THEN WRITE(6,'(T2,A,T15,3I5)')'X.X: NOTOT:', + (ELNOTOT(ITSEC),ITSEC=1,NSECELLIB+1) WRITE(6,'(T2,A,T15,3I5)')' LENTOT:', + (ELLENTOT(ITSEC),ITSEC=1,NSECELLIB+1) ELSEIF (NSECELLIB.EQ.4) THEN WRITE(6,'(T2,A,T15,5I5)')'X.X: NOTOT:', + (ELNOTOT(ITSEC),ITSEC=1,NSECELLIB+1) WRITE(6,'(T2,A,T15,5I5)')' LENTOT:', + (ELLENTOT(ITSEC),ITSEC=1,NSECELLIB+1) END IF WRITE(6,*) WRITE(6,*)' distribution of predicted elements' WRITE(6,'(T2,A2,T5,30I3)') + 'H:',(MATLENDIS(ITHISTO,(NSECELLIB+1)),ITHISTO=1,30) IF (NSECELLIB.EQ.3) THEN WRITE(6,'(T2,A2,T5,30I3)') + 'E:',(MATLENDIS(ITHISTO,(NSECELLIB+2)),ITHISTO=1,30) WRITE(6,'(T2,A2,T5,30I3)') + 'L:',(MATLENDIS(ITHISTO,(NSECELLIB+3)),ITHISTO=1,30) ELSEIF (NSECELLIB.EQ.2) THEN WRITE(6,'(T2,A2,T5,30I3)') + 'L:',(MATLENDIS(ITHISTO,(NSECELLIB+2)),ITHISTO=1,30) ELSEIF (NSECELLIB.EQ.4) THEN WRITE(6,'(T2,A2,T5,30I3)') + 'E:',(MATLENDIS(ITHISTO,(NSECELLIB+2)),ITHISTO=1,30) WRITE(6,'(T2,A2,T5,30I3)') + 'T:',(MATLENDIS(ITHISTO,(NSECELLIB+3)),ITHISTO=1,30) WRITE(6,'(T2,A2,T5,30I3)') + 'L:',(MATLENDIS(ITHISTO,(NSECELLIB+4)),ITHISTO=1,30) END IF END IF END ***** end of SEVALLEN ***** ------------------------------------------------------------------ ***** SUB SEVALPO ***** ------------------------------------------------------------------ C---- C---- NAME : SEVALPO C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Apr, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The pay-offs of a certain prediction are computed* * -------- i.e.: MATNUM, asf. * * input variables:NSECELLIB,LENGTHLIB,DSSPCHAR,PREDCHAR * * output variab.: MATNUM,MATOFDSSP,MATOFPRED,Q3,SQ,CORR * * SBRs calling: SEVALQUO: computes MATOF*, Q3, SQ, CORR with * * -------------- passing MATNUM * * called by: SEVALSEC (in lib-prot.f) * *----------------------------------------------------------------------* SUBROUTINE SEVALPO(NSECELLIB,MAXNSECEL,LENGTHLIB,MAXLENGTH, + DSSPCHAR,PREDCHAR,MATNUM,MATQOFDSSP,MATQOFPRED,Q3,SQ,CORR) IMPLICIT NONE C---- variables passed INTEGER MAXNSECEL,MAXLENGTH,NSECELLIB,LENGTHLIB, + MATNUM(1:(MAXNSECEL+1),1:(MAXNSECEL+1)) REAL Q3,SQ,CORR(1:MAXNSECEL), + MATQOFDSSP(1:MAXNSECEL,1:MAXNSECEL), + MATQOFPRED(1:MAXNSECEL,1:MAXNSECEL) CHARACTER*1 SSCHAR(1:8) CHARACTER*1 DSSPCHAR(1:MAXLENGTH),PREDCHAR(1:MAXLENGTH) C---- local variables INTEGER ITSEC,ITSEC2,MUE,ISUM1,ISUM2 LOGICAL LHELP,LDSSP,LNET ******------------------------------*-----------------------------****** * MUE,ITSEC,ITSEC2 serve as iteration variables * * CORR(i) correlation for class i, see POTRAIN/TESTCOR * * DSSPCHAR(i) secondary structure according to DSSP for a par- * * ticular protein * * ISUM1,2 help variables required for computing sums * * LENGTHLIB current length of protein * * LHELP logical help variable for intermediately check * * LDSSP,LNET intermediate flags, used for checking whether for* * a particular residue there is any of the three * * classes: if not there is a fault * * MATNUM(i,j) the number of residues in a certain secondary * * structure, i labels DSSP assignment, i.e. all * * numbers with i=1 are according to DSSP helices, * * j labels the prediction. That means, e.g.: * * MATNUM(1,1) are all DSSP helices predicted to be * * a helix, MATNUM(1,2) those DSSP helices predicted* * as strands and MATNUM(1,4) all DSSP helices, resp. * MATNUM(4,4) all residues predicted. * * MATNUMALL MATNUM summed over all proteins of all files read* * MATOFDSSP(i,j) stores according to the same scheme as MATNUM the* * percentages of residues predicted divided by the * * numbers of DSSP (note there is no element (4,4) )* * MATOFPRED(i,j) same as previous but now percentages of prediction * MAXLENGTH maximal length of current protein allowed * * MAXNHISTO maximal number of columns for histogram * * MAXNUMPROT maximal number of proteins per read file * * MAXNSECEL maximal number of secondary structures allowed * * NSECELLIB currently read number of secondary structures * * PREDCHAR(i) secondary structure according to prediction for a* * particular protein * * Q3 =properly predicted for all classes/all residues * * SQ first divide predicted/DSSP in each class then * * sum all classes and divide by e.g. 3 * * SSCHAR(i) character giving the one-letter symbol for i-th * * secondary structure class * ******------------------------------*-----------------------------****** C---- check variables passed IF (LENGTHLIB.GT.MAXLENGTH) THEN WRITE(6,'(T5,A)') + ' The length of the protein passed to SBR SEVALPO' WRITE(6,'(T5,A)') + ' exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current length: ',LENGTHLIB,' allocated:',MAXLENGTH WRITE(6,'(T5,A)')' Stopped in SEVALPO 12-2-92:1' STOP END IF IF (NSECELLIB.GT.MAXNSECEL) THEN WRITE(6,'(T5,A)') + 'The number of secondary structures passed to SBR SEVALPO' WRITE(6,'(T5,A)') + 'exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current number: ',NSECELLIB,' allocated:',MAXNSECEL WRITE(6,'(T5,A)')' Stopped in SEVALPO 12-2-92:2' STOP END IF C---- assign secondary characters SSCHAR(1)='H' SSCHAR(2)='E' SSCHAR(NSECELLIB)='L' IF (NSECELLIB.EQ.4) THEN SSCHAR(3)='T' ELSEIF (NSECELLIB.EQ.5) THEN SSCHAR(3)='T' SSCHAR(4)='S' ELSEIF (NSECELLIB.GT.5) THEN WRITE(6,'(T5,A)') + 'Caution: current version of SEVALPO distinguishes' WRITE(6,'(T5,A)')'only five different secondary structures!' WRITE(6,'(T5,A)')'Stopped in SBR SEVALPO: 12-2-92:3' STOP END IF C---- to be on the save side: substitute potential blanks by 'L' DO MUE=1,LENGTHLIB LHELP=.TRUE. DO ITSEC=1,NSECELLIB IF (PREDCHAR(MUE).EQ.SSCHAR(ITSEC)) THEN LHELP=.FALSE. END IF END DO IF (LHELP .EQV. .TRUE.) THEN PREDCHAR(MUE)='L' END IF LHELP=.TRUE. DO ITSEC=1,NSECELLIB IF (DSSPCHAR(MUE).EQ.SSCHAR(ITSEC)) THEN LHELP=.FALSE. END IF END DO IF (LHELP .EQV. .TRUE.) THEN DSSPCHAR(MUE)='L' END IF END DO C---- initialize by setting zero DO ITSEC=1,(MAXNSECEL+1) DO ITSEC2=1,(MAXNSECEL+1) MATNUM(ITSEC,ITSEC2)=0 END DO END DO C-------------------------------------------------- C---- new number matrix ----- C-------------------------------------------------- C IF (.TRUE.) THEN C------- loop over all residues DO MUE=1,LENGTHLIB LDSSP=.TRUE. LNET=.TRUE. DO ITSEC=1,NSECELLIB IF (DSSPCHAR(MUE).EQ.SSCHAR(ITSEC)) THEN LDSSP=.FALSE. DO ITSEC2=1,NSECELLIB IF (PREDCHAR(MUE).EQ.SSCHAR(ITSEC2)) THEN LNET=.FALSE. MATNUM(ITSEC,ITSEC2)=MATNUM(ITSEC,ITSEC2)+1 END IF END DO END IF END DO C---------- consistency check IF (LNET.OR.LDSSP) THEN WRITE(6,*)'for mue=',mue,' :ldssp',ldssp, + ' lnet ',lnet,' with dssp=', + dsspchar(mue),' net:',predchar(mue) END IF END DO C------- summing up DO ITSEC=1,NSECELLIB DO ITSEC2=1,NSECELLIB MATNUM(ITSEC,(NSECELLIB+1))= + MATNUM(ITSEC,(NSECELLIB+1))+MATNUM(ITSEC,ITSEC2) MATNUM((NSECELLIB+1),ITSEC)= + MATNUM((NSECELLIB+1),ITSEC)+MATNUM(ITSEC2,ITSEC) END DO END DO ISUM1=0 ISUM2=0 DO ITSEC=1,NSECELLIB ISUM1=ISUM1+MATNUM(ITSEC,(NSECELLIB+1)) ISUM2=ISUM2+MATNUM((NSECELLIB+1),ITSEC) END DO C END IF IF (ISUM1.EQ.ISUM2) THEN MATNUM((NSECELLIB+1),(NSECELLIB+1))=ISUM1 ELSE WRITE(6,*)'number for dssp and net not equal!' WRITE(6,*)'new: evalpo,resp SEVALPO' WRITE(6,*)'for net:',ISUM2,' for DSSP:',ISUM1 END IF C---- compute quotients C ============= CALL SEVALQUO(NSECELLIB,MAXNSECEL,MATNUM, + MATQOFDSSP,MATQOFPRED,Q3,SQ,CORR) C ============= END ***** end of SEVALPO ***** ------------------------------------------------------------------ ***** SUB SEVALQUO ***** ------------------------------------------------------------------ C---- C---- NAME : SEVALQUO C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Apr, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The pay-offs of a certain prediction are computed* * -------- i.e.: quotients. * * input variables:NSECELLIB,MATNUM * * output variab.: MATOFDSSP,MATOFPRED,Q3,SQ,CORR * * called by: SEVALSEC (in lib-prot.f): computes MATNUM * * ---------- SEVALPO: (in lib-prot.f): computes MATNUM * *----------------------------------------------------------------------* SUBROUTINE SEVALQUO(NSECELLIB,MAXNSECEL,MATNUM, + MATQOFDSSP,MATQOFPRED,Q3,SQ,CORR) IMPLICIT NONE C---- variables passed INTEGER MAXNSECEL,NSECELLIB, + MATNUM(1:(MAXNSECEL+1),1:(MAXNSECEL+1)) REAL Q3,SQ,CORR(1:MAXNSECEL) REAL MATQOFDSSP(1:MAXNSECEL,1:MAXNSECEL) REAL MATQOFPRED(1:MAXNSECEL,1:MAXNSECEL) C---- local variables INTEGER ITSEC,ITSEC2,ITSEC3,ISUM1 INTEGER PRED(1:8),REJ(1:8),OVEREST(1:8),UNDEREST(1:8) REAL SQRT,DNM,DNM1,DNM2,DNM3,DNM4,CNT,CNT1,CNT2,RSUM ******------------------------------*-----------------------------****** * MUE,ITSEC,ITSEC2,ITSEC3 serve as iteration variables * * CNT/DNM used for intermediateyly computing a quotient * * CORR(i) correlation for class i, see POTRAIN/TESTCOR * * definition (Matthew) * * pred(i)*rej(i)-underest(i)*overest(i) * * /sqrt( (pred+under)(pred+over)(rej+under)(rej+over) )* * LENGTHLIB current length of protein * * LHELP logical help variable for intermediately check * * LDSSP,LNET intermediate flags, used for checking whether for* * a particular residue there is any of the three * * classes: if not there is a fault * * MATNUM(i,j) the number of residues in a certain secondary * * structure, i labels DSSP assignment, i.e. all * * numbers with i=1 are according to DSSP helices, * * j labels the prediction. That means, e.g.: * * MATNUM(1,1) are all DSSP helices predicted to be * * a helix, MATNUM(1,2) those DSSP helices predicted* * as strands and MATNUM(1,4) all DSSP helices, resp. * MATNUM(4,4) all residues predicted. * * MATNUMALL MATNUM summed over all proteins of all files read* * MATOFDSSP(i,j) stores according to the same scheme as MATNUM the* * percentages of residues predicted divided by the * * numbers of DSSP (note there is no element (4,4) )* * MATOFPRED(i,j) same as previous but now percentages of prediction * MAXNHISTO maximal number of columns for histogram * * MAXNSECEL maximal number of secondary structures allowed * * NSECELLIB currently read number of secondary structures * * OVEREST(i) number of wrongly predicted secondary structure * * elements of class i (perceptron says it is in i * * but nature say, this is a lie) * * PRED(i) number of properly predicted secondary structure * * elements of class i * * Q3 =properly predicted for all classes/all residues * * REJ(i) number of properly rejected secondary structure * * elements of class i (reject: not being i) * * SQ first divide predicted/DSSP in each class then * * sum all classes and divide by e.g. 3 * * UNDEREREST(i) number of wrongly rejected secondary structure * * elements of class i (perceptron says it is not in* * i but nature say, this is a lie) * ******------------------------------*-----------------------------****** DNM= 0 CNT= 0 C-------------------------------------------------- C---- compute quotients ----- C-------------------------------------------------- DO ITSEC=1,NSECELLIB DO ITSEC2=1,NSECELLIB IF ((MATNUM(ITSEC,(NSECELLIB+1)).NE.0).AND. + (MATNUM((NSECELLIB+1),ITSEC2).NE.0)) THEN MATQOFDSSP(ITSEC,ITSEC2)= + 100*MATNUM(ITSEC,ITSEC2) + /REAL(MATNUM(ITSEC,(NSECELLIB+1))) MATQOFPRED(ITSEC,ITSEC2)= + 100*MATNUM(ITSEC,ITSEC2) + /REAL(MATNUM((NSECELLIB+1),ITSEC2)) ELSEIF ((MATNUM(ITSEC,(NSECELLIB+1)).NE.0).AND. + (MATNUM((NSECELLIB+1),ITSEC2).EQ.0)) THEN MATQOFDSSP(ITSEC,ITSEC2)= + 100*MATNUM(ITSEC,ITSEC2) + /REAL(MATNUM(ITSEC,(NSECELLIB+1))) MATQOFPRED(ITSEC,ITSEC2)=0 ELSEIF ((MATNUM(ITSEC,(NSECELLIB+1)).EQ.0).AND. + (MATNUM((NSECELLIB+1),ITSEC2).NE.0)) THEN MATQOFDSSP(ITSEC,ITSEC2)=0 MATQOFPRED(ITSEC,ITSEC2)= + 100*MATNUM(ITSEC,ITSEC2) + /REAL(MATNUM((NSECELLIB+1),ITSEC2)) END IF END DO END DO ISUM1=0 RSUM=0. DO ITSEC=1,NSECELLIB ISUM1=ISUM1+MATNUM(ITSEC,ITSEC) RSUM=RSUM+MATQOFDSSP(ITSEC,ITSEC) END DO IF (MATNUM((NSECELLIB+1),(NSECELLIB+1)).NE.0) THEN Q3=100*ISUM1/REAL(MATNUM((NSECELLIB+1),(NSECELLIB+1))) ELSE Q3=0 END IF IF (NSECELLIB.NE.0) THEN SQ=RSUM/REAL(NSECELLIB) ELSE SQ=0 END IF C---- correlation (Matthews) C---- for helix examples with M(ii) as MATNUM(i,i) DO ITSEC=1,NSECELLIB C------- = M(11) PRED(ITSEC)=MATNUM(ITSEC,ITSEC) C------- = M(22)+M(23)+M(32)+M(33) ISUM1=0 DO ITSEC2=1,NSECELLIB IF (ITSEC2.NE.ITSEC) THEN DO ITSEC3=1,NSECELLIB IF (ITSEC3.NE.ITSEC) THEN ISUM1=ISUM1+MATNUM(ITSEC2,ITSEC3) END IF END DO END IF END DO REJ(ITSEC)=ISUM1 C------- = M(12)+M(13) ISUM1=0 DO ITSEC2=1,NSECELLIB IF (ITSEC2.NE.ITSEC) THEN ISUM1=ISUM1+MATNUM(ITSEC,ITSEC2) END IF END DO UNDEREST(ITSEC)=ISUM1 C------- = M(21)+M(31) ISUM1=0 DO ITSEC2=1,NSECELLIB IF (ITSEC2.NE.ITSEC) THEN ISUM1=ISUM1+MATNUM(ITSEC2,ITSEC) END IF END DO OVEREST(ITSEC)=ISUM1 END DO DO ITSEC=1,NSECELLIB CNT1=PRED(ITSEC)*REJ(ITSEC) CNT2=OVEREST(ITSEC)*UNDEREST(ITSEC) DNM1=REJ(ITSEC)+UNDEREST(ITSEC) DNM2=REJ(ITSEC)+OVEREST(ITSEC) DNM3=PRED(ITSEC)+OVEREST(ITSEC) DNM4=PRED(ITSEC)+UNDEREST(ITSEC) C------- take care of potential overflow IF ((DNM1*DNM2*DNM3*DNM4).GT.(10.E18)) THEN CORR(ITSEC)=0. ELSE CNT=REAL(CNT1-CNT2) DNM=SQRT(REAL(DNM1*DNM2*DNM3*DNM4)) END IF IF ((ABS(CNT).LE.(10.E-16)).OR.(DNM.GT.(10.E16))) THEN CORR(ITSEC)=0. ELSE CORR(ITSEC)=CNT/DNM END IF END DO END ***** end of SEVALQUO ***** ------------------------------------------------------------------ ***** SUB SEVALSEG ***** ------------------------------------------------------------------ C---- C---- NAME : SEVALSEG C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1992 version 0.1 * * changed: Mar, 1993 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The measures related to segments are computed. * * input variables:NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES * * ----------------DSSPCHAR,PREDCHAR * * output variab.: NUMSEGOVERL, QSEGFOV * * called by: SEVALPRED (in lib-prot.f) * * SBRs calling: * from lib-prot.f: * * SSEGBEGIN, SSEGLOV, SSEGSOV, SSEGFOV, STABLESEG * * procedure: * overlapp NUMSEGOVERL(3/4,ITSEC) ,3=%OBS, 4=%PRED * * ---------- for H, E, T * * if overlapp > L/2 * * for L: * * if overlapp > 2 * * * correct: NUMSEGOVERL(5,ITSEC) * * for L < 5: | L(OBS)-L(PRED) | <= 1 * * .AND. shift by 1 allowed * * for 5<=L<10: | L(OBS)-L(PRED) | <= 2 * * .AND. shift by 2 allowed * * for L >= 10: | L(OBS)-L(PRED) | <= 3 * * .AND. shift by 3 allowed * * * overlapping fraction: QSEGFOV(1/2,ITSEC) * * number of overlapping residues * * QSEGFOV(i)= ------------------------------ * * end (max) - begin (min) * * where * * max= maximum (end(pred),end(obs)) * * min= minimum (beg(pred),beg(obs)) * *----------------------------------------------------------------------* SUBROUTINE SEVALSEG(KSEG,LWRITEFILE,PROTNAME, + NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES,CHVP1, + DSSPCHAR,PREDCHAR,CHVP2,NUMSEGOVERL, + COUNTSEGMAT,QSEGLOV,QSEGSOV,QSEGFOV,DEVNOM,CHVPL) IMPLICIT NONE C---- variables/ parameters from calling SBR INTEGER KSEG,MAXNSECEL,NSECELLIB,MAXNUMRES,NUMRESLIB, + CHVPM(1:50),CHVPL,CHVP1,CHVP2, + NUMSEGOVERL(1:9,1:(MAXNSECEL+1)), + COUNTSEGMAT(1:2,1:(MAXNSECEL+1)),DEVNOM REAL QSEGFOV(1:2,1:(MAXNSECEL+1)), + QSEGLOV(1:2,1:(MAXNSECEL+1)),QSEGSOV(1:2,1:(MAXNSECEL+1)) CHARACTER*1 DSSPCHAR(1:MAXNUMRES),PREDCHAR(1:MAXNUMRES) CHARACTER*222 PROTNAME LOGICAL LWRITEFILE C---- local parameters INTEGER MAXSEG PARAMETER (MAXSEG= 5000) C---- local variables resp. passed to SBRs called INTEGER MUE,ITSEC,COUNTSEG,ITER INTEGER NUMCOR(1:2,1:8), + POINTDSSP(1:2000),POINTPRED(1:2000), + BEGSEGDSSP(1:MAXSEG),ENDSEGDSSP(1:MAXSEG),LENSEGDSSP(1:MAXSEG), + BEGSEGPRED(1:MAXSEG),ENDSEGPRED(1:MAXSEG),LENSEGPRED(1:MAXSEG) LOGICAL LHELP,LWRITE,LERRCHVP CHARACTER*1 SSCHAR(1:8) ******------------------------------*-----------------------------****** * MUE,ITER serve as iteration variables * * DEVNOM allowed deviation in nominator : * * overlapping length + DEVNOM * * QSEGFOV = --------------------------- * * common length * * NUMSEGOVERL(i,j) number of overlapping/correct segments * * i=1 number of DSSP segments in secondary structure * * j, for last: sum over all * * i=2 number of residues in structure i, summed up over* * all segments (in i=1) * * i=3 number of predicted segments in class j * * i=4 number of residues in structure i, summed up over* * all segments (in i=1) for the prediction * * i=5 number of overlapping predicted segments related * * to those being observed. Correct means: * * overlap >= length of segment / 2, for H, E, T * * and for loop: at least loop of 2, resp 1, if the* * DSSP loop is 1. * * i=6 number of overlapping segments multiplied by * * length: related to %observed * * i=7 same as 5, but other way round: %pred! * * i=8 same as 6, but other way round: %pred! * * j, for last: sum over all * * i=9 number of correct segments: * * L +/- 1, and shift by 1, if L<=5 * * L +/- 1, and shift by 2, if 510 * * noted: j, for last: sum over all * * QSEGLOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the loose overlap (half length overlap) * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * QSEGSOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the strict overlap * * for L < 5: | L(OBS)-L(PRED) | <= 1 * * .AND. shift by 1 allowed * * for 5<=L<10: | L(OBS)-L(PRED) | <= 2 * * .AND. shift by 2 allowed * * for L >= 10: | L(OBS)-L(PRED) | <= 3 * * .AND. shift by 3 allowed * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * QSEGFOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the fractional overlap: * * overlapping length * * as given by: ------------------ * * common length * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * LWRITE variable used, to call subroutines such that the * * result they compute is written out (true) or not * ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- initial check of variables passed ----- C-------------------------------------------------- IF (CHVPL.NE.2) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'WARNING: SEVALSEG: number of passed variables not fitting' END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for SEVALSEG: variables passed not correct !' END IF C---- check variables passed IF (NUMRESLIB.GT.MAXNUMRES) THEN WRITE(6,'(T5,A)') + ' The length of the protein passed to SBR SEVALSEG' WRITE(6,'(T5,A)') + ' exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current length: ',NUMRESLIB,' allocated:',MAXNUMRES WRITE(6,'(T5,A)')' Stopped in SEVALSEG 12-11-92:3' STOP END IF IF (NSECELLIB.GT.MAXNSECEL) THEN WRITE(6,'(T5,A)') + 'The number of secondary structures passed to SBR SEVALSEG' WRITE(6,'(T5,A)') + 'exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current number: ',NSECELLIB,' allocated:',MAXNSECEL WRITE(6,'(T5,A)')' Stopped in SEVALSEG 12-11-92:4' STOP END IF C---- set zero * CALL SISTZ2(NUMSEGOVERL,9,(MAXNSECEL+1)) DO ITSEC=1,(NSECELLIB+1) DO MUE=1,9 NUMSEGOVERL(MUE,ITSEC)=0 END DO END DO C-------------------------------------------------- C---- assign secondary characters ----- C-------------------------------------------------- SSCHAR(1)='H' SSCHAR(2)='E' SSCHAR(NSECELLIB)='L' IF (NSECELLIB.EQ.4) THEN SSCHAR(3)='T' ELSEIF (NSECELLIB.EQ.5) THEN SSCHAR(3)='T' SSCHAR(4)='S' ELSEIF (NSECELLIB.GT.5) THEN WRITE(6,'(T5,A)') + 'Caution: current version of SEVALSEG distinguishes' WRITE(6,'(T5,A)')'only five different secondary structures!' WRITE(6,'(T5,A)')'Stopped in SBR SEVALSEG: 12-11-92:5' STOP END IF C---- to be on the save side: substitute potential blanks by 'L' DO MUE=1,NUMRESLIB LHELP=.TRUE. DO ITSEC=1,(NSECELLIB-1) IF (LHELP.AND.(PREDCHAR(MUE).EQ.SSCHAR(ITSEC))) THEN LHELP=.FALSE. END IF END DO IF (LHELP .EQV. .TRUE.) THEN PREDCHAR(MUE)='L' END IF END DO LWRITE=.FALSE. IF (LWRITE .EQV. .TRUE.) THEN WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,A,T10,A,T60,A7)')'---', + 'SEVALSEG: overlapping segments for: ',PROTNAME END IF C-------------------------------------------------- C---- storing begin and end of segments ----- C-------------------------------------------------- C---------------------------------------- C---- assign begin and ends for DSSP ---- C---------------------------------------- C ============== CALL SSEGBEGIN(NUMRESLIB,MAXNUMRES,1,MAXSEG,DSSPCHAR,2, + BEGSEGDSSP,ENDSEGDSSP,3,LENSEGDSSP,COUNTSEG,3) C ============== C---- store separately number of helices, strands, turns, and loops DO MUE=1,COUNTSEG DO ITSEC=1,NSECELLIB IF (DSSPCHAR(BEGSEGDSSP(MUE)).EQ.SSCHAR(ITSEC)) THEN NUMSEGOVERL(1,ITSEC)=NUMSEGOVERL(1,ITSEC)+1 NUMSEGOVERL(2,ITSEC)=NUMSEGOVERL(2,ITSEC)+LENSEGDSSP(MUE) END IF END DO END DO NUMSEGOVERL(1,(NSECELLIB+1))=COUNTSEG DO ITSEC=1,NSECELLIB NUMSEGOVERL(2,(NSECELLIB+1))=NUMSEGOVERL(2,(NSECELLIB+1)) + +NUMSEGOVERL(2,ITSEC) END DO C---- consistency check lengths DO MUE=1,NUMSEGOVERL(1,(NSECELLIB+1)) IF (LENSEGDSSP(MUE).NE. + (ENDSEGDSSP(MUE)-BEGSEGDSSP(MUE))+1) THEN WRITE(6,'(T2,A,T10,A,T50,I4)')'***', + 'SEVALSEG: fault for observed segment: ',MUE END IF END DO C---- assign pointers COUNTSEG=1 DO MUE=1,NUMRESLIB POINTDSSP(MUE)=COUNTSEG IF (MUE.EQ.ENDSEGDSSP(COUNTSEG)) THEN COUNTSEG=COUNTSEG+1 END IF END DO C---------------------------------------- C---- assign begin and ends for PRED ---- C---------------------------------------- C ============== CALL SSEGBEGIN(NUMRESLIB,MAXNUMRES,1,MAXSEG,PREDCHAR,2, + BEGSEGPRED,ENDSEGPRED,3,LENSEGPRED,COUNTSEG,3) C ============== C---- store separately number of helices, strands, turns, and loops DO MUE=1,COUNTSEG DO ITSEC=1,NSECELLIB IF (PREDCHAR(BEGSEGPRED(MUE)).EQ.SSCHAR(ITSEC)) THEN NUMSEGOVERL(3,ITSEC)=NUMSEGOVERL(3,ITSEC)+1 NUMSEGOVERL(4,ITSEC)=NUMSEGOVERL(4,ITSEC)+LENSEGPRED(MUE) END IF END DO END DO NUMSEGOVERL(3,(NSECELLIB+1))=COUNTSEG DO ITSEC=1,NSECELLIB NUMSEGOVERL(4,(NSECELLIB+1))=NUMSEGOVERL(4,(NSECELLIB+1)) + +NUMSEGOVERL(4,ITSEC) END DO C---- consistency check: correctly counted? DO MUE=1,NUMSEGOVERL(3,(NSECELLIB+1)) IF (LENSEGPRED(MUE).NE. + (ENDSEGPRED(MUE)-BEGSEGPRED(MUE))+1) THEN WRITE(6,'(T2,A,T10,A,T50,I4)')'***', + 'SEVALSEG: fault for predicted segment: ',MUE END IF END DO C---- assign pointers COUNTSEG=1 DO MUE=1,NUMRESLIB POINTPRED(MUE)=COUNTSEG IF (MUE.EQ.ENDSEGPRED(COUNTSEG)) THEN COUNTSEG=COUNTSEG+1 END IF END DO C-------------------------------------------------- C---- overlapp % observed and % predicted ----- C-------------------------------------------------- C ============= CALL SSEGLOV(NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES, + MAXSEG,1,DSSPCHAR,PREDCHAR,2,LENSEGDSSP,LENSEGPRED, + BEGSEGDSSP,ENDSEGDSSP,BEGSEGPRED,ENDSEGPRED,3, + NUMSEGOVERL,QSEGLOV,3) C ============= C-------------------------------------------------- C---- computing correct elements ----- C-------------------------------------------------- C ============ CALL SSEGSOV(NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES,MAXSEG,1, + DSSPCHAR,PREDCHAR,SSCHAR,2,LENSEGDSSP,LENSEGPRED, + POINTDSSP,POINTPRED,BEGSEGDSSP,BEGSEGPRED, + 3,NUMCOR,NUMSEGOVERL(1,(NSECELLIB+1)), + NUMSEGOVERL(3,(NSECELLIB+1)),QSEGSOV,3) C ============ DO ITSEC=1,NSECELLIB NUMSEGOVERL(9,ITSEC)=NUMCOR(1,ITSEC) END DO DO ITSEC=1,NSECELLIB NUMSEGOVERL(9,(NSECELLIB+1))=NUMSEGOVERL(9,(NSECELLIB+1)) + +NUMSEGOVERL(9,ITSEC) END DO C-------------------------------------------------- C---- computing overlapping lengths quotients ----- C-------------------------------------------------- C ============= CALL SSEGFOV(NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES, + MAXSEG,1,DSSPCHAR,PREDCHAR,SSCHAR,2,BEGSEGDSSP, + BEGSEGPRED,ENDSEGDSSP,ENDSEGPRED,POINTDSSP,POINTPRED, + 3,NUMSEGOVERL(1,(NSECELLIB+1)),NUMSEGOVERL(3,(NSECELLIB+1)), + COUNTSEGMAT,QSEGFOV,3,DEVNOM) C ============= C-------------------------------------------------- C---- writing result onto printer ----- C-------------------------------------------------- C---- first: intermediately normalise the quotients DO ITSEC=1,(NSECELLIB+1) DO ITER=1,2 IF (NUMSEGOVERL(2*ITER,ITSEC).NE.0) THEN QSEGLOV(ITER,ITSEC)=100*QSEGLOV(ITER,ITSEC) + /REAL(NUMSEGOVERL(2*ITER,ITSEC)) QSEGSOV(ITER,ITSEC)=100*QSEGSOV(ITER,ITSEC) + /REAL(NUMSEGOVERL(2*ITER,ITSEC)) QSEGFOV(ITER,ITSEC)=100*QSEGFOV(ITER,ITSEC) + /REAL(NUMSEGOVERL(2*ITER,ITSEC)) C------------- search a potential bug/artefact IF (QSEGLOV(ITER,ITSEC).GT.100) THEN QSEGLOV(ITER,ITSEC)=0 WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR: in Sevalseg: QSEGLOV > 100%,' WRITE(6,'(T2,A,T10,A,t25,i3,t30,a,t40,i3)')'***', + 'for iter=',iter,'itsec=',itsec END IF IF (QSEGSOV(ITER,ITSEC).GT.100) THEN QSEGSOV(ITER,ITSEC)=0 WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR: in Sevalseg: QSEGSOV > 100%,' WRITE(6,'(T2,A,T10,A,t25,i3,t30,a,t40,i3)')'***', + 'for iter=',iter,'itsec=',itsec END IF IF (QSEGFOV(ITER,ITSEC).GT.100) THEN QSEGFOV(ITER,ITSEC)=0 WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR: in Sevalseg: QSEGFOV > 100%,' WRITE(6,'(T2,A,T10,A,t25,i3,t30,a,t40,i3)')'***', + 'for iter=',iter,'itsec=',itsec END IF ELSE QSEGLOV(ITER,ITSEC)=0 QSEGSOV(ITER,ITSEC)=0 QSEGFOV(ITER,ITSEC)=0 END IF END DO END DO C---- writing result into file FILESEG (should be open!) IF (LWRITEFILE .EQV. .TRUE.) THEN C ============== CALL STABLESEG(KSEG,NSECELLIB,MAXNSECEL,PROTNAME,NUMSEGOVERL, + QSEGLOV,QSEGSOV,QSEGFOV,DEVNOM) C ============== END IF END ***** end of SEVALSEG ***** ------------------------------------------------------------------ ***** SUB SEXP_NOINBIN_2VEC ***** ------------------------------------------------------------------ C---- C---- NAME : SEXP_NOINBIN_2VEC C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1994 version 0.1 * * changed: dd , 1994 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Compares the two vectors of projected relative * * -------- exposure (0-9) for observation and prediction * * and returns the matrix of number in bins. * * Definition: * EXP_NOINBIN(i,j) = N means, for N residues the * * exposure is: * * observed in i (=> relative exposure = i*i /100), * * predicted in j (=> relative exposure = j*j /100).* * in variables: NUMRESMAX, NUMRES, DSSPBIN, PREDBIN, * * out variables: EXP_NOINBIN * * SBRs calling: from lib-unix.f: * * -------------- SCHECKPASS * *----------------------------------------------------------------------* SUBROUTINE SEXP_NOINBIN_2VEC(NUMRESMAX,NUMRES,CHVP1, + DSSPBIN,CHVP2,PREDBIN,CHVP3,EXP_NOINBIN,CHVPL) IMPLICIT NONE C---- variables passed INTEGER CHVPM(1:50),CHVPL,CHVP1,CHVP2,CHVP3, + NUMRESMAX,NUMRES,EXP_NOINBIN(0:9,0:9) INTEGER*2 DSSPBIN(1:NUMRESMAX),PREDBIN(1:NUMRESMAX) C---- local variables * INTEGER MUE,IT1,IT2 LOGICAL LERRCHVP ******------------------------------*-----------------------------****** *--------------------- * * passed variables * *--------------------- * * LWRITE variable used, to call subroutines such that the * * result they compute is written out (true) or not * *--------------------- * * local variables * *--------------------- * * MUE,ITER serve as iteration variables * ******------------------------------*-----------------------------****** C---- defaults C----------------------------------------------------------------------* C---- initial check of variables passed -----* C----------------------------------------------------------------------* IF (CHVPL.NE.3) THEN WRITE(6,'(T2,A,T10,A)')'***','WARNING: SEXP_NOINBIN_2VEC: '// + 'number of passed variables not fitting' END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 CHVPM(3)=CHVP3 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for FDUMMY: variables passed not correct !' END IF C----------------------------------------------------------------------* C---- end of checking variables -----* C----------------------------------------------------------------------* C-------------------------------------------------- C---- C-------------------------------------------------- DO IT1=0,9 DO IT2=0,9 EXP_NOINBIN(IT2,IT1)=0 END DO END DO DO MUE=1,NUMRES EXP_NOINBIN(DSSPBIN(MUE),PREDBIN(MUE))= + EXP_NOINBIN(DSSPBIN(MUE),PREDBIN(MUE))+1 END DO END ***** end of SEXP_NOINBIN_2VEC ***** ------------------------------------------------------------------ ***** SUB SEXP_NOINSTATES ***** ------------------------------------------------------------------ C---- C---- NAME : SEXP_NOINSTATES C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1993 version 0.1 * * changed: Dec, 1993 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: For a set of numbers of bins (obs,pred), the num-* * -------- ber of correct ones is returned for three models:* * 2states: 0-20, 20-100, e.g. 0-4, 5-9 * * 3states: 0-5, 5-25, 25-100, e.g. 0-2, 3-5, 6-9 * * 10 : per bin * * in variables: EXP_NOINBIN, THRESH2, THRESH3A, THRESH3B * * output variab.: EXP_NO2STATES, EXP_NO3STATES, EXP_NO10STATES * * --------------- how often occurs: obs = n, pred = m, * * note: 25 = sum * *----------------------------------------------------------------------* SUBROUTINE SEXP_NOINSTATES(EXP_NOINBIN,THRESH2,THRESH3A, + THRESH3B,CHVP1, + OBS_NO2STATES,OBS_NO3STATES,OBS_NO10STATES,CHVP2, + EXP_NO2STATES,EXP_NO3STATES,EXP_NO10STATES,CHVPL) IMPLICIT NONE C---- variables passed INTEGER EXP_NO2STATES(1:3),EXP_NO3STATES(1:4), + EXP_NO10STATES(1:11),EXP_NOINBIN(0:9,0:9), + OBS_NO2STATES(1:3),OBS_NO3STATES(1:4),OBS_NO10STATES(1:11), + THRESH2,THRESH3A,THRESH3B,CHVPM(1:50),CHVPL,CHVP1,CHVP2 C---- local variables INTEGER ICOUNT,IT1,IT2,ICOUNT2,ICOUNT3 LOGICAL LERRCHVP ******------------------------------*-----------------------------****** ******------------------------------*-----------------------------****** C---- default C----------------------------------------------------------------------* C---- initial check of variables passed -----* C----------------------------------------------------------------------* IF (CHVPL.NE.2) THEN WRITE(6,'(T2,A,T10,A)')'***','WARNING: SEXP_NOINSTATES: '// + 'number of passed variables not fitting' WRITE(6,'(T2,A,T10,A,T40,4I5)')'***', + 'they are: CHVPL: 1,2,3:',CHVPL,CHVP1,CHVP2 STOP END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for SEXP_NOINSTATES: variables passed not correct !' END IF C---- check variables passed C----------------------------------------------------------------------* C---- end of checking variables -----* C----------------------------------------------------------------------* C-------------------------------------------------- C---- compute number of bins per AA: obs: n, pred m C-------------------------------------------------- C---- 10 states ICOUNT=0 ICOUNT2=0 DO IT1=0,9 ICOUNT3=0 DO IT2=0,9 ICOUNT3=ICOUNT3+EXP_NOINBIN(IT1,IT2) END DO ICOUNT2=ICOUNT2+ICOUNT3 OBS_NO10STATES(IT1+1)=ICOUNT3 ICOUNT=ICOUNT+EXP_NOINBIN(IT1,IT1) EXP_NO10STATES(IT1+1)=EXP_NOINBIN(IT1,IT1) END DO EXP_NO10STATES(11)=ICOUNT OBS_NO10STATES(11)=ICOUNT2 C---- 3 states DO IT1=1,3 EXP_NO3STATES(IT1)=0 END DO ICOUNT=0 ICOUNT2=0 DO IT1=0,(THRESH3A-1) ICOUNT3=0 DO IT2=0,9 ICOUNT3=ICOUNT3+EXP_NOINBIN(IT1,IT2) END DO ICOUNT2=ICOUNT2+ICOUNT3 DO IT2=0,(THRESH3A-1) ICOUNT=ICOUNT+EXP_NOINBIN(IT1,IT2) EXP_NO3STATES(1)=EXP_NO3STATES(1)+EXP_NOINBIN(IT1,IT2) END DO END DO OBS_NO3STATES(1)=ICOUNT2 ICOUNT2=0 DO IT1=THRESH3A,(THRESH3B-1) ICOUNT3=0 DO IT2=0,9 ICOUNT3=ICOUNT3+EXP_NOINBIN(IT1,IT2) END DO ICOUNT2=ICOUNT2+ICOUNT3 DO IT2=THRESH3A,(THRESH3B-1) ICOUNT=ICOUNT+EXP_NOINBIN(IT1,IT2) EXP_NO3STATES(2)=EXP_NO3STATES(2)+EXP_NOINBIN(IT1,IT2) END DO END DO OBS_NO3STATES(2)=ICOUNT2 ICOUNT2=0 DO IT1=THRESH3B,9 ICOUNT3=0 DO IT2=0,9 ICOUNT3=ICOUNT3+EXP_NOINBIN(IT1,IT2) END DO ICOUNT2=ICOUNT2+ICOUNT3 DO IT2=THRESH3B,9 ICOUNT=ICOUNT+EXP_NOINBIN(IT1,IT2) EXP_NO3STATES(3)=EXP_NO3STATES(3)+EXP_NOINBIN(IT1,IT2) END DO END DO OBS_NO3STATES(3)=ICOUNT2 EXP_NO3STATES(4)=ICOUNT ICOUNT=0 DO IT1=1,3 ICOUNT=ICOUNT+OBS_NO3STATES(IT1) END DO OBS_NO3STATES(4)=ICOUNT C---- 2 states DO IT1=1,2 EXP_NO2STATES(IT1)=0 END DO ICOUNT=0 ICOUNT2=0 DO IT1=0,(THRESH2-1) ICOUNT3=0 DO IT2=0,9 ICOUNT3=ICOUNT3+EXP_NOINBIN(IT1,IT2) END DO ICOUNT2=ICOUNT2+ICOUNT3 DO IT2=0,(THRESH2-1) ICOUNT=ICOUNT+EXP_NOINBIN(IT1,IT2) EXP_NO2STATES(1)=EXP_NO2STATES(1)+EXP_NOINBIN(IT1,IT2) END DO END DO OBS_NO2STATES(1)=ICOUNT2 ICOUNT2=0 DO IT1=THRESH2,9 ICOUNT3=0 DO IT2=0,9 ICOUNT3=ICOUNT3+EXP_NOINBIN(IT1,IT2) END DO ICOUNT2=ICOUNT2+ICOUNT3 DO IT2=THRESH2,9 ICOUNT=ICOUNT+EXP_NOINBIN(IT1,IT2) EXP_NO2STATES(2)=EXP_NO2STATES(2)+EXP_NOINBIN(IT1,IT2) END DO END DO OBS_NO2STATES(2)=ICOUNT2 EXP_NO2STATES(3)=ICOUNT OBS_NO2STATES(3)=ICOUNT2+OBS_NO2STATES(1) END ***** end of SEXP_NOINSTATES ***** ------------------------------------------------------------------ ***** SUB SFILEOPEN ***** ------------------------------------------------------------------ C---- C---- NAME : SFILEOPEN C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE SFILEOPEN(UNIT,FILENAME,ACTSTATUS,LENGTH,ACTTASK) IMPLICIT NONE C---- local function INTEGER FILEN_STRING C---- local variables INTEGER UNIT,LENGTH,IEND CHARACTER*(*) FILENAME,ACTSTATUS,ACTTASK CHARACTER*222 CHFILE ******------------------------------*-----------------------------****** C purge blanks from file name IEND=FILEN_STRING(FILENAME) CHFILE(1:IEND)=FILENAME(1:IEND) C---- hack br 2001-01: avoid trouble with LINUX IF (ACTSTATUS(1:3).EQ.'OLD') THEN OPEN(UNIT,FILE=CHFILE(1:IEND),STATUS='OLD') ELSEIF (ACTSTATUS(1:3).EQ.'NEW') THEN OPEN(UNIT,FILE=CHFILE(1:IEND),STATUS='NEW') ELSE OPEN(UNIT,FILE=CHFILE(1:IEND),STATUS='UNKNOWN') END IF C---- bullshit to avoid warnings IF (ACTTASK.EQ.'XX') THEN CONTINUE END IF IF (LENGTH.LT.1) THEN CONTINUE END IF RETURN END ***** end of SFILEOPEN ***** ------------------------------------------------------------------ ***** SUB SILEN_STRING ***** ------------------------------------------------------------------ C---- C---- NAME : SILEN_STRING C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The length of a given character string is returned * -------- resp. non-blank begin (ibeg) and end (iend) * * input: STRING string of CHARACTER*222 * * output: ibeg,iend * *----------------------------------------------------------------------* SUBROUTINE SILEN_STRING(STRING,IBEG,IEND) C---- variables passing CHARACTER*222 STRING C---- local variables INTEGER ICOUNT,ITER,IBEG,IEND CHARACTER*222 HSTRING LOGICAL LHELP ******------------------------------*-----------------------------****** C---- defaults HSTRING=STRING ICOUNT=0 LHELP=.TRUE. DO ITER=1,80 IF (LHELP .EQV. .TRUE.) THEN IF (HSTRING(ITER:ITER).NE.' ') THEN IF (ICOUNT.EQ.0) THEN IBEG=ITER END IF ICOUNT=ICOUNT+1 ELSE IF (ICOUNT.NE.0) THEN IEND=ITER-1 LHELP=.FALSE. END IF END IF END IF END DO IF (ICOUNT.EQ.0) THEN WRITE(6,'(T2,A,T10,A,A1,A,A1)')'***', + 'ERROR: Sbr SILEN_STRING: empty string:','|',STRING,'|' END IF END ***** end of SILEN_STRING ***** ------------------------------------------------------------------ ***** SUB SINTTOCHAR ***** ------------------------------------------------------------------ C---- C---- NAME : SINTTOCHAR C---- ARG : IINT,TXT C---- DES : converts the integer (<100) to a textstring (1:3) C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: convertion of INTEGER IINT into a character (*3) * C input variables:IINT * C output: TXT * *----------------------------------------------------------------------* SUBROUTINE SINTTOCHAR(IINT,TXT) INTEGER IINT CHARACTER*3 TXT ************************************************************************ C---- warning IF (IINT.GE.100) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR in SINTTOCHAR library lib-comp!' WRITE(6,'(T2,A,T10,A)')'***', + 'The number to be converted must be < 100.' END IF C---- convert integer to character IF (IINT.EQ.1) THEN TXT=' 1' ELSEIF (IINT.EQ.2) THEN TXT=' 2' ELSEIF (IINT.EQ.3) THEN TXT=' 3' ELSEIF (IINT.EQ.4) THEN TXT=' 4' ELSEIF (IINT.EQ.5) THEN TXT=' 5' ELSEIF (IINT.EQ.6) THEN TXT=' 6' ELSEIF (IINT.EQ.7) THEN TXT=' 7' ELSEIF (IINT.EQ.8) THEN TXT=' 8' ELSEIF (IINT.EQ.9) THEN TXT=' 9' ELSEIF (IINT.EQ.10) THEN TXT=' 10' ELSEIF (IINT.EQ.11) THEN TXT=' 11' ELSEIF (IINT.EQ.12) THEN TXT=' 12' ELSEIF (IINT.EQ.13) THEN TXT=' 13' ELSEIF (IINT.EQ.14) THEN TXT=' 14' ELSEIF (IINT.EQ.15) THEN TXT=' 15' ELSEIF (IINT.EQ.16) THEN TXT=' 16' ELSEIF (IINT.EQ.17) THEN TXT=' 17' ELSEIF (IINT.EQ.18) THEN TXT=' 18' ELSEIF (IINT.EQ.19) THEN TXT=' 19' ELSEIF (IINT.EQ.20) THEN TXT=' 20' ELSEIF (IINT.EQ.21) THEN TXT=' 21' ELSEIF (IINT.EQ.22) THEN TXT=' 22' ELSEIF (IINT.EQ.23) THEN TXT=' 23' ELSEIF (IINT.EQ.24) THEN TXT=' 24' ELSEIF (IINT.EQ.25) THEN TXT=' 25' ELSEIF (IINT.EQ.26) THEN TXT=' 26' ELSEIF (IINT.EQ.27) THEN TXT=' 27' ELSEIF (IINT.EQ.28) THEN TXT=' 28' ELSEIF (IINT.EQ.29) THEN TXT=' 29' ELSEIF (IINT.EQ.30) THEN TXT=' 30' ELSEIF (IINT.EQ.31) THEN TXT=' 31' ELSEIF (IINT.EQ.32) THEN TXT=' 32' ELSEIF (IINT.EQ.33) THEN TXT=' 33' ELSEIF (IINT.EQ.34) THEN TXT=' 34' ELSEIF (IINT.EQ.35) THEN TXT=' 35' ELSEIF (IINT.EQ.36) THEN TXT=' 36' ELSEIF (IINT.EQ.37) THEN TXT=' 37' ELSEIF (IINT.EQ.38) THEN TXT=' 38' ELSEIF (IINT.EQ.39) THEN TXT=' 39' ELSEIF (IINT.EQ.40) THEN TXT=' 40' ELSEIF (IINT.EQ.41) THEN TXT=' 41' ELSEIF (IINT.EQ.42) THEN TXT=' 42' ELSEIF (IINT.EQ.43) THEN TXT=' 43' ELSEIF (IINT.EQ.44) THEN TXT=' 44' ELSEIF (IINT.EQ.45) THEN TXT=' 45' ELSEIF (IINT.EQ.46) THEN TXT=' 46' ELSEIF (IINT.EQ.47) THEN TXT=' 47' ELSEIF (IINT.EQ.48) THEN TXT=' 48' ELSEIF (IINT.EQ.49) THEN TXT=' 49' ELSEIF (IINT.EQ.50) THEN TXT=' 50' ELSEIF (IINT.EQ.51) THEN TXT=' 51' ELSEIF (IINT.EQ.52) THEN TXT=' 52' ELSEIF (IINT.EQ.53) THEN TXT=' 53' ELSEIF (IINT.EQ.54) THEN TXT=' 54' ELSEIF (IINT.EQ.55) THEN TXT=' 55' ELSEIF (IINT.EQ.56) THEN TXT=' 56' ELSEIF (IINT.EQ.57) THEN TXT=' 57' ELSEIF (IINT.EQ.58) THEN TXT=' 58' ELSEIF (IINT.EQ.59) THEN TXT=' 59' ELSEIF (IINT.EQ.60) THEN TXT=' 60' ELSEIF (IINT.EQ.61) THEN TXT=' 61' ELSEIF (IINT.EQ.62) THEN TXT=' 62' ELSEIF (IINT.EQ.63) THEN TXT=' 63' ELSEIF (IINT.EQ.64) THEN TXT=' 64' ELSEIF (IINT.EQ.65) THEN TXT=' 65' ELSEIF (IINT.EQ.66) THEN TXT=' 66' ELSEIF (IINT.EQ.67) THEN TXT=' 67' ELSEIF (IINT.EQ.68) THEN TXT=' 68' ELSEIF (IINT.EQ.69) THEN TXT=' 69' ELSEIF (IINT.EQ.70) THEN TXT=' 70' ELSEIF (IINT.EQ.71) THEN TXT=' 71' ELSEIF (IINT.EQ.72) THEN TXT=' 72' ELSEIF (IINT.EQ.73) THEN TXT=' 73' ELSEIF (IINT.EQ.74) THEN TXT=' 74' ELSEIF (IINT.EQ.75) THEN TXT=' 75' ELSEIF (IINT.EQ.76) THEN TXT=' 76' ELSEIF (IINT.EQ.77) THEN TXT=' 77' ELSEIF (IINT.EQ.78) THEN TXT=' 78' ELSEIF (IINT.EQ.79) THEN TXT=' 79' ELSEIF (IINT.EQ.80) THEN TXT=' 80' ELSEIF (IINT.EQ.81) THEN TXT=' 81' ELSEIF (IINT.EQ.82) THEN TXT=' 82' ELSEIF (IINT.EQ.83) THEN TXT=' 83' ELSEIF (IINT.EQ.84) THEN TXT=' 84' ELSEIF (IINT.EQ.85) THEN TXT=' 85' ELSEIF (IINT.EQ.86) THEN TXT=' 86' ELSEIF (IINT.EQ.87) THEN TXT=' 87' ELSEIF (IINT.EQ.88) THEN TXT=' 88' ELSEIF (IINT.EQ.89) THEN TXT=' 89' ELSEIF (IINT.EQ.90) THEN TXT=' 90' ELSEIF (IINT.EQ.91) THEN TXT=' 91' ELSEIF (IINT.EQ.92) THEN TXT=' 92' ELSEIF (IINT.EQ.93) THEN TXT=' 93' ELSEIF (IINT.EQ.94) THEN TXT=' 94' ELSEIF (IINT.EQ.95) THEN TXT=' 95' ELSEIF (IINT.EQ.96) THEN TXT=' 96' ELSEIF (IINT.EQ.97) THEN TXT=' 97' ELSEIF (IINT.EQ.98) THEN TXT=' 98' ELSEIF (IINT.EQ.99) THEN TXT=' 99' END IF END ***** end of SINTTOCHAR ***** ------------------------------------------------------------------ ***** SUB SISTZ1 ***** ------------------------------------------------------------------ C---- C---- NAME : SISTZ1 C---- ARG : IVEC,IROW C---- DES : sets zero a 1-dimensional integer vector (IROW C---- DES : elements) C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Apr, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: an integer 1-dimensional vector IVEC (IROW) is * C set to zero for all elements * C input parameter: IROW * C input variables: IVEC(integer vector) * C output variables: IVEC=0 for all elements * *----------------------------------------------------------------------* SUBROUTINE SISTZ1(IVEC,IROW) INTEGER IROW,ITER1 INTEGER IVEC(1:IROW) DO ITER1=1,IROW IVEC(ITER1)=0 END DO END ***** end of SISTZ1 ***** ------------------------------------------------------------------ ***** SUB SISTZ2 ***** ------------------------------------------------------------------ C---- C---- NAME : SISTZ2 C---- ARG : IMAT,IROW,ICOL C---- DES : sets zero a 2-dimensional integer matrix(IROW,ICOL) C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Jun, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: an integer 2-dimensional matrix IMAT (IROW,ICOL) * C is set to zero for all elements * C input parameter: IROW,ICOL * C input variables: IMAT(integer matrix) * C output variables: IMAT=0 for all elements * *----------------------------------------------------------------------* SUBROUTINE SISTZ2(IMAT,IROW,ICOL) INTEGER IROW,ICOL,ITROW,ITCOL INTEGER IMAT(1:IROW,1:ICOL) DO ITCOL=1,ICOL DO ITROW=1,IROW IMAT(ITROW,ITCOL)=0 END DO END DO END ***** end of SISTZ2 ***** ------------------------------------------------------------------ ***** SUB SRMAX1 ***** ------------------------------------------------------------------ C---- C---- NAME : SRMAX1 C---- ARG : RVEC,IROW,MAXVAL,MAXPOS C---- DES : returns the maximal value of the components of the C---- DES : real C---- DES : vector RVEC(IROW) = MAXVAL, plus the position of that C---- DES : value within the vector = MAXPOS C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: computation of maximal value of the elements of * C a real vector plus return of the position of that* C value within the vector. * C input parameter:IROW * C input variables:RVEC * C output: MAXVAL,MAXPOS * *----------------------------------------------------------------------* SUBROUTINE SRMAX1(RVEC,IROW,MAXVAL,MAXPOS) INTEGER IROW,MAXPOS,ITER REAL MAXVAL REAL RVEC(1:IROW) MAXVAL=RVEC(1) MAXPOS=0 DO ITER=1,IROW IF (MAXVAL.LE.RVEC(ITER)) THEN MAXVAL=RVEC(ITER) MAXPOS=ITER END IF END DO C---- check whether one value regarded as maximum or not IF ((MAXPOS.EQ.0).AND.(MAXVAL.NE.RVEC(1))) THEN WRITE(6,'(T2,A)')'***' WRITE(6,'(T2,A)')'***' WRITE(6,'(T2,A,T10,A)')'***', + 'probably an ERROR in library SBR SRMAX1 detected.' WRITE(6,'(T2,A,T10,A)')'***', + 'The subroutine is expected to compute the maximum of a' WRITE(6,'(T2,A,T10,A)')'***', + 'vector but there seems to be none.' WRITE(6,'(T2,A,T10,A,T45,I5,A)')'***', + 'Components are: (with IROW = ',IROW,')' WRITE(6,'(T2,A,T10,20F5.2)')'***', + (RVEC(ITER),ITER=1,IROW) WRITE(6,'(T2,A,T10,A,T45,F8.5)')'***', + 'Maximum is computed to be: ',MAXVAL WRITE(6,'(T2,A)')'***' WRITE(6,'(T2,A)')'***' END IF END ***** end of SRMAX1 ***** ------------------------------------------------------------------ ***** SUB SRSORTVEC ***** ------------------------------------------------------------------ C---- C---- NAME : SRSORTVEC C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: May, 1993 version 0.1 * * changed: May, 1993 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The components of the real vector VEC are sorted * * -------- according to their seize. The succession is * * returned in ISORT. * * in variables: NROW,NROWMAX,VEC * * out variables: ISORT * *----------------------------------------------------------------------* SUBROUTINE SRSORTVEC(NROW,NROWMAX,CHVP1,RVEC,CHVP2,ISORT,CHVPL) IMPLICIT NONE C---- variables passed INTEGER CHVPM(1:2),CHVPL,CHVP1,CHVP2, + NROW,NROWMAX,ISORT(1:NROWMAX) REAL RVEC(1:NROWMAX) C---- local variables * INTEGER ITER,ITER2,POSMAX REAL HMAX LOGICAL LERRCHVP,LFOUND(1:1000) ******------------------------------*-----------------------------****** C---- defaults POSMAX= 0 IF (NROWMAX.GT.1000) THEN WRITE(6,'(T2,A,T10,A,T50,I6)')'***', + 'ERROR in SRSORTVEC: watch out, NROWMAX =',NROWMAX WRITE(6,'(T2,A,T10,A)')'***', + ' however, maximum for logicals LFOUND is 1000!' END IF C----------------------------------------------------------------------* C---- initial check of variables passed -----* C----------------------------------------------------------------------* IF (CHVPL.NE.2) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'WARNING: SSEGFOV: number of passed variables not fitting' END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C CALL SCHECKPASS(LERRCHVP,CHVPL,CHVPM) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for : variables passed not correct !' END IF C---- check variables passed C----------------------------------------------------------------------* C---- end of checking variables -----* C----------------------------------------------------------------------* C---- initialize DO ITER=1,NROW LFOUND(ITER)=.FALSE. END DO C---- first sweep: look for maximum HMAX=0 DO ITER=1,NROW HMAX=MAX(HMAX,RVEC(ITER)) IF (HMAX.EQ.RVEC(ITER)) THEN POSMAX=ITER END IF END DO ISORT(1)=POSMAX LFOUND(POSMAX)=.TRUE. C---- now determine all the others DO ITER=2,NROW HMAX= 0 POSMAX=0 DO ITER2=1,NROW IF (LFOUND(ITER2) .EQV. .FALSE. ) THEN HMAX=MAX(HMAX,RVEC(ITER2)) IF (HMAX.EQ.RVEC(ITER2)) THEN POSMAX=ITER2 END IF END IF END DO IF (POSMAX .EQ. 0) THEN WRITE(6,'(T2,A,T10,A,T60,I3)')'***', + 'ERROR: non found in SRSORTVEC for iter=',ITER END IF ISORT(ITER)=POSMAX LFOUND(POSMAX)=.TRUE. END DO END ***** end of SRSORTVEC ***** ------------------------------------------------------------------ ***** SUB SRSTZ1 ***** ------------------------------------------------------------------ C---- C---- NAME : SRSTZ1 C---- ARG : RVECT,IROW C---- DES : Sets zero a 1-dimens. real vector with the row-length C---- DES : IROW C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: a real vector RVEC is set to zero * C input parameter: IROW * C input variables: RVEC(real vector) * C output variables: RVEC=0. for all elements * *----------------------------------------------------------------------* SUBROUTINE SRSTZ1(RVEC,IROW) REAL RVEC(1:IROW) DO ITER1=1,IROW RVEC(ITER1)=0. END DO END ***** end of SRSTZ1 ***** ------------------------------------------------------------------ ***** SUB SRSTZ2 ***** ------------------------------------------------------------------ C---- C---- NAME : SRSTZ2 C---- ARG : RMAT,IROW,ICOL C---- DES : Sets zero a 2-dimensional real matrix with the C---- DES : row-length C---- DES : IROW, the column-length ICOL :RMAT(IROW,ICOL) C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: a real two dimensional matrix RMAT(rows,columns) is set * C to zero * C input parameter: IROW,ICOL * C input variables: RMAT(real matrix) * C output variables: RMAT=0. for all elements * *----------------------------------------------------------------------* SUBROUTINE SRSTZ2(RMAT,IROW,ICOL) REAL RMAT(1:IROW,1:ICOL) DO ITER2=1,ICOL DO ITER1=1,IROW RMAT(ITER1,ITER2)=0. END DO END DO END ***** end of SRSTZ2 ***** ------------------------------------------------------------------ ***** SUB SSEGBEGIN ***** ------------------------------------------------------------------ C---- C---- NAME : SSEGBEGIN C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: The begins and ends of the segments are found. * C input variables:NSECELLIB, MAXNSECEL, NUMRESLIB, MAXNUMRES * C ----------------RESCHAR, * C output variab.: BEG, END, LEN, COUNTSEG * C called by: SEVALSEG (in lib-prot.f) * C SBRs calling: from lib-unix.f: * C SCHECKPASS * *----------------------------------------------------------------------* SUBROUTINE SSEGBEGIN(NUMRESLIB,MAXNUMRES, + CHVP1,MAXSEG,RESCHAR,CHVP2,BEG,END,CHVP3,LEN, + COUNTSEG,CHVPL) IMPLICIT NONE C---- variables passed INTEGER MAXNUMRES,NUMRESLIB,MAXSEG, + BEG(1:MAXSEG),END(1:MAXSEG),LEN(1:MAXSEG), + CHVPL,CHVP1,CHVP2,CHVP3 CHARACTER*1 RESCHAR(1:MAXNUMRES) C---- local variables * INTEGER MUE,COUNTRES,COUNTSEG INTEGER CHVPM(1:50) LOGICAL LERRCHVP CHARACTER*1 CURSTR CURSTR= CHAR(0) COUNTRES= 0 ******------------------------------*-----------------------------****** C MUE,ITER serve as iteration variables * ******------------------------------*-----------------------------****** C---- CHeck passed parameter IF (CHVPL.NE.3) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'WARNING: SSEGBEGIN: number of passed variables not fitting' END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 CHVPM(3)=CHVP3 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for SSEGBEGIN: variables passed not correct !' END IF C-------------------------------------------------- C---- storing begin and end of segments ----- C-------------------------------------------------- C---- assign begin and ends for RES DO MUE=1,NUMRESLIB IF (MUE.EQ.1) THEN CURSTR=RESCHAR(1) BEG(1)=1 COUNTSEG=1 COUNTRES=1 ELSEIF ((MUE.EQ.NUMRESLIB).AND.(RESCHAR(MUE).EQ.CURSTR)) THEN END(COUNTSEG)=MUE LEN(COUNTSEG)=COUNTRES+1 ELSEIF ((MUE.EQ.NUMRESLIB).AND.(RESCHAR(MUE).NE.CURSTR)) THEN END(COUNTSEG)=MUE-1 LEN(COUNTSEG)=COUNTRES COUNTSEG=COUNTSEG+1 BEG(COUNTSEG)=MUE END(COUNTSEG)=MUE LEN(COUNTSEG)=1 ELSEIF (RESCHAR(MUE).EQ.CURSTR) THEN COUNTRES=COUNTRES+1 ELSE END(COUNTSEG)=MUE-1 LEN(COUNTSEG)=COUNTRES COUNTRES=1 CURSTR=RESCHAR(MUE) COUNTSEG=COUNTSEG+1 BEG(COUNTSEG)=MUE END IF END DO END ***** end of SSEGBEGIN ***** ------------------------------------------------------------------ ***** SUB SSEGFOV ***** ------------------------------------------------------------------ C---- C---- NAME : SSEGFOV C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The quotient of overlapping/ summed length is * * -------- computed. * * input variables:NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES, * * ----------------DSSPCHAR,PREDCHAR,SSCHAR, * * BEGSEGDSSP,BEGSEGPRED,ENDSEGDSSP,ENDSEGPRED, * * POINTDSSP,POINTPRED,NUMSEGDSSP,NUMSEGPRED, * * output variab.: QSEGAVOV * * called by: SEVALSEG (in lib-prot.f) * * SBRs calling: from lib-comp.f: * * -------------- SISTZ1, SRSTZ2 * * from lib-unix.f: * * SCHECKPASS * * procedure: If two segments overlap (predict and observed) * * ---------- the quotient of overlapping segment score is given * by: * * number of overlapping residues * * QSEGAVOV(i)= ------------------------------ * * end (max) - begin (min) * * where max= maximum (end(pred),end(obs)) * * min= minimum (beg(pred),beg(obs)) * *----------------------------------------------------------------------* SUBROUTINE SSEGFOV(NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES, + MAXSEGPASS,CHVP1,DSSPCHAR,PREDCHAR,SSCHAR,CHVP2, + BEGSEGDSSP,BEGSEGPRED,ENDSEGDSSP,ENDSEGPRED,POINTDSSP, + POINTPRED,CHVP3,NUMSEGDSSP,NUMSEGPRED,COUNTSEG, + QSEGFOV,CHVPL,DEVNOM) IMPLICIT NONE C---- variables passed INTEGER MAXNSECEL,NSECELLIB,MAXNUMRES,NUMRESLIB,DEVNOM, + MAXSEGPASS,CHVPM(1:50),CHVPL,CHVP1,CHVP2,CHVP3, + COUNTSEG(1:2,1:(MAXNSECEL+1)),NUMSEGDSSP,NUMSEGPRED, + POINTPRED(1:MAXNUMRES),POINTDSSP(1:MAXNUMRES), + BEGSEGDSSP(1:MAXSEGPASS),BEGSEGPRED(1:MAXSEGPASS), + ENDSEGDSSP(1:MAXSEGPASS),ENDSEGPRED(1:MAXSEGPASS) REAL QSEGFOV(1:2,1:(MAXNSECEL+1)) CHARACTER*1 DSSPCHAR(1:MAXNUMRES),PREDCHAR(1:MAXNUMRES) CHARACTER*1 SSCHAR(1:8) C---- local variables * INTEGER MUE,ITSEC,ITER,ITSEG,IHELP,BEGMUE,MUEFOUND, + IMAXOV,IMINOV,INTERCOUNTSEG,MAXDEV LOGICAL LERRCHVP,LOVER * CHARACTER*10 TXT1(1:5) ******------------------------------*-----------------------------****** * MUE,ITER serve as iteration variables * * DEVNOM allowed deviation in nominator : * * overlapping length + DEVNOM * * as given by: --------------------------- * * common length * * IMINOV =minimal overlapping length (minimal region * * spanned by both strings) * * IMAXOV =maximal overlapping length (maximal region * * spanned by either of the two) * * QSEGFOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the fractional overlap: * * overlapping length * * as given by: ------------------ * * common length * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * LWRITE variable used, to call subroutines such that the * * result they compute is written out (true) or not * ******------------------------------*-----------------------------****** C---- defaults MUEFOUND= 0 C----------------------------------------------------------------------* C---- initial check of variables passed -----* C----------------------------------------------------------------------* IF (CHVPL.NE.3) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'WARNING: SSEGFOV: number of passed variables not fitting' END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 CHVPM(3)=CHVP3 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for SSEGFOV: variables passed not correct !' END IF C---- check variables passed IF (NUMRESLIB.GT.MAXNUMRES) THEN WRITE(6,'(T5,A)') + ' The length of the protein passed to SBR SSEGFOV' WRITE(6,'(T5,A)') + ' exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T50,I4)') + ' Current length: ',NUMRESLIB,' allocated:',MAXNUMRES WRITE(6,'(T5,A)')' Stopped in SSEGFOV 12-2-92:1' STOP END IF IF (NSECELLIB.GT.MAXNSECEL) THEN WRITE(6,'(T5,A)') + 'The number of secondary structures passed to SBR SSEGFOV' WRITE(6,'(T5,A)') + 'exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current number: ',NSECELLIB,' allocated:',MAXNSECEL WRITE(6,'(T5,A)')' Stopped in SSEGFOV 12-11-92:2' STOP END IF C----------------------------------------------------------------------* C---- end of checking variables -----* C----------------------------------------------------------------------* C-------------------------------------------------- C---- computing overlapping lengths %obs ----- C-------------------------------------------------- C---- set zero C ----------- CALL SISTZ2(COUNTSEG,2,(MAXNSECEL+1)) C ----------- CALL SRSTZ2(QSEGFOV,2,(MAXNSECEL+1)) C ----------- DO MUE=1,NUMSEGDSSP BEGMUE=BEGSEGDSSP(MUE) LOVER=.FALSE. DO ITSEC=1,NSECELLIB IF ((LOVER .EQV. .FALSE.).AND. + (DSSPCHAR(BEGMUE).EQ.SSCHAR(ITSEC))) THEN C------------- search for closest segment predicted IF (DSSPCHAR(BEGMUE).EQ.PREDCHAR(BEGMUE)) THEN LOVER=.TRUE. MUEFOUND=BEGMUE ELSE DO ITSEG=1,(ENDSEGDSSP(MUE)-BEGSEGDSSP(MUE)) IF ((LOVER .EQV. .FALSE.) .AND. + (DSSPCHAR(BEGMUE+ITSEG)) .EQ. + PREDCHAR(BEGMUE+ITSEG)) THEN LOVER=.TRUE. MUEFOUND=BEGMUE+ITSEG END IF END DO END IF IF (LOVER .EQV. .TRUE.) THEN IHELP=POINTPRED(MUEFOUND) IMINOV= + (-MAX(BEGSEGDSSP(MUE),BEGSEGPRED(IHELP)) + +MIN(ENDSEGDSSP(MUE),ENDSEGPRED(IHELP))+1) IMAXOV= + (-MIN(BEGSEGDSSP(MUE),BEGSEGPRED(IHELP)) + +MAX(ENDSEGDSSP(MUE),ENDSEGPRED(IHELP))+1) C---------------- allow deviation IF (DEVNOM.EQ.50) THEN MAXDEV=MIN(IMINOV, + INT((ENDSEGDSSP(MUE)-BEGSEGDSSP(MUE)+1)/2.)) ELSEIF (DEVNOM.EQ.100) THEN MAXDEV=MIN(IMINOV, + (ENDSEGDSSP(MUE)-BEGSEGDSSP(MUE)+1)) ELSE MAXDEV=MIN(IMINOV,DEVNOM) END IF DO ITER=1,MAXDEV IF (IMAXOV.GT.IMINOV) THEN IMINOV=IMINOV+1 END IF END DO C---------------- COUNTSEG(1,ITSEC)=COUNTSEG(1,ITSEC)+1 IF (IMAXOV.GT.0) THEN QSEGFOV(1,ITSEC)=QSEGFOV(1,ITSEC) + +IMINOV/REAL(IMAXOV) + *(ENDSEGDSSP(MUE)-BEGSEGDSSP(MUE)+1) ELSE WRITE(6,'(T2,A,T10,A,T50,I3)')'***', + 'ERROR in SSEGFOV: length=0 for',IMAXOV WRITE(6,'(T2,A,T10,A,T40,I4,A,T60,A1)')'***', + 'for obs seg:',MUE,' which is a: ', + SSCHAR(ITSEC) END IF ELSE COUNTSEG(1,ITSEC)=COUNTSEG(1,ITSEC)+1 END IF END IF END DO C------- end of computation for H, E, T END DO C---- end of loop over observed segments C---- normalize with number of respective segments QSEGFOV(1,(NSECELLIB+1))=0. INTERCOUNTSEG=0 DO ITSEC=1,NSECELLIB IF (COUNTSEG(1,ITSEC).NE.0) THEN QSEGFOV(1,(NSECELLIB+1))=QSEGFOV(1,(NSECELLIB+1)) + +QSEGFOV(1,ITSEC) INTERCOUNTSEG=INTERCOUNTSEG+COUNTSEG(1,ITSEC) C-------------------------------------------------- C---- out now, since normalisation with number of residues C QSEGFOV(1,ITSEC)=QSEGFOV(1,ITSEC)/REAL(COUNTSEG(1,ITSEC)) C-------------------------------------------------- END IF END DO COUNTSEG(1,(NSECELLIB+1))=INTERCOUNTSEG C-------------------------------------------------- C---- out now, since normalisation with number of residues C QSEGFOV(1,(NSECELLIB+1))= C + QSEGFOV(1,(NSECELLIB+1))/REAL(INTERCOUNTSEG) C-------------------------------------------------- C write(6,*)'x.x lib-x.f' C write(6,*)'dssp' C write(6,'(60A1)')(dsspchar(mue),mue=1,numreslib) C write(6,*)'pred' C write(6,'(60A1)')(predchar(mue),mue=1,numreslib) C write(6,'(A,T20,4I5)')'countseg = ',(countseg(1,iter),iter=1,4) C write(6,'(A,T20,4I5)')'fov=',(int(100*qSEGFOV(1,iter)),iter=1,4) C---- end computing overlapping lengths %obs ----- C-------------------------------------------------- C-------------------------------------------------- C---- computing overlapping lengths %pred ----- C-------------------------------------------------- DO MUE=1,NUMSEGPRED BEGMUE=BEGSEGPRED(MUE) LOVER=.FALSE. DO ITSEC=1,NSECELLIB IF ((LOVER .EQV. .FALSE.).AND. + (PREDCHAR(BEGMUE).EQ.SSCHAR(ITSEC))) THEN IF (PREDCHAR(BEGMUE).EQ.DSSPCHAR(BEGMUE)) THEN LOVER=.TRUE. MUEFOUND=BEGMUE ELSE DO ITSEG=1,(ENDSEGPRED(MUE)-BEGSEGPRED(MUE)) IF ((LOVER .EQV. .FALSE.).AND. + (PREDCHAR(BEGMUE+ITSEG).EQ. + DSSPCHAR(BEGMUE+ITSEG))) THEN LOVER=.TRUE. MUEFOUND=BEGMUE+ITSEG END IF END DO END IF IF (LOVER .EQV. .TRUE.) THEN IHELP=POINTDSSP(MUEFOUND) IMINOV= + (-MAX(BEGSEGPRED(MUE),BEGSEGDSSP(IHELP)) + +MIN(ENDSEGPRED(MUE),ENDSEGDSSP(IHELP))+1) IMAXOV= + (-MIN(BEGSEGPRED(MUE),BEGSEGDSSP(IHELP)) + +MAX(ENDSEGPRED(MUE),ENDSEGDSSP(IHELP))+1) C---------------- allow deviation IF (DEVNOM.EQ.50) THEN MAXDEV=MIN(IMINOV, + INT((ENDSEGPRED(MUE)-BEGSEGPRED(MUE)+1)/2.)) ELSEIF (DEVNOM.EQ.100) THEN MAXDEV=MIN(IMINOV, + (ENDSEGPRED(MUE)-BEGSEGPRED(MUE)+1)) ELSE MAXDEV=MIN(IMINOV,DEVNOM) END IF DO ITER=1,MAXDEV IF (IMAXOV.GT.IMINOV) THEN IMINOV=IMINOV+1 END IF END DO C---------------- COUNTSEG(2,ITSEC)=COUNTSEG(2,ITSEC)+1 IF (IMAXOV.GT.0) THEN QSEGFOV(2,ITSEC)=QSEGFOV(2,ITSEC) + +IMINOV/REAL(IMAXOV) + *(ENDSEGPRED(MUE)-BEGSEGPRED(MUE)+1) ELSE WRITE(6,'(T2,A,T10,A,T50,I3)')'***', + 'ERROR in SSEGFOV: length=0 for',IMAXOV WRITE(6,'(T2,A,T10,A,T40,I4,A,T60,A1)')'***', + 'for obs seg:',MUE,' which is a: ', + SSCHAR(ITSEC) END IF ELSE COUNTSEG(2,ITSEC)=COUNTSEG(2,ITSEC)+1 END IF END IF END DO C------- end of computation for H, E, T END DO C---- end of loop over observed segments C---- normalize with number of respective segments QSEGFOV(2,(NSECELLIB+1))=0. INTERCOUNTSEG=0 DO ITSEC=1,NSECELLIB IF (COUNTSEG(2,ITSEC).NE.0) THEN QSEGFOV(2,(NSECELLIB+1))=QSEGFOV(2,(NSECELLIB+1)) + +QSEGFOV(2,ITSEC) INTERCOUNTSEG=INTERCOUNTSEG+COUNTSEG(2,ITSEC) C-------------------------------------------------- C---- out now, since normalisation with number of residues C QSEGFOV(2,ITSEC)=QSEGFOV(2,ITSEC)/REAL(COUNTSEG(2,ITSEC)) C-------------------------------------------------- END IF END DO COUNTSEG(2,(NSECELLIB+1))=INTERCOUNTSEG C-------------------------------------------------- C---- out now, since normalisation with number of residues C QSEGFOV(2,(NSECELLIB+1))= C + QSEGFOV(2,(NSECELLIB+1))/REAL(INTERCOUNTSEG) C-------------------------------------------------- C---- end computing overlapping lengths %obs ----- C-------------------------------------------------- END ***** end of SSEGFOV ***** ------------------------------------------------------------------ ***** SUB SSEGLOV ***** ------------------------------------------------------------------ C---- C---- NAME : SSEGLOV C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1992 version 0.1 * * changed: Mar, 1993 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The measures related to segments are computed. * * input variables:NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES * * ----------------DSSPCHAR,PREDCHAR * * output variab.: NUMSEGOVERL * * called by: SEVALPRED (in lib-prot.f) * * SBRs calling: from lib-comp.f: * * -------------- SISTZ1, * * from lib-unix.f: * * SCHECKPASS * * from lib-prot.f: * * SSEGBEGIN, STABLESEG * * procedure: overlapp NUMSEGOVERL(3/4,ITSEC) ,3=%OBS, 4=%PRED * * ---------- for H, E, T * * if overlapp > L/2 * * for L: * * if overlapp > 2 * * correct: NUMSEGOVERL(5,ITSEC) * * for L < 5: | L(OBS)-L(PRED) | <= 1 * * .AND. shift by 1 allowed * * for 5<=L<10: | L(OBS)-L(PRED) | <= 2 * * .AND. shift by 2 allowed * * for L >= 10: | L(OBS)-L(PRED) | <= 3 * * .AND. shift by 3 allowed * *----------------------------------------------------------------------* SUBROUTINE SSEGLOV(NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES, + MAXSEGPASS,CHVP1,DSSPCHAR,PREDCHAR,CHVP2,LENSEGDSSP, + LENSEGPRED,BEGSEGDSSP,ENDSEGDSSP,BEGSEGPRED,ENDSEGPRED, + CHVP3,NUMSEGOVERL,QSEGLOV,CHVPL) IMPLICIT NONE C---- variables passed INTEGER MAXNSECEL,NSECELLIB,MAXNUMRES,NUMRESLIB,MAXSEGPASS, + CHVPM(1:50),CHVPL,CHVP1,CHVP2,CHVP3, + NUMSEGOVERL(1:9,1:(MAXNSECEL+1)), + BEGSEGDSSP(1:MAXSEGPASS),ENDSEGDSSP(1:MAXSEGPASS), + LENSEGDSSP(1:MAXSEGPASS),LENSEGPRED(1:MAXSEGPASS), + BEGSEGPRED(1:MAXSEGPASS),ENDSEGPRED(1:MAXSEGPASS) REAL QSEGLOV(1:2,1:(MAXNSECEL+1)) CHARACTER*1 DSSPCHAR(1:MAXNUMRES),PREDCHAR(1:MAXNUMRES) C---- local variables * INTEGER MUE,ITSEC,ITOVER,ITER,IHELP,BEGMUE,ENDMUE LOGICAL LERRCHVP,LOVER ******------------------------------*-----------------------------****** * MUE,ITER serve as iteration variables * * NUMSEGOVERL(i,j) number of overlapping/correct segments * * i=1 number of DSSP segments in secondary structure * * j, for last: sum over all * * i=2 number of residues in structure i, summed up over* * all segments (in i=1) * * i=3 number of predicted segments in class j * * i=4 number of residues in structure i, summed up over* * all segments (in i=1) for the prediction * * i=5 number of overlapping predicted segments related * * to those being observed. Correct means: * * overlap >= length of segment / 2, for H, E, T * * and for loop: at least loop of 2, resp 1, if the* * DSSP loop is 1. * * i=6 number of overlapping segments multiplied by * * length: related to %observed * * i=7 same as 5, but other way round: %pred! * * i=8 same as 6, but other way round: %pred! * * j, for last: sum over all * * i=9 number of correct segments: * * L +/- 1, and shift by 1, if L<=5 * * L +/- 1, and shift by 2, if 510 * * noted: j, for last: sum over all * * QSEGLOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the loose overlap (half length overlap) * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * LWRITE variable used, to call subroutines such that the * * result they compute is written out (true) or not * ******------------------------------*-----------------------------****** C---- initial check of variables passed IF (CHVPL.NE.3) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'WARNING: SSEGLOV: number of passed variables not fitting' END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 CHVPM(3)=CHVP3 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for SSEGLOV: variables passed not correct !' END IF C---- check variables passed IF (NUMRESLIB.GT.MAXNUMRES) THEN WRITE(6,'(T5,A)') + ' The length of the protein passed to SBR SSEGLOV' WRITE(6,'(T5,A)') + ' exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current length: ',NUMRESLIB,' allocated:',MAXNUMRES WRITE(6,'(T5,A)')' Stopped in SSEGLOV 12-11-92:3' STOP END IF IF (NSECELLIB.GT.MAXNSECEL) THEN WRITE(6,'(T5,A)') + 'The number of secondary structures passed to SBR SSEGLOV' WRITE(6,'(T5,A)') + 'exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current number: ',NSECELLIB,' allocated:',MAXNSECEL WRITE(6,'(T5,A)')' Stopped in SSEGLOV 12-11-92:4' STOP END IF C---- set zero C ----------- CALL SRSTZ2(QSEGLOV,2,(MAXNSECEL+1)) C ----------- DO ITER=1,4 DO ITSEC=1,(NSECELLIB+1) NUMSEGOVERL((4+ITER),ITSEC)=0 END DO END DO C-------------------------------------------------- C---- overlapp % observed ----- C-------------------------------------------------- DO MUE=1,NUMSEGOVERL(1,(NSECELLIB+1)) BEGMUE=BEGSEGDSSP(MUE) ENDMUE=ENDSEGDSSP(MUE) C---------------------------------------- C------- helix, strand, turn -------- C---------------------------------------- IF ((DSSPCHAR(BEGMUE).EQ.'H').OR.(DSSPCHAR(BEGMUE).EQ.'E').OR. + (DSSPCHAR(BEGMUE).EQ.'T')) THEN LOVER=.TRUE. IF (INT(LENSEGDSSP(MUE)).LT.2) THEN WRITE(6,'(T2,A,T10,A,T40,A1,A,T60,I3)')'***', + 'segment too short for:',DSSPCHAR(MUE), + 'seg no:',MUE LOVER=.FALSE. ELSEIF (INT(LENSEGDSSP(MUE)).GT.NUMRESLIB) THEN WRITE(6,'(T2,A,T10,A,T40,A1,A,T60,I3)')'***', + 'segment too long for:',DSSPCHAR(MUE), + 'seg no:',MUE LOVER=.FALSE. ELSE C------------- overlapp with N-terminal end of segment? DO ITOVER=1,INT(LENSEGDSSP(MUE)/2.) IHELP=BEGMUE+ITOVER-1 IF (LOVER.AND. + (PREDCHAR(IHELP).NE.DSSPCHAR(IHELP))) THEN LOVER=.FALSE. C------------------- allow H H -> HHH IF ((IHELP.GT.1).AND.(IHELP.LT.NUMRESLIB)) THEN IF ((PREDCHAR(IHELP-1).EQ.DSSPCHAR(IHELP)).AND. + (PREDCHAR(IHELP+1).EQ.DSSPCHAR(IHELP))) THEN LOVER=.TRUE. END IF END IF END IF END DO END IF C---------- overlapp with C-terminal end of segment? IF ((LOVER.EQV. .FALSE.).AND.(LENSEGDSSP(MUE).GT.2).AND. + (LENSEGDSSP(MUE).LT.NUMRESLIB)) THEN LOVER=.TRUE. DO ITOVER=1,INT(LENSEGDSSP(MUE)/2.) IHELP=ENDMUE-INT(LENSEGDSSP(MUE)/2.)+ITOVER-1 IF (IHELP.LT.0) THEN LOVER=.FALSE. ELSE IF (LOVER.EQV. .TRUE. .AND.(PREDCHAR(IHELP).NE. + DSSPCHAR(IHELP))) THEN LOVER=.FALSE. C------------------- allow H H -> HHH IF ((IHELP.GT.1).AND.(IHELP.LT.NUMRESLIB)) THEN IF ((PREDCHAR(IHELP-1).EQ.DSSPCHAR(IHELP)).AND. + (PREDCHAR(IHELP+1).EQ.DSSPCHAR(IHELP))) THEN LOVER=.TRUE. END IF END IF END IF END DO END IF C---------- overlapped? IF (LOVER .EQV. .TRUE.) THEN IF (DSSPCHAR(BEGMUE).EQ.'H') THEN NUMSEGOVERL(5,1)=NUMSEGOVERL(5,1)+1 NUMSEGOVERL(6,1)=NUMSEGOVERL(6,1)+LENSEGDSSP(MUE) QSEGLOV(1,1)=QSEGLOV(1,1)+LENSEGDSSP(MUE) ELSEIF (DSSPCHAR(BEGMUE).EQ.'E') THEN NUMSEGOVERL(5,2)=NUMSEGOVERL(5,2)+1 NUMSEGOVERL(6,2)=NUMSEGOVERL(6,2)+LENSEGDSSP(MUE) QSEGLOV(1,2)=QSEGLOV(1,2)+LENSEGDSSP(MUE) ELSEIF (DSSPCHAR(BEGMUE).EQ.'T') THEN NUMSEGOVERL(5,3)=NUMSEGOVERL(5,3)+1 NUMSEGOVERL(6,3)=NUMSEGOVERL(6,3)+LENSEGDSSP(MUE) QSEGLOV(1,3)=QSEGLOV(1,3)+LENSEGDSSP(MUE) END IF END IF C---------------------------------------- C------- loop overlap > 2 -------- C---------------------------------------- ELSEIF (DSSPCHAR(BEGMUE).EQ.'L') THEN LOVER=.FALSE. C---------- overlapp with loop anywhere > 2? IF (LENSEGDSSP(MUE).EQ.1) THEN IF (PREDCHAR(BEGMUE).EQ.'L') THEN LOVER=.TRUE. END IF ELSEIF (LENSEGDSSP(MUE).EQ.2) THEN IF (PREDCHAR(BEGMUE).EQ.'L') THEN LOVER=.TRUE. ELSEIF ((BEGMUE.LT.NUMRESLIB).AND. + (PREDCHAR(BEGMUE+1).EQ.'L')) THEN LOVER=.TRUE. END IF ELSEIF (LENSEGDSSP(MUE).GT.NUMRESLIB) THEN LOVER=.FALSE. ELSEIF (ENDMUE.GT.NUMRESLIB) THEN LOVER=.FALSE. ELSE DO ITOVER=BEGMUE,ENDMUE IF ((LOVER.EQV. .FALSE.).AND. + (PREDCHAR(ITOVER).EQ.'L')) THEN IF (ITOVER.GT.BEGMUE) THEN IF (PREDCHAR(ITOVER-1).EQ.'L') THEN LOVER=.TRUE. END IF ELSEIF (ITOVER.LT.ENDMUE) THEN IF (PREDCHAR(ITOVER+1).EQ.'L') THEN LOVER=.TRUE. END IF END IF END IF END DO END IF C---------- overlapped? IF (LOVER .EQV. .TRUE.) THEN NUMSEGOVERL(5,NSECELLIB)=NUMSEGOVERL(5,NSECELLIB)+1 NUMSEGOVERL(6,NSECELLIB)=NUMSEGOVERL(6,NSECELLIB) + +LENSEGDSSP(MUE) QSEGLOV(1,NSECELLIB)=QSEGLOV(1,NSECELLIB)+LENSEGDSSP(MUE) END IF END IF END DO C---- compute number of all overlapping segments DO ITSEC=1,NSECELLIB NUMSEGOVERL(5,(NSECELLIB+1))=NUMSEGOVERL(5,(NSECELLIB+1)) + +NUMSEGOVERL(5,ITSEC) NUMSEGOVERL(6,(NSECELLIB+1))=NUMSEGOVERL(6,(NSECELLIB+1)) + +NUMSEGOVERL(6,ITSEC) QSEGLOV(1,(NSECELLIB+1))=QSEGLOV(1,(NSECELLIB+1)) + +QSEGLOV(1,ITSEC) END DO C-------------------------------------------------- C---- overlapp % predicted ----- C-------------------------------------------------- DO MUE=1,NUMSEGOVERL(3,(NSECELLIB+1)) BEGMUE=BEGSEGPRED(MUE) ENDMUE=ENDSEGPRED(MUE) C---------------------------------------- C------- helix, strand, turn -------- C---------------------------------------- IF ((PREDCHAR(BEGMUE).EQ.'H').OR. + (PREDCHAR(BEGMUE).EQ.'E').OR. + (PREDCHAR(BEGMUE).EQ.'T')) THEN LOVER=.TRUE. IF (INT(LENSEGPRED(MUE)).LT.2) THEN WRITE(6,'(T2,A,T10,A,T40,A1,A,T60,I3)')'***', + 'pred seg too short for:',PREDCHAR(MUE), + 'seg no:',MUE LOVER=.FALSE. ELSEIF (INT(LENSEGPRED(MUE)).GT.NUMRESLIB) THEN WRITE(6,'(T2,A,T10,A,T40,A1,A,T60,I3)')'***', + 'pred seg too long for:',PREDCHAR(MUE), + 'seg no:',MUE LOVER=.FALSE. ELSE C------------- overlapp with N-terminal end of segment? DO ITOVER=1,INT(LENSEGPRED(MUE)/2.) IHELP=BEGMUE+ITOVER-1 IF (LOVER.EQV. .TRUE. .AND.(IHELP.LT.NUMRESLIB).AND. + (DSSPCHAR(IHELP).NE.PREDCHAR(IHELP))) THEN LOVER=.FALSE. C------------------- allow H H -> HHH IF ((IHELP.GT.1).AND.(IHELP.LT.NUMRESLIB)) THEN IF ((DSSPCHAR(IHELP-1).EQ.PREDCHAR(IHELP)).AND. + (DSSPCHAR(IHELP+1).EQ.PREDCHAR(IHELP))) THEN LOVER=.TRUE. END IF END IF END IF END DO END IF C---------- overlapp with C-terminal end of segment? IF ((LOVER.EQV. .FALSE.).AND.(LENSEGPRED(MUE).GT.2).AND. + (LENSEGPRED(MUE).LT.NUMRESLIB)) THEN LOVER=.TRUE. DO ITOVER=1,INT(LENSEGPRED(MUE)/2.) IHELP=ENDMUE-INT(LENSEGPRED(MUE)/2.)+ITOVER-1 C---------------- hack 2-06-97 IF ((IHELP.GT.0).AND.(IHELP.LE.NUMRESLIB)) THEN IF (LOVER.EQV. .TRUE. .AND.(IHELP.GE.1).AND. + (IHELP.LE.NUMRESLIB).AND. + (PREDCHAR(IHELP).NE.DSSPCHAR(IHELP))) THEN LOVER=.FALSE. C------------------- allow H H -> HHH IF ((IHELP.GT.1).AND.(IHELP.LT.NUMRESLIB)) THEN IF ((DSSPCHAR(IHELP-1).EQ. + PREDCHAR(IHELP)).AND. + (DSSPCHAR(IHELP+1).EQ. + PREDCHAR(IHELP))) THEN LOVER=.TRUE. END IF END IF ELSE LOVER=.FALSE. END IF C---------------- hack 2-06-97 ELSE LOVER=.FALSE. END IF END DO ELSE LOVER=.FALSE. END IF C---------- overlapped? IF (LOVER .EQV. .TRUE.) THEN IF (PREDCHAR(BEGMUE).EQ.'H') THEN NUMSEGOVERL(7,1)=NUMSEGOVERL(7,1)+1 NUMSEGOVERL(8,1)=NUMSEGOVERL(8,1)+LENSEGPRED(MUE) QSEGLOV(2,1)=QSEGLOV(2,1)+LENSEGPRED(MUE) ELSEIF (PREDCHAR(BEGMUE).EQ.'E') THEN NUMSEGOVERL(7,2)=NUMSEGOVERL(7,2)+1 NUMSEGOVERL(8,2)=NUMSEGOVERL(8,2)+LENSEGPRED(MUE) QSEGLOV(2,2)=QSEGLOV(2,2)+LENSEGPRED(MUE) ELSEIF (PREDCHAR(BEGMUE).EQ.'T') THEN NUMSEGOVERL(7,3)=NUMSEGOVERL(7,3)+1 NUMSEGOVERL(8,3)=NUMSEGOVERL(8,3)+LENSEGPRED(MUE) QSEGLOV(2,3)=QSEGLOV(2,3)+LENSEGPRED(MUE) END IF END IF C---------------------------------------- C------- loop overlap > 2 -------- C---------------------------------------- ELSEIF (PREDCHAR(BEGMUE).EQ.'L') THEN LOVER=.FALSE. C---------- overlapp with loop anywhere > 2? IF (LENSEGPRED(MUE).EQ.1) THEN IF (DSSPCHAR(BEGMUE).EQ.'L') THEN LOVER=.TRUE. END IF ELSEIF (LENSEGPRED(MUE).EQ.2) THEN IF (DSSPCHAR(BEGMUE).EQ.'L') THEN LOVER=.TRUE. ELSEIF ((BEGMUE.LT.NUMRESLIB).AND. + (DSSPCHAR(BEGMUE+1).EQ.'L')) THEN LOVER=.TRUE. END IF ELSEIF (LENSEGPRED(MUE).GT.NUMRESLIB) THEN LOVER=.FALSE. ELSE DO ITOVER=BEGMUE,ENDMUE IF ((LOVER.EQV. .FALSE.).AND. + (PREDCHAR(ITOVER).EQ.'L')) THEN IF (ITOVER.GT.BEGMUE) THEN IF (DSSPCHAR(ITOVER-1).EQ.'L') THEN LOVER=.TRUE. END IF ELSEIF (ITOVER.LT.ENDMUE) THEN IF (DSSPCHAR(ITOVER+1).EQ.'L') THEN LOVER=.TRUE. END IF END IF END IF END DO END IF C---------- overlapped? IF (LOVER .EQV. .TRUE.) THEN NUMSEGOVERL(7,NSECELLIB)=NUMSEGOVERL(7,NSECELLIB)+1 NUMSEGOVERL(8,NSECELLIB)=NUMSEGOVERL(8,NSECELLIB) + +LENSEGPRED(MUE) QSEGLOV(2,NSECELLIB)= + QSEGLOV(2,NSECELLIB)+LENSEGPRED(MUE) END IF END IF END DO C---- compute number of all overlapping segments DO ITSEC=1,NSECELLIB NUMSEGOVERL(7,(NSECELLIB+1))=NUMSEGOVERL(7,(NSECELLIB+1)) + +NUMSEGOVERL(4,ITSEC) NUMSEGOVERL(8,(NSECELLIB+1))=NUMSEGOVERL(8,(NSECELLIB+1)) + +NUMSEGOVERL(8,ITSEC) QSEGLOV(2,(NSECELLIB+1))=QSEGLOV(2,(NSECELLIB+1)) + +QSEGLOV(2,ITSEC) END DO C-------------------------------------------------- C---- end of scanning PRED segments ----- C-------------------------------------------------- END ***** end of SSEGLOV ***** ------------------------------------------------------------------ ***** SUB SSEGSOV ***** ------------------------------------------------------------------ C---- C---- NAME : SSEGSOV C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The number of correctly predicted elements is * * -------- computed. * * input variables:NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES, * * ----------------DSSPCHAR,PREDCHAR,SSCHAR,LENSEGDSSP,LENSEGPRED, * * POINTPRED,BEGSEGDSSP,COUNTSEG * * output variab.: NUMCOR * * called by: SEVALSEG (in lib-prot.f) * * SBRs calling: from lib-comp.f: * * -------------- SISTZ1, * * from lib-unix.f: * * SCHECKPASS * * procedure: correct: NUMSEGOVERL(5,ITSEC) * * ---------- for L < 5: | L(OBS)-L(PRED) | <= 1 * * .AND. shift by 1 allowed * * for 5<=L<10: | L(OBS)-L(PRED) | <= 2 * * .AND. shift by 2 allowed * * for L >= 10: | L(OBS)-L(PRED) | <= 3 * * .AND. shift by 3 allowed * *----------------------------------------------------------------------* SUBROUTINE SSEGSOV(NSECELLIB,MAXNSECEL,NUMRESLIB,MAXNUMRES, + MAXSEGPASS,CHVP1,DSSPCHAR,PREDCHAR,SSCHAR,CHVP2, + LENSEGDSSP,LENSEGPRED,POINTDSSP,POINTPRED, + BEGSEGDSSP,BEGSEGPRED,CHVP3, + NUMCOR,COUNTSEGDSSP,COUNTSEGPRED,QSEGSOV,CHVPL) IMPLICIT NONE C---- variables passed INTEGER MAXNSECEL,NSECELLIB,MAXNUMRES,NUMRESLIB, + MAXSEGPASS,CHVPM(1:50),CHVPL,CHVP1,CHVP2,CHVP3, + NUMCOR(1:2,1:8),COUNTSEGDSSP,COUNTSEGPRED, + POINTDSSP(1:MAXNUMRES),POINTPRED(1:MAXNUMRES), + BEGSEGDSSP(1:MAXSEGPASS),BEGSEGPRED(1:MAXSEGPASS), + LENSEGDSSP(1:MAXSEGPASS),LENSEGPRED(1:MAXSEGPASS) REAL QSEGSOV(1:2,1:(MAXNSECEL+1)) CHARACTER*1 DSSPCHAR(1:MAXNUMRES),PREDCHAR(1:MAXNUMRES) CHARACTER*1 SSCHAR(1:8) C---- local variables * INTEGER MUE,ITSEC,IHELP LOGICAL LERRCHVP,LOVER ******------------------------------*-----------------------------****** * MUE,ITER serve as iteration variables * * QSEGSOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the strict overlap * * for L < 5: | L(OBS)-L(PRED) | <= 1 * * .AND. shift by 1 allowed * * for 5<=L<10: | L(OBS)-L(PRED) | <= 2 * * .AND. shift by 2 allowed * * for L >= 10: | L(OBS)-L(PRED) | <= 3 * * .AND. shift by 3 allowed * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * LWRITE variable used, to call subr such that the * * result they compute is written out (true) or not * ******------------------------------*-----------------------------****** C---- initial check of variables passed IF (CHVPL.NE.3) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'WARNING: SSEGSOV: number of passed variables not fitting' END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 CHVPM(3)=CHVP3 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for SSEGSOV: variables passed not correct !' END IF C---- check variables passed IF (NUMRESLIB.GT.MAXNUMRES) THEN WRITE(6,'(T5,A)') + ' The length of the protein passed to SBR SSEGSOV' WRITE(6,'(T5,A)') + ' exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current length: ',NUMRESLIB,' allocated:',MAXNUMRES WRITE(6,'(T5,A)')' Stopped in SSEGSOV 12-2-92:1' STOP END IF IF (NSECELLIB.GT.MAXNSECEL) THEN WRITE(6,'(T5,A)') + 'The number of secondary structures passed to SBR SSEGSOV' WRITE(6,'(T5,A)') + 'exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current number: ',NSECELLIB,' allocated:',MAXNSECEL WRITE(6,'(T5,A)')' Stopped in SSEGSOV 12-11-92:2' STOP END IF C---- set zero C ----------- CALL SISTZ2(NUMCOR,2,8) C ----------- CALL SRSTZ2(QSEGSOV,2,(MAXNSECEL+1)) C ----------- C---------------------------------------------------------------------- C---- computing correct elements for %observed ----- C---------------------------------------------------------------------- DO MUE=1,COUNTSEGDSSP LOVER=.FALSE. IF (LENSEGDSSP(MUE).LE.2) THEN IHELP=BEGSEGDSSP(MUE) IF (PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)) THEN LOVER=.TRUE. END IF ELSEIF (LENSEGDSSP(MUE).LE.5) THEN IHELP=BEGSEGDSSP(MUE) IF ((PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP)).LE. + (LENSEGDSSP(MUE)+1)).AND. + (LENSEGPRED(POINTPRED(IHELP)).GE. + (LENSEGDSSP(MUE)-1))) THEN LOVER=.TRUE. ELSEIF (IHELP.LT.0) THEN LOVER=.FALSE. ELSEIF (IHELP.EQ.1) THEN IF (PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)) THEN LOVER=.TRUE. ELSE LOVER=.FALSE. END IF ELSEIF (IHELP.EQ.NUMRESLIB) THEN IF (PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)) THEN LOVER=.TRUE. ELSE LOVER=.FALSE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.1)) THEN IF ( (PREDCHAR(IHELP-1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP-1)).LE. + (LENSEGDSSP(MUE)+1)).AND. + (LENSEGPRED(POINTPRED(IHELP-1)).GE. + (LENSEGDSSP(MUE)-1))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.NUMRESLIB)) THEN IF ( (PREDCHAR(IHELP+1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP+1)).LE. + (LENSEGDSSP(MUE)+1)).AND. + (LENSEGPRED(POINTPRED(IHELP+1)).GE. + (LENSEGDSSP(MUE)-1))) THEN LOVER=.TRUE. END IF END IF ELSEIF (LENSEGDSSP(MUE).LE.10) THEN IHELP=BEGSEGDSSP(MUE) IF ( (PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP)).LE. + (LENSEGDSSP(MUE)+2)).AND. + (LENSEGPRED(POINTPRED(IHELP)).GE. + (LENSEGDSSP(MUE)-2))) THEN LOVER=.TRUE. ELSEIF (IHELP.LT.0) THEN LOVER=.FALSE. ELSEIF (IHELP.EQ.1) THEN IF (PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)) THEN LOVER=.TRUE. ELSE LOVER=.FALSE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.1)) THEN IF ((PREDCHAR(IHELP-1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP-1)).LE. + (LENSEGDSSP(MUE)+2)).AND. + (LENSEGPRED(POINTPRED(IHELP-1)).GE. + (LENSEGDSSP(MUE)-2))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.2)) THEN IF ( (PREDCHAR(IHELP-2).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP-2)).LE. + (LENSEGDSSP(MUE)+2)).AND. + (LENSEGPRED(POINTPRED(IHELP-2)).GE. + (LENSEGDSSP(MUE)-2))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.NUMRESLIB)) THEN IF ( (PREDCHAR(IHELP+1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP+1)).LE. + (LENSEGDSSP(MUE)+2)).AND. + (LENSEGPRED(POINTPRED(IHELP+1)).GE. + (LENSEGDSSP(MUE)-2))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.(NUMRESLIB-1))) THEN IF ( (PREDCHAR(IHELP+2).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP+2)).LE. + (LENSEGDSSP(MUE)+2)).AND. + (LENSEGPRED(POINTPRED(IHELP+2)).GE. + (LENSEGDSSP(MUE)-2))) THEN LOVER=.TRUE. END IF END IF ELSEIF (LENSEGDSSP(MUE).GT.NUMRESLIB) THEN LOVER=.FALSE. ELSEIF (LENSEGDSSP(MUE).GT.10) THEN IHELP=BEGSEGDSSP(MUE) IF ((PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP)).LE. + (LENSEGDSSP(MUE)+3)).AND. + (LENSEGPRED(POINTPRED(IHELP)).GE. + (LENSEGDSSP(MUE)-3))) THEN LOVER=.TRUE. END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.1)) THEN IF ( (PREDCHAR(IHELP-1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP-1)).LE. + (LENSEGDSSP(MUE)+3)).AND. + (LENSEGPRED(POINTPRED(IHELP-1)).GE. + (LENSEGDSSP(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.2)) THEN IF ( (PREDCHAR(IHELP-2).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP-2)).LE. + (LENSEGDSSP(MUE)+3)).AND. + (LENSEGPRED(POINTPRED(IHELP-2)).GE. + (LENSEGDSSP(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.3)) THEN IF ( (PREDCHAR(IHELP-3).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP-3)).LE. + (LENSEGDSSP(MUE)+3)).AND. + (LENSEGPRED(POINTPRED(IHELP-3)).GE. + (LENSEGDSSP(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.NUMRESLIB)) THEN IF ( (PREDCHAR(IHELP+1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP+1)).LE. + (LENSEGDSSP(MUE)+3)).AND. + (LENSEGPRED(POINTPRED(IHELP+1)).GE. + (LENSEGDSSP(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.(NUMRESLIB-1))) THEN IF ( (PREDCHAR(IHELP+2).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP+2)).LE. + (LENSEGDSSP(MUE)+3)).AND. + (LENSEGPRED(POINTPRED(IHELP+2)).GE. + (LENSEGDSSP(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.(NUMRESLIB-2))) THEN IF ( (PREDCHAR(IHELP+3).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGPRED(POINTPRED(IHELP+3)).LE. + (LENSEGDSSP(MUE)+3)).AND. + (LENSEGPRED(POINTPRED(IHELP+3)).GE. + (LENSEGDSSP(MUE)-3))) THEN LOVER=.TRUE. END IF END IF END IF C------- count number of correct elements IF (LOVER .EQV. .TRUE.) THEN DO ITSEC=1,NSECELLIB IF (DSSPCHAR(BEGSEGDSSP(MUE)).EQ.SSCHAR(ITSEC)) THEN NUMCOR(1,ITSEC)=NUMCOR(1,ITSEC)+1 QSEGSOV(1,ITSEC)=QSEGSOV(1,ITSEC)+LENSEGDSSP(MUE) END IF END DO END IF END DO C---- end of loop over observed segments C-------------------------------------------------- C-------------------------------------------------- C---- compute SOV for NSECELLIB+1 (i.e. all states) C-------------------------------------------------- DO ITSEC=1,NSECELLIB QSEGSOV(1,(NSECELLIB+1))=QSEGSOV(1,(NSECELLIB+1)) + +QSEGSOV(1,ITSEC) NUMCOR(1,(NSECELLIB+1))=NUMCOR(1,(NSECELLIB+1)) + +NUMCOR(1,ITSEC) END DO C---- end of computation for correct elements as % of observed ----- C---------------------------------------------------------------------- C---------------------------------------------------------------------- C---- computing correct elements for %predicted ----- C---------------------------------------------------------------------- DO MUE=1,COUNTSEGPRED LOVER=.FALSE. IF (LENSEGPRED(MUE).LE.5) THEN IHELP=BEGSEGPRED(MUE) IF ((PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP)).LE. + (LENSEGPRED(MUE)+1)).AND. + (LENSEGDSSP(POINTDSSP(IHELP)).GE. + (LENSEGPRED(MUE)-1))) THEN LOVER=.TRUE. ELSEIF (IHELP.EQ.1) THEN IF (PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)) THEN LOVER=.TRUE. ELSE LOVER=.FALSE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.1)) THEN IF ( (PREDCHAR(IHELP-1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-1)).LE. + (LENSEGPRED(MUE)+1)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-1)).GE. + (LENSEGPRED(MUE)-1))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.NUMRESLIB)) THEN IF ( (PREDCHAR(IHELP+1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+1)).LE. + (LENSEGPRED(MUE)+1)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+1)).GE. + (LENSEGPRED(MUE)-1))) THEN LOVER=.TRUE. END IF END IF C---------- correction for short helices/strands IF ((PREDCHAR(IHELP).EQ.'H').OR. + (PREDCHAR(IHELP).EQ.'E')) THEN LOVER=.FALSE. END IF ELSEIF (LENSEGPRED(MUE).LE.10) THEN IHELP=BEGSEGPRED(MUE) IF ((PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP)).LE. + (LENSEGPRED(MUE)+2)).AND. + (LENSEGDSSP(POINTDSSP(IHELP)).GE. + (LENSEGPRED(MUE)-2))) THEN LOVER=.TRUE. ELSEIF (IHELP.EQ.1) THEN IF (PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)) THEN LOVER=.TRUE. ELSE LOVER=.FALSE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.1)) THEN IF ( (PREDCHAR(IHELP-1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-1)).LE. + (LENSEGPRED(MUE)+2)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-1)).GE. + (LENSEGPRED(MUE)-2))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.2)) THEN IF ( (PREDCHAR(IHELP-2).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-2)).LE. + (LENSEGPRED(MUE)+2)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-2)).GE. + (LENSEGPRED(MUE)-2))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.NUMRESLIB)) THEN IF ( (PREDCHAR(IHELP+1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+1)).LE. + (LENSEGPRED(MUE)+2)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+1)).GE. + (LENSEGPRED(MUE)-2))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.(NUMRESLIB-1))) THEN IF ( (PREDCHAR(IHELP+2).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+2)).LE. + (LENSEGPRED(MUE)+2)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+2)).GE. + (LENSEGPRED(MUE)-2))) THEN LOVER=.TRUE. END IF END IF ELSEIF (LENSEGPRED(MUE).GT.10) THEN IHELP=BEGSEGPRED(MUE) IF ((PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP)).LE. + (LENSEGPRED(MUE)+3)).AND. + (LENSEGDSSP(POINTDSSP(IHELP)).GE. + (LENSEGPRED(MUE)-3))) THEN LOVER=.TRUE. ELSEIF (IHELP.EQ.1) THEN IF (PREDCHAR(IHELP).EQ.DSSPCHAR(IHELP)) THEN LOVER=.TRUE. ELSE LOVER=.FALSE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.1)) THEN IF ( (PREDCHAR(IHELP-1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-1)).LE. + (LENSEGPRED(MUE)+3)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-1)).GE. + (LENSEGPRED(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.2)) THEN IF ( (PREDCHAR(IHELP-2).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-2)).LE. + (LENSEGPRED(MUE)+3)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-2)).GE. + (LENSEGPRED(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.GT.3)) THEN IF ( (PREDCHAR(IHELP-3).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-3)).LE. + (LENSEGPRED(MUE)+3)).AND. + (LENSEGDSSP(POINTDSSP(IHELP-3)).GE. + (LENSEGPRED(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.NUMRESLIB)) THEN IF ( (PREDCHAR(IHELP+1).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+1)).LE. + (LENSEGPRED(MUE)+3)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+1)).GE. + (LENSEGPRED(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.(NUMRESLIB-1))) THEN IF ( (PREDCHAR(IHELP+2).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+2)).LE. + (LENSEGPRED(MUE)+3)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+2)).GE. + (LENSEGPRED(MUE)-3))) THEN LOVER=.TRUE. END IF END IF IF ((LOVER.EQV. .FALSE.).AND.(IHELP.LT.(NUMRESLIB-2))) THEN IF ( (PREDCHAR(IHELP+3).EQ.DSSPCHAR(IHELP)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+3)).LE. + (LENSEGPRED(MUE)+3)).AND. + (LENSEGDSSP(POINTDSSP(IHELP+3)).GE. + (LENSEGPRED(MUE)-3))) THEN LOVER=.TRUE. END IF END IF END IF C---- count number of correct elements IF (LOVER .EQV. .TRUE.) THEN DO ITSEC=1,NSECELLIB IF (DSSPCHAR(BEGSEGPRED(MUE)).EQ.SSCHAR(ITSEC)) THEN NUMCOR(2,ITSEC)=NUMCOR(2,ITSEC)+1 QSEGSOV(2,ITSEC)=QSEGSOV(2,ITSEC)+LENSEGPRED(MUE) END IF END DO END IF END DO C---- end of loop over predicted segments C-------------------------------------------------- C-------------------------------------------------- C---- compute SOV for NSECELLIB+1 (i.e. all states) C-------------------------------------------------- DO ITSEC=1,NSECELLIB QSEGSOV(2,(NSECELLIB+1))=QSEGSOV(2,(NSECELLIB+1)) + +QSEGSOV(2,ITSEC) NUMCOR(2,(NSECELLIB+1))=NUMCOR(2,(NSECELLIB+1)) + +NUMCOR(2,ITSEC) END DO END ***** end of SSEGSOV ***** ------------------------------------------------------------------ ***** SUB STABLEPOLENFILE ***** ------------------------------------------------------------------ C---- C---- NAME : STABLEPOLENFILE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1992 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The pay-offs of a certain prediction are written * * -------- as a table onto unit KOUT * * input variables:NSECELLIB, PROTNAMELIB, NUMRESLIB, TITLE * * ----------------MATNUM, MATQOFDSSP, MATQOFPRED, INTERQ3, INTERSQ * * INTERCORR, MATLEN * * called by: SEVALSEC (in lib-prot.f) * * calling: SEVALQUO (in lib-prot.f) (if q3,sq=0, mat not) * *----------------------------------------------------------------------* SUBROUTINE STABLEPOLENFILE(KUNIT,NSECELLIB,MAXNSECELLIB, + PROTNAMELIB,NUMRESLIB,TITLE,MATNUM,MATQOFDSSP,MATQOFPRED, + INTERQ3,INTERSQ,INTERCORR,MATLEN) IMPLICIT NONE C---- local variables * INTEGER MAXNSECELLIB INTEGER ITER,ITSEC,NUMRESLIB,NSECELLIB,IHELP,KUNIT,ICOUNT INTEGER MATNUM(1:(MAXNSECELLIB+1),1:(MAXNSECELLIB+1)) INTEGER MATLEN(1:(MAXNSECELLIB+1),1:4),IBEG,IEND REAL MATQOFDSSP(1:MAXNSECELLIB,1:MAXNSECELLIB) REAL MATQOFPRED(1:MAXNSECELLIB,1:MAXNSECELLIB) REAL INTERCORR(1:MAXNSECELLIB),INTERQ3,INTERSQ REAL INTERAVLENGTH(1:8,1:2) CHARACTER*1 INTERTITLE(1:40) CHARACTER*222 PROTNAMELIB,INTERNAME CHARACTER*10 INTERDSSP(1:8) CHARACTER TITLE*(*) LOGICAL LFLAG ******------------------------------*-----------------------------****** * ITSEC,ITER iteration variables * * INTERAVLENGTH(i,k) intermediately store average length of elements * (required to avoid division by zero) * * INTERCORR(i) correlation for class i, (Mathews) * * INTERQ3 =properly predicted for all classes/all residues * * INTERSQ first divide predicted/DSSP in each class then * * sum all classes and divide by e.g. 3 * * INTERTITLE intermediate variable storing a character 40 with* * the title (potentially truncated) * * KUNIT =6, or 10, according to whether the table is to * * be written onto printer or into a file (FILETABLE) * MATLEN(i,j) matrix with the lengths of the elements: * * i=1,4 => H,E,C,all * * j=1 => number of elements DSSP * * j=2 => number of elements PRED * * j=2 => summed length of all elements for DSSP * * j=2 => summed length of all elements for PRED * * MATNUM(i,j) the number of residues in a certain secondary * * structure, i labels DSSP assignment, i.e. all * * numbers with i=1 are according to DSSP helices, * * j labels the prediction. That means, e.g.: * * MATNUM(1,1) are all DSSP helices predicted to be * * a helix, MATNUM(1,2) those DSSP helices predicted* * as strands and MATNUM(1,4) all DSSP helices, resp. * MATNUM(4,4) all residues predicted. * * MATOFDSSP(i,j) stores according to the same scheme as MATNUM the* * percentages of residues predicted divided by the * * numbers of DSSP (note there is no element (4,4) )* * MATOFPRED(i,j) same as previous but now percentages of prediction * MAXNSECELLIB maximal number of secondary structures allowed * * NSECELLIB currently read number of secondary structures * * NUMRESLIB number of residues of protein for current table * * PROTNAMELIB the name of the protein for current table * * TITLE title of job which generated the prediction * ******------------------------------*-----------------------------****** IHELP= 0 C---------------------------------------------------------------------- C---- check the size of the quantities passed: ----- C---- if Q3=SQ=0 and MATNUM(i,i) not 0 --> compute newly ----- C---------------------------------------------------------------------- LFLAG=.TRUE. IF ((INTERQ3.EQ.0.).AND.(INTERSQ.EQ.0.)) THEN DO ITSEC=1,NSECELLIB IF (LFLAG.EQV. .TRUE. .AND.(MATNUM(ITSEC,ITSEC).NE.0)) THEN LFLAG=.FALSE. END IF END DO IF (LFLAG.EQV. .FALSE.) THEN C ============= CALL SEVALQUO(NSECELLIB,MAXNSECELLIB,MATNUM,MATQOFDSSP, + MATQOFPRED,INTERQ3,INTERSQ,INTERCORR) C ============= END IF END IF C---------------------------------------------------------------------- C---- TABLE ----- C---------------------------------------------------------------------- C KUNIT=6 C---- count length of string 'TITLE' LFLAG=.TRUE. DO ITER=1,50 IF (LFLAG .EQV. .TRUE.) THEN IF (TITLE(ITER:ITER).EQ.' ') THEN LFLAG=.FALSE. IHELP=ITER END IF END IF END DO DO ITER=1,IHELP INTERTITLE(ITER)=TITLE(ITER:ITER) END DO DO ITER=(IHELP+1),40 INTERTITLE(ITER)=' ' END DO C---- length of protein name ok? CALL SILEN_STRING(PROTNAMELIB,IBEG,IEND) ICOUNT=IEND-IBEG+1 IF ((ICOUNT+IBEG).LT.7) THEN INTERNAME(1:ICOUNT+IBEG)=PROTNAMELIB(1:ICOUNT+IBEG) INTERNAME((ICOUNT+IBEG+1):7)=' ' ELSE INTERNAME(1:7)=PROTNAMELIB(1:7) END IF C---- avoid division by zero! DO ITER=1,2 DO ITSEC=1,(NSECELLIB+1) IF (MATLEN(ITSEC,ITER).NE.0) THEN INTERAVLENGTH(ITSEC,ITER)= + MATLEN(ITSEC,(2+ITER))/REAL(MATLEN(ITSEC,ITER)) ELSE INTERAVLENGTH(ITSEC,ITER)=0 END IF END DO END DO C-------------------------------------------------- C---- write all numbers into a table ----- C-------------------------------------------------- C---------------------------------------- C---- 3 secondary structures ----- C---------------------------------------- IF (NSECELLIB.EQ.3) THEN C------- header WRITE(KUNIT,'(T2,A1,16A1,A1,49A1,A1,T70,A)') + '+',('-',ITER=1,16),'+',('-',ITER=1,49),'+', + '-------------------+' WRITE(KUNIT,'(T2,A2,A7,A1,I5,T19,A9,40A1,T69,A1,T70,A14,T89, + A1)')'| ',INTERNAME,':',NUMRESLIB,'| method:', + (INTERTITLE(ITER),ITER=1,40),'|',' segments','|' WRITE(KUNIT,'(T2,A1,16A1,A1,19A1,A1,17A1,A1,11A1,A1,T70,2A10)') + '+',('-',ITER=1,16),'+',('-',ITER=1,19),'+',('-',ITER=1, + 17),'+',('-',ITER=1,11),'+',('---------+',ITER=1,2) WRITE(KUNIT,'(T2,A,T40,A,T57,A1,A,T69,A1,T70,2A10)') + '| number of residues with H,E,C |', + ' % of DSSP','|',' % of Net','|',' number |', + 'av length|' WRITE(KUNIT,'(T2,A1,A,T12,4A7,3A6,3A4,T70,4A5)') + '+','--------+',('------+',ITER=1,(NSECELLIB+1)), + ('-----+',ITER=1,NSECELLIB),('---+',ITER=1,NSECELLIB), + ('----+',ITER=1,4) WRITE(KUNIT,'(T2,A10,4A7,3A6,3A4,T70,4A5)') + '| |','net H |','net E |','net C |','sum DS|', + ' H |',' E |',' C |',' H |',' E |',' C |', + 'DSSP|',' Net|','DSSP|',' Net|' WRITE(KUNIT,'(T2,A1,A,T12,4A7,3A6,3A4,T70,4A5)') + '+','--------+',('------+',ITER=1,(NSECELLIB+1)), + ('-----+',ITER=1,NSECELLIB),('---+',ITER=1,NSECELLIB), + ('----+',ITER=1,4) C------- number for all secondary elements INTERDSSP(1)='| DSSP H |' INTERDSSP(2)='| DSSP E |' INTERDSSP(3)='| DSSP C |' DO ITSEC=1,NSECELLIB WRITE(KUNIT,'(T2,A10,4(I5,A2),3(F5.1,A1),3(I3,A1), + T70,2(I4,A1),2(F4.1,A1))') + INTERDSSP(ITSEC),(MATNUM(ITSEC,ITER),' |',ITER=1, + (NSECELLIB+1)),(MATQOFDSSP(ITSEC,ITER),'|',ITER=1, + NSECELLIB),(INT(MATQOFPRED(ITSEC,ITER)),'|',ITER=1, + NSECELLIB),(MATLEN(ITSEC,ITER),'|',ITER=1,2), + (INTERAVLENGTH(ITSEC,ITER),'|',ITER=1,2) END DO C------- sums WRITE(KUNIT,'(T2,A1,A,T12,4A7,3A6,3A4,T70,4A5)') + '+','--------+',('------+',ITER=1,(NSECELLIB+1)), + ('-----+',ITER=1,NSECELLIB),'---+','-+-+','---+', + ('----+',ITER=1,4) WRITE(KUNIT,'(T2,A10,4(I5,A2),3A6,2A6,T70,2(I4,A1),2(F4.1, + A1))')'| sum Net|',(MATNUM((NSECELLIB+1),ITER),' |', + ITER=1,(NSECELLIB+1)),'corH |','corE |','corC |',' Q3 |', + ' SQ |',(MATLEN((NSECELLIB+1),ITER),'|',ITER=1,2), + (INTERAVLENGTH((NSECELLIB+1),ITER),'|',ITER=1,2) WRITE(KUNIT,'(T2,A1,36A1,A1,3(F4.2,A2),2(F5.1,A1),T89,A1)') + '|',(' ',ITER=1,36),'|',(INTERCORR(ITSEC),' |',ITSEC=1, + NSECELLIB),INTERQ3,'|',INTERSQ,'|','|' WRITE(KUNIT,'(T2,A1,36A1,A1,3A6,2A6,T70,A)') + '+',('-',ITER=1,36),'+',('-----+',ITER=1,NSECELLIB), + ('*****+',ITER=1,2),'-------------------+' C---------------------------------------- C---- 4 secondary structures ----- C---------------------------------------- ELSEIF (NSECELLIB.EQ.4) THEN C------- header WRITE(KUNIT,'(T2,A1,16A1,A1,50A1,A1,T71,A)') + '+',('-',ITER=1,16),'+',('-',ITER=1,50),'+', + '-------------------+' WRITE(KUNIT,'(T2,A2,A7,A1,I5,T19,A9,40A1,T70,A1,T71,A14,T90, + A1)')'| ',INTERNAME,':',NUMRESLIB,'| method:', + (INTERTITLE(ITER),ITER=1,40),'|',' segments','|' WRITE(KUNIT,'(T2,A1,16A1,A1,18A1,A2,14A1,A1,14A1,A2,T71,2A10)') + '+',('-',ITER=1,16),'+',('-',ITER=1,18),'+-',('-',ITER=1, + 14),'+',('-',ITER=1,14),'-+',('---------+',ITER=1,2) WRITE(KUNIT,'(T2,A,T39,A,T54,A1,A,T70,A1,2A10)') + '| number of residues with H,E,T,L |', + ' % of DSSP','|',' % of Net','|',' number |', + 'av length|' WRITE(KUNIT,'(T2,A7,5A6,8A4,T71,4A5)')'+-----+',('-----+', + ITER=1,(NSECELLIB+1)),('---+',ITER=1,2*NSECELLIB), + ('----+',ITER=1,4) WRITE(KUNIT,'(T2,A7,5A6,8A4,T71,4A5)') + '| |','net H|','net E|','net T|','net L|','sum o|', + ' H |','E |',' T |',' L |',' H |',' E |',' T |',' L |', + 'DSSP|',' Net|','DSSP|',' Net|' WRITE(KUNIT,'(T2,A7,5A6,8A4,T71,4A5)')'+-----+',('-----+', + ITER=1,(NSECELLIB+1)),('---+',ITER=1,2*NSECELLIB), + ('----+',ITER=1,4) C------- number for all secondary elements INTERDSSP(1)='|obs H|' INTERDSSP(2)='|obs E|' INTERDSSP(3)='|obs T|' INTERDSSP(4)='|obs L|' DO ITSEC=1,NSECELLIB WRITE(KUNIT,'(T2,A7,5(I5,A1),8(I3,A1), + T71,2(I4,A1),2(F4.1,A1))') + INTERDSSP(ITSEC),(MATNUM(ITSEC,ITER),'|',ITER=1, + (NSECELLIB+1)),(INT(MATQOFDSSP(ITSEC,ITER)),'|',ITER=1, + NSECELLIB),(INT(MATQOFPRED(ITSEC,ITER)),'|',ITER=1, + NSECELLIB),(MATLEN(ITSEC,ITER),'|',ITER=1,2), + (INTERAVLENGTH(ITSEC,ITER),'|',ITER=1,2) END DO C------- sums WRITE(KUNIT,'(T2,A7,5A6,A32,T71,4A5)')'+-----+',('-----+', + ITER=1,(NSECELLIB+1)),'---+--++---++--+--++---++--+---+', + ('----+',ITER=1,4) WRITE(KUNIT,'(T2,A7,5(I5,A1),A1,4A6,A7, + T71,2(I4,A1),2(F4.1,A1))') + '|sum N|',(MATNUM((NSECELLIB+1),ITER),'|',ITER=1, + (NSECELLIB+1)),' ','cor H|','cor E|','cor T|','cor L|', + ' Q3 |',(MATLEN((NSECELLIB+1),ITER),'|',ITER=1,2), + (INTERAVLENGTH((NSECELLIB+1),ITER),'|',ITER=1,2) WRITE(KUNIT,'(T2,A1,35A1,A2,4(F5.2,A1),F6.1,A1,T90,A1)') + '|',(' ',ITER=1,35),'| ',(INTERCORR(ITSEC),'|',ITSEC=1, + NSECELLIB),INTERQ3,'|','|' WRITE(KUNIT,'(T2,A1,35A1,A2,4A6,A7,T71,A)') + '+',('-',ITER=1,35),'+-',('-----+',ITER=1,NSECELLIB), + '******+','-------------------+' END IF END ***** end of STABLEPOLENFILE ***** ------------------------------------------------------------------ ***** SUB STABLESEG ***** ------------------------------------------------------------------ C---- C---- NAME : STABLESEG C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Nov, 1992 version 0.1 * * changed: Mar, 1993 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The results of the analysis of overlapping, resp.* * -------- correct segments is written onto unit KUNIT * * input variables:KUNIT, NSECELLIB, MAXNSECEL, NUMSEGOVERL * * called by: SEVALSEG (in lib-prot.f) * *----------------------------------------------------------------------* SUBROUTINE STABLESEG(KUNIT,NSECELLIB,MAXNSECEL, + PROTNAME,NUMSEGOVERL,QSEGLOV,QSEGSOV,QSEGFOV,DEVNOM) IMPLICIT NONE C---- variables passed INTEGER MAXNSECEL,NSECELLIB,KUNIT, + NUMSEGOVERL(1:9,1:(MAXNSECEL+1)),DEVNOM REAL QSEGLOV(1:2,1:(MAXNSECEL+1)), + QSEGSOV(1:2,1:(MAXNSECEL+1)),QSEGFOV(1:2,1:(MAXNSECEL+1)) CHARACTER*222 PROTNAME C---- local variables * INTEGER ITER,ITSEC,ICOUNT,IBEG,IEND REAL*4 ROVERL(1:2,1:10) CHARACTER*10 TXT1(1:5) CHARACTER*11 TXTFOV CHARACTER*7 INTERNAME ******------------------------------*-----------------------------****** * MUE,ITER serve as iteration variables * * NUMSEGOVERL(i,j) number of overlapping/correct segments * * i=1 number of DSSP segments in secondary structure * * j, for last: sum over all * * i=2 number of residues in structure i, summed up over* * all segments (in i=1) * * i=3 number of predicted segments in class j * * i=4 number of residues in structure i, summed up over* * all segments (in i=1) for the prediction * * i=5 number of overlapping predicted segments related * * to those being observed. Correct means: * * overlap >= length of segment / 2, for H, E, T * * and for loop: at least loop of 2, resp 1, if the* * DSSP loop is 1. * * i=6 number of overlapping segments multiplied by * * length: related to %observed * * i=7 same as 5, but other way round: %pred! * * i=8 same as 6, but other way round: %pred! * * j, for last: sum over all * * i=9 number of correct segments: * * L +/- 1, and shift by 1, if L<=5 * * L +/- 1, and shift by 2, if 510 * * noted: j, for last: sum over all * * QSEGLOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the loose overlap (half length overlap) * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * QSEGSOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the strict overlap * * for L < 5: | L(OBS)-L(PRED) | <= 1 * * .AND. shift by 1 allowed * * for 5<=L<10: | L(OBS)-L(PRED) | <= 2 * * .AND. shift by 2 allowed * * for L >= 10: | L(OBS)-L(PRED) | <= 3 * * .AND. shift by 3 allowed * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * QSEGFOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the fractional overlap: * * overlapping length * * as given by: ------------------ * * common length * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- writing the overlapping results ----- C-------------------------------------------------- TXT1(1)='% H' TXT1(2)='% E' TXT1(NSECELLIB)='% L' IF (NSECELLIB.EQ.4) THEN TXT1(3)='% T' END IF TXT1(NSECELLIB+1)='sum' IF (DEVNOM.EQ.0) THEN TXTFOV='| Fov0 |' ELSEIF (DEVNOM.EQ.1) THEN TXTFOV='| Fov1 |' ELSEIF (DEVNOM.EQ.2) THEN TXTFOV='| Fov2 |' ELSEIF (DEVNOM.EQ.3) THEN TXTFOV='| Fov3 |' ELSEIF (DEVNOM.EQ.4) THEN TXTFOV='| Fov4 |' ELSEIF (DEVNOM.EQ.50) THEN TXTFOV='| Fov50% |' ELSEIF (DEVNOM.EQ.100) THEN TXTFOV='| Fov100% |' ELSE TXTFOV='| frac ov |' END IF CALL SILEN_STRING(PROTNAME,IBEG,IEND) ICOUNT=IEND-IBEG+1 IF ((ICOUNT+IBEG).LT.7) THEN INTERNAME(1:ICOUNT+IBEG)=PROTNAME(1:ICOUNT+IBEG) INTERNAME((ICOUNT+IBEG+1):7)=' ' ELSE INTERNAME(1:7)=PROTNAME(1:7) END IF C---- take care about divisions by 0, non weighted measures DO ITSEC=1,(NSECELLIB+1) IF (NUMSEGOVERL(1,ITSEC).EQ.0) THEN ROVERL(1,ITSEC)=0 ELSE ROVERL(1,ITSEC)= + NUMSEGOVERL(5,ITSEC)/REAL(NUMSEGOVERL(1,ITSEC)) END IF IF (NUMSEGOVERL(3,ITSEC).EQ.0) THEN ROVERL(2,ITSEC)=0 ELSE ROVERL(2,ITSEC)= + NUMSEGOVERL(7,ITSEC)/REAL(NUMSEGOVERL(3,ITSEC)) END IF END DO C-------------------------------------------------- C---- starting a hack! C---- hack since the %predicted for NSECEL+1 (roverl(2,4)) seems to be C---- wrong and I dont want to locate the bug: NUMSEGOVERL(7,(NSECELLIB+1))=0 NUMSEGOVERL(3,(NSECELLIB+1))=0 DO ITSEC=1,NSECELLIB NUMSEGOVERL(7,(NSECELLIB+1))=NUMSEGOVERL(7,(NSECELLIB+1))+ + NUMSEGOVERL(7,ITSEC) NUMSEGOVERL(3,(NSECELLIB+1))=NUMSEGOVERL(3,(NSECELLIB+1))+ + NUMSEGOVERL(3,ITSEC) END DO IF (NUMSEGOVERL(3,(NSECELLIB+1)).EQ.0) THEN ROVERL(2,ITSEC)=0 ELSE ROVERL(2,(NSECELLIB+1))= + NUMSEGOVERL(7,ITSEC)/REAL(NUMSEGOVERL(3,ITSEC)) END IF C---- end of hack! C-------------------------------------------------- WRITE(KUNIT,'(T2,A)')'---' IF (NSECELLIB.EQ.3) THEN WRITE(KUNIT,'(T2,A,T10,A11,2A36)')'---','+---------+', + ('-----------------------------------+',ITER=1,2) WRITE(KUNIT,'(T2,A,T10,A2,A7,A2,2A36)')'---', + '| ',INTERNAME,' |', + ' % of observed overlapping seg. |', + ' % of predicted overlapping seg. |' WRITE(KUNIT,'(T2,A,T10,A11,8(A3,A1,A4,A1))') + '---','+---------+', + ('-----','+','----','+',ITSEC=1,2*(NSECELLIB+1)) WRITE(KUNIT,'(T2,A,T10,A11,8(A3,A1,A4,A1))') + '---','| |', + (TXT1(ITSEC),'|','Nobs','|',ITSEC=1,(NSECELLIB+1)), + (TXT1(ITSEC),'|','Nprd','|',ITSEC=1,(NSECELLIB+1)) WRITE(KUNIT,'(T2,A,T10,A11,8(A3,A1,A4,A1))') + '---','+---------+', + ('-----','+','----','+',ITSEC=1,2*(NSECELLIB+1)) WRITE(KUNIT,'(T2,A,T10,A11,8(I3,A1,I4,A1))') + '---','| no ov s |', + (INT(100*ROVERL(1,ITSEC)),'|',NUMSEGOVERL(1,ITSEC),'|', + ITSEC=1,(NSECELLIB+1)), + (INT(100*ROVERL(2,ITSEC)),'|',NUMSEGOVERL(3,ITSEC),'|', + ITSEC=1,(NSECELLIB+1)) WRITE(KUNIT,'(T2,A,T10,A11,8(I3,A1,I4,A1))') + '---','| Lov |', + (INT(QSEGLOV(1,ITSEC)), + '|',NUMSEGOVERL(2,ITSEC),'|',ITSEC=1,(NSECELLIB+1)), + (INT(QSEGLOV(2,ITSEC)), + '|',NUMSEGOVERL(4,ITSEC),'|',ITSEC=1,(NSECELLIB+1)) WRITE(KUNIT,'(T2,A,T10,A11,8(A3,A1,A4,A1))') + '---','+---------+', + ('-----','+','----','+',ITSEC=1,2*(NSECELLIB+1)) WRITE(KUNIT,'(T2,A,T10,A11,2(4(A3,A3,A3)))') + '---','| |', + ((' ',TXT1(ITSEC),' |',ITSEC=1,(NSECELLIB+1)),ITER=1,2) WRITE(KUNIT,'(T2,A,T10,A11,8(A7,A2))')'---', + '+---------+',('-------','-+',ITSEC=1,2*(NSECELLIB+1)) WRITE(KUNIT,'(T2,A,T10,A11,8(F7.2,A2))') + '---','| Sov |', + (QSEGSOV(1,ITSEC),' |',ITSEC=1,(NSECELLIB+1)), + (QSEGSOV(2,ITSEC),' |',ITSEC=1,(NSECELLIB+1)) WRITE(KUNIT,'(T2,A,T10,A11,8(F7.2,A2))')'---',TXTFOV, + ((QSEGFOV(ITER,ITSEC),' |',ITSEC=1,(NSECELLIB+1)), + ITER=1,2) WRITE(KUNIT,'(T2,A,T10,A11,8(A7,A2))')'---','+---------+', + ('-------','-+',ITSEC=1,2*(NSECELLIB+1)) ELSEIF (NSECELLIB.EQ.4) THEN WRITE(KUNIT,'(T2,A,T10,2A40,T90,A1)')'---', + ('+---------------------------------------',ITER=1,2),'+' WRITE(KUNIT,'(T2,A,T10,A,T50,A,T90,A1)')'---', + '| % of observed overlapping seg.', + '| % of predicted overlapping seg.','|' WRITE(KUNIT,'(T2,A,T10,A1,2(4(A3,A1,A4,A1),A3,A1))')'---', + '+',(('-----','+','----','+',ITSEC=1,NSECELLIB),'---','+', + ITER=1,2) WRITE(KUNIT,'(T2,A,T10,A1,2(4(A3,A1,A4,A1),A3,A1))')'---', + '|',(TXT1(ITSEC),'|','Nobs','|',ITSEC=1,NSECELLIB), + TXT1(NSECELLIB+1),'|', + (TXT1(ITSEC),'|','Nprd','|',ITSEC=1,NSECELLIB), + TXT1(NSECELLIB+1),'|' WRITE(KUNIT,'(T2,A,T10,A1,2(4(A3,A1,A4,A1),A3,A1))')'---', + '+',(('-----','+','----','+',ITSEC=1,NSECELLIB),'---','+', + ITER=1,2) WRITE(KUNIT,'(T2,A,T10,A1,2(4(I3,A1,I4,A1),I3,A1),A4)') + '---','|',(INT(100*ROVERL(1,ITSEC)), + '|',NUMSEGOVERL(1,ITSEC),'|',ITSEC=1,NSECELLIB), + INT(100*ROVERL(1,NSECELLIB)),'|', + (INT(100*ROVERL(2,ITSEC)), + '|',NUMSEGOVERL(3,ITSEC),'|',ITSEC=1,NSECELLIB), + INT(100*ROVERL(2,NSECELLIB)),'|',' no ' WRITE(KUNIT,'(T2,A,T10,A1,2(4(I3,A1,I4,A1),I3,A1),A4)') + '---','|',(INT(QSEGLOV(1,ITSEC)), + '|',NUMSEGOVERL(2,ITSEC),'|',ITSEC=1,NSECELLIB), + INT(QSEGLOV(1,(NSECELLIB+1))),'|', + (INT(QSEGLOV(2,ITSEC)), + '|',NUMSEGOVERL(4,ITSEC),'|',ITSEC=1,NSECELLIB), + INT(QSEGLOV(2,(NSECELLIB+1))),'|',' Lov' WRITE(KUNIT,'(T2,A,T10,A1,2(4(A3,A1,A4,A1),A3,A1))')'---', + '+',(('-----','+','----','+',ITSEC=1,NSECELLIB),'---','+', + ITER=1,2) WRITE(KUNIT,'(T2,A,A)') + '+-----+-----------------------------+'// + '+-----------------------------+' WRITE(KUNIT,'(T2,A,A)') + '| | % H | % E | % T | % L | sum |'// + '| % H | % E | % T | % L | sum |' WRITE(KUNIT,'(T2,A,A)') + '+-----+-----+-----+-----+-----+-----+'// + '+-----+-----+-----+-----+-----+' WRITE(KUNIT,'(T2,A7,5(F5.1,A1),A1,5(F5.1,A1))')'|Sov |', + (QSEGSOV(1,ITSEC),'|',ITSEC=1,(NSECELLIB+1)),'|', + (QSEGSOV(2,ITSEC),'|',ITSEC=1,(NSECELLIB+1)) WRITE(KUNIT,'(T2,A1,A6,A1,5(F5.1,A1),A1,5(F5.1,A1))') + '|',TXTFOV(2:7), + '|',(QSEGFOV(1,ITSEC),'|',ITSEC=1,(NSECELLIB+1)),'|', + (QSEGFOV(2,ITSEC),'|',ITSEC=1,(NSECELLIB+1)) WRITE(KUNIT,'(T2,A,A)') + '+-----+-----+-----+-----+-----+-----+'// + '+-----+-----+-----+-----+-----+' END IF END ***** end of STABLESEG ***** ------------------------------------------------------------------ ***** SUB STABLE_EXPNOINBIN ***** ------------------------------------------------------------------ C---- C---- NAME : STABLE_EXPNOINBIN C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1993 version 0.1 * * changed: Feb, 1994 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: For a set of proteins the average relative expo- * * -------- sure per residue is computed (possibly for DSSP * * and PRED). * * in variables: NUMPROT,NUMRES * * ------------- RESNAME,EXPDSSP,EXPPRED * * output variab.: EXPDSSP_AV,EXPPRED_AV,EXPDSSP_AVSIGMA,EXPPRED_AVSI *----------------------------------------------------------------------* SUBROUTINE STABLE_EXPNOINBIN(KUNIT,CHVP1,EXP_NOINBIN,TXT,CHVPL) IMPLICIT NONE C---- variables passed INTEGER KUNIT,EXP_NOINBIN(0:9,0:9), + CHVPM(1:50),CHVPL,CHVP1 CHARACTER*222 TXT C---- local variables INTEGER IT1,IT2,SUMDSSP(0:9),SUMPRED(0:9),SUM REAL RTMP LOGICAL LERRCHVP ******------------------------------*-----------------------------****** C---- default C----------------------------------------------------------------------* C---- initial check of variables passed -----* C----------------------------------------------------------------------* IF (CHVPL.NE.1) THEN WRITE(6,'(T2,A,T10,A)')'***','WARNING: STABLE_EXPNOINBIN: '// + 'number of passed variables not fitting' WRITE(6,'(T2,A,T10,A,T40,4I5)')'***', + 'they are: CHVPL: 1,2,3:',CHVPL,CHVP1 STOP END IF CHVPM(1)=CHVP1 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C CALL SCHECKPASS(LERRCHVP,CHVPL,CHVPM) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for STABLE_EXPNOINBIN: variables passed not correct !' END IF C---- check variables passed C----------------------------------------------------------------------* C---- end of checking variables -----* C----------------------------------------------------------------------* C-------------------------------------------------- C---- computing percentages/sums C-------------------------------------------------- SUM=0 DO IT1=0,9 SUMDSSP(IT1)=0 SUMPRED(IT1)=0 DO IT2=0,9 SUMDSSP(IT1)=SUMDSSP(IT1)+EXP_NOINBIN(IT1,IT2) SUMPRED(IT1)=SUMPRED(IT1)+EXP_NOINBIN(IT2,IT1) END DO SUM=SUM+SUMDSSP(IT1) END DO C-------------------------------------------------- C---- writing C-------------------------------------------------- WRITE(KUNIT,'(T2,A)')'---' WRITE(KUNIT,'(T2,A,T10,A,T40,A20)')'---','numbers per bin for:', + TXT WRITE(KUNIT,'(T2,A)')'---' WRITE(KUNIT,'(T2,A)')'no in bin' WRITE(KUNIT,'(T2,A,T11,A1,T13,10I5,A4,A6,A7)')'pred:', + '|',(IT2,IT2=0,9),' | ',' SUM',' %DSSP' WRITE(KUNIT,'(T2,9A1,A1,53A1,A1,16A1)')('-',IT1=1,9),'+', + ('-',IT1=1,53),'+',('-',IT1=1,16) DO IT1=0,9 IF (SUM.NE.0) THEN RTMP=100*SUMDSSP(IT1)/REAL(SUM) ELSE RTMP=0 END IF WRITE(KUNIT,'(T2,A,T8,I1,T11,A1,T13,10I5,A4,I6,F7.1)') + 'DSSP ',IT1,'|', + (EXP_NOINBIN(IT1,IT2),IT2=0,9), + ' | ',SUMDSSP(IT1),RTMP END DO WRITE(KUNIT,'(T2,9A1,A1,53A1,A1,16A1)')('-',IT1=1,9),'+', + ('-',IT1=1,53),'+',('-',IT1=1,16) WRITE(KUNIT,'(T2,A,T11,A1,T13,10I5,A4)') + 'PRED SUM','|',(SUMPRED(IT2),IT2=0,9),' | ' WRITE(KUNIT,'(T2,A,T11,A1,T13,10F5.1,A4)') + 'PRED %','|',(100*SUMPRED(IT2)/REAL(MIN(1,SUM)),IT2=0,9), + ' | ' WRITE(KUNIT,'(T2,9A1,A1,53A1,A1,16A1)')('-',IT1=1,9),'+', + ('-',IT1=1,53),'+',('-',IT1=1,16) WRITE(KUNIT,'(T2,A)')'---' END ***** end of STABLE_EXPNOINBIN ***** ------------------------------------------------------------------ ***** SUB STABLE_EXPSTATES ***** ------------------------------------------------------------------ C---- C---- NAME : STABLE_EXPSTATES C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1994 version 0.1 * * changed: Mar, 1994 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The percentages of 2state, 3state, 10state * * -------- exposure accuracy are written for one protein. * *----------------------------------------------------------------------* SUBROUTINE STABLE_EXPSTATES(KUNIT,LTOPLINE,LBOTTOMLINE, + PROTNAME,CHVP1,EXP_NOINBIN,T2,T3A,T3B,CHVP2,EXP_NO2ST, + EXP_NO3ST,CHVP3,EXP_NO10ST,EXP_CORR,CHVPL) IMPLICIT NONE C---- variables passed INTEGER KUNIT,EXP_NO2ST(1:3),EXP_NO3ST(1:4), + EXP_NO10ST(1:11),EXP_NOINBIN(0:9,0:9),T2,T3A,T3B, + CHVPM(1:50),CHVPL,CHVP1,CHVP2,CHVP3 REAL EXP_CORR CHARACTER*222 PROTNAME LOGICAL LTOPLINE,LBOTTOMLINE C---- local functions INTEGER FILEN_STRING,FIEXP_NOINBIN_SUM REAL FRDIVIDE_SAFE CHARACTER*222 FCUT_SPACES C---- local variables INTEGER IT1,IT2,ILEN, + NUMRES,TMPT2(1:3),TMPT3(1:4),INUM,ICHECK,ICOUNT REAL RES2(1:5),RES3(1:7),RES10(1:20),RES10S(1:2) CHARACTER*222 NAME6 CHARACTER*10 COBS,CPRED LOGICAL LERRCHVP ******------------------------------*-----------------------------****** C---- default C----------------------------------------------------------------------* C---- initial check of variables passed -----* C----------------------------------------------------------------------* IF (CHVPL.NE.3) THEN WRITE(6,'(T2,A,T10,A)')'***','WARNING: STABLE_EXPSTATES'// + ': number of passed variables not fitting' WRITE(6,'(T2,A,T10,A,T40,4I5)')'***', + 'they are: CHVPL: 1,2,3:',CHVPL,CHVP1,CHVP2,CHVP3 STOP END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 CHVPM(3)=CHVP3 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C CALL SCHECKPASS(LERRCHVP,CHVPL,CHVPM) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for STABLE_EXPSTATES: variables passed not correct !' END IF C---- check variables passed IF ( (T2.LT.0).OR.(T2.GT.10).OR. + (T3A.LT.0).OR.(T3A.GT.10).OR. + (T3B.LT.0).OR.(T3B.GT.10) ) THEN WRITE(6,'(T2,A,T10,A)')'***','STABLE_EXPSTATES: '// + 'thresholds wrong! ' WRITE(6,'(T2,A,T10,A,T20,i3,a,t30,i3,A,T40,I3)') + '***','T2= ',T2,' T3A = ',T3A,' T3B = ',T3B STOP END IF C----------------------------------------------------------------------* C---- end of checking variables -----* C----------------------------------------------------------------------* C---- defaults COBS='obs' CPRED='pred' TMPT2(1)=0 TMPT2(2)=T2 TMPT2(3)=10 TMPT3(1)=0 TMPT3(2)=T3A TMPT3(3)=T3B TMPT3(4)=10 C---- cut off spaces: ILEN=FILEN_STRING(PROTNAME) IF (ILEN.LT.6) THEN NAME6(1:ILEN)=FCUT_SPACES(PROTNAME) NAME6((ILEN+1):6)=' ' ELSE NAME6(1:6)=FCUT_SPACES(PROTNAME) END IF C---- headline IF (LTOPLINE .EQV. .TRUE.) THEN WRITE(KUNIT,'(A1,6A1,A2,21A1,A2,29A1,A2,8A1,A2,2(6A1,A2))') + '+',('-',IT1=1,6),'-+',('-',IT1=1,21),'-+', + ('-',IT1=1,29),'-+',('-',IT1=1,8),'-+', + (('-',IT1=1,6),'-+',IT2=1,2) WRITE(KUNIT,'(A1,A,T9,A1,A5,4A4,A2,A5,6A4,A2, + 2A4,A2,A6,A2,A6,A2)')'|','name','|', + ' Q2 ',' b%o',' %p',' e%o',' %p',' |', + ' Q3 ',' b%o',' %p',' i%o',' %p ',' e%o', + ' %p',' |','Q10o',' %p',' |', + ' c10 ',' |',' N',' |' WRITE(KUNIT,'(A1,6A1,A2,21A1,A2,29A1,A2,8A1,A2,2(6A1,A2))') + '+',('-',IT1=1,6),'-+',('-',IT1=1,21),'-+', + ('-',IT1=1,29),'-+',('-',IT1=1,8),'-+', + (('-',IT1=1,6),'-+',IT2=1,2) END IF C-------------------------------------------------- C---- computing percentages C-------------------------------------------------- NUMRES=0 ICHECK=0 DO IT1=1,2 INUM=FIEXP_NOINBIN_SUM(EXP_NOINBIN,TMPT2(IT1),TMPT2(IT1+1), + COBS) NUMRES=NUMRES+INUM RES2((IT1-1)*2+1)=100*FRDIVIDE_SAFE(REAL(EXP_NO2ST(IT1)), + REAL(INUM)) INUM=FIEXP_NOINBIN_SUM(EXP_NOINBIN,TMPT2(IT1),TMPT2(IT1+1), + CPRED) RES2((IT1-1)*2+2)=100*FRDIVIDE_SAFE(REAL(EXP_NO2ST(IT1)), + REAL(INUM)) ICHECK=ICHECK+INUM END DO RES2(5)=100*FRDIVIDE_SAFE(REAL(EXP_NO2ST(3)),REAL(NUMRES)) C---- consistency check IF (ICHECK.NE.NUMRES) THEN WRITE(6,'(T2,A,T10,A)')'***','STABLE_EXPSTATES '// + 'ERROR not same number for observed and predicted!' WRITE(6,'(T2,A,T10,A,T20,I5,A,T40,I5)')'***', + 'NUMRES = ',NUMRES,' ICHECK = ',ICHECK DO IT1=0,9 WRITE(kunit,'(T10,10I5)')(EXP_NOINBIN(IT1,IT2),IT2=0,9) END DO STOP END IF DO IT1=1,3 INUM=FIEXP_NOINBIN_SUM(EXP_NOINBIN,TMPT3(IT1),TMPT3(IT1+1), + COBS) RES3((IT1-1)*2+1)=100*FRDIVIDE_SAFE(REAL(EXP_NO3ST(IT1)), + REAL(INUM)) INUM=FIEXP_NOINBIN_SUM(EXP_NOINBIN,TMPT3(IT1),TMPT3(IT1+1), + CPRED) RES3((IT1-1)*2+2)=100*FRDIVIDE_SAFE(REAL(EXP_NO3ST(IT1)), + REAL(INUM)) END DO RES3(7)=100*FRDIVIDE_SAFE(REAL(EXP_NO3ST(4)),REAL(NUMRES)) RES10S(1)=0 RES10S(2)=0 ICOUNT=0 DO IT1=1,10 INUM=FIEXP_NOINBIN_SUM(EXP_NOINBIN,(IT1-1),IT1,COBS) RES10((IT1-1)*2+1)=100*FRDIVIDE_SAFE(REAL(EXP_NO10ST(IT1)), + REAL(INUM)) RES10S(1)=RES10S(1)+REAL(EXP_NO10ST(IT1)) INUM=FIEXP_NOINBIN_SUM(EXP_NOINBIN,(IT1-1),IT1,CPRED) RES10((IT1-1)*2+2)=100*FRDIVIDE_SAFE(REAL(EXP_NO10ST(IT1)), + REAL(INUM)) RES10S(2)=RES10S(2)+RES10((IT1-1)*2+2) IF (INUM.GT.0) THEN ICOUNT=ICOUNT+1 END IF END DO RES10S(1)=100*FRDIVIDE_SAFE(RES10S(1),REAL(NUMRES)) RES10S(2)=FRDIVIDE_SAFE(RES10S(2),REAL(ICOUNT)) C-------------------------------------------------- C---- writing percentages C-------------------------------------------------- WRITE(KUNIT,'(A1,A,T9,A1,F5.1,4I4,A2,F5.1,6I4,A2, + 2I4,A2,F6.3,A2,I6,A2)')'|',NAME6,'|', + RES2(5),(INT(RES2(IT1)),IT1=1,4),' |', + RES3(7),(INT(RES3(IT1)),IT1=1,6),' |', + (INT(RES10S(IT1)),IT1=1,2),' |',EXP_CORR,' |',NUMRES,' |' C-------------------------------------------------- C---- write bottom line? IF (LBOTTOMLINE .EQV. .TRUE.) THEN WRITE(KUNIT,'(A1,6A1,A2,21A1,A2,29A1,A2,8A1,A2,2(6A1,A2))') + '+',('-',IT1=1,6),'-+',('-',IT1=1,21),'-+', + ('-',IT1=1,29),'-+',('-',IT1=1,8),'-+', + (('-',IT1=1,6),'-+',IT2=1,2) END IF END ***** end of STABLE_EXPSTATES ***** ------------------------------------------------------------------ ***** SUB STABLE_QILS ***** ------------------------------------------------------------------ C---- C---- NAME : STABLE_QILS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Apr, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The pay-offs of a certain prediction are written * * -------- as a table onto unit KUNIT: * * in variables: NSECEL, MAXNSECEL, KUNIT, NUMRES, PROTNAME, TITLE* * ------------- MATNUM, MATLEN, NUMSEGOVERL, * * MATQOFDSSP,MATQOFPRED,Q3,SQ,CORR,INFO,INFO_INV, * * QSEGLOV,QSEGSOV,QSEGFOV,DEVNOM,CHVPL * * called by: typically SEVALSEG, resp. Xevalpred * * SBRs calling: from lib-prot.f: * * -------------- SEVALQUO, SEVALINFOFILE * * from lib-unix.f: * * SCHECKPASS * * from lib-comp.f: * * SISTZ1, SRSTZ2, SILEN_STRING * * from lib-prot.f: * *----------------------------------------------------------------------* SUBROUTINE STABLE_QILS(KUNIT,NSECEL,MAXNSECEL,NUMRES,CHVP1, + PROTNAME,TITLE,CHVP2,MATNUM,MATLEN,CHVP3, + MATQOFDSSP,MATQOFPRED,Q3,SQ,CORR,INFO,INFO_INV,CHVP4, + QSEGSOV,QSEGFOV,DEVNOM,CHVPL) IMPLICIT NONE C---- variables passed INTEGER CHVPM(1:50),CHVPL,CHVP1,CHVP2,CHVP3,CHVP4, + MAXNSECEL,NSECEL,NUMRES,KUNIT, + MATNUM(1:(MAXNSECEL+1),1:(MAXNSECEL+1)), + MATLEN(1:(MAXNSECEL+1),1:4),DEVNOM REAL MATQOFDSSP(1:MAXNSECEL,1:MAXNSECEL), + MATQOFPRED(1:MAXNSECEL,1:MAXNSECEL), + CORR(1:MAXNSECEL),Q3,SQ,INFO,INFO_INV, + QSEGSOV(1:2,1:(MAXNSECEL+1)),QSEGFOV(1:2,1:(MAXNSECEL+1)) CHARACTER*222 TITLE,PROTNAME C---- local variables * INTEGER ITER,ITSEC,ILEN,IBEG,IEND,ICOUNT REAL INTERAVLENGTH(1:8,1:2) CHARACTER*222 INTERTITLE CHARACTER*7 INTERNAME CHARACTER*10 INTERDSSP(1:8) CHARACTER*11 TXTFOV LOGICAL LFLAG,LERRCHVP ******------------------------------*-----------------------------****** *--------------------- * * passed variables * * KUNIT number of unit to write the files upon * * MAXNSECEL maximal number of secondary structures for array * * boundaries * * NSECEL number of secondary structure types used * * PROTNAME the name of the chain for which the class is * * determined * *--------------------- * * local variables * * ITSEC,ITER iteration variables * * INTERAVLENGTH(i,k) intermediately store average length of elements * (required to avoid division by zero) * * CORR(i) correlation for class i, (Mathews) * * Q3 =properly predicted for all classes/all residues * * SQ first divide predicted/DSSP in each class then * * sum all classes and divide by e.g. 3 * * INTERTITLE intermediate variable storing a character 40 with* * the title (potentially truncated) * * KUNIT =6, or 10, according to whether the table is to * * be written onto printer or into a file (FILETABLE) * MATLEN(i,j) matrix with the lengths of the elements: * * i=1,4 => H,E,C,all * * j=1 => number of elements DSSP * * j=2 => number of elements PRED * * j=2 => summed length of all elements for DSSP * * j=2 => summed length of all elements for PRED * * MATNUM(i,j) the number of residues in a certain secondary * * structure, i labels DSSP assignment, i.e. all * * numbers with i=1 are according to DSSP helices, * * j labels the prediction. That means, e.g.: * * MATNUM(1,1) are all DSSP helices predicted to be * * a helix, MATNUM(1,2) those DSSP helices predicted* * as strands and MATNUM(1,4) all DSSP helices, resp. * MATNUM(4,4) all residues predicted. * * MATOFDSSP(i,j) stores according to the same scheme as MATNUM the* * percentages of residues predicted divided by the * * numbers of DSSP (note there is no element (4,4) )* * MATOFPRED(i,j) same as previous but now percentages of prediction * MAXNSECEL maximal number of secondary structures allowed * * NSECEL currently read number of secondary structures * * NUMRES number of residues of protein for current table * * PROTNAME the name of the protein for current table * * QSEGSOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the strict overlap * * for L < 5: | L(OBS)-L(PRED) | <= 1 * * .AND. shift by 1 allowed * * for 5<=L<10: | L(OBS)-L(PRED) | <= 2 * * .AND. shift by 2 allowed * * for L >= 10: | L(OBS)-L(PRED) | <= 3 * * .AND. shift by 3 allowed * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * QSEGFOV(i,j) i=1: %observed * * i=2: %predicted * * j=1-4 (helix,strand,loop,3-states) * * gives the fractional overlap: * * overlapping length * * as given by: ------------------ * * common length * * multiplication with length of segment, normali- * * sation will be done by calling SBR with N=number * * of all residues in the data set * * TITLE title of job which generated the prediction * ******------------------------------*-----------------------------****** C---------------------------------------------------------------------- C---- check the size of the quantities passed: ----- C---- if Q3=SQ=0 and MATNUM(i,i) not 0 --> compute newly ----- C---------------------------------------------------------------------- IF (CHVPL.NE.4) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'WARNING: SEVALSEG: number of passed variables not fitting' END IF CHVPM(1)=CHVP1 CHVPM(2)=CHVP2 CHVPM(3)=CHVP3 CHVPM(4)=CHVP4 C --------------- CALL SCHECKPASS(CHVPM,CHVPL,LERRCHVP) C --------------- IF (LERRCHVP .EQV. .TRUE.) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR for SEVALSEG: variables passed not correct !' END IF C---- check variables passed IF (NSECEL.GT.MAXNSECEL) THEN WRITE(6,'(T2,A,T10,A,A)')'***','ERROR: The number of '// + 'secondary structures passed to SBR STABLE_QILS' WRITE(6,'(t2,A,T10,A)')'***', + 'exceeds the locally allocated array dimensions.' WRITE(6,'(T5,A,T25,I4,T30,A,T40,I4)') + ' Current number: ',NSECEL,' allocated:',MAXNSECEL WRITE(6,'(T5,A)')' Stopped at 31-3-93a' STOP END IF C---- end of initially checking consistency of ---- C---- variables passed ----- C-------------------------------------------------- C-------------------------------------------------- C---- if the quotient Q3 passed 0, call SBR ----- C-------------------------------------------------- LFLAG=.TRUE. IF ((Q3.EQ.0.).AND.(SQ.EQ.0.)) THEN DO ITSEC=1,NSECEL IF (LFLAG.EQV. .TRUE. .AND.(MATNUM(ITSEC,ITSEC).NE.0)) THEN LFLAG=.FALSE. END IF END DO IF (LFLAG.EQV. .FALSE.) THEN C ============= CALL SEVALQUO(NSECEL,MAXNSECEL,MATNUM,MATQOFDSSP, + MATQOFPRED,Q3,SQ,CORR) C ============= LFLAG=.FALSE. C ============== CALL SEVALINFOFILE(6,NSECEL,MAXNSECEL, + MATNUM,INFO,INFO_INV,LFLAG) C ============== END IF END IF C-------------------------------------------------- C---- check length of Protname and Title ----- C-------------------------------------------------- C---- count length of string 'TITLE' CALL SILEN_STRING(TITLE,IBEG,IEND) ILEN=IEND-IBEG+1 IF (ILEN.LT.40) THEN INTERTITLE(1:ILEN)=TITLE(IBEG:IEND) DO ITER=(ILEN+1),40 INTERTITLE(ITER:ITER)=' ' END DO ELSE INTERTITLE(1:40)=TITLE(IBEG:IBEG+39) END IF C---- length of protein name ok? CALL SILEN_STRING(PROTNAME,IBEG,IEND) ICOUNT=IEND-IBEG+1 IF ((ICOUNT+IBEG).LT.7) THEN INTERNAME(1:ICOUNT+IBEG)=PROTNAME(1:ICOUNT+IBEG) INTERNAME((ICOUNT+IBEG+1):7)=' ' ELSE INTERNAME(1:7)=PROTNAME(1:7) END IF C---- assign names for txt used in table IF (DEVNOM.EQ.0) THEN TXTFOV='| Fov0 |' ELSEIF (DEVNOM.EQ.1) THEN TXTFOV='| Fov1 |' ELSEIF (DEVNOM.EQ.2) THEN TXTFOV='| Fov2 |' ELSEIF (DEVNOM.EQ.3) THEN TXTFOV='| Fov3 |' ELSEIF (DEVNOM.EQ.4) THEN TXTFOV='| Fov4 |' ELSEIF (DEVNOM.EQ.50) THEN TXTFOV='| Fov50% |' C changed 1-8-95 TXTFOV='| SOV |' ELSEIF (DEVNOM.EQ.100) THEN TXTFOV='| Fov100% |' ELSE TXTFOV='| frac ov |' END IF C-------------------------------------------------- C---- check length of Protname and Title ----- C-------------------------------------------------- C---- avoid division by zero for average lengths! DO ITER=1,2 DO ITSEC=1,(NSECEL+1) IF (MATLEN(ITSEC,ITER).NE.0) THEN INTERAVLENGTH(ITSEC,ITER)= + MATLEN(ITSEC,(2+ITER))/REAL(MATLEN(ITSEC,ITER)) ELSE INTERAVLENGTH(ITSEC,ITER)=0 END IF END DO END DO C---------------------------------------------------------------------- C---- TABLE ----- C---------------------------------------------------------------------- C-------------------------------------------------- C---- 3 secondary structures ----- C-------------------------------------------------- IF (NSECEL.EQ.3) THEN C---------------------------------------- C------- single residue quotients ----- C---------------------------------------- C------- header WRITE(KUNIT,'(T2,A1,17A1,A1,48A1,A1,T70,A)') + '+',('-',ITER=1,17),'+',('-',ITER=1,48),'+', + '-------------------+' WRITE(KUNIT,'(T2,A2,A7,A1,I6,T20,A9,A39,T69,A1,T70,A14,T89, + A1)')'| ',INTERNAME,':',NUMRES,'| method:', + INTERTITLE,'|',' segments','|' WRITE(KUNIT,'(T2,A1,17A1,A1,48A1,A1,T70,A)') + '+',('-',ITER=1,17),'+',('-',ITER=1,48),'+', + '-------------------+' WRITE(KUNIT,'(T2,A,T40,A,T57,A1,A,T69,A1,T70,2A10)') + '| number of residues with H,E,C |', + ' % of DSSP','|',' % of Net','|',' number |', + 'av length|' WRITE(KUNIT,'(T2,A1,A,T12,4A7,3A6,3A4,T70,4A5)') + '+','--------+',('------+',ITER=1,(NSECEL+1)), + ('-----+',ITER=1,NSECEL),('---+',ITER=1,NSECEL), + ('----+',ITER=1,4) WRITE(KUNIT,'(T2,A10,4A7,3A6,3A4,T70,4A5)') + '| |','net H |','net E |','net C |','sum DS|', + ' H |',' E |',' C |',' H |',' E |',' C |', + 'DSSP|',' Net|','DSSP|',' Net|' WRITE(KUNIT,'(T2,A1,A,T12,4A7,3A6,3A4,T70,4A5)') + '+','--------+',('------+',ITER=1,(NSECEL+1)), + ('-----+',ITER=1,NSECEL),('---+',ITER=1,NSECEL), + ('----+',ITER=1,4) C------- number for all secondary elements INTERDSSP(1)='| DSSP H |' INTERDSSP(2)='| DSSP E |' INTERDSSP(3)='| DSSP C |' DO ITSEC=1,NSECEL WRITE(KUNIT,'(T2,A10,4(I6,A1),3(F5.1,A1),3(I3,A1), + T70,2(I4,A1),2(F4.1,A1))') + INTERDSSP(ITSEC), + (MATNUM(ITSEC,ITER),'|',ITER=1,(NSECEL+1)), + (MATQOFDSSP(ITSEC,ITER),'|',ITER=1,NSECEL), + (INT(MATQOFPRED(ITSEC,ITER)),'|',ITER=1,NSECEL), + (MATLEN(ITSEC,ITER),'|',ITER=1,2), + (INTERAVLENGTH(ITSEC,ITER),'|',ITER=1,2) END DO C------- sums WRITE(KUNIT,'(T2,A1,A,T12,4A7,3A6,3A4,T70,4A5)') + '+','--------+',('------+',ITER=1,(NSECEL+1)), + ('-----+',ITER=1,NSECEL),'---+','-+-+','---+', + ('----+',ITER=1,4) WRITE(KUNIT,'(T2,A10,4(I6,A1),3A6,2A6,T70,2(I4,A1),2(F4.1, + A1))') + '| sum Net|', + (MATNUM((NSECEL+1),ITER),'|',ITER=1,(NSECEL+1)), + 'corH |','corE |','corC |',' Q3 |', + ' SQ |',(MATLEN((NSECEL+1),ITER),'|',ITER=1,2), + (INTERAVLENGTH((NSECEL+1),ITER),'|',ITER=1,2) WRITE(KUNIT,'(T2,A1,36A1,A1,3(F4.2,A2),2(F5.1,A1),T89,A1)') + '|',(' ',ITER=1,36),'|',(CORR(ITSEC),' |',ITSEC=1, + NSECEL),Q3,'|',SQ,'|','|' C WRITE(KUNIT,'(T2,A1,36A1,A1,3A6,2A6,T70,A)') C + '+',('-',ITER=1,36),'+',('-----+',ITER=1,NSECEL), C + ('*****+',ITER=1,2),'-------------------+' WRITE(KUNIT,'(T2,A,A)') + '+---------+--------------------------++'// + '+---+-----+-----++****+*****+-------------------+' C------- information C WRITE(KUNIT,'(T57,A10,F6.3,A9,F6.3,A2)') C + '| I %obs= ',INFO,', %pred= ',INFO_INV,' |' C WRITE(KUNIT,'(T57,A)') C + '+-------------------------------+' C WRITE(KUNIT,'(T2,A)')'---' C------- end of single residue stuff ---- C---------------------------------------- C---------------------------------------- C------- segment based measures ----- C---------------------------------------- WRITE(KUNIT,'(T2,A,A)') + '| segments| % of observed |'// + '| % of predicted | information |' WRITE(KUNIT,'(T2,A,A)') + '+---------+------+------+------+------+'// + '+------+------+------+------+---------+---------+' WRITE(KUNIT,'(T2,A,A)') + '| measure | % H | % E | % L | sum |'// + '| % H | % E | % L | sum | I %obs | I %pred |' WRITE(KUNIT,'(T2,A,A)') + '+---------+------+------+------+------+'// + '+------+------+------+------+---------+---------+' C commented out 1-8-95 if (1.eq.0) then WRITE(KUNIT,'(T2,A11,4(F5.1,A2),A1,4(F5.1,A2), + T70,2(F6.3,A4))')'| Sov |', + (QSEGSOV(1,ITSEC),' |',ITSEC=1,(NSECEL+1)),'|', + (QSEGSOV(2,ITSEC),' |',ITSEC=1,(NSECEL+1)), + INFO,' |',INFO_INV,' |' endif C changed 5.8.95 C WRITE(KUNIT,'(T2,A11,4(F5.1,A2),A1,4(F5.1,A2), C + T70,2(A5,I3,A2))')TXTFOV, C + (QSEGFOV(1,ITSEC),' |',ITSEC=1,(NSECEL+1)),'|', C + (QSEGFOV(2,ITSEC),' |',ITSEC=1,(NSECEL+1)), C + ' ',INT(100*INFO/0.62),'%|', C + ' ',INT(100*INFO_INV/0.62),'%|' WRITE(KUNIT,'(T2,A11,4(F5.1,A2),A1,4(F5.1,A2), + T70,2(F4.2,A1,I3,A2))')TXTFOV, + (QSEGFOV(1,ITSEC),' |',ITSEC=1,(NSECEL+1)),'|', + (QSEGFOV(2,ITSEC),' |',ITSEC=1,(NSECEL+1)), + INFO,' ',INT(100*INFO/0.62),'%|', + INFO_INV,' ',INT(100*INFO_INV/0.62),'%|' WRITE(KUNIT,'(T2,A,A)') + '+---------+------+------+------+------+'// + '+------+------+------+------+---------+---------+' C-------------------------------------------------- C---- end of 3 secondary structures ----- C-------------------------------------------------- C---------------------------------------- C---- 4 secondary structures ----- C---------------------------------------- ELSEIF (NSECEL.EQ.4) THEN C------- header WRITE(KUNIT,'(T2,A1,16A1,A1,50A1,A1,T71,A)') + '+',('-',ITER=1,16),'+',('-',ITER=1,50),'+', + '-------------------+' WRITE(KUNIT,'(T2,A2,A7,A1,I5,T19,A9,A40,T70,A1,T71,A14,T90, + A1)')'| ',INTERNAME,':',NUMRES,'| method:', + INTERTITLE,'|',' segments','|' WRITE(KUNIT,'(T2,A1,16A1,A1,18A1,A2,14A1,A1,14A1,A2,T71,2A10)') + '+',('-',ITER=1,16),'+',('-',ITER=1,18),'+-',('-',ITER=1, + 14),'+',('-',ITER=1,14),'-+',('---------+',ITER=1,2) WRITE(KUNIT,'(T2,A,T39,A,T54,A1,A,T70,A1,2A10)') + '| number of residues with H,E,T,L |', + ' % of DSSP','|',' % of Net','|',' number |', + 'av length|' WRITE(KUNIT,'(T2,A7,5A6,8A4,T71,4A5)')'+-----+',('-----+', + ITER=1,(NSECEL+1)),('---+',ITER=1,2*NSECEL), + ('----+',ITER=1,4) WRITE(KUNIT,'(T2,A7,5A6,8A4,T71,4A5)') + '| |','net H|','net E|','net T|','net L|','sum o|', + ' H |','E |',' T |',' L |',' H |',' E |',' T |',' L |', + 'DSSP|',' Net|','DSSP|',' Net|' WRITE(KUNIT,'(T2,A7,5A6,8A4,T71,4A5)')'+-----+',('-----+', + ITER=1,(NSECEL+1)),('---+',ITER=1,2*NSECEL), + ('----+',ITER=1,4) C------- number for all secondary elements INTERDSSP(1)='|obs H|' INTERDSSP(2)='|obs E|' INTERDSSP(3)='|obs T|' INTERDSSP(4)='|obs L|' DO ITSEC=1,NSECEL WRITE(KUNIT,'(T2,A7,5(I5,A1),8(I3,A1), + T71,2(I4,A1),2(F4.1,A1))') + INTERDSSP(ITSEC),(MATNUM(ITSEC,ITER),'|',ITER=1, + (NSECEL+1)),(INT(MATQOFDSSP(ITSEC,ITER)),'|',ITER=1, + NSECEL),(INT(MATQOFPRED(ITSEC,ITER)),'|',ITER=1, + NSECEL),(MATLEN(ITSEC,ITER),'|',ITER=1,2), + (INTERAVLENGTH(ITSEC,ITER),'|',ITER=1,2) END DO C------- sums WRITE(KUNIT,'(T2,A7,5A6,A32,T71,4A5)')'+-----+',('-----+', + ITER=1,(NSECEL+1)),'---+--++---++--+--++---++--+---+', + ('----+',ITER=1,4) WRITE(KUNIT,'(T2,A7,5(I5,A1),A1,4A6,A7, + T71,2(I4,A1),2(F4.1,A1))') + '|sum N|',(MATNUM((NSECEL+1),ITER),'|',ITER=1, + (NSECEL+1)),' ','cor H|','cor E|','cor T|','cor L|', + ' Q3 |',(MATLEN((NSECEL+1),ITER),'|',ITER=1,2), + (INTERAVLENGTH((NSECEL+1),ITER),'|',ITER=1,2) WRITE(KUNIT,'(T2,A1,35A1,A2,4(F5.2,A1),F6.1,A1,T90,A1)') + '|',(' ',ITER=1,35),'| ',(CORR(ITSEC),'|',ITSEC=1, + NSECEL),Q3,'|','|' C WRITE(KUNIT,'(T2,A1,35A1,A2,4A6,A7,T71,A)') C + '+',('-',ITER=1,35),'+-',('-----+',ITER=1,NSECEL), C + '******+','-------------------+' WRITE(KUNIT,'(T2,A,A)') + '+-----+-----------------------------+'// + '+-----+-----+-----+-----+******+-------------------+' WRITE(KUNIT,'(T2,A,A)') + '|seg | % of observed |'// + '| % of predicted | information |' WRITE(KUNIT,'(T2,A,A)') + '+-----+-----------------------------+'// + '+-----------------------------++---------+---------+' WRITE(KUNIT,'(T2,A,A)') + '| | % H | % E | % T | % L | sum |'// + '| % H | % E | % T | % L | sum || I %obs | I %pred |' WRITE(KUNIT,'(T2,A,A)') + '+-----+-----+-----+-----+-----+-----+'// + '+-----+-----+-----+-----+-----++---------+---------+' WRITE(KUNIT,'(T2,A7,5(F5.1,A1),A1,5(F5.1,A1), + T70,A1,2(F6.3,A4))')'|Sov |', + (QSEGSOV(1,ITSEC),'|',ITSEC=1,(NSECEL+1)),'|', + (QSEGSOV(2,ITSEC),'|',ITSEC=1,(NSECEL+1)),'|', + INFO,' |',INFO_INV,' |' WRITE(KUNIT,'(T2,A1,A5,A1,5(F5.1,A1),A1,5(F5.1,A1), + T70,A1,2(A5,I3,A2))')'|',TXTFOV(3:7),'|', + (QSEGFOV(1,ITSEC),'|',ITSEC=1,(NSECEL+1)),'|', + (QSEGFOV(2,ITSEC),'|',ITSEC=1,(NSECEL+1)),'|', + ' ',INT(100*INFO/0.62),'%|', + ' ',INT(100*INFO_INV/0.62),'%|' WRITE(KUNIT,'(T2,A,A)') + '+-----+-----+-----+-----+-----+-----+'// + '+-----+-----+-----+-----+-----++---------+---------+' END IF WRITE(KUNIT,*) END ***** end of STABLE_QILS ***** ------------------------------------------------------------------ ***** SUB StrPos ***** ------------------------------------------------------------------ C---- C---- NAME : StrPos C---- ARG : C---- DES : StrPos(Source,IStart,IStop): Finds the positions of the C---- DES : first and last non-blank/non-TAB in Source. C---- DES : IStart=IStop=0 for empty Source C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE StrPos(Source,IStart,IStop) CHARACTER*222 SOURCE INTEGER ISTART,ISTOP ISTART=0 ISTOP=0 DO J=1,LEN(SOURCE) IF(SOURCE(J:J).NE.' ')THEN ISTART=J GOTO 20 ENDIF ENDDO RETURN 20 DO J=LEN(SOURCE),1,-1 IF(SOURCE(J:J).NE.' ')THEN ISTOP=J RETURN ENDIF ENDDO ISTART=0 ISTOP=0 RETURN END ***** end of STRPOS ***** ------------------------------------------------------------------ ***** SUB WRITELINES ***** ------------------------------------------------------------------ C---- C---- NAME : WRITELINES C---- ARG : C---- DES : if 'cstring' contains '/n' (new line) this routine writes C---- DES : cstring line by line on screen; called by GETINT,GETREAL.. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRITELINES(CSTRING) CHARACTER*222 CSTRING INTEGER ICUTBEGIN(10),ICUTEND(10) CALL StrPos(CSTRING,ISTART,ISTOP) ILINE=1 ICUTBEGIN(ILINE)=1 ICUTEND(ILINE)=ISTOP DO I=1,ISTOP-1 IF(CSTRING(I:I+1).EQ.'/n')THEN ILINE=ILINE+1 ICUTBEGIN(ILINE)=I+2 ICUTEND(ILINE-1)=I-1 ICUTEND(ILINE)=ISTOP ENDIF ENDDO DO I=1,ILINE WRITE(*,*)CSTRING(ICUTBEGIN(I):ICUTEND(I)) ENDDO RETURN END ***** end of WRITELINES C vim:et:ts=2: profnet-1.0.22/src-phd/lib-sys-MACIBM.f0000644015075101507510000001562712021362704016576 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** FCT FCTIME_DATE ***** ------------------------------------------------------------------ C---- C---- NAME : FCTIME_DATE C---- ARG : C---- DES : C---- OUT : character*24 'YYYY_MM_DD - hh:mm:ss' C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns date * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: char*8 YYYYMMDD * * input : NOM, DEN * *----------------------------------------------------------------------* CHARACTER*24 FUNCTION FCTIME_DATE() IMPLICIT NONE C---- variables passed from/to SBR calling CHARACTER*24 CTEMP,CTEMP2 ******------------------------------*-----------------------------****** * execution of function * CTEMP=' ' CALL DATE_AND_TIME(CTEMP) FCTIME_DATE= ' ' FCTIME_DATE(1:4)= CTEMP(1:4) FCTIME_DATE(5:5)= '_' FCTIME_DATE(6:7)= CTEMP(5:6) FCTIME_DATE(8:8)= '_' FCTIME_DATE(9:10)= CTEMP(7:8) FCTIME_DATE(11:13)=' - ' FCTIME_DATE(14:15)=CTEMP2(1:2) FCTIME_DATE(16:16)=':' FCTIME_DATE(17:18)=CTEMP2(3:4) FCTIME_DATE(19:19)=':' FCTIME_DATE(20:21)=CTEMP2(5:6) END ***** end of FCTIME_DATE ***** ------------------------------------------------------------------ ***** FCT FRTIME_SECNDS ***** ------------------------------------------------------------------ C---- C---- NAME : FRTIME_SECNDS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns CPU time seconds * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: cputime * * input : T1: time to start (from previous call for unix) * *----------------------------------------------------------------------* REAL FUNCTION FRTIME_SECNDS(T1) IMPLICIT NONE C---- variables passed from/to SBR calling REAL T1 ******------------------------------*-----------------------------****** * execution of function * CALL CPU_TIME(T1) FRTIME_SECNDS=T1 END ***** end of FRTIME_SECNDS ***** ------------------------------------------------------------------ ***** SUB SCFDATE ***** ------------------------------------------------------------------ C---- C---- NAME : SCFDATE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE SCFDATE(ITERCALL,LOGIWRITE,DATEOLD) IMPLICIT NONE CHARACTER*24 ACTDATE,DATEOLD,CTEMP INTEGER ITER,ITERCALL LOGICAL LOGIWRITE C C ACTDATE=FDATE() ACTDATE='' CTEMP=' ' CALL DATE_AND_TIME(CTEMP) ACTDATE=CTEMP IF (LOGIWRITE .EQV. .TRUE.) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) IF (ITERCALL.EQ.2) THEN WRITE(6,'(T10,A11,A24)')'started: ',DATEOLD WRITE(6,'(T10,A11,A24)')' ended: ',ACTDATE ELSE WRITE(6,'(T10,A11,A24)')' time: ',ACTDATE END IF WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF IF (ITERCALL.EQ.1) THEN DATEOLD=ACTDATE END IF END ***** end of SCFDATE ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix C REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME,TIME_TMP INTEGER ITER LOGICAL LOGIWRITE C---- br 2003-08-23: bullshit to avoid warning TIME_TMP= 0.0 Cunix C TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) C TIMEDIFF=DTIME(TIMEARRAYM) Clinux C TIMEDIFF=DTIME(TIMEARRAYM) Cibm CALL CPU_TIME(TIMEDIFF) IF (LOGIWRITE .EQV. .TRUE.) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src-phd/lib-sys-SGI.f0000644015075101507510000001464412021362704016266 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** FCT FCTIME_DATE ***** ------------------------------------------------------------------ C---- C---- NAME : FCTIME_DATE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns date * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: char*8 YYYYMMDD * * input : NOM, DEN * *----------------------------------------------------------------------* CHARACTER*24 FUNCTION FCTIME_DATE() IMPLICIT NONE ******------------------------------*-----------------------------****** * execution of function * C FCTIME_DATE=FDATE() FCTIME_DATE='' END ***** end of FCTIME_DATE ***** ------------------------------------------------------------------ ***** FCT FRTIME_SECNDS ***** ------------------------------------------------------------------ C---- C---- NAME : FRTIME_SECNDS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns CPU time seconds * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: cputime * * input : NOM, DEN * *----------------------------------------------------------------------* REAL FUNCTION FRTIME_SECNDS(T1) IMPLICIT NONE C---- variables passed from/to SBR calling REAL T1 ******------------------------------*-----------------------------****** * execution of function * FRTIME_SECNDS=SECNDS(T1) END ***** end of FRTIME_SECNDS ***** ------------------------------------------------------------------ ***** SUB SCFDATE ***** ------------------------------------------------------------------ C---- C---- NAME : SCFDATE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE SCFDATE(ITERCALL,LOGIWRITE,DATEOLD) IMPLICIT NONE CHARACTER*24 ACTDATE,DATEOLD,CTEMP INTEGER ITER,ITERCALL LOGICAL LOGIWRITE C C ACTDATE=FDATE() ACTDATE='' C ibm C CTEMP=' ' C CALL DATE_AND_TIME(CTEMP) C ACTDATE=CTEMP IF (LOGIWRITE .EQV. .TRUE.) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) IF (ITERCALL.EQ.2) THEN WRITE(6,'(T10,A11,A24)')'started: ',DATEOLD WRITE(6,'(T10,A11,A24)')' ended: ',ACTDATE ELSE WRITE(6,'(T10,A11,A24)')' time: ',ACTDATE END IF WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF IF (ITERCALL.EQ.1) THEN DATEOLD=ACTDATE END IF END ***** end of SCFDATE ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux C REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME,TIME_TMP INTEGER ITER LOGICAL LOGIWRITE C---- br 2003-08-23: bullshit to avoid warning TIME_TMP= 0.0 Cunix TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) TIMEDIFF=DTIME(TIMEARRAYM) Clinux C TIMEDIFF=DTIME(TIMEARRAYM) Cibm C TIMEDIFF=DTIME(TIMEARRAYM) C CALL CPU_TIME(TIMEDIFF) IF (LOGIWRITE .EQV. .TRUE.) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src-phd/lib-sys.f0000644015075101507510000001464512021362705015650 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** FCT FCTIME_DATE ***** ------------------------------------------------------------------ C---- C---- NAME : FCTIME_DATE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns date * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: char*8 YYYYMMDD * * input : NOM, DEN * *----------------------------------------------------------------------* CHARACTER*24 FUNCTION FCTIME_DATE() IMPLICIT NONE ******------------------------------*-----------------------------****** * execution of function * C FCTIME_DATE=FDATE() FCTIME_DATE='' END ***** end of FCTIME_DATE ***** ------------------------------------------------------------------ ***** FCT FRTIME_SECNDS ***** ------------------------------------------------------------------ C---- C---- NAME : FRTIME_SECNDS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns CPU time seconds * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: cputime * * input : NOM, DEN * *----------------------------------------------------------------------* REAL FUNCTION FRTIME_SECNDS(T1) IMPLICIT NONE C---- variables passed from/to SBR calling REAL T1 ******------------------------------*-----------------------------****** * execution of function * FRTIME_SECNDS=SECNDS(T1) END ***** end of FRTIME_SECNDS ***** ------------------------------------------------------------------ ***** SUB SCFDATE ***** ------------------------------------------------------------------ C---- C---- NAME : SCFDATE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE SCFDATE(ITERCALL,LOGIWRITE,DATEOLD) IMPLICIT NONE CHARACTER*24 ACTDATE,DATEOLD,CTEMP INTEGER ITER,ITERCALL LOGICAL LOGIWRITE C C ACTDATE=FDATE() ACTDATE='' C ibm C CTEMP=' ' C CALL DATE_AND_TIME(CTEMP) C ACTDATE=CTEMP IF (LOGIWRITE .EQV. .TRUE.) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) IF (ITERCALL.EQ.2) THEN WRITE(6,'(T10,A11,A24)')'started: ',DATEOLD WRITE(6,'(T10,A11,A24)')' ended: ',ACTDATE ELSE WRITE(6,'(T10,A11,A24)')' time: ',ACTDATE END IF WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF IF (ITERCALL.EQ.1) THEN DATEOLD=ACTDATE END IF END ***** end of SCFDATE ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix C REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME,TIME_TMP INTEGER ITER LOGICAL LOGIWRITE C---- br 2003-08-23: bullshit to avoid warning TIME_TMP= 0.0 Cunix C TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) C TIMEDIFF=DTIME(TIMEARRAYM) Clinux TIMEDIFF=DTIME(TIMEARRAYM) Cibm C TIMEDIFF=DTIME(TIMEARRAYM) C CALL CPU_TIME(TIMEDIFF) IF (LOGIWRITE .EQV. .TRUE.) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src-phd/phd.f0000644015075101507510000122151512021412433015030 0ustar lkajanlkajan*----------------------------------------------------------------------* * FORTRAN code for program PHD * * (Profile based neural network prediction of secondary * * structure, solvent accessibility, and transmembrane * * helices) * *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 0.2 * *----------------------------------------------------------------------* * * * General notes: - The program uses a parameter files (INCLUDE): * * phdParameter.f.f * * - Library routines are taken from: * * lib-phd.f * * * * Organisation: (1) main program PHD * * (2) MAIN_STOP_EMPTYHSSP * * then all subroutines alphabetically * * * * parameters/variables defined in: * * Doc-code-phd.txt * * * * To port it: hard coded is only the path for the *.com file * * currently: /home/rost/pub * * or: /home/phd/net (if arg5=server) * * or: explicitly given in arg6 * * NOTE: defined in 'iniphd.f', * * --> grep 'change to port' * * * * Input arg: arg1: HSSP file * * arg2: optional flag if = "mach", then the output * * (of secondary structure) comes with "# 1" * * arg3: optional flag if = "whatif", an output file* * with extension ".whatif" is created, which * * can be read by e.g. KaleidaGraph * * arg4: optional flag if * * = "sec" -> prediction of secondary str. * * = "exp" -> prediction of exposure * * = "htm" -> prediction of helical trans- * * membrane regions * * default: sec * * arg5: optional if phd LSERVER=TRUE, default: FALSE * arg6: specifies the Parameter file to be chosen * * arg7: optional flag: = "rdb", an output file is * * written (extension ".rdb") with a format * * for interchange, i.e. merging the results * * from sec and exp- predictions * * arg8: if = DEC or ALPHA, LDEC=TRUE * * arg9: working directory, default=local * * arg10: name for .pred file * * arg11: name for .rdb file * * arg12: not used * * * *----------------------------------------------------------------------* PROGRAM PHD C---- include parameter files INCLUDE 'phdParameter.f' C---- local variables INTEGER ITER,MUE,NUMARGUMENTS,IHELP REAL TIME0,FRTIME_SECNDS LOGICAL LWRITE ******------------------------------*-----------------------------****** * LDSSPREAD is set true, if there is an observed secondary * * structure in the HSSP file (then Evaldssp is * * called and the pay-off table written into the out* * put) * * LFILTER controls whether the prediction ought to filterd * * LOUTBINPROB if true, the probabilities for the assignment of * * the secondary structures is computed and written * * into the output. * * LSERVER if true the name of FILEPRED, FILEOUTPUT are * * chosen equal to the name of the HSSP file, other-* * wise according to the name of the protein in the * * HSSP file. * * LWRITE controls whether calls of time and date are writ-* * ten into the printer * * SECNDS external function returning seconds elapsed since* * midnight * ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- assigning parameters ----- C-------------------------------------------------- C---- note: now determined by arguments: LSERVER= .FALSE. LDEC= .FALSE. C---- security FILE_HSSP= ' ' C---- call SRDTIME(CALL,LWRITE) from personal lib-syst.f LWRITE= .FALSE. c$$$ CALL SRDTIME(1,LWRITE) C---- call SCFDATE(1,LWRITE) from personal lib-syst.f LWRITE= .FALSE. C CALL SCFDATE(1,LWRITE,STARTDATE) C---- elapsed time: real: seconds since midnight-supplied arg TIME0= 0.0 C TIMESTART= SECNDS(TIME0) C TIMESTART= FRTIME_SECNDS(TIME0) C-------------------------------------------------- C---- requesting HSSP file name and further C---- input variables to run program C-------------------------------------------------- C ------------------- CALL GET_ARG_NUMBER(NUMARGUMENTS) C ------------------- IF (NUMARGUMENTS.GT.0) THEN C ------------------- CALL GET_ARGUMENT(1,FILE_HSSP) C ------------------- CHAR_ARG_READ(1)=FILE_HSSP ELSE WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,70A1)')('-',ITER=1,70) WRITE(6,'(T2,3A1,T10,A)')('-',ITER=1,3), + 'Dear User, Welcome to PredictProtein !' WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,3A1,T10,A)')('-',ITER=1,3), + 'Please select a HSSP file for the prediction:' WRITE(6,'(T2,A)')'---' C ------------ CALL GETCHAR(80,FILE_HSSP,' HSSP file ? ') C ------------ END IF IF (NUMARGUMENTS.GE.2) THEN DO ITER=2,NUMARGUMENTS C ----------------- CALL GET_ARGUMENT(ITER,CHAR_ARG_READ(ITER)) C ----------------- END DO END IF C---- initialise according to input C =========== CALL INIPHD(NUMARGUMENTS) C =========== C-------------------------------------------------- C---- initialise the parameter names for all C---- particular jobs (architectures) C-------------------------------------------------- C ------------ CALL READPAR C ------------ C---- 21 amino acid names (20+unknown) and solvent into AACODE C ------------ CALL TRANSAA C ------------ C-------------------------------------------------- C---- adjust filename for output file ----- C-------------------------------------------------- C-------------------------------------------------- C---- reading sequence from HSSP file ----- C-------------------------------------------------- WRITE(6,'(T2,70A1)')('-',ITER=1,70) WRITE(6,'(T2,3A1,T10,A,T30,A50)')('-',ITER=1,3), + 'Protein from HSSP:',FILE_HSSP WRITE(6,'(T2,70A1)')('-',ITER=1,70) WRITE(6,'(T2,A)')'---' C --------------- CALL RS_GETHSSP C --------------- C stop if no sequence in HSSP IF (NUMNALIGN(1).EQ.0) THEN WRITE(6,'(T2,A,T10,60A1)')'***',('*',ITER=1,60) WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR in reading HSSP (?), claimed to be empty (main PHD)' WRITE(6,'(T2,A,T10,60A1)')'***',('*',ITER=1,60) STOP END IF C-------------------------------------------------- C---- if somehow a fault occurred stop program ---- C-------------------------------------------------- IF (NUMRES.EQ.0) THEN C ------------------------ CALL MAIN_STOP_EMPTYHSSP C ------------------------ C!GOTO! !!!!!!!!! C ========= GOTO 9999 C ========= C!GOTO! !!!!!!!!! END IF C-------------------------------------------------- C---- is there a DSSP assignmnet in the HSSP file? C-------------------------------------------------- IHELP=0 DO MUE=1,NUMRES IF ((RESSECSTR(MUE).EQ.'H').OR. + (RESSECSTR(MUE).EQ.'G').OR. + (RESSECSTR(MUE).EQ.'E')) THEN IHELP=IHELP+1 END IF END DO IF ((IHELP.GT.5).AND.(LSERVER.EQV. .FALSE.)) THEN LDSSPREAD=.TRUE. ELSE LDSSPREAD=.FALSE. END IF WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,3A1,T10,A)')('-',ITER=1,3), + 'end of reading protein data' WRITE(6,'(T2,70A1)')('-',ITER=1,70) WRITE(6,'(T2,A)')'---' C-------------------------------------------------- C---- loop over all networks ----- C-------------------------------------------------- C ============ CALL NETWORK C ============ IF (LFILTER .EQV. .TRUE.) THEN C =========== CALL FILTER C =========== END IF C-------------------------------------------------- C---- saving data/output file ----- C-------------------------------------------------- C---- convert DSSP (8) -> 3 structure types (lib-prot.f) IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(6,'(T2,A)')'---' LWRITE=.TRUE. C ============= CALL EVALDSSP C ============= WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,70A1)')('-',ITER=1,70) WRITE(6,'(T2,A)')'---' END IF C ============ CALL CONTENT C ============ C---- write results into output file C ----------- CALL DATAOT C ----------- C---- write results on printer C ----------- CALL TXTRES C ----------- C-------------------------------------------------- C---- branch for misread HSSP file ----- C-------------------------------------------------- C!GOTO!!!!!!!! C ======== 9999 CONTINUE C ======== C!GOTO!!!!!!!! END ***** end of MAIN ***** ------------------------------------------------------------------ ***** SUB MAIN_STOP_EMPTYHSSP ***** ------------------------------------------------------------------ C---- C---- NAME : MAIN_STOP_EMPTYHSSP C---- ARG : C---- DES : For an empty HSSP file blabla written C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: For an empty HSSP file blabla written. * *----------------------------------------------------------------------* SUBROUTINE MAIN_STOP_EMPTYHSSP C---- local variables INTEGER ITER ******------------------------------*-----------------------------****** WRITE(6,'(T2,70A1)')('*',ITER=1,70) WRITE(6,'(T2,A3)')'***' WRITE(6,'(T2,3A1,T10,A,T30,A50)')('*',ITER=1,3), + 'An error occurred: the adressed HSSP file is empty.' WRITE(6,'(T2,3A1,T10,A,T30,A50)')('*',ITER=1,3), + 'Program has stopped consequently !' WRITE(6,'(T2,A3)')'***' WRITE(6,'(T2,3A1,T10,A,T30,A50)')('*',ITER=1,3), + 'A potential cause is you mistyped the file name.' WRITE(6,'(T2,3A1,T10,A,T30,A50)')('*',ITER=1,3), + 'Either start the program with: ' WRITE(6,'(T2,3A1,T10,A,T30,A50)')('*',ITER=1,3), + '"dir/PredictProtein.MACHINE filename"' WRITE(6,'(T2,3A1,T10,A,T30,A50)')('*',ITER=1,3), + 'or check the path of the file you want to be read.' WRITE(6,'(T2,A3)')'***' WRITE(6,'(T2,3A1,T10,A,T30,A50)')('*',ITER=1,3), + 'Sorry !' WRITE(6,'(T2,A3)')'***' WRITE(6,'(T2,70A1)')('*',ITER=1,70) END ***** end of MAIN_STOP_EMPTYHSSP ***** ------------------------------------------------------------------ ***** SUB BINFIL ***** ------------------------------------------------------------------ C---- C---- NAME : BINFIL C---- ARG : C---- DES : Executes the output decision, i.e., actual network C---- DES : prediction C---- DES : in terms of binary values (for filtered output). C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: This SBR executes the output decision, i.e. the * * -------- actual prediciton of the network in terms of * * binary output values. * * input: OUTFIL, (THREXP10ST, MAXEXP, EXPCODE) * * var. read: SSCODE, EXPCODE, MAXEXP, THREXP10ST * * output: OUTEXPFIL, OUTBINCHARFIL * * called by: SBR FILTEREXP * * calling: lib-comp.f: SRSTZ1, SRMAX1 * *----------------------------------------------------------------------* SUBROUTINE BINFIL C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE,ITOUT,IMAX REAL OUTLOC(1:(NUMOUTMAX)),RMAX ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- loop over all residues ----- C-------------------------------------------------- DO MUE=1,NUMRES C ----------- CALL SRSTZ1(OUTLOC,NUMOUTMAX) C ----------- DO ITOUT=1,NUMOUT OUTLOC(ITOUT)=OUTFIL(ITOUT,MUE) END DO C---------------------------------------- C------- WTO decision C---------------------------------------- C ----------- CALL SRMAX1(OUTLOC,NUMOUTMAX,RMAX,IMAX) C ----------- IF (RMAX.EQ.0) THEN OUTEXPFIL(MUE)=MAXEXP OUTBINCHARFIL(MUE)='e' ELSE OUTEXPFIL(MUE)=THREXP10ST(IMAX) OUTBINCHARFIL(MUE)=EXPCODE(IMAX) END IF C---------------------------------------- C------- end of WTO decision C---------------------------------------- END DO C-------------------------------------------------- C---- end of loop over all residues ---- C-------------------------------------------------- END ***** end of BINFIL ***** ------------------------------------------------------------------ ***** SUB BINOUT ***** ------------------------------------------------------------------ C---- C---- NAME : BINOUT C---- ARG : C---- DES : Executes the output decision, i.e., actual network C---- DES : prediction C---- DES : in terms of binary values. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: This SBR executes the output decision, i.e. the * * -------- actual prediciton of the network in terms of * * binary output values. * * const. passed: NUMRES, NSECEL, NUMOUT, NUMEXP, MODESECSTRON * * -------------- NUMOUTMAX, * * var. passed: in: OUTPUT; out: OUTBIN, OUTBINCHAR, OUTEXP * * var. read: SSCODE, EXPCODE, MAXEXP, THREXP10ST * * called by: SBR NETWORK * * calling: lib-comp.f: SRSTZ1, SRMAX1 * *----------------------------------------------------------------------* SUBROUTINE BINOUT C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE,ITOUT,IMAX REAL OUTLOC(1:(NUMOUTMAX)),RMAX ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- loop over all residues ----- C-------------------------------------------------- DO MUE=1,NUMRES C ----------- CALL SRSTZ1(OUTLOC,NUMOUTMAX) C ----------- DO ITOUT=1,NUMOUT OUTLOC(ITOUT)=OUTPUT(ITOUT,MUE) END DO C---------------------------------------- C------- WTO decision C---------------------------------------- C ----------- CALL SRMAX1(OUTLOC,NUMOUTMAX,RMAX,IMAX) C ----------- DO ITOUT=1,NUMOUT OUTBIN(ITOUT,MUE)=0 END DO C------------------------------ C------- secondary structure C------------------------------ IF (MODESECSTRON(1:9).EQ.'SECONDARY') THEN OUTBIN(IMAX,MUE)=1 OUTBINCHAR(MUE)= SSCODE(IMAX) OUTBINCHARFIL(MUE)=SSCODE(IMAX) C------------------------------ C------- exposure C------------------------------ ELSE IF (RMAX.EQ.0) THEN OUTBIN(NUMOUT,MUE)=1 OUTEXP(MUE)= MAXEXP OUTBINCHAR(MUE)= 'e' ELSE OUTBIN(IMAX,MUE)= 1 OUTEXP(MUE)= THREXP10ST(IMAX) OUTBINCHAR(MUE)= EXPCODE(IMAX) END IF END IF C---------------------------------------- C------- end of WTO decision C---------------------------------------- END DO C-------------------------------------------------- C---- end of loop over all residues ---- C-------------------------------------------------- END ***** end of BINOUT ***** ------------------------------------------------------------------ ***** SUB CODEIN ***** ------------------------------------------------------------------ C---- C---- NAME : CODEIN C---- ARG : C---- DES : The 20 amino acid one letter names (+solvent) are C---- DES : 'transcribed' into a vector with NCODEUNT components C---- DES : 0,1. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The 20 amino acid one letter names (+solvent) are* * -------- 'transcribed' into a vector with NCODEUNT * * components 0,1. * * input var.: MODEASSCAS, PROFACC, NBIOLOBJ * * ----------- CODEVECPROF, LOGI_CONS, *_INDEL, * * output var.: CODEVECTOR * * exchange var.: to ASSCAS: CODEVECTOR * * -------------- from : CODEVECPROF * * called from: ASSCAS * * procedure: The actual residue ACTRESIDUE taken from SBR * * --------- ASSCAS is compared with the amino acid code vector * AACODE(i). In case of being equal the integer * * number i is transposed into a binary number by * * NCODEUNT units. * * for: MODECODEIN='PROFILE' the profiles are given * * by CODEVECPROF(i), i=1,21, for each residue from * * all those read from the databank. In ASSCAS the * * maximum of all these numbers is searched (PROFMAX) * For the binary approach (MODECODEIN='PROFILE-BIN') * the following way is used to transmit the integers * to binaries: * * nprof in first intervall -> 000 (for PROFACC =4)* * in second -> 100 * * in third -> 110 * * in fourth -> 111 * *----------------------------------------------------------------------* SUBROUTINE CODEIN C---- global parameter * INCLUDE 'phdParameter.f' C---- local parameter * INTEGER LOWEST PARAMETER (LOWEST= 2) C---- local variables INTEGER CHECKNUM,ITER1,ITER2,ITPROF,ITACC LOGICAL CHECKFLAG(1:NBIOLOBJMAX),LHELP CHARACTER*1 CHELP ******------------------------------*-----------------------------****** * ITER1,2,ITPROF,ITACC iteration variables * * ACTRESIDUE gives the one letter name of the actual residue * * which by calling of CODEIN ought to be translated* * into a vector with 21 components (one 1, rest 0) * * alternatively such a vector is given by a binary * * vector with NCODEUNITS-1 components:2**unit... * * CODEVECTOR is this translated coding for every amino acid * * type (for further information, see SR CODEIN). * * LOWEST for MODECODEIN='PROFILE-BIN': the 000.. vector is* * used for RESPROF < lowest, the 111.. for > * * PROFMAX-LOWEST * ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- for alphabetical coding ----- C-------------------------------------------------- IF (MODEASSCAS(ACTCHI).EQ.'ALPHABET') THEN C------- all lower case letters -> C CHELP=ACTRESIDUE IF ((CHELP.EQ.'a').OR.(CHELP.EQ.'b').OR.(CHELP.EQ.'c').OR. A (CHELP.EQ.'d').OR.(CHELP.EQ.'e').OR.(CHELP.EQ.'f').OR. B (CHELP.EQ.'g').OR.(CHELP.EQ.'h').OR.(CHELP.EQ.'i').OR. C (CHELP.EQ.'j').OR.(CHELP.EQ.'k').OR.(CHELP.EQ.'l').OR. D (CHELP.EQ.'m').OR.(CHELP.EQ.'n').OR.(CHELP.EQ.'o').OR. E (CHELP.EQ.'p').OR.(CHELP.EQ.'q').OR.(CHELP.EQ.'r').OR. F (CHELP.EQ.'s').OR.(CHELP.EQ.'t').OR.(CHELP.EQ.'u').OR. G (CHELP.EQ.'v').OR.(CHELP.EQ.'w').OR.(CHELP.EQ.'y').OR. H (CHELP.EQ.'x').OR.(CHELP.EQ.'z').OR.(CHELP.EQ.'X')) THEN ACTRESIDUE='C' C------- Z -> E ELSEIF (CHELP.EQ.'Z') THEN ACTRESIDUE='E' C------- B -> D ELSEIF (CHELP.EQ.'B') THEN ACTRESIDUE='D' C------- for alignments: . -> E ELSEIF (CHELP.EQ.'.') THEN ACTRESIDUE='O' C------- for alignments: . -> E ELSEIF (CHELP.EQ.' ') THEN ACTRESIDUE='U' WRITE(6,'(T2,A,T10,A,T30,I6,A,T40,A1)') + '---','CODEIN for pos:',ACTPOS,'residue =',ACTRESIDUE C------- for breaks: -> U ELSEIF (CHELP.EQ.'!') THEN ACTRESIDUE='U' END IF C------- upper case letters DO ITER1=1,NBIOLOBJ IF (ACTRESIDUE.EQ.AACODE(ITER1)) THEN DO ITER2=1,NCODEUNT CODEVECTOR(ITER2)=REAL(AABIT(ITER1,ITER2)) END DO CHECKFLAG(ITER1)=.TRUE. ELSE CHECKFLAG(ITER1)=.FALSE. END IF END DO C------- consistency check CHECKNUM=0 DO ITER1=1,NBIOLOBJ IF (CHECKFLAG(ITER1) .EQV. .TRUE.) THEN CHECKNUM=CHECKNUM+1 END IF END DO IF (CHECKNUM.NE.1) THEN WRITE(6,*)' FAULT in CODEIN: checknum = ',CHECKNUM WRITE(6,*)' for residue: ',ACTRESIDUE STOP END IF C-------------------------------------------------- C---- for encoding with profiles ----- C-------------------------------------------------- ELSEIF (MODEASSCAS(ACTCHI).EQ.'PROFILE-BIN') THEN C change insertion C IF ((ACTRESIDUE.EQ.'!').OR.(ACTRESIDUE.EQ.'.')) THEN IF (ACTRESIDUE.EQ.'!') THEN DO ITPROF=1,(NBIOLOBJ-1) CODEVECPROF(ITPROF)=0 END DO CODEVECPROF(ITPROF)=100 END IF DO ITPROF=1,NBIOLOBJ LHELP=.TRUE. C---------- resprof = 0 (+lowest)? IF (CODEVECPROF(ITPROF).GT.LOWEST) THEN CODEVECTOR(((ITPROF-1)*(PROFACC-1))+1)=1. ELSE LHELP=.FALSE. DO ITACC=1,(PROFACC-1) CODEVECTOR(((ITPROF-1)*(PROFACC-1))+ITACC)=0. END DO END IF C---------- profmax (-lowest)? IF (LHELP .EQV. .TRUE.) THEN IF (CODEVECPROF(ITPROF).GT.(PROFMAX-LOWEST)) THEN DO ITACC=1,(PROFACC-1) CODEVECTOR(((ITPROF-1)*(PROFACC-1))+ITACC)=1. END DO LHELP=.FALSE. ELSE CODEVECTOR(ITPROF*(PROFACC-1))=0. END IF END IF C---------- in between: sort into intervalls IF (LHELP .EQV. .TRUE.) THEN DO ITACC=2,(PROFACC-2) IF (CODEVECPROF(ITPROF).GT. + ((ITACC-1)*PROFINTERV)) THEN CODEVECTOR((ITPROF-1)*(PROFACC-1)+ITACC)=1. ELSE CODEVECTOR((ITPROF-1)*(PROFACC-1)+ITACC)=0. END IF END DO END IF END DO C-------------------------------------------------- C---- real profiles ----- C-------------------------------------------------- ELSEIF ( (MODEASSCAS(ACTCHI).EQ.'PROFILE-REAL').OR. + LOGI_CONS ) THEN IF ((ACTRESIDUE.EQ.'!').OR.(ACTRESIDUE.EQ.' ')) THEN DO ITPROF=1,(NBIOLOBJ-1) CODEVECPROF(ITPROF)=0 END DO CODEVECPROF(ITPROF)=100 END IF DO ITPROF=1,NBIOLOBJ C---------- resprof = 0 (+lowest)? IF (CODEVECPROF(ITPROF).GT.LOWEST) THEN CODEVECTOR(ITPROF)= + REAL(CODEVECPROF(ITPROF))/REAL(PROFMAX) ELSE CODEVECTOR(ITPROF)=0. END IF END DO ELSE WRITE(6,*)'CODEIN: wrong mode chosen: MODEASSCAS(ACTCHI)=', + MODEASSCAS(ACTCHI) STOP END IF C-------------------------------------------------- C---- end of MODEASSCAS ----- C-------------------------------------------------- END ***** end of CODEIN ***** ------------------------------------------------------------------ ***** SUB CODESTR ***** ------------------------------------------------------------------ C---- C---- NAME : CODESTR C---- ARG : C---- DES : The NSECEL secondary structures generated by net1 are C---- DES : 'transcribed' into vectors with NSECEL components 0,1 C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The NSECEL secondary structures generated by net1* * -------- are 'transcribed' into vectors with NSECEL * * components 0,1 * * purpose: The NSECEL secondary structures generated by net1* * -------- are 'transcribed' into vectors with NSECEL * * components 0,1 * * input var.: MODEASSSTR, CASCACC, NSECEL * * ----------- CODEVECINCASC * * output var.: CODEVECTOR * * exchange var.: to ASSSTR: CODEVECTOR * * -------------- from : CODEVECINCASC * * called from: ASSSTR * * procedure: The actual residue ACTSTR is compared to SSCODE * * --------- if ACTSTR.eq.SSCODE(i), CODEVECTOR(i) is set to 1* * CODEVECTOR(j), with j=1,NSECEL except i * *----------------------------------------------------------------------* SUBROUTINE CODESTR C---- global parameter * INCLUDE 'phdParameter.f' C---- local parameter * INTEGER LOWEST PARAMETER (LOWEST= 2) INTEGER ITSEC,ITACC,INTERMAX,POSMAX,IHELP,ITOUT LOGICAL INTERFLAG ******------------------------------*-----------------------------****** * ITER1 iteration variable * * CODEVECTOR is this translated coding for every structure * * type (for further information, see SR CODEIN). * * LOWEST for MODECODEIN='PROFILE-BIN': the 000.. vector is* * used for RESPROF < lowest, the 111.. for > * * PROFMAX-LOWEST * ******------------------------------*-----------------------------****** POSMAX= 0 C---------------------------------------- C---- real-new 2 -------- C---------------------------------------- IF ( (MODEASSSTR(ACTCHI).EQ.'REAL-OCT').OR. + (MODEASSSTR(ACTCHI).EQ.'REAL-CONS').OR. + ((.NOT.LOGI_REALINPUT).AND.LOGI_CONS) ) THEN IF (CODEVECINCASC(NSECEL+1).NE.100) THEN C---------------------------------------- C---------- secondary part DO ITSEC=1,NSECEL C------------- intrj = 0 (+lowest)? IF (CODEVECINCASC(ITSEC).GT.LOWEST) THEN CODEVECTOR(((ITSEC-1)*(CASCACC-1))+1)=1. ELSE DO ITACC=1,(CASCACC-1) CODEVECTOR(((ITSEC-1)*(CASCACC-1))+ITACC)=0. END DO END IF C------------- > 100 (-lowest)? IF (CODEVECINCASC(ITSEC).GT.(100-LOWEST)) THEN CODEVECTOR(ITSEC*(CASCACC-1))=1. ELSE CODEVECTOR(ITSEC*(CASCACC-1))=0. END IF C------------- in between: sort into intervalls DO ITACC=2,(CASCACC-2) IF ((CODEVECINCASC(ITSEC).GE. + ((ITACC-1)*CASCINTERV))) THEN CODEVECTOR(((ITSEC-1)*(CASCACC-1))+ITACC)=1. ELSE CODEVECTOR(((ITSEC-1)*(CASCACC-1))+ITACC)=0. END IF END DO END DO C---------------------------------------- C---------- no conservation weight IF (MODEASSSTR(ACTCHI).EQ.'REAL-OCT') THEN C------------- spacer DO ITACC=(NSECEL*(CASCACC-1)+1),((NSECEL+1)*(CASCACC-1)) CODEVECTOR(ITACC)=0 END DO IHELP=(NSECEL+1)*(CASCACC-1) C---------------------------------------- C---------- conservation weight 1992: H-E-L-cons-spacer C---------- ----------------- ELSEIF (MODEASSSTR(ACTCHI).EQ.'REAL-CONS') THEN C------------- spacer = 0 DO ITACC=((NSECEL+1)*(CASCACC-1)+1), + ((NSECEL+2)*(CASCACC-1)) CODEVECTOR(ITACC)=0. END DO C------------- coding conservation weight with additional DO ITACC=1,(CASCACC-1) IF ((ACTCONSWEIGHT.GE.((ITACC-1)*2./(CASCACC-1))).AND. + (ACTCONSWEIGHT.LT.(ITACC*2./(CASCACC-1)))) THEN CODEVECTOR(NSECEL*(CASCACC-1)+ITACC)=1. ELSE CODEVECTOR(NSECEL*(CASCACC-1)+ITACC)=0. END IF END DO IHELP=(NSECEL+1)*(CASCACC-1) C---------------------------------------- C---------- conservation weight 1993: H-E-L-spacer-expos-cons-indel C---------- ----------------------------- ELSEIF (LOGI_CONS.AND.(.NOT.LOGI_INDEL)) THEN C------------- spacer DO ITACC=(NSECEL*(CASCACC-1)+1),((NSECEL+1)*(CASCACC-1)) CODEVECTOR(ITACC)=0 END DO IHELP=(NSECEL+1)*(CASCACC-1) C------------- conservation weight new DO ITACC=1,(CASCACC-1) IF ((ACTCONSWEIGHT.GE.((ITACC-1)*2. + /REAL(CASCACC-1))).AND. + (ACTCONSWEIGHT.LT.(ITACC*2./REAL(CASCACC-1)))) THEN CODEVECTOR(IHELP+ITACC)=1. ELSE CODEVECTOR(IHELP+ITACC)=0. END IF END DO IHELP=(NSECEL+2)*(CASCACC-1) C---------------------------------------- C---------- insertions and deletions number deletions/insertions ELSEIF (LOGI_CONS.AND.LOGI_INDEL) THEN C------------- spacer DO ITACC=(NSECEL*(CASCACC-1)+1),((NSECEL+1)*(CASCACC-1)) CODEVECTOR(ITACC)=0 END DO IHELP=(NSECEL+1)*(CASCACC-1) C------------- conservation weight new DO ITACC=1,(CASCACC-1) IF (((ACTNDEL/REAL(ACTNALIGN)) + .GE.((ITACC-1)/REAL(CASCACC-1))).AND. + ((ACTNDEL/REAL(ACTNALIGN)) + .LT.(ITACC*2./REAL(CASCACC-1)))) THEN CODEVECTOR(IHELP+ITACC)=1. ELSE CODEVECTOR(IHELP+ITACC)=0. END IF END DO IHELP=IHELP+(CASCACC-1) DO ITACC=1,(CASCACC-1) IF (((ACTNINS/REAL(ACTNALIGN)) + .GE.((ITACC-1)/REAL(CASCACC-1))).AND. + ((ACTNINS/REAL(ACTNALIGN)) + .LT.(ITACC*2./REAL(CASCACC-1)))) THEN CODEVECTOR(IHELP+ITACC)=1. ELSE CODEVECTOR(IHELP+ITACC)=0. END IF END DO END IF C------- spacer ? ELSE DO ITACC=1,(NSECEL*(CASCACC-1)) CODEVECTOR(ITACC)=0. END DO IF (LOGI_CONS .EQV. .TRUE.) THEN DO ITACC=(NSECEL*(CASCACC-1)+1),((NSECEL+1)*(CASCACC-1)) CODEVECTOR(ITACC)=0. END DO DO ITACC=((NSECEL+1)*(CASCACC-1)+1),NCODEUNT CODEVECTOR(ITACC)=1. END DO ELSE DO ITACC=(NSECEL*(CASCACC-1)+1),((NSECEL+1)*(CASCACC-1)) CODEVECTOR(ITACC)=0. END DO DO ITACC=((NSECEL+1)*(CASCACC-1)+1),NCODEUNT CODEVECTOR(ITACC)=1. END DO END IF END IF C---------------------------------------- C---- binary : winner takes all ------ C---------------------------------------- ELSEIF (MODEASSSTR(ACTCHI).EQ.'BIN-EXCL') THEN C------- code secondary structure IF (CODEVECINCASC(NSECEL+1).NE.100) THEN INTERMAX=0 INTERFLAG=.TRUE. DO ITSEC=1,NSECEL IF (CODEVECINCASC(ITSEC).GT.INTERMAX) THEN INTERFLAG=.FALSE. POSMAX=ITSEC INTERMAX=CODEVECINCASC(ITSEC) END IF END DO C---------- consistency check (one found?) IF (INTERFLAG .EQV. .TRUE.) THEN WRITE(6,*)'fault in CODESTR no example regarded as' WRITE(6,*)'"winner". For test and mue =', + ACTPOS,' and the respective outputs:' WRITE(6,*)'stopped 17-12-91-1b' STOP END IF C---------- winner takes all DO ITSEC=1,(NSECEL+1) CODEVECTOR(ITSEC)=0. END DO CODEVECTOR(POSMAX)=1. C------- spacer ? ELSE CODEVECTOR(NSECEL+1)=1. DO ITSEC=1,NSECEL CODEVECTOR(ITSEC)=0. END DO END IF C---------------------------------------- C---- real-new -------- C---------------------------------------- ELSEIF (MODEASSSTR(ACTCHI).EQ.'REAL-NEW') THEN IF (CODEVECINCASC(NSECEL+1).NE.100) THEN DO ITSEC=1,NSECEL C------------- intrj = 0 (+lowest)? IF (CODEVECINCASC(ITSEC).GT.LOWEST) THEN CODEVECTOR(((ITSEC-1)*(CASCACC-1))+1)=1. ELSE DO ITACC=1,(CASCACC-1) CODEVECTOR(((ITSEC-1)*(CASCACC-1))+ITACC)=0. END DO END IF C------------- > 100 (-lowest)? IF (CODEVECINCASC(ITSEC).GT.(100-LOWEST)) THEN CODEVECTOR(ITSEC*(CASCACC-1))=1. ELSE CODEVECTOR(ITSEC*(CASCACC-1))=0. END IF C------------- in between: sort into intervalls DO ITACC=2,(CASCACC-2) IF ((CODEVECINCASC(ITSEC).GE. + ((ITACC-1)*CASCINTERV))) THEN CODEVECTOR(((ITSEC-1)*(CASCACC-1))+ITACC)=1. ELSE CODEVECTOR(((ITSEC-1)*(CASCACC-1))+ITACC)=0. END IF END DO END DO C------- spacer ? ELSE DO ITACC=1,(NSECEL*(CASCACC-1)) CODEVECTOR(ITACC)=0 END DO DO ITACC=(NSECEL*(CASCACC-1)+1),((NSECEL+1)*(CASCACC-1)) CODEVECTOR(ITACC)=1 END DO END IF C---------------------------------------- C---- real real -------- C---------------------------------------- ELSEIF ( (MODEASSSTR(ACTCHI).EQ.'REAL-REAL').OR. + (MODEASSSTR(ACTCHI)(1:3).EQ.'RR-') ) THEN IF (CODEVECINCASC(NSECEL+1).NE.100) THEN DO ITOUT=1,NUMOUT C------------- intrj = 0 (+lowest)? IF (CODEVECINCASC(ITOUT).GT.LOWEST) THEN CODEVECTOR(ITOUT)=CODEVECINCASC(ITOUT)/100. ELSE CODEVECTOR(ITOUT)=0. END IF END DO C---------- spacer = 0 CODEVECTOR(NUMOUT+1)=0. IHELP=(NUMOUT+1) C---------- conservation weight CODEVECTOR(IHELP+1)=ACTCONSWEIGHT/2. IHELP=(NUMOUT+2) C---------- number deletions/insertions IF (LOGI_INDEL .EQV. .TRUE.) THEN CODEVECTOR(IHELP+1)=ACTNDEL/MAX(1.,REAL(ACTNALIGN)) CODEVECTOR(IHELP+2)=ACTNINS/MAX(1.,REAL(ACTNALIGN)) END IF C------- spacer ? ELSE DO ITOUT=1,NUMOUT CODEVECTOR(ITOUT)=0. END DO CODEVECTOR(NUMOUT+1)=1. DO ITOUT=(NUMOUT+2),NCODEUNT CODEVECTOR(ITOUT)=0. END DO END IF ELSE WRITE(6,'(T2,A,T10,A)')'***','CODESTR: mode strange!' WRITE(6,'(T2,A,T10,A)')'***','stopped 6-3-94d' STOP END IF C---------------------------------------- C---- end of modeassstr ------- C---------------------------------------- END ***** end of CODESTR ***** ------------------------------------------------------------------ ***** SUB CONTENT ***** ------------------------------------------------------------------ C---- C---- NAME : CONTENT C---- ARG : C---- DES : The content in secondary structure, resp. relative C---- DES : percentage of occurrence per amino acid is computed. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The content in secondary structure, resp. relative * -------- percentage of occurrence per amino acid is * * computed. * * input variables:OUTBINCHARFIL, OUTBINCHAR, DSSPCHAR, RESNAME * * output variab.: CONTPRED,CONTDSSP,CONTAA * * called by: MAIN * * calling: lib-comp.f SISTZ1 * * procedure: See SEVALPO, SEVALQUO, STABLEPO * *----------------------------------------------------------------------* SUBROUTINE CONTENT C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE,ITAA,COUNT(1:8),ICOUNT,ITSEC CHARACTER*24 TXTAA CHARACTER*1 INTERCHAR ******------------------------------*-----------------------------****** C---- default TXTAA(1:24)='ABCDEFGHIKLMNPQRSTVWXYZU' C---------------------------------------- C---- computing the content of acids -- C---------------------------------------- DO ITAA=1,24 ICOUNT=0 DO MUE=1,NUMRES IF (TXTAA(ITAA:ITAA).EQ.RESNAME(MUE)) THEN ICOUNT=ICOUNT+1 END IF END DO CONTAA(ITAA)=100*ICOUNT/REAL(NUMRES) END DO C------------------------------------------------------------- C---- secondary structure prediction ----- C------------------------------------------------------------- IF (MODESECSTRON(1:9).EQ.'SECONDARY') THEN C------------------------------------------- C------- computing the content of pred SS -- C------------------------------------------- C------- initially set equal content=prediction C =========== CALL SISTZ1(COUNT,8) C =========== DO MUE=1,NUMRES IF (LFILTER .EQV. .TRUE.) THEN INTERCHAR=OUTBINCHARFIL(MUE) ELSE INTERCHAR=OUTBINCHAR(MUE) END IF IF (INTERCHAR.EQ.'H') THEN COUNT(1)=COUNT(1)+1 ELSEIF (INTERCHAR.EQ.'E') THEN COUNT(2)=COUNT(2)+1 ELSEIF ((INTERCHAR.EQ.'L').OR.(INTERCHAR.EQ.' ')) THEN COUNT(NSECEL)=COUNT(NSECEL)+1 ELSEIF (NSECEL.GT.3) THEN IF (INTERCHAR.EQ.'T') THEN COUNT(3)=COUNT(3)+1 END IF END IF END DO DO ITSEC=1,NSECEL CONTPRED(ITSEC)=100*COUNT(ITSEC)/REAL(NUMRES) END DO C------------------------------------------- C------- computing the content of obs SS -- C------------------------------------------- IF (LDSSPREAD .EQV. .TRUE.) THEN C---------- initially set equal content=prediction C =========== CALL SISTZ1(COUNT,8) C =========== DO MUE=1,NUMRES INTERCHAR=CONVSECSTR(MUE) IF (INTERCHAR.EQ.'H') THEN COUNT(1)=COUNT(1)+1 ELSEIF (INTERCHAR.EQ.'E') THEN COUNT(2)=COUNT(2)+1 ELSEIF ((INTERCHAR.EQ.'L').OR.(INTERCHAR.EQ.' ')) THEN COUNT(NSECEL)=COUNT(NSECEL)+1 ELSEIF (NSECEL.GT.3) THEN IF (INTERCHAR.EQ.'T') THEN COUNT(3)=COUNT(3)+1 END IF END IF END DO DO ITSEC=1,NSECEL CONTDSSP(ITSEC)=100*COUNT(ITSEC)/REAL(NUMRES) END DO END IF END IF C---- end of content ----- C-------------------------------------------------- END ***** end of CONTENT ***** ------------------------------------------------------------------ ***** SUB DATAOT ***** ------------------------------------------------------------------ C---- C---- NAME : DATAOT C---- ARG : C---- DES : The prediction is written into FILEPRED. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The prediction is written into FILEPRED. * * const. passed: LWHATIF, LRDB, MODESECSTRON * * var. read: FILEPRED, FILEOUTPUT, FILE_WHATIF, FILE_RDB * * ext. SBR: SFILEOPEN (lib-unix) * * called by: MAIN * * calling: SCOUNT_HYDROPHOB, DATAOT_OUTPUT, * * -------- DATAOT_WHATIF, DATAOT_RDBSEC,DATAOT_RDBEXP, * * WRTCONTENT, WRTPRED, WRTEXP, WRTE, WRTF * *----------------------------------------------------------------------* SUBROUTINE DATAOT C---- global parameters * INCLUDE 'phdParameter.f' C---- local parameter INTEGER KOUT PARAMETER (KOUT= 10) C---- local function INTEGER FILEN_STRING C---- local variables LOGICAL LWRTOUTPUT CHARACTER*222 CHFILE INTEGER IEND ******------------------------------*-----------------------------****** LWRTOUTPUT= .FALSE. C-------------------------------------------------- C---- write prediction for testing set ----- C-------------------------------------------------- C---- write into fileotpredtest IEND= FILEN_STRING(FILEPRED) CHFILE= ' ' CHFILE(1:IEND)= FILEPRED(1:IEND) CALL SFILEOPEN(KOUT,CHFILE(1:IEND),'UNKNOWN',222,' ') C write(6,*)'xy filepred=',CHFILE(1:IEND) C---- general information C ================== C CALL WRTHEADER(KOUT) C ================== C---- writing content C =================== CALL WRTCONTENT(KOUT) C =================== C---- write prediction + header IF (MODESECSTRON(1:9).EQ.'SECONDARY') THEN C ================ C CALL WRTPRED(6) CALL WRTPRED(KOUT) C ================ ELSEIF (MODESECSTRON.EQ.'EXPOSURE') THEN C =============== CALL WRTEXP(KOUT) C =============== END IF CALL WRTE(KOUT) CALL WRTF(KOUT) C---- for i/o checks: WRITE(KOUT,'(A3)')'END' C-------------------------------------------------- C---- search for potential trans-membrane regions - C-------------------------------------------------- C---- count hydrophobic residues C ========================= CALL SCOUNT_HYDROPHOB(KOUT) C ========================= CLOSE(KOUT) C---- close FILEPRED C-------------------------------------------------- C---- write real outputs of prediction into file -- C-------------------------------------------------- IF (LWRTOUTPUT .EQV. .TRUE.) THEN C------- write into fileotpredtest IEND= FILEN_STRING(FILEOUTPUT) CHFILE= ' ' CHFILE(1:IEND)=FILEOUTPUT(1:IEND) CALL SFILEOPEN(KOUT,CHFILE(1:IEND),'UNKNOWN',222,' ') C CALL SFILEOPEN(KOUT,FILEOUTPUT,'UNKNOWN',222,' ') C ================== CALL DATAOT_OUTPUT(KOUT) C ================== CLOSE(KOUT) END IF C-------------------------------------------------- C---- write format for interchange C-------------------------------------------------- IF (LRDB .EQV. .TRUE.) THEN C------- write into fileotpredtest IEND= FILEN_STRING(FILE_RDB) CHFILE= ' ' CHFILE(1:IEND)=FILE_RDB(1:IEND) CALL SFILEOPEN(KOUT,CHFILE(1:IEND),'UNKNOWN',222,' ') C CALL SFILEOPEN(KOUT,FILE_RDB,'UNKNOWN',222,' ') IF (MODESECSTRON.EQ.'SECONDARY') THEN C ================== CALL DATAOT_RDBSEC(KOUT) C ================== ELSEIF (MODESECSTRON.EQ.'EXPOSURE') THEN C ================== CALL DATAOT_RDBEXP(KOUT) C ================== ELSEIF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN C ================== CALL DATAOT_RDBHTM(KOUT) C ================== END IF CLOSE(KOUT) END IF END ***** end of DATAOT ***** ------------------------------------------------------------------ ***** SUB DATAOT_OUTPUT ***** ------------------------------------------------------------------ C---- C---- NAME : DATAOT_OUTPUT C---- ARG : C---- DES : The real values of a prediction are written into a file: C---- DES : name.OUTPUT C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The real values of a prediction are written into * * -------- a file: name.OUTPUT * * in variables: kunit * * out variables: OUTPUT(itsec,mue), OUTBINCHAR(mue) * * called by: DATAOT * *----------------------------------------------------------------------* SUBROUTINE DATAOT_OUTPUT(KUNIT) C---- global parameters * INCLUDE 'phdParameter.f' C---- local variables * INTEGER KUNIT,ITSEC,MUE CHARACTER*1 INTERCHAR ******------------------------------*-----------------------------****** C---- write real output values WRITE(KUNIT,'(T10,A,T40,I5)')'number of residues:',NUMRES WRITE(KUNIT,'(T10,A,T40,I5)')'number of sec str:',NSECEL IF (NSECEL.EQ.3) THEN WRITE(KUNIT,'(T10,3A6,T40,A6)') + 'out H ','out E ','out L',' WTO ' ELSE WRITE(KUNIT,'(T10,4A6,T40,I6)') + 'out H ','out E ','out T ','out L ',' WTO ' END IF DO MUE=1,NUMRES C------- convert loop from blank to "L" IF ((OUTBINCHAR(MUE).NE.'H').AND.(OUTBINCHAR(MUE).NE.'E').AND. + (OUTBINCHAR(MUE).NE.'T')) THEN INTERCHAR='L' ELSE INTERCHAR=OUTBINCHAR(MUE) END IF IF (NSECEL.EQ.3) THEN WRITE(KUNIT,'(T10,3F6.2,T40,A6)') + (OUTPUT(ITSEC,MUE),ITSEC=1,NSECEL),INTERCHAR ELSE WRITE(KUNIT,'(T10,4F6.2,T40,A6)') + (OUTPUT(ITSEC,MUE),ITSEC=1,NSECEL),INTERCHAR END IF END DO END ***** end of DATAOT_OUTPUT ***** ------------------------------------------------------------------ ***** SUB DATAOT_RDBSEC ***** ------------------------------------------------------------------ C---- C---- NAME : DATAOT_RDBSEC C---- ARG : C---- DES : The prediction is written into a file to merge secondary C---- DES : structure and exposure prediction by calling perl script. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The prediction is written into a file to merge * * -------- secondary structure and exposure prediction by * * the perl script calling phd. * * in variables: KUNIT * * called by: DATAOT * *----------------------------------------------------------------------* SUBROUTINE DATAOT_RDBSEC(KUNIT) C---- global parameters * INCLUDE 'phdParameter.f' INTEGER FILEN_STRING C---- local variables * INTEGER KUNIT,ITSEC,MUE,IT CHARACTER*1 XC,INTERDSSP,INTERPRED CHARACTER*222 CTMP ******------------------------------*-----------------------------****** C---- default XC=CHAR(9) C---- header WRITE(KUNIT,'(A)')'# Perl-RDB' WRITE(KUNIT,'(A)')'# ' WRITE(KUNIT,'(A)')'# PHDsec: secondary structure prediction' CTMP=PROTNAME(1) WRITE(KUNIT,'(A)')'# ' WRITE(KUNIT,'(A,T19,A)') + '# PDBID :',CTMP(1:FILEN_STRING(CTMP)) WRITE(KUNIT,'(A,T19,I5)')'# LENGTH :',NUMRES WRITE(KUNIT,'(A)')'# NOTATION No : residue number ' WRITE(KUNIT,'(A)')'# NOTATION AA : amino acid one letter code' IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(A)') + '# NOTATION OHEL : observed secondary structure' END IF WRITE(KUNIT,'(A)') + '# NOTATION PHEL : predicted secondary structure' WRITE(KUNIT,'(A)')'# NOTATION PHEL : '// + 'H=helix, E=strand, L=non-regular (taken from DSSP)' WRITE(KUNIT,'(A)')'# NOTATION RI_S : '// + 'reliability of secondary structure prediction , 0-9' WRITE(KUNIT,'(A)')'# NOTATION pH : '// + 'probability of predicting helix, 0-9' WRITE(KUNIT,'(A)') + '# NOTATION pE : probability of predicting strand' WRITE(KUNIT,'(A)') + '# NOTATION pL : probability of predicting loop' WRITE(KUNIT,'(A)') + '# NOTATION OtH : network output for helix, 0-100' WRITE(KUNIT,'(A)')'# NOTATION OtE : network output for strand' WRITE(KUNIT,'(A)')'# NOTATION OtL : network output for loop' WRITE(KUNIT,'(A)')'# ' C---- column names and width IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(A2,A,A2,A,2(A4,A),A4,3(A,A2),3(A,A3))') + 'No',XC,'AA',XC,'OHEL',XC,'PHEL',XC,'RI_S', + XC,'pH',XC,'pE',XC,'pL',XC,'OtH',XC,'OtE',XC,'OtL' WRITE(KUNIT,'(A2,3(A,A1),4(A,A2),3(A,A2))') + '4N',(XC,'1',it=1,3),(XC,'1N',IT=1,4),(XC,'3N',IT=1,3) ELSE WRITE(KUNIT,'(A2,A,A2,A,A4,A,A4,3(A,A2),3(A,A3))') + 'No',XC,'AA',XC,'PHEL',XC,'RI_S', + XC,'pH',XC,'pE',XC,'pL',XC,'OtH',XC,'OtE',XC,'OtL' WRITE(KUNIT,'(A2,2(A,A1),4(A,A2),3(A,A2))') + '4N',(XC,'1',it=1,2),(XC,'1N',IT=1,4),(XC,'3N',IT=1,3) END IF C---- prediction: number, sequence, DSSP, prediction, Rel, Prob(H,E,L) DO MUE=1,NUMRES IF (LDSSPREAD .EQV. .TRUE.) THEN INTERDSSP=CONVSECSTR(MUE) ELSE INTERDSSP='U' END IF IF ( (OUTBINCHARFIL(MUE).NE.'H').AND. + (OUTBINCHARFIL(MUE).NE.'G').AND. + (OUTBINCHARFIL(MUE).NE.'B').AND. + (OUTBINCHARFIL(MUE).NE.'E') ) THEN INTERPRED='L' ELSE INTERPRED=OUTBINCHARFIL(MUE) END IF IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(I4,A,A1,A,2(A1,A),I1,3(A,I1),3(A,I3))')MUE,XC, + RESNAME(MUE),XC,INTERDSSP,XC,INTERPRED,XC,RELIND(MUE), + (XC,OUTBINPROB(ITSEC,MUE),ITSEC=1,NSECEL), + (XC,INT(100*OUTPUT(ITSEC,MUE)),ITSEC=1,NSECEL) ELSE WRITE(KUNIT,'(I4,A,A1,A,A1,A,I1,3(A,I1),3(A,I3))')MUE,XC, + RESNAME(MUE),XC,INTERPRED,XC,RELIND(MUE), + (XC,OUTBINPROB(ITSEC,MUE),ITSEC=1,NSECEL), + (XC,INT(100*OUTPUT(ITSEC,MUE)),ITSEC=1,NSECEL) END IF END DO END ***** end of DATAOT_RDBSEC ***** ------------------------------------------------------------------ ***** SUB DATAOT_RDBEXP ***** ------------------------------------------------------------------ C---- C---- NAME : DATAOT_RDBEXP C---- ARG : C---- DES : The prediction is written into a file to merge secondary C---- DES : structure and exposure prediction by calling perl script. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The prediction is written into a file to merge * * -------- secondary structure and exposure prediction by * * the perl script calling phd. * * in variables: KUNIT * * called by: DATAOT * *----------------------------------------------------------------------* SUBROUTINE DATAOT_RDBEXP(KUNIT) C---- global parameters * INCLUDE 'phdParameter.f' C---- local function INTEGER FILEN_STRING REAL FR_REXP_TO_EXP,FR_EXP_TO_REXP CHARACTER*1 FC_REXP_TO_3STCHAR,FC_REXPI_TO_3STCHAR C---- local variables * INTEGER KUNIT,ITEXP,MUE, + OBSEXP,OBSREXP,PHDEXP,PHDREXP,IT,PHDBINLOC(1:NUMOUTMAX) CHARACTER*1 XC,OBSCHAR,PHDCHARLOC CHARACTER*222 CTMP ******------------------------------*-----------------------------****** C---- default XC=CHAR(9) C---- header WRITE(KUNIT,'(A)')'# Perl-RDB' WRITE(KUNIT,'(A)') + '# PHDacc: solvent accessibility prediction' WRITE(KUNIT,'(A)')'# ' CTMP=PROTNAME(1) WRITE(KUNIT,'(A,T19,A)') + '# PDBID :',CTMP(1:FILEN_STRING(CTMP)) WRITE(KUNIT,'(A,T19,I5)')'# LENGTH :',NUMRES WRITE(KUNIT,'(A)')'# NOTATION No : residue number ' WRITE(KUNIT,'(A)')'# NOTATION AA : amino acid one letter code' IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(A)')'# NOTATION OACC : '// + 'observed accessible surface area (from DSSP), 0-300 A' END IF WRITE(KUNIT,'(A)')'# NOTATION PACC : '// + 'predicted accessible surface area, 0-300 A' IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(A)')'# NOTATION OREL : '// + 'observed relative accessible surface area, 0-100' END IF WRITE(KUNIT,'(A)')'# NOTATION PREL : '// + 'predicted relative accessible surface area' WRITE(KUNIT,'(A)') + '# NOTATION RI_A : reliability of accessibility prediction, 0-9' IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(A)')'# NOTATION Obie : observed exposure state' END IF WRITE(KUNIT,'(A)')'# NOTATION Pbie : predicted exposure state' WRITE(KUNIT,'(A)') + '# NOTATION Pbie : b=buried, i=intermediate, e=exposed' WRITE(KUNIT,'(A)')'# NOTATION Ot(n): '// + 'network output for relative accessibility = n*n%, 0-100' WRITE(KUNIT,'(A)')'# ' C---- column names and width IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(A2,A,A2,7(A,A4),10(A,A2,I1))') + 'No',XC,'AA',XC,'OACC',XC,'PACC',XC,'OREL',XC,'PREL',XC, + 'RI_A',XC,'Obie',XC,'Pbie',(XC,'Ot',(IT-1),IT=1,10) WRITE(KUNIT,'(A2,A,A1,4(A,A2),A,A2,2(A,A1),10(A,A3))') + '4N',XC,'1',(XC,'3N',IT=1,4),XC,'1N', + (XC,'1',IT=1,2),(XC,'3N',IT=1,10) ELSE WRITE(KUNIT,'(A2,A,A2,4(A,A4),10(A,A2,I1))') + 'No',XC,'AA',XC,'PACC',XC,'PREL',XC, + 'RI_A',XC,'Pbie',(XC,'Ot',(IT-1),IT=1,10) WRITE(KUNIT,'(A2,A,A1,2(A,A2),A,A2,A,A1,10(A,A3))') + '4N',XC,'1',(XC,'3N',IT=1,2),XC,'1N', + XC,'1',(XC,'3N',IT=1,10) END IF C---- prediction: number, sequence, DSSP, prediction, Rel, Prob(H,E,L) DO MUE=1,NUMRES IF (LFILTER .EQV. .TRUE.) THEN PHDREXP=INT(100*OUTEXPFIL(MUE)) PHDEXP=INT(FR_REXP_TO_EXP(OUTEXPFIL(MUE),RESNAME(MUE))) DO ITEXP=1,NUMOUT PHDBINLOC(ITEXP)=INT(100*OUTFIL(ITEXP,MUE)) END DO PHDCHARLOC=OUTBINCHARFIL(MUE) ELSE PHDREXP=INT(100*OUTEXP(MUE)) PHDEXP=INT(FR_REXP_TO_EXP(OUTEXP(MUE),RESNAME(MUE))) DO ITEXP=1,NUMOUT PHDBINLOC(ITEXP)=INT(100*OUTPUT(ITEXP,MUE)) END DO PHDCHARLOC=OUTBINCHAR(MUE) END IF IF (LDSSPREAD .EQV. .TRUE.) THEN OBSEXP=RESACC(MUE) OBSREXP=INT(100*FR_EXP_TO_REXP(OBSEXP,RESNAME(MUE))) C ------------------ C version: real value (0 - 1) C OBSCHAR=FC_REXP_TO_3STCHAR(DESEXP(MUE), C + THREXP3ST(2),THREXP3ST(3)) C version: integer value (0 - 100) OBSCHAR=FC_REXPI_TO_3STCHAR(INT(100*DESEXP(MUE)), + THREXP3STI(2),THREXP3STI(3)) C ------------------ ELSE OBSEXP= 0 OBSREXP=0 OBSCHAR='U' END IF IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(I4,A,A1,A,4(I3,A),I1,2(A,A1),10(A,I3))') + MUE,XC,RESNAME(MUE),XC,OBSEXP,XC,PHDEXP,XC, + OBSREXP,XC,PHDREXP,XC,RELIND(MUE), + XC,OBSCHAR,XC,PHDCHARLOC, + (XC,PHDBINLOC(ITEXP),ITEXP=1,NUMOUT) ELSE WRITE(KUNIT,'(I4,A,A1,A,2(I3,A),I1,A,A1,10(A,I3))') + MUE,XC,RESNAME(MUE),XC,PHDEXP,XC, + PHDREXP,XC,RELIND(MUE),XC,PHDCHARLOC, + (XC,PHDBINLOC(ITEXP),ITEXP=1,NUMOUT) END IF END DO END ***** end of DATAOT_RDBEXP ***** ------------------------------------------------------------------ ***** SUB DATAOT_RDBHTM ***** ------------------------------------------------------------------ C---- C---- NAME : DATAOT_RDBHTM C---- ARG : C---- DES : The prediction is written into a RDB file. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The prediction is written into a RDB file. * * in variables: KUNIT * * called by: DATAOT * *----------------------------------------------------------------------* SUBROUTINE DATAOT_RDBHTM(KUNIT) C---- global parameters * INCLUDE 'phdParameter.f' C---- local functions INTEGER FILEN_STRING C---- local variables * INTEGER KUNIT,ITSEC,MUE,IT CHARACTER*1 XC,INTERDSSP,INTERPRED CHARACTER*222 CTMP ******------------------------------*-----------------------------****** C---- default XC=CHAR(9) C---- header WRITE(KUNIT,'(A)')'# Perl-RDB' WRITE(KUNIT,'(A)')'# ' WRITE(KUNIT,'(A)')'# PHDhtm: prediction of helical '// + 'transmembrane regions' WRITE(KUNIT,'(A)')'# ' CTMP=PROTNAME(1) WRITE(KUNIT,'(A,T19,A)') + '# PDBID :',CTMP(1:FILEN_STRING(CTMP)) WRITE(KUNIT,'(A,T19,I5)')'# LENGTH :',NUMRES WRITE(KUNIT,'(A)')'# NOTATION No : residue number ' WRITE(KUNIT,'(A)')'# NOTATION AA : amino acid one letter code' IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(A)')'# NOTATION OHL : observed transmembrane '// + 'helices' END IF WRITE(KUNIT,'(A)') + '# NOTATION PHL : predicted transmembrane helices' WRITE(KUNIT,'(A)')'# NOTATION PHL : '// + 'H=helical membrane, L=no helical transmembrane' WRITE(KUNIT,'(A)')'# NOTATION RI_S : '// + 'reliability of secondary structure prediction , 0-9' WRITE(KUNIT,'(A)')'# NOTATION pH : '// + 'probability of predicting helix, 0-9' WRITE(KUNIT,'(A)') + '# NOTATION pL : probability of predicting loop' WRITE(KUNIT,'(A)') + '# NOTATION OtH : network output for helix, 0-100' WRITE(KUNIT,'(A)')'# NOTATION OtL : network output for loop' WRITE(KUNIT,'(A)')'# ' C---- column names and width IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(A2,A,A2,A,2(A4,A),A4,2(A,A2),2(A,A3))') + 'No',XC,'AA',XC,'OHL ',XC,'PHL ',XC,'RI_S', + XC,'pH',XC,'pL',XC,'OtH',XC,'OtL' WRITE(KUNIT,'(A2,3(A,A1),3(A,A2),2(A,A2))') + '4N',(XC,'1',it=1,3),(XC,'1N',IT=1,3),(XC,'3N',IT=1,2) ELSE WRITE(KUNIT,'(A2,A,A2,A,A4,A,A4,2(A,A2),2(A,A3))') + 'No',XC,'AA',XC,'PHL ',XC,'RI_S', + XC,'pH',XC,'pL',XC,'OtH',XC,'OtL' WRITE(KUNIT,'(A2,2(A,A1),3(A,A2),2(A,A2))') + '4N',(XC,'1',it=1,2),(XC,'1N',IT=1,3),(XC,'3N',IT=1,2) END IF C---- prediction: number, sequence, DSSP, prediction, Rel, Prob(H,E,L) DO MUE=1,NUMRES IF (LDSSPREAD .EQV. .TRUE.) THEN INTERDSSP=CONVSECSTR(MUE) ELSE INTERDSSP='U' END IF IF ( (OUTBINCHARFIL(MUE).NE.'H').AND. + (OUTBINCHARFIL(MUE).NE.'G').AND. + (OUTBINCHARFIL(MUE).NE.'B').AND. + (OUTBINCHARFIL(MUE).NE.'E') ) THEN INTERPRED='L' ELSE INTERPRED=OUTBINCHARFIL(MUE) END IF IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(I4,A,3(A1,A),I1,2(A,I1),2(A,I3))')MUE,XC, + RESNAME(MUE),XC,INTERDSSP,XC,INTERPRED,XC,RELIND(MUE), + (XC,OUTBINPROB(ITSEC,MUE),ITSEC=1,NSECEL), + (XC,INT(100*OUTPUT(ITSEC,MUE)),ITSEC=1,NSECEL) ELSE WRITE(KUNIT,'(I4,A,2(A1,A),I1,2(A,I1),2(A,I3))')MUE,XC, + RESNAME(MUE),XC,INTERPRED,XC,RELIND(MUE), + (XC,OUTBINPROB(ITSEC,MUE),ITSEC=1,NSECEL), + (XC,INT(100*OUTPUT(ITSEC,MUE)),ITSEC=1,NSECEL) END IF END DO END ***** end of DATAOT_RDBHTM ***** ------------------------------------------------------------------ ***** SUB EVALDSSP ***** ------------------------------------------------------------------ C---- C---- NAME : EVALDSSP C---- ARG : C---- DES : The pay-off of the perceptron, i.e. its success is C---- DES : evaluated C---- DES : by computing certain measures of quality of the C---- DES : prediction. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The pay-off of the perceptron, i.e. its success * * -------- is evaluated by computing certain measures of * * quality of the prediction. * * called by: MAIN * * calling: EVALSEC, EVALEXP * *----------------------------------------------------------------------* SUBROUTINE EVALDSSP C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE ******------------------------------*-----------------------------****** C--------------------------------------------------- C---- convert secondary structure 8 -> 3 C--------------------------------------------------- DO MUE=1,NUMRES IF (RESSECSTR(MUE).EQ.'G') THEN CONVSECSTR(MUE)='H' ELSEIF ((RESSECSTR(MUE).EQ.'I').OR. + (RESSECSTR(MUE).EQ.'S').OR. + (RESSECSTR(MUE).EQ.'B').OR. + (RESSECSTR(MUE).EQ.'T').OR. + (RESSECSTR(MUE).EQ.'L')) THEN CONVSECSTR(MUE)=' ' ELSE CONVSECSTR(MUE)=RESSECSTR(MUE) END IF END DO C--------------------------------------------------- C---- secondary structure prediction ----- C--------------------------------------------------- IF (MODESECSTRON(1:9).EQ.'SECONDARY') THEN write(6,*)'--- now entering: EVALSEC' C ============ CALL EVALSEC C ============ C--------------------------------------------------- C---- prediction of solvent exposure prediction --- C--------------------------------------------------- ELSEIF (MODESECSTRON.EQ.'EXPOSURE') THEN write(6,*)'--- now entering: EVALEXP' C ============ CALL EVALEXP C ============ END IF END ***** end of EVALDSSP ***** ------------------------------------------------------------------ ***** SUB EVALSEC ***** ------------------------------------------------------------------ C---- C---- NAME : EVALSEC C---- ARG : C---- DES : Secondary structure prediction accuracy. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The pay-off of the perceptron, i.e. its success * * -------- is evaluated by computing certain measures of * * quality of the prediction * * input variables:CONVSECSTR, OUTBINCHAR * * output variab.: MATNUM, MATLEN, MATLENDIS * * --------------- RMATQOFDSSP, RMATQOFPRED, Q3, SQ, CORR, INFO * * called by: EVALDSSP * * calling: lib-prot.f: * * SEVALPO, SEVALQUO, * * procedure: See SEVALPO, SEVALQUO, * *----------------------------------------------------------------------* SUBROUTINE EVALSEC C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE,DEVNOM,NSECEL_LOC CHARACTER*3 TXT3 LOGICAL LWRITE ******------------------------------*-----------------------------****** * MUE,NUE,ITSEC,ITSEC2,ITER,ITHISTO,ITFILES iteration variables * * CORR(i) correlation for class i, (Mathews) * * MATLEN(i,j) matrix with the lengths of the elements: * * i=1,4 => H,E,C,all * * j=1 => number of elements DSSP * * j=2 => number of elements PRED * * j=2 => summed length of all elements for DSSP * * j=2 => summed length of all elements for PRED * * MATLENDIS(i,j) gives the distribution of the elements * * i=1,50=> for histogram (lengths 1-50) * * j=1,3 => H,E,C for DSSP * * j=4,6 => H,E,C for PRED * * MATNUM(i,j) the number of residues in a certain secondary * * structure, i labels DSSP assignment, i.e. all * * numbers with i=1 are according to DSSP helices, * * j labels the prediction. That means, e.g.: * * MATNUM(1,1) are all DSSP helices predicted to be * * a helix,MATNUM(1,2) those DSSP helices predicted * * as strands and MATNUM(1,4) all DSSP helices,resp.* * MATNUM(4,4) all residues predicted. * * RMATQOFDSSP(i,j) stores according to the same scheme as MATNUM * * the percentages of residues predicted divided by * * the numbers of DSSP (note no element (4,4) ) * * RMATQOFPRED(i,j)same as previous but now percentages of prediction * Q3 =properly predicted for all classes/all residues * * SQ first divide predicted/DSSP in each class then * * sum all classes and divide by e.g. 3 * ******------------------------------*-----------------------------****** C---- blow up states for TM prediction IF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN NSECEL_LOC=3 ELSE NSECEL_LOC=NSECEL END IF C---- evaluate filtered version IF (.NOT.LFILTER) THEN DO MUE=1,NUMRES OUTBINCHARFIL(MUE)=OUTBINCHAR(MUE) END DO END IF DO MUE=(NUMRES+1),NUMRESMAX OUTBINCHARFIL(MUE)='x' CONVSECSTR(MUE)='x' END DO C---- evaluating the pay-off numbers C ============ CALL SEVALPO(NSECEL_LOC,NUMOUTMAX,NUMRES,NUMRESMAX, + CONVSECSTR,OUTBINCHARFIL, + MATNUM,RMATQOFDSSP,RMATQOFPRED,Q3,SQ,CORR) C ============ C---- compute lengths of secondary structure elements C ============= CALL SEVALLEN(NSECEL_LOC,NUMOUTMAX,NUMRES,NUMRESMAX, + 50,NHISTOMAX,RESSECSTR,OUTBINCHARFIL,MATLEN,MATLENDIS) C ============= TITLE(1:8)='jury on ' C ---------------- CALL SINTTOCHAR(NUMNETJURY,TXT3) C ---------------- TITLE(9:11)=TXT3 TITLE(12:20)='nets. ' LWRITE=.FALSE. DEVNOM=50 C ============== IF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN WRITE(6,*)'--- skip SEVALLEN for htm' C CALL SEVALSEG(6,LWRITE,PROTNAME(1), C + NSECEL_LOC,NUMOUTMAX,NUMRES,NUMRESMAX,1, C + CONVSECSTR,OUTBINCHARFIL,2,NUMSEGOVERL, C + COUNTSEGMAT,QLOV,QSOV,QFOV,DEVNOM,2) ELSE C ============= CALL SEVALSEG(6,LWRITE,PROTNAME(1), + NSECEL_LOC,NUMOUTMAX,NUMRES,NUMRESMAX,1, + CONVSECSTR,OUTBINCHARFIL,2,NUMSEGOVERL, + COUNTSEGMAT,QLOV,QSOV,QFOV,DEVNOM,2) C ============== END IF C---- reconvert 'L' -> ' ' DO MUE=1,NUMRES IF (OUTBINCHAR(MUE).EQ.'L') THEN OUTBINCHAR(MUE)=' ' END IF END DO END ***** end of EVALSEC ***** ------------------------------------------------------------------ ***** SUB EVALEXP ***** ------------------------------------------------------------------ C---- C---- NAME : EVALEXP C---- ARG : C---- DES : Solvent accessibility prediction accuracy. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Evaluates the prediction of solvent exposure. * * const. passed: NUMRESMAX, NUMRES, * * var. passed: in: RESACC, RESNAME, OUTEXP * * ------------ -> out: DESEXP, DSSPVEC_I2, PREDVEC_I2, * * EXP_NOINBIN, * * OBS_NO2ST, *_NO3ST, *_NO10ST, * * EXP_NO2ST, *_NO3ST, *_NO10ST, EXP_CORR * * var. read: THREXP2ST, THREXP3ST * * ext. SBR: lib-prot.f: SEXP_NOINBIN_2VEC, SEXP_NOINSTATES * * ext. function lib-comp.f: FRCORRVEC_REAL4 * * ------------- lib-prot.f: FR_EXP_TO_REXP * * called by: EVALDSSP * * calling: *----------------------------------------------------------------------* SUBROUTINE EVALEXP C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local function REAL FR_EXP_TO_REXP,FRCORRVEC_REAL4 C---- local variables INTEGER MUE ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- convert exposure to bins 0-9 C-------------------------------------------------- DO MUE=1,NUMRES C -------------- DESEXP(MUE)=FR_EXP_TO_REXP(RESACC(MUE),RESNAME(MUE)) C -------------- DSSPVEC_I2(MUE)=INT2(MIN(9.,SQRT(100*DESEXP(MUE)))) IF (LFILTER .EQV. .TRUE.) THEN PREDVEC_I2(MUE)=INT2(MIN(9.,SQRT(100*OUTEXPFIL(MUE)))) ELSE PREDVEC_I2(MUE)=INT2(MIN(9.,SQRT(100*OUTEXP(MUE)))) END IF END DO C-------------------------------------------------- C---- compute matrix of bin identities C-------------------------------------------------- C ====================== CALL SEXP_NOINBIN_2VEC(NUMRESMAX,NUMRES,1, + DSSPVEC_I2,2,PREDVEC_I2,3,EXP_NOINBIN,3) C ====================== C-------------------------------------------------- C---- evaluate correct predictions per state C-------------------------------------------------- C ==================== CALL SEXP_NOINSTATES(EXP_NOINBIN,T2,T3A,T3B,1, + OBS_NOIN2ST,OBS_NOIN3ST,OBS_NOIN10ST,2, + EXP_NOIN2ST,EXP_NOIN3ST,EXP_NOIN10ST,2) C ==================== C-------------------------------------------------- C---- evaluate correlation C-------------------------------------------------- C --------------- EXP_CORR=FRCORRVEC_REAL4(NUMRESMAX,NUMRES,DESEXP,OUTEXP,1.) C --------------- END ***** end of EVALEXP ***** ------------------------------------------------------------------ ***** SUB EVALOUTBINPROB ***** ------------------------------------------------------------------ C---- C---- NAME : EVALOUTBINPROB C---- ARG : C---- DES : The real output values are used to compute the C---- DES : probability C---- DES : of the assignment to either secondary structure. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The real output values are used to compute the * * -------- probability of the assignment to either secondary* * structure. * * in variables: OUTPUT * * out variables: OUTBINPROB * * called by: NETWORK * * procedure: The real values are projected onto a grid of 0-9 * * ---------- OUTBINPROB(i)=ngrid, if: * * OUTPUT(i) * * ----------------- > 0.ngrid and < 0.(ngrid-1) * * sum/i {output(i)} * *----------------------------------------------------------------------* SUBROUTINE EVALOUTBINPROB C---- global parameters * INCLUDE 'phdParameter.f' C---- local variables * INTEGER ITOUT,ITOUT2,MUE,ITGRID REAL SUM LOGICAL LFOUND ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- compute probabilities of assignment ----- C-------------------------------------------------- DO MUE=1,NUMRES C------- compute sum SUM=0. DO ITOUT=1,NUMOUT SUM=SUM+OUTPUT(ITOUT,MUE) END DO C------- mind potential division by zero IF (SUM.LT.0.0001) THEN SUM=1 DO ITOUT=1,NUMOUT OUTPUT(ITOUT,MUE)=0 END DO END IF C------- now project onto grid: DO ITOUT=1,NUMOUT LFOUND=.FALSE. DO ITGRID=1,10 IF ( (LFOUND.EQV. .FALSE.).AND. + ((OUTPUT(ITOUT,MUE)/SUM).GE.((ITGRID-1)/10.)).AND. + ((OUTPUT(ITOUT,MUE)/SUM).LE.(ITGRID/10.)) ) THEN OUTBINPROB(ITOUT,MUE)=ITGRID-1 LFOUND=.TRUE. END IF END DO IF (LFOUND.EQV. .FALSE.) THEN WRITE(6,'(T2,A,T10,A,T60,I3)')'***', + 'ERROR in EVALOUTBINPROB: non found for numout=', + NUMOUT WRITE(6,'(T2,A,T10,A,T16,I5,T25,A,T35,3F5.2, + T55,A,T65,F5.2)')'***','mue=',MUE,'OUTPUT:', + (OUTPUT(ITOUT2,MUE),ITOUT2=1,NUMOUT),'sum=',SUM END IF END DO END DO C---- end of loop over mue=1,numres END ***** end of EVALOUTBINPROB ***** ------------------------------------------------------------------ ***** SUB EVALRELIND ***** ------------------------------------------------------------------ C---- C---- NAME : EVALRELIND C---- ARG : C---- DES : Computation of reliability indices. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Computation of reliability indices. * * called by: NETWORK * * calling: EVALRELSEC, EVALRELEXP, EVALRELTM * *----------------------------------------------------------------------* SUBROUTINE EVALRELIND(LFILTERLOC) C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables LOGICAL LFILTERLOC ******------------------------------*-----------------------------****** ******------------------------------*-----------------------------****** C--------------------------------------------------- C---- secondary structure prediction ----- C--------------------------------------------------- IF (MODESECSTRON.EQ.'SECONDARY') THEN C =============== CALL EVALRELSEC C =============== C--------------------------------------------------- C---- prediction of solvent exposure prediction --- C--------------------------------------------------- ELSEIF (MODESECSTRON.EQ.'EXPOSURE') THEN C =============== CALL EVALRELEXP(LFILTERLOC) C =============== C--------------------------------------------------- C---- prediction of trans-membrane regions --- C--------------------------------------------------- ELSEIF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN C =============== CALL EVALRELHTM(LFILTERLOC) C =============== END IF END ***** end of EVALRELIND ***** ------------------------------------------------------------------ ***** SUB EVALRELSEC ***** ------------------------------------------------------------------ C---- C---- NAME : EVALRELSEC C---- ARG : C---- DES : Computation of the reliability of the assignment of C---- DES : secondary C---- DES : structure according to the real values of the network C---- DES : output. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Computation of the reliability of the assignment * * -------- of secondary structure according to the real * * values of the output of a network. * * in parameter: NSECEL,NUMRESMAX * * in variables: NUMRES, OUTPUT * * out variables: MAXPOS, NUMRELIND, RELIND * * called from: NETWORK * * SBRs calling: * * from personal libraries: * * lib-comp.f: SRMAX1, SISTZ1, SISTZ2, SRSTZ1, * * lib-unix.f: SFILEOPEN * *----------------------------------------------------------------------* SUBROUTINE EVALRELSEC C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE,ITSEC,DIFF INTEGER*2 ITER,INTERMAXPOS C---- ********* INTEGER*2 MAXPOS(1:NUMRESMAX),SNDMAXPOS C---- ********* REAL INTERMAXVAL,INTERMAX(1:NUMOUTMAX) LOGICAL LHELP ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- compute the reliability index (first: maxima) C-------------------------------------------------- C---------------------------------------- C---- compute positions of maxima ----- C---------------------------------------- DO MUE=1,NUMRES C security set zero CALL SRSTZ1(INTERMAX,NUMOUTMAX) C array -> vector DO ITSEC=1,NSECEL INTERMAX(ITSEC)=REAL(OUTPUT(ITSEC,MUE))/100. END DO C get maximum CALL SRMAX1(INTERMAX,NUMOUTMAX,INTERMAXVAL,INTERMAXPOS) MAXPOS(MUE)=INTERMAXPOS C get second largest value INTERMAX(INTERMAXPOS)=0 CALL SRMAX1(INTERMAX,NUMOUTMAX,INTERMAXVAL,INTERMAXPOS) SNDMAXPOS=INTERMAXPOS C---------------------------------------- C------- compute reliability index ------ C---------------------------------------- DIFF=INT(100*(OUTPUT(MAXPOS(MUE),MUE)-OUTPUT(SNDMAXPOS,MUE))) C------- consistency IF (DIFF.LT.0) THEN WRITE(6,'(T2,A,T10,A,T60,I5)')'***', + 'ERROR IN EVALRELSEC: difference negative =',DIFF WRITE(6,'(T2,A,T10,A,T20,I3,A,T35,I3,T45,3I4)')'***', + 'pos max: ',MAXPOS(MUE),'snd max:',SNDMAXPOS, + (OUTPUT(ITSEC,MUE),ITSEC=1,NSECEL) WRITE(6,'(T2,A,T10,A,T20,I5,A)')'***', + 'for mue =',MUE,'stopped 28-10-92-1' STOP END IF C------- search intervalls IF (DIFF.EQ.0) THEN RELIND(MUE)=0 ELSEIF (DIFF.GE.90) THEN RELIND(MUE)=9 ELSE LHELP=.TRUE. DO ITER=1,9 IF ((LHELP.EQV. .TRUE.) .AND. + (DIFF.GE.((ITER-1)*10)) .AND. + (DIFF.LT.(ITER*10))) THEN RELIND(MUE)=ITER LHELP=.FALSE. END IF END DO END IF C------- end of computing reliability --- C---------------------------------------- END DO C-------------------------------------------------- C---- end of computation ----- C-------------------------------------------------- END ***** end of EVALRELSEC ***** ------------------------------------------------------------------ ***** SUB EVALRELEXP ***** ------------------------------------------------------------------ C---- C---- NAME : EVALRELEXP C---- ARG : C---- DES : Computes reliability indices for the exposure prediction. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Computes the reliability indices for the * * -------- prediction of exposure. * * called by: EVALDSSP * *----------------------------------------------------------------------* SUBROUTINE EVALRELEXP(LFILTERLOC) C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local function INTEGER FIRELIND_2ND3OFF C---- local variables INTEGER MUE,ITEXP REAL OUTLOC(1:(NUMOUTMAX)) LOGICAL LFILTERLOC ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- loop over all residues ----- C-------------------------------------------------- DO MUE=1,NUMRES C ----------- CALL SRSTZ1(OUTLOC,NUMOUTMAX) C ----------- IF (LFILTERLOC .EQV. .TRUE.) THEN DO ITEXP=1,NUMOUT OUTLOC(ITEXP)=OUTFIL(ITEXP,MUE) END DO ELSE DO ITEXP=1,NUMOUT OUTLOC(ITEXP)=OUTPUT(ITEXP,MUE) END DO END IF C---------------------------------------- C------- relind C---------------------------------------- C ---------------- RELIND(MUE)=INT2(FIRELIND_2ND3OFF(NUMOUTMAX,NUMOUT,OUTLOC)) C ---------------- C write(6,*)'xx mue=',mue,' ri=',relind(mue),' fil=',LFILTERLOC END DO C-------------------------------------------------- C---- end of loop over all residues ---- C-------------------------------------------------- END ***** end of EVALRELEXP ***** ------------------------------------------------------------------ ***** SUB EVALRELHTM ***** ------------------------------------------------------------------ C---- C---- NAME : EVALRELHTM C---- ARG : C---- DES : Reliability indices for the transmembrane regions. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Computes the reliability indices for the * * -------- prediction of transmembrane regions. * * called by: EVALDSSP * *----------------------------------------------------------------------* SUBROUTINE EVALRELHTM(LFILTERLOC) C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local function INTEGER FIRELIND_2ND C---- local variables INTEGER MUE,ITEXP REAL OUTLOC(1:(NUMOUTMAX)) LOGICAL LFILTERLOC ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- loop over all residues ----- C-------------------------------------------------- DO MUE=1,NUMRES C security: set zero CALL SRSTZ1(OUTLOC,NUMOUTMAX) IF (LFILTERLOC .EQV. .TRUE.) THEN DO ITEXP=1,NUMOUT OUTLOC(ITEXP)=OUTFIL(ITEXP,MUE) END DO ELSE DO ITEXP=1,NUMOUT OUTLOC(ITEXP)=OUTPUT(ITEXP,MUE) END DO END IF C---------------------------------------- C------- relind C---------------------------------------- C ------------ RELIND(MUE)=INT2(FIRELIND_2ND(NUMOUTMAX,NUMOUT,OUTLOC,1.)) C ------------ END DO C-------------------------------------------------- C---- end of loop over all residues ---- C-------------------------------------------------- END ***** end of EVALRELHTM ***** ------------------------------------------------------------------ ***** SUB FILTER ***** ------------------------------------------------------------------ C---- C---- NAME : FILTER C---- ARG : C---- DES : The prediction is filtered (see FILTERSEC and C---- DES : FILTEREXP) C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The prediction is filtered according to: * * SECONDARY STRUCTURE prediction * * for helix of length 1,2: * * if relindex >=4 -> extend in direction of * * lowest relindex, until length =3 * * else -> cut helix (make it 'L') * * EXPOSURE prediction * * averages over groups of 3 output units * * input: OUTBINCHAR, RELIND, OUTPUT * * output: OUTEXPFIL, OUTFIL, OUTBINCHARFIL * * called by: MAIN * * calling: FILTERSEC, FILTEREXP * *----------------------------------------------------------------------* SUBROUTINE FILTER C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables LOGICAL LFILTERLOC ******------------------------------*-----------------------------****** C------------------------------------------------------------- C---- secondary structure prediction ----- C------------------------------------------------------------- IF (MODESECSTRON.EQ.'SECONDARY') THEN C ============== CALL FILTERSEC C ============== ELSEIF (MODESECSTRON.EQ.'EXPOSURE') THEN C ============== CALL FILTEREXP C ============== LFILTERLOC=.TRUE. C =============== CALL EVALRELIND(LFILTERLOC) C =============== END IF END ***** end of FILTER ***** ------------------------------------------------------------------ ***** SUB FILTERSEC ***** ------------------------------------------------------------------ C---- C---- NAME : FILTERSEC C---- ARG : C---- DES : The prediction is filtered according to: for helix of C---- DES : length 1,2: C---- DES : if relindex >=4 -> extend in direction of C---- DES : lowest relindex, until length =3 C---- DES : else -> cut helix (make it 'L') C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The prediction is filtered according to: * * -------- for helix of length 1,2: * * if relindex >=4 -> extend in direction of * * lowest relindex, until length =3 * * else -> cut helix (make it 'L') * * input variables:OUTBINCHAR, RELIND * * output variab.: OUTBINCHARFIL * * called by: FILTER * *----------------------------------------------------------------------* SUBROUTINE FILTERSEC C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE,ITLEN,COUNTLEN LOGICAL FLAGINTER ******------------------------------*-----------------------------****** C---------------------------------------- C---- applying the filter -------- C---------------------------------------- C---- initially set equal filter=prediction DO MUE=1,NUMRES OUTBINCHARFIL(MUE)=OUTBINCHAR(MUE) END DO MUE=0 DO WHILE (MUE.LT.NUMRES) MUE=MUE+1 C------- boundary check IF (MUE.GT.NUMRES) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR: FILTERSEC (from phd) max number of samples exceeded!' WRITE(6,'(T2,A,T10,A,T20,I4,T28,A,T38,I6)')'***', + 'mue=',mue,'numres=',numres STOP END IF C------- look for helices IF (OUTBINCHAR(MUE).EQ.'H') THEN C---------- measure lengths of helical segments FLAGINTER=.TRUE. COUNTLEN=1 DO ITLEN=1,100 IF (FLAGINTER .EQV. .TRUE.) THEN IF ((MUE.LE.(NUMRES-ITLEN)).AND. + (OUTBINCHAR(MUE+ITLEN).EQ.'H')) THEN COUNTLEN=COUNTLEN+1 ELSE FLAGINTER=.FALSE. END IF END IF END DO C---------- helix of length < 3? IF (COUNTLEN.LT.3) THEN FLAGINTER=.TRUE. DO ITLEN=1,COUNTLEN IF ( (FLAGINTER .EQV. .TRUE.) .AND. + (RELIND(MUE+ITLEN-1).GE.4)) THEN FLAGINTER=.FALSE. END IF END DO C------------- Relind < 4 for all residues -> cut IF (FLAGINTER .EQV. .TRUE.) THEN DO ITLEN=1,COUNTLEN OUTBINCHARFIL(MUE+ITLEN-1)=' ' END DO C------------- Relind >= 4 for one residue -> elongate! ELSE DO ITLEN=1,(3-COUNTLEN) IF (MUE.LE.(NUMRES-(COUNTLEN+ITLEN))) THEN C br: hack 2000-05-31: avoid going for 0 .. IF ( (MUE.GE.2) .AND. + ((MUE-ITLEN).GT.0) ) THEN IF (RELIND(MUE+COUNTLEN-1+ITLEN) + .LT.RELIND(MUE-ITLEN)) THEN OUTBINCHARFIL(MUE+COUNTLEN-1+ITLEN)='H' COUNTLEN=COUNTLEN+1 ELSE OUTBINCHARFIL(MUE-ITLEN)='H' END IF ELSE OUTBINCHARFIL(MUE+COUNTLEN-1+ITLEN)='H' COUNTLEN=COUNTLEN+1 END IF ELSE OUTBINCHARFIL(MUE-ITLEN)='H' END IF END DO END IF END IF MUE=MUE+COUNTLEN-1 END IF END DO C---- end of FILTERSEC ----- C-------------------------------------------------- END ***** end of FILTERSEC ***** ------------------------------------------------------------------ ***** SUB FILTEREXP ***** ------------------------------------------------------------------ C---- C---- NAME : FILTEREXP C---- ARG : C---- DES : The prediction is filtered according to: averages over C---- DES : groups of 3 output units C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Filters the jury decision: averages over 3 * * -------- nearest output neighbours. * * input: OUTPUT, * * in control: NUMRES, NUMOUT, NUMOUTMAX, * * output: OUTFIL, OUTEXPFIL, OUTBINCHARFIL * * called by: FILTER * * calling: SR_FILTER_EXP, BINFIL * * lib-prot.f: SRSTZ1 * *----------------------------------------------------------------------* SUBROUTINE FILTEREXP C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE,ITEXP REAL OUTLOC(1:NUMOUTMAX),OUTLOCFIL(1:NUMOUTMAX) ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- loop over all residues C-------------------------------------------------- DO MUE=1,NUMRES DO ITEXP=1,NUMOUT OUTLOC(ITEXP)=OUTPUT(ITEXP,MUE) END DO C------- shift emphasis away from buried, by subtracting C------- from most buried state (0.04, 0.02 for 0 and 1, if >0.10) IF (LREDUCE_BURRIED .EQV. .TRUE.) THEN IF (OUTLOC(1).GT.REDUCE_MINSIZE) THEN OUTLOC(1)=OUTLOC(1)-REDUCE_STATE0 END IF IF (OUTLOC(2).GT.REDUCE_MINSIZE) THEN OUTLOC(2)=OUTLOC(2)-REDUCE_STATE1 END IF END IF C ----------- CALL SRSTZ1(OUTLOCFIL,NUMOUTMAX) C ----------- C------- nearest neighbour average C ================== CALL SR_FILTER_EXP(NUMOUTMAX,NUMOUT,OUTLOC,OUTLOCFIL) C ================== C------- store filtered output DO ITEXP=1,NUMOUT OUTFIL(ITEXP,MUE)=OUTLOCFIL(ITEXP) END DO C------- store filtered output DO ITEXP=1,NUMOUT OUTFIL(ITEXP,MUE)=OUTLOCFIL(ITEXP) END DO END DO C---- end loop over all residues C-------------------------------------------------- C-------------------------------------------------- C---- WTO decision ----- C-------------------------------------------------- C =========== CALL BINFIL C =========== END ***** end of FILTEREXP ***** ------------------------------------------------------------------ ***** SUB INIPHD ***** ------------------------------------------------------------------ C---- C---- NAME : INIPHD C---- ARG : C---- DES : The variables passed when calling phd are interpreted. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The variables passed when calling phd are * * -------- interpreted (many ifs). * *----------------------------------------------------------------------* SUBROUTINE INIPHD(NUMARGUMENTS) C---- include parameter files INCLUDE 'phdParameter.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER NUMARGUMENTS,LENTMPDIR,ITER,IHELP,IEND,IDIR CHARACTER*222 TMPDIR,TMPLIST,INTERNAME,TXT80 LOGICAL LDEFAULT,LHELP,LOK,LFILE_PRED_DONE,LFILE_RDB_DONE ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- defaults C-------------------------------------------------- IEND= 0 LFILE_PRED_DONE=.FALSE. LFILE_RDB_DONE= .FALSE. FILEPRED= ' ' FILE_RDB= ' ' FILEOUTPUT= ' ' INTERNAME= ' ' C-------------------------------------------------- C---- arguments passed C-------------------------------------------------- C LHELP=.FALSE. LHELP=.TRUE. IF (LHELP .EQV. .TRUE.) THEN WRITE(6,'(T2,A3)')'---' WRITE(6,'(T2,A3,T10,A)')'---', + 'Arguments given for calling FORTRAN program phd:' DO ITER=1,NUMARGUMENTS WRITE(6,'(A,T10,I3,T15,a1,A,A1)')' --- Arg ',ITER,'|', + CHAR_ARG_READ(ITER)(1:FILEN_STRING(CHAR_ARG_READ(ITER))),'|' END DO END IF C-------------------------------------------------- C---- arg 2: read machine readable? C-------------------------------------------------- IF ( (NUMARGUMENTS.GE.2).AND. + ((CHAR_ARG_READ(2).EQ.'MACH').OR. + (CHAR_ARG_READ(2).EQ.'mach').OR. + (CHAR_ARG_READ(2).EQ.'machine').OR. + (CHAR_ARG_READ(2).EQ.'MACHINE').OR. + (CHAR_ARG_READ(2).EQ.'MACHINE_READABLE').OR. + (CHAR_ARG_READ(2).EQ.'machine_readable')) ) THEN LMACHINE_READABLE=.TRUE. ELSE LMACHINE_READABLE=.FALSE. END IF C-------------------------------------------------- C---- arg 3: write WhatIf output? C-------------------------------------------------- IF ( (NUMARGUMENTS.GE.3).AND. + ((CHAR_ARG_READ(3).EQ.'WHATIF').OR. + (CHAR_ARG_READ(3).EQ.'WhatIf').OR. + (CHAR_ARG_READ(3).EQ.'whatif').OR. + (CHAR_ARG_READ(3).EQ.'Whatif').OR. + (CHAR_ARG_READ(3).EQ.'KG').OR. + (CHAR_ARG_READ(3).EQ.'kg')) ) THEN LWHATIF=.TRUE. ELSE LWHATIF=.FALSE. END IF C-------------------------------------------------- C---- arg 4: prediction of exposure, or secondary structure? C-------------------------------------------------- IF (NUMARGUMENTS.GE.4) THEN IF ( (CHAR_ARG_READ(4)(1:3).EQ.'exp').OR. + (CHAR_ARG_READ(4)(1:3).EQ.'EXP').OR. + (CHAR_ARG_READ(4)(1:3).EQ.'acc').OR. + (CHAR_ARG_READ(4)(1:3).EQ.'ACC') ) THEN MODESECSTRON='EXPOSURE' NSECEL=0 ELSEIF ( (CHAR_ARG_READ(4)(1:3).EQ.'sec').OR. + (CHAR_ARG_READ(4)(1:3).EQ.'SEC') ) THEN MODESECSTRON='SECONDARY' NSECEL=3 ELSEIF ( (CHAR_ARG_READ(4)(1:3).EQ.'htm').OR. + (CHAR_ARG_READ(4)(1:3).EQ.'HTM') ) THEN MODESECSTRON='SECONDARY_HTM' NSECEL=2 ELSE MODESECSTRON='SECONDARY' NSECEL=3 END IF ELSE MODESECSTRON='SECONDARY' END IF C-------------------------------------------------- C---- arg 5: user phd -> LSERVER = True C-------------------------------------------------- IF ( (NUMARGUMENTS.GE.5).AND. + ((CHAR_ARG_READ(5).EQ.'server').OR. + (CHAR_ARG_READ(5).EQ.'SERVER').OR. + (CHAR_ARG_READ(5).EQ.'phd').OR. + (CHAR_ARG_READ(5).EQ.'PHD')) ) THEN LSERVER=.TRUE. ELSE LSERVER=.FALSE. C------- be nice, say hello! WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,70A1)')('-',ITER=1,70) WRITE(6,'(T2,A3,T10,A)')'---', + 'Dear User, Welcome to PredictProtein !' WRITE(6,'(T2,A)')'---' END IF C-------------------------------------------------- C---- set environment (change to port) C-------------------------------------------------- IF (LSERVER .EQV. .TRUE.) THEN PATH_PARACOM='/home/phd/net/' ELSE PATH_PARACOM='/home/rost/pub/' END IF LENPATH_PARACOM=FILEN_STRING(PATH_PARACOM) C-------------------------------------------------- C---- arg 6: arch list -> see below C---- C---- arg 7: write into interchange formatted file ? C-------------------------------------------------- IF ( (NUMARGUMENTS.GE.7).AND. + ((CHAR_ARG_READ(7).EQ.'RDB').OR. + (CHAR_ARG_READ(7).EQ.'rdb').OR. + (CHAR_ARG_READ(7).EQ.'TMPRDB').OR. + (CHAR_ARG_READ(7).EQ.'tmprdb')) ) THEN LRDB=.TRUE. ELSE LRDB=.FALSE. END IF C-------------------------------------------------- C---- arg 8: machine = DEC or ALPHA ? C-------------------------------------------------- IF ( (NUMARGUMENTS.GE.8).AND. + ((CHAR_ARG_READ(8).EQ.'DEC').OR. + (CHAR_ARG_READ(8).EQ.'dec').OR. + (CHAR_ARG_READ(8).EQ.'ALPHA').OR. + (CHAR_ARG_READ(8).EQ.'alpha')) ) THEN LDEC=.TRUE. ELSE LDEC=.FALSE. END IF C-------------------------------------------------- C---- arg 6: read list of architectures C-------------------------------------------------- FILE_ARCHLIST(1:LENPATH_PARACOM)=PATH_PARACOM(1:LENPATH_PARACOM) LDEFAULT=.FALSE. LOK=.FALSE. IF (NUMARGUMENTS.GE.6) THEN IF (CHAR_ARG_READ(6).EQ.'nov93') THEN LDEFAULT=.TRUE. ELSEIF (CHAR_ARG_READ(6).EQ.'cic') THEN TXT80='Para-cic.com' ELSEIF (CHAR_ARG_READ(6)(1:7).EQ.'cic-152') THEN TMPDIR(1:LENPATH_PARACOM)=PATH_PARACOM TMPDIR((LENPATH_PARACOM+1):(LENPATH_PARACOM+5))='cross/' LENTMPDIR=LENPATH_PARACOM+5 TMPLIST( 1:12)='Para-cic-152' TMPLIST(13:13)=CHAR_ARG_READ(6)(8:8) TMPLIST(14:17)='.com' LOK=.TRUE. FILE_ARCHLIST(1:LENTMPDIR)=TMPDIR(1:LENTMPDIR) FILE_ARCHLIST((LENTMPDIR+1):(LENTMPDIR+17))=TMPLIST(1:17) ELSEIF (CHAR_ARG_READ(6).EQ.'ind') THEN TXT80='Para-ind.com' ELSEIF (CHAR_ARG_READ(6).EQ.'crb') THEN TXT80='Para-crb.com' ELSEIF (CHAR_ARG_READ(6)(1:4).EQ.'Para') THEN FILE_ARCHLIST=CHAR_ARG_READ(6) LOK=.TRUE. ELSEIF ( (CHAR_ARG_READ(6)(1:5).EQ.'para:').OR. + (CHAR_ARG_READ(6)(1:5).EQ.'para_') ) THEN FILE_ARCHLIST=' ' IEND=FILEN_STRING(CHAR_ARG_READ(6)) FILE_ARCHLIST=CHAR_ARG_READ(6)(6:IEND) LOK=.TRUE. ELSEIF ( CHAR_ARG_READ(6)(1:1).EQ.'/' ) THEN FILE_ARCHLIST=CHAR_ARG_READ(6) LOK=.TRUE. ELSE LDEFAULT=.TRUE. END IF IF (LOK .EQV. .FALSE.) THEN IHELP=FILEN_STRING(TXT80) FILE_ARCHLIST((LENPATH_PARACOM+1):(LENPATH_PARACOM+IHELP))= + TXT80(1:IHELP) END IF ELSE LDEFAULT=.TRUE. END IF C-------------------------------------------------- C---- arg 9-11: working directory and output files C-------------------------------------------------- IF (NUMARGUMENTS.GE.9) THEN IDIR=FILEN_STRING(CHAR_ARG_READ(9)) IF (IDIR.GT.3) THEN PATH_WORK=CHAR_ARG_READ(9)(1:IDIR) WRITE(6,'(A,T30,A1,A,A1)')' --- working directory ', + '"',PATH_WORK(1:FILEN_STRING(PATH_WORK)),'"' END IF END IF IF (NUMARGUMENTS.GE.10) THEN IDIR=FILEN_STRING(CHAR_ARG_READ(10)) IF (IDIR.GT.3) THEN FILEPRED=CHAR_ARG_READ(10)(1:IDIR) LFILE_PRED_DONE=.TRUE. IEND=FILEN_STRING(FILEPRED) WRITE(6,'(A,T30,A1,A,A1)')' --- FILEPRED ', + '"',FILEPRED(1:IEND),'"' END IF END IF IF (NUMARGUMENTS.GE.11) THEN IDIR=FILEN_STRING(CHAR_ARG_READ(11)) IF (IDIR.GT.3) THEN FILE_RDB=CHAR_ARG_READ(11)(1:IDIR) LFILE_RDB_DONE=.TRUE. WRITE(6,'(A,T30,A1,A,A1)')' --- FILE_RDB ', + '"',FILE_RDB(1:FILEN_STRING(FILE_RDB)),'"' END IF END IF C-------------------------------------------------- C default archictectures C-------------------------------------------------- C VERSION_SEC=' 4.94_252 ' C VERSION_EXP=' 4.94_252 ' VERSION_SEC=' 5.94_317 ' VERSION_EXP=' 4.94_317 ' VERSION_HTM=' 8.94_69 ' IF (LDEFAULT .EQV. .TRUE.) THEN IF (MODESECSTRON.EQ.'EXPOSURE') THEN TXT80='Para-exp-mar94.com' TXT80='Para-exp-apr94.com' TXT80='Para-exp317-apr94.com' ELSEIF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN TXT80='Para-htm69-aug94.com' ELSE TXT80='Para-nov93.com' TXT80='Para-apr94.com' TXT80='Para-sec317-may94.com' END IF IHELP=FILEN_STRING(TXT80) FILE_ARCHLIST((LENPATH_PARACOM+1):(LENPATH_PARACOM+IHELP))= + TXT80(1:IHELP) WRITE(6,'(T2,A,T10,A)')'---', + 'Read default architecture list for prediction: ' WRITE(6,'(T2,A,T10,A1,A,A1)')'---','|', + FILE_ARCHLIST(1:FILEN_STRING(FILE_ARCHLIST)),'|' ELSEIF ( (FILE_ARCHLIST(1:11).EQ.'Para-exp317').OR. + (FILE_ARCHLIST(1:11).EQ.'Para-sec317') ) THEN VERSION_SEC=' 5.94_317 ' VERSION_EXP=' 5.94_317 ' VERSION_HTM=' 8.94_69 ' END IF C-------------------------------------------------- C---- adjust filename for output file ----- C-------------------------------------------------- IF (LSERVER .EQV. .FALSE.) THEN C------- get out chain identifier LHELP=.TRUE. DO ITER=1,80 IF (LHELP .EQV. .TRUE.) THEN IF ( FILE_HSSP(ITER:ITER+2).EQ.'_!_' ) THEN LHELP=.FALSE. IEND=ITER-1 END IF END IF END DO IF (LHELP .EQV. .TRUE.) THEN FILE_HSSP_NOCHAIN=FILE_HSSP ELSE FILE_HSSP_NOCHAIN(1:IEND)=FILE_HSSP(1:IEND) END IF C------- get unique file id LHELP=.TRUE. DO ITER=1,80 IF (LHELP .EQV. .TRUE.) THEN IF ( (FILE_HSSP(ITER:ITER+3).EQ.'hssp').OR. + (FILE_HSSP(ITER:ITER+3).EQ.'Hssp').OR. + (FILE_HSSP(ITER:ITER+3).EQ.'HSSP') ) THEN LHELP=.FALSE. IEND=ITER-2 END IF END IF END DO C------- pred file IF (.NOT.LFILE_PRED_DONE) THEN FILEPRED(1:IEND)=FILE_HSSP(1:IEND) FILEPRED((IEND+1):(IEND+5))='.pred' WRITE(6,'(A,T30,A1,A,A1)')' --- FILEPRED ', + '"',FILEPRED(1:FILEN_STRING(FILEPRED)),'"' END IF C------- *.rdb IF (LRDB.AND.(.NOT.LFILE_RDB_DONE)) THEN FILE_RDB=FILE_HSSP(1:IEND) IF (MODESECSTRON.EQ.'SECONDARY') THEN FILE_RDB(IEND+1:IEND+7)='.rdbsec' ELSEIF (MODESECSTRON.EQ.'EXPOSURE') THEN FILE_RDB(IEND+1:IEND+7)='.rdbexp' ELSEIF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN FILE_RDB(IEND+1:IEND+7)='.rdbhtm' END IF WRITE(6,'(A,T30,A1,A,A1)')' --- FILE_RDB ', + '"',FILE_RDB(1:FILEN_STRING(FILE_RDB)),'"' END IF C------- output (into working) IDIR=FILEN_STRING(PATH_WORK) IF (IDIR.GT.3) THEN FILEOUTPUT(1:IDIR)=PATH_WORK(1:IDIR) ELSE IDIR=0 END IF FILEOUTPUT(IDIR+1:IDIR+IEND)=FILE_HSSP(1:IEND) FILEOUTPUT(IDIR+IEND+1:IDIR+IEND+7) ='.output' C-------------------------------------------------- C---- for phd on server: read name of HSSP file C-------------------------------------------------- ELSE C------- get unique file id LHELP=.TRUE. DO ITER=1,222 IF (LHELP .EQV. .TRUE.) THEN IF (FILE_HSSP(ITER:ITER).NE.'.') THEN INTERNAME(ITER:ITER)=FILE_HSSP(ITER:ITER) ELSE IEND=ITER-1 LHELP=.FALSE. END IF END IF END DO FILE_HSSP_NOCHAIN=FILE_HSSP C------- pred file IF (LFILE_PRED_DONE .EQV. .FALSE.) THEN FILEPRED(1:IEND)=INTERNAME(1:IEND) FILEPRED((IEND+1):(IEND+5))='.pred' END IF C------- *.rdb IF ((LRDB .EQV. .TRUE.) .AND. (.NOT.LFILE_RDB_DONE)) THEN FILE_RDB=FILE_HSSP(1:IEND) IF (MODESECSTRON.EQ.'SECONDARY') THEN FILE_RDB(IEND+1:IEND+7)='.rdbsec' ELSEIF (MODESECSTRON.EQ.'EXPOSURE') THEN FILE_RDB(IEND+1:IEND+7)='.rdbexp' ELSEIF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN FILE_RDB(IEND+1:IEND+7)='.rdbhtm' END IF END IF C------- output (into working) IDIR=FILEN_STRING(PATH_WORK) IF (IDIR.GT.3) THEN FILEOUTPUT(1:IDIR)=PATH_WORK(1:IDIR) ELSE IDIR=0 END IF FILEOUTPUT(IDIR+1:IDIR+IEND)=INTERNAME(1:IEND) FILEOUTPUT(IDIR+IEND+1:IDIR+IEND+7)='.output' END IF C-------------------------------------------------- C---- filter asf C-------------------------------------------------- IF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN LFILTER=.FALSE. ELSE C LFILTER=.FALSE. LFILTER=.TRUE. END IF LOUTBINPROB=.TRUE. C-------------------------------------------------- C---- initialise length intervals C-------------------------------------------------- C---- note: unit i = 1, if length <= split_length(i) IF (NUNITS_LENGTH.NE.4) THEN WRITE(6,'(T2,A,T10,A)')'***','ERROR in INIPHD: '// + 'currently only for NUNITS_LENGTH = 4 (phdParameter.f) !' WRITE(6,'(T2,A,T10,A,T40,I5,T50,A)')'***', + 'instead it is: ',NUNITS_LENGTH,'stopped 29-12-93-1.' STOP ELSE SPLIT_LENGTH(1)=60 SPLIT_LENGTH(2)=120 SPLIT_LENGTH(3)=240 SPLIT_LENGTH(4)=500 SPLIT_LENGTH(4)=NUMRESMAX END IF C---- note: unit i = 1, if distcaps <= split_distcaps(i) IF (NUNITS_DISTCAPS.NE.4) THEN WRITE(6,'(T2,A,T10,A)')'***','ERROR in INIPHD: '// + 'currently only for NUNITS_DISTCAPS = 4 (phdParameter.f) !' WRITE(6,'(T2,A,T10,A,T40,I5,T50,A)')'***', + 'instead it is: ',NUNITS_DISTCAPS,'stopped 29-12-93-1.' STOP ELSE SPLIT_DISTCAPS(1)=10 SPLIT_DISTCAPS(2)=20 SPLIT_DISTCAPS(3)=30 SPLIT_DISTCAPS(4)=40 SPLIT_DISTCAPS(5)=NUMRESMAX END IF C-------------------------------------------------- C---- exposure thresholds and filtering stuff C-------------------------------------------------- IF (MODESECSTRON.EQ.'EXPOSURE') THEN MAXEXP=1 DO ITER=1,10 THREXP10ST(ITER)=(ITER-1)*(ITER-1)*MAXEXP/100. C convert to integer THREXP10STI(ITER)=INT(100*THREXP10ST(ITER)) END DO THREXP2ST(1)= 0. THREXP2ST(2)= (16/100.)*MAXEXP THREXP2ST(3)= MAXEXP C convert to integer DO ITER=1,3 THREXP2STI(ITER)=INT(100*THREXP2ST(ITER)) END DO THREXP3ST(1)=0. THREXP3ST(2)=( 9/100.)*MAXEXP THREXP3ST(3)=( 36/100.)*MAXEXP THREXP3ST(4)=MAXEXP C convert to integer DO ITER=1,4 THREXP3STI(ITER)=INT(100*THREXP3ST(ITER)) END DO T2= 4 T3A=3 T3B=6 C------- filter variables (reduce the emphasis on states 0 and 1%) LREDUCE_BURRIED=.TRUE. LREDUCE_BURRIED=.FALSE. REDUCE_MINSIZE=0.1 REDUCE_STATE0=0.04 REDUCE_STATE1=0.02 END IF END ***** end of INIPHD ***** ------------------------------------------------------------------ ***** SUB NETWORK ***** ------------------------------------------------------------------ C---- C---- NAME : NETWORK C---- ARG : C---- DES : This SBR first executes the networks trigger function by C---- DES : calling SBR TRIGGER for all architectures. Then, the out- C---- DES : puts are summed up to finally compute the jury decision. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: This SBR first executes the networks trigger * * -------- function by calling SBR TRIGGER for all archi- * * tectures. Then, the outputs are summed up to * * finally compute the jury decision. * * const. passed: NUMRES, NUMOUT, NUMNETSND, NUMNETFST * * var. passed: in: INPUT, FILEARCHFST, FILEARCHSND * * ------------ out: OUTPUT, OUTBIN, OUTBINCHAR * * var. read: NUMIN,NUMHID,NUMOUT,JUNCTION1ST,JUNCTION2ND * * ---------- NUMINFST, NUMINSND, NCODEUNTSND, NCODEUNT * * NUMNEIGH, CASCAC* * * calling: SBR: READARCH, WINDIR, TRIGGER, BINOUT, * * -------- EVALRELIND, EVALOUTBINPROB * * lib-comp.f: SRSTZ1 * * called by: main program * *----------------------------------------------------------------------* SUBROUTINE NETWORK C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local parameters LOGICAL LCHECK_WRITE PARAMETER (LCHECK_WRITE=.FALSE.) C PARAMETER (LCHECK_WRITE=.TRUE.) C---- local variables INTEGER CHI,MUE,ITOUT,MSTOP REAL INTEROUT(1:(NUMOUTMAX)) C CHARACTER*24 FDATE LOGICAL LFILTERLOC ******------------------------------*-----------------------------****** * CHI,MUE,ITSEC,ITOUT: iteration variables * * CONTROLCHAR controls how the header is to be read: * * 'FST' -> first network * * 'SND' -> second network * * INTEROUT(itout) used to sum up the outputs over all jury networks* ******------------------------------*-----------------------------****** C XDTE=FDATE() C-------------------------------------------------- C---- loop over all first architectures ----- C-------------------------------------------------- DO CHI=1,NUMNETFST ACTCHI=CHI ACTFILE=FILEARCHFST(CHI) C---------------------------------------- C------- read architecture ACTCHI ----- C---------------------------------------- CONTROLCHAR='FST' C ============= CALL READARCH C ============= C------- assign input C =========== CALL WINDIR C =========== C---------------------------------------- C------- compute output of 1st nets ----- C---------------------------------------- C ============ CALL TRIGGER C ============ C------- store output in OUTFST DO MUE=1,NUMRES DO ITOUT=1,NUMOUT OUTFST(ITOUT,MUE,CHI)=OUTPUT(ITOUT,MUE) END DO C---------- check output MSTOP=10 IF (LCHECK_WRITE .EQV. .TRUE.) THEN IF (MUE.LE.MSTOP) THEN WRITE(6,'(I3,A5,10I4,a5,i3)')MUE,' -> ', + (INT(100*OUTPUT(ITOUT,MUE)),ITOUT=1,NUMOUT), + ' obs ',RESACC(MUE) ELSEIF (MUE.EQ.(MSTOP+1)) THEN WRITE(6,*)'STOPPED IN NETWORK YY' C STOP END IF END IF END DO END DO C-------------------------------------------------- C---- end of loop over all first architectures ---- C-------------------------------------------------- C-------------------------------------------------- C---- loop over all second architectures ----- C-------------------------------------------------- DO CHI=1,NUMNETSND ACTCHI=CHI ACTFILE=FILEARCHSND(CHI) C---------------------------------------- C------- read architecture ACTCHI ----- C---------------------------------------- CONTROLCHAR='SND' C ============= CALL READARCH C ============= C---------------------------------------- C------- compute output of 2nd nets ----- C---------------------------------------- C------- assign windows for input C =========== CALL WINDIR C =========== C------- compute network trigger C ============ CALL TRIGGER C ============ C------- store output in OUTSND DO MUE=1,NUMRES DO ITOUT=1,NUMOUT OUTSND(ITOUT,MUE,CHI)=OUTPUT(ITOUT,MUE) END DO END DO END DO WRITE(6,'(T2,A,T10,A)')'---','end of READARCH' WRITE(6,'(T2,70A1)')('-',ITOUT=1,70) WRITE(6,'(T2,A)')'---' C-------------------------------------------------- C---- end of loop over all second architectures --- C-------------------------------------------------- C-------------------------------------------------- C---- add up outputs for jury decision ----- C-------------------------------------------------- C---------------------------------------- C---- loop over all residues ----- C---------------------------------------- DO MUE=1,NUMRES C ----------- CALL SRSTZ1(INTEROUT,NUMOUTMAX) C ----------- DO ITOUT=1,NUMOUT C---------- loop over all jury 2ND nets IF (NUMNETSND.NE.0) THEN DO CHI=1,NUMNETSND INTEROUT(ITOUT)=INTEROUT(ITOUT)+OUTSND(ITOUT,MUE,CHI) END DO INTEROUT(ITOUT)=INTEROUT(ITOUT)/REAL(NUMNETSND) C---------- loop over all jury 1ST nets ELSE DO CHI=1,NUMNETFST INTEROUT(ITOUT)=INTEROUT(ITOUT)+OUTFST(ITOUT,MUE,CHI) END DO INTEROUT(ITOUT)=INTEROUT(ITOUT)/REAL(NUMNETFST) END IF OUTPUT(ITOUT,MUE)=INTEROUT(ITOUT) END DO C write(6,'(a,t20,10i3)')'xxx network out', C + (int(100*output(itout,mue)),itout=1,numout) END DO C-------------------------------------------------- C---- end of jury decision ----- C-------------------------------------------------- C-------------------------------------------------- C------- WTO decision ----- C-------------------------------------------------- C =========== CALL BINOUT C =========== C-------------------------------------------------- C---- assigning reliability index ----- C-------------------------------------------------- cxx check exposure LFILTERLOC=.FALSE. C =============== CALL EVALRELIND(LFILTERLOC) C =============== C-------------------------------------------------- C---- computing probability of assignment ----- C---- i.e. the 0-9 % values for each outpt unit C-------------------------------------------------- IF (LOUTBINPROB .EQV. .TRUE.) THEN C =================== CALL EVALOUTBINPROB C =================== END IF END ***** end of NETWORK ***** ------------------------------------------------------------------ ***** SUB READARCH ***** ------------------------------------------------------------------ C---- C---- NAME : READARCH C---- ARG : C---- DES : The data is read from files containing the junctions. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The data is read from files containing the * * -------- junctions. * * input var.: ACTFILE, ACTCHI, CONTROLPAR * * note: The parameters and variables are taken from the * * ----- file parsecstron, see there for further details * *----------------------------------------------------------------------* SUBROUTINE READARCH C---- global parameter * INCLUDE 'phdParameter.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER ITER,ITER1,IEND CHARACTER*20 DUMMY20 CHARACTER*3 DUMMY3 LOGICAL LOK C LOGICAL FL_OTHER ******------------------------------*-----------------------------****** C---- write note into output IEND= FILEN_STRING(ACTFILE) WRITE(6,'(T2,A,T10,A,T20,A3,A2,T26,I2,T30,A)')'---', + 'READARCH ',CONTROLCHAR(1:3),': ',ACTCHI,ACTFILE(1:IEND) C---- read file CALL SFILEOPEN(10,ACTFILE(1:IEND),'OLD',222,'READONLY') C---- header = 15 lines DO ITER=1,15 READ(10,*) END DO C---- architecture parameters = 11 lines --> 25 so far IF (CONTROLCHAR.EQ.'FST') THEN READ(10,'(A20,A20)')DUMMY20,DUMMY20 C LOK=FL_OTHER(XDTE) Cxxpass LOK=FL_OTHER(XDTE) LOK=.TRUE. IF ((DUMMY20(1:5).NE.'FIRST').OR.(LOK .EQV. .FALSE.)) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR in READARCH for reading in an expected first net' CLOSE(10) STOP END IF READ(10,*) READ(10,'(A20,A20)')DUMMY20,MODEASSCAS(ACTCHI) IF (MODEASSCAS(ACTCHI).EQ.'ALPHABET') THEN MODEASSCAS(ACTCHI)='PROFILE-REAL' END IF ELSE READ(10,'(A20,A20)')DUMMY20,DUMMY20 IF (DUMMY20(1:6).NE.'SECOND') THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR in READARCH for reading in an expected snd net' CLOSE(10) STOP END IF READ(10,'(A20,I6)')DUMMY20,CASCACC READ(10,'(A20,A20)')DUMMY20,MODEASSSTR(ACTCHI) END IF READ(10,'(A20,I6)')DUMMY20,NUMIN READ(10,'(A20,I6)')DUMMY20,NUMHID READ(10,'(A20,I6)')DUMMY20,NUMOUT READ(10,'(A20,I6)')DUMMY20,NCODEUNT READ(10,'(A20,I6)')DUMMY20,NUMNEIGH READ(10,*) READ(10,*) C---- architecture rest C-------------------------------------------------- C---- unfortunately the new format does not have -- C---- mode DIL, thus the last units (nmach) not -- C---- there -- C-------------------------------------------------- READ(10,*) DO ITER=1,NUMHID READ(10,'(10F10.4)') + (JUNCTION1ST(ITER1,ITER),ITER1=1,(NUMIN+NUMOUT)) C write(6,'(10F10.4)') C + (JUNCTION1ST(ITER1,ITER),ITER1=1,(NUMIN+NUMOUT)) END DO READ(10,*) DO ITER=1,(NUMHID+NUMOUT) READ(10,'(10F10.4)')(JUNCTION2ND(ITER,ITER1),ITER1=1,NUMOUT) C write(6,'(10F10.4)')(JUNCTION2ND(ITER,ITER1),ITER1=1,NUMOUT) END DO C---- control READ(10,'(A3)')dummy3 CLOSE(10) IF (DUMMY3.NE.'END') THEN WRITE(6,'(T2,A,T10,A)')'*****', + 'ERROR for reading in the architectures, here for:' WRITE(6,'(T2,A,T10,A,T25,A,T30,A,T40,I4,T45,A,T52,A)')'*****', + 'controlchar=',CONTROLCHAR,'actchi=',ACTCHI,'ACTFILE=', + ACTFILE STOP END IF END ***** end of READARCH ***** ------------------------------------------------------------------ ***** SUB READPAR ***** ------------------------------------------------------------------ C---- C---- NAME : READPAR C---- ARG : C---- DES : Reads in the required parameters from the parameter file: C---- DES : Parameter.com. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: This SBR reads in the required parameters from * * -------- the parameter file: Parameter.com. * * const. passed: NUMNETSND,NUMNETFST * * var. read: MAXVAR, MAXACC, PROFACC, CASCACC * * ---------- NUMNETFST,NUMNETSND,NUMNETJURY * * NCODEUNTFST, NCODEUNTSND(1:NUMNETSND) * * TRANS2FROM1(1:NUMNETSND), * * MODEASSCAS(1:NUMNETFST),MODEASSSTR(1:NUMNETSND) * * FILEPRED,FILEARCHFST(1:FST)/SND(1:SND) * * ext. SBR: SFILEOPEN (lib-unix) * * called by: main program * *----------------------------------------------------------------------* SUBROUTINE READPAR C---- include parameter files INCLUDE 'phdParameter.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER ITER,INTER,IBEG,IEND CHARACTER*3 DUMMY3 CHARACTER*20 DUMMY20 CHARACTER*222 HC ******------------------------------*-----------------------------****** C---- read parameters from file Parameter.f cxx C FILE_ARCHLIST='Para-test.com' C write(6,*)'xx in READPAR: forced change of parameter file to:' C write(6,*)'xx ',FILE_ARCHLIST CALL SFILEOPEN(10,FILE_ARCHLIST,'OLD',222,'READONLY') C---- header = 14 lines DO ITER=1,14 READ(10,*) END DO C---- paths READ(10,*) C READ(10,'(T21,A)')PATH_PRED READ(10,'(T21,A)')PATH_ARCH C READ(10,'(T21,A)')PATH_WORK C---- architecture parameters = 11 lines --> 25 so far READ(10,*) READ(10,'(A20,I6)')DUMMY20,MAXVAR READ(10,'(A20,I6)')DUMMY20,MAXACC READ(10,'(A20,I6)')DUMMY20,PROFACC READ(10,'(A20,I6)')DUMMY20,CASCACC READ(10,'(A20,I6)')DUMMY20,NBIOLOBJ READ(10,*) READ(10,'(A20,I6)')DUMMY20,NUMNETFST READ(10,'(A20,I6)')DUMMY20,NUMNETSND READ(10,'(A20,I6)')DUMMY20,NUMNETJURY C >***** C > TRANS2FROM1(1:NUMNETSND) (20I4) IF (NUMNETSND.NE.0) THEN READ(10,*) READ(10,*) READ(10,'(20I4)')(TRANS2FROM1(ITER),ITER=1,NUMNETSND) END IF C >***** C > MODEASSCAS(1:NUMNETFST) (row: no. A25) READ(10,*) READ(10,*) DO ITER=1,NUMNETFST READ(10,'(I10,T21,A)')INTER,MODEASSCAS(ITER) END DO C >***** C > MODEASSSTR(1:NUMNETSND) (row: no. A25) IF (NUMNETSND.NE.0) THEN READ(10,*) READ(10,*) DO ITER=1,NUMNETSND READ(10,'(I10,T21,A)')INTER,MODEASSSTR(ITER) END DO END IF C >***** C > FILEARCHFST(1:NUMNETFST) (row: no. A50) READ(10,*) READ(10,*) DO ITER=1,NUMNETFST READ(10,'(I10,T21,A)')INTER,FILEARCHFST(ITER) END DO C > FILEASND(1:NUMNETSND) (row: no. A50) IF (NUMNETSND.NE.0) THEN READ(10,*) DO ITER=1,NUMNETSND READ(10,'(I10,T21,A)')INTER,FILEARCHSND(ITER) END DO END IF C---- control READ(10,'(A3)')DUMMY3 CLOSE(10) IF (DUMMY3.NE.'END') THEN WRITE(6,'(T2,A,T10,A,T50,A40)')'*****', + 'ERROR for reading in the parameter file ', + FILE_ARCHLIST stop END IF C-------------------------------------------------- C---- adding path_arch to file names C-------------------------------------------------- IF (FILEN_STRING(PATH_ARCH).GT.1) THEN DO ITER=1,NUMNETFST HC=PATH_ARCH IBEG=FILEN_STRING(PATH_ARCH)+1 IEND=IBEG+FILEN_STRING(FILEARCHFST(ITER))-1 HC(IBEG:IEND)=FILEARCHFST(ITER) FILEARCHFST(ITER)(1:IEND)=HC(1:IEND) END DO DO ITER=1,NUMNETSND HC=PATH_ARCH IBEG=FILEN_STRING(PATH_ARCH)+1 IEND=IBEG+FILEN_STRING(FILEARCHSND(ITER))-1 HC(IBEG:IEND)=FILEARCHSND(ITER) FILEARCHSND(ITER)(1:IEND)=HC(1:IEND) END DO END IF C---- bullshit to avoid warning IF (INTER.GT.1) THEN CONTINUE END IF IF (DUMMY20.EQ.'XX') THEN CONTINUE END IF END ***** end of READPAR ***** ------------------------------------------------------------------ ***** SUB RS_GETHSSP ***** ------------------------------------------------------------------ C---- C---- NAME : RS_GETHSSP C---- ARG : C---- DES : Reading the protein from an HSSP file: FILE_HSSP C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * * changed: Aug, 2003 version 1.2 * *----------------------------------------------------------------------* C purpose: Reading the protein from an HSSP file: FILE_HSSP * C input parameter:NUMPROTMAX,NUMRESMAX * C input variable: FILE_HSSP * C output variable:PROTNAME,RESNAME,NUMRES * C ----------------POINTBEG,POINTEND,RESSECSTR,RESACC,RESVAR * C RESPROF * C Note: Program taken from Reinhard Schneider * C======================================================================= C NUMPROT: number of proteins in compressed database C POINTBEG: pointer to begining of protein C POINTEND: pointer to end of protein C PROTNAME Brookhaven Data Bank identifier C RESNAME: sequential storage for the SEQUENCE C NOTE: lower case characters are 'C'; lower case of C HSSP-files (insertions) are converted in RS_GETHSSPBASE C RESSECSTR: sequential storage for the SECONDARY STRUCTURE C NOTE: original DSSP definition C======================================================================= C CAUTION: RESVAR and RESACC are INTEGER*2 C======================================================================= C RESACC: solvated residue surface area in A**2 C RESVAR: sequence variability as derived from the nalign C alignments C OFFSET: offset of aligned sequence (HSSP-alignment) to PDBSEQ C======================================================================= C----------------------------------------------------------------------- C Reinhard Schneider December, 1991 * C----------------------------------------------------------------------- *----------------------------------------------------------------------* SUBROUTINE RS_GETHSSP C---- global parameters INCLUDE 'phdParameter.f' C---- local parameters and variables INTEGER KDSSP C INTEGER MAXRESBASE C PARAMETER (MAXRESBASE= NUMRESMAX) PARAMETER (KDSSP= 12) C INTEGER MAXRES,MAXAA C C now defined in parameter file!! C C PARAMETER (MAXALIGNS= 3000) C PARAMETER (MAXALIGNS= 5000) C PARAMETER (MAXCORE= 500000) C PARAMETER (MAXCORE= 100000) C PARAMETER (MAXAA= 20) C.. Attributes of individual proteins INTEGER ACCBASE(NUMRESMAX) INTEGER VARIABILITY(NUMRESMAX) INTEGER PROFILE(NUMRESMAX,MAXAA) INTEGER WRT_NINS(NUMRESMAX),WRITENDEL(NUMRESMAX) C INTEGER WRT_NALIGN(NUMPROTMAX) INTEGER WRT_NALIGN(MAXALIGNS) REAL*4 WRT_CONSWEIGHT(NUMRESMAX) C.. attributes of all proteins INTEGER PROTBEGIN(MAXALIGNS),PROTEND(0:MAXALIGNS) CHARACTER CSEQBASE(NUMRESMAX) CHARACTER CSTRBASE(NUMRESMAX) CHARACTER*132 CPROTID(MAXALIGNS) INTEGER NPROT,NCHAINBREAK,NPROTBREAK, + OFFSET(MAXALIGNS) C THRESHOLD for HSSP alignments C.. LOGICAL LOGICAL LERROR,LOGIPROFILE,LOGICONSWEIGHT INTEGER I,J,K,ISTART,ISTOP,LEN,KRESBASE,IPOS C====================================================================== C need to read HSSP files C====================================================================== C Reinhard Schneider 1989, BIOcomputing EMBL, D-6900 Heidelberg, FRG C please report any bug, e-mail (INTERNET): C schneider@EMBL-Heidelberg.DE C or sander@EMBL-Heidelberg.DE C======================================================================= C INCREASE THE NUMBER OF FOLLOWING THREE PARAMETER IF NECESSARY C Note: increase also in calling program C======================================================================= C maxaligns = maximal number of alignments in a HSSP-file C maxres= maximal number of residues in a PDB-protein C maxcore= maximal space for storing the alignments C======================================================================= C maxaa= 20 amino acids C nblocksize= number of alignments in one line C pdbid= Brookhaven Data Bank identifier C header,compound,source,author= informations about the PDB-protein C pdbseq= amino acid sequence of the PDB-protein C chainid= chain identifier (chain A etc.) C secstr= DSSP secondary structure summary C bp1,bp2= beta-bridge partner C cols= DSSP hydrogen bonding patterns for turns and helices, C geometrical bend, chirality, one character name of beta-ladder C and of beta-sheet C sheetlabel= chain identifier of beta bridge partner C seqlength= number of amino acids in the PDB-protein C pdbno= residue number as in PDB file C nchain= number of different chains in pdbid.DSSP data set C kchain= number of chains used in HSSP data set C nalign= number of alignments C acc= solvated residue surface area in A**2 C emblid= EMBL/SWISSPROT identifier of the alignend protein C strid= if the 3-D structure of this protein is known, then strid C (structure ID)is the Protein Data Bank identifier as taken C from the EMBL/SWISSPROT entry C protname= one line description of alignend protein C aliseq= sequential storage for the alignments C alipointer= points to the beginning of alignment X ( 1>= X <=nalign ) C ifir,ilas= first and last position of the alignment in the test C protein C jfir,jlas= first and last position of the alignment in the alignend C protein C lali= length of the alignment excluding insertions and deletions C ngap= number of insertions and deletions in the alignment C lgap= total length of all insertions and deletions C lenseq= length of the entire sequence of the alignend protein C ide= percentage of residue identity of the alignment C var= sequence variability as derived from the nalign alignments C seqprof= relative frequency for each of the 20 amino acids C nocc= number of alignend sequences spanning this position (including C the test sequence C ndel= number of sequences with a deletion in the test protein at this C position C nins= number of sequences with an insertion in the test protein at C this position C LOGIPROFILE if true the profile is written into output file C entropy= entropy measure of sequence variability at this position C relent= relative entropy (entropy normalized to the range 0-100) C======================================================================= C============================ import ================================== C attributes of sequence with known structure CHARACTER*132 PDBID,HEADER,COMPOUND,SOURCE,AUTHOR CHARACTER PDBSEQ(NUMRESMAX),CHAINID(NUMRESMAX), + SECSTR(NUMRESMAX) C.......LENGHT*7 CHARACTER*7 COLS(NUMRESMAX) CHARACTER*132 CHAINREMARK INTEGER SEQLENGTH,NCHAIN,KCHAIN,NALIGN INTEGER ACC(NUMRESMAX) C br 2003-08-23: save space C CHARACTER SHEETLABEL(NUMRESMAX) C INTEGER BP1(NUMRESMAX),BP2(NUMRESMAX),PDBNO(NUMRESMAX) CHARACTER SHEETLABEL(1) INTEGER BP1(1),BP2(1),PDBNO(1) C br 2003-08-23: end save space C ATTRIBUTES OF ALIGNED SEQUENCES CHARACTER*132 EMBLID(MAXALIGNS),STRID(MAXALIGNS), + IPROTNAME(MAXALIGNS),ACCNUM(MAXALIGNS), + EXCLUDEFLAG(MAXALIGNS) C br 2003-08-23: save space C CHARACTER ALISEQ(MAXCORE) CHARACTER ALISEQ(1) C br 2003-08-23: end save space INTEGER ALIPOINTER(MAXALIGNS), + IFIR(MAXALIGNS),ILAS(MAXALIGNS),JFIR(MAXALIGNS), + JLAS(MAXALIGNS),LALI(MAXALIGNS),NGAP(MAXALIGNS), + LGAP(MAXALIGNS),LENSEQ(MAXALIGNS) REAL IDE(MAXALIGNS),SIM(MAXALIGNS) C ATTRIBUTES OF PROFILE INTEGER SEQPROF(NUMRESMAX,MAXAA), + NOCC(NUMRESMAX),NDEL(NUMRESMAX),NINS(NUMRESMAX) REAL CONSWEIGHT(NUMRESMAX) C br 2003-08-23: save space C INTEGER VAR(NUMRESMAX),RELENT(NUMRESMAX) C REAL ENTROPY(NUMRESMAX) INTEGER VAR(1),RELENT(1) REAL ENTROPY(1) C br 2003-08-23: end save space C br 2003-08-23: save space C br 2003-08-23: end save space C....... LOGICAL LCONSERV,LOLDVERSION C Compiler bug patch C write data in loop, because the SUN4 compiler has a limit stacksize of C 4096 (before it was 8192 MURKS) in a routine(do_u_out, rwrite or w4cp) C integer NPACK C parameter (NPACK=1000) C...... LOGICAL LSCREEN INTEGER MAXALIGNS_LOC,MAXRES C======================================================================= C.... init MAXRES= NUMRESMAX MAXALIGNS_LOC= MAXALIGNS NPROT= 0 NCHAINBREAK= 0 NPROTBREAK= 0 DO I=1,MAXALIGNS_LOC emblid(i)= ' ' ENDDO DO I=1,MAXALIGNS PROTBEGIN(I)= 0 PROTEND(I)= 0 WRT_NALIGN(I)= 0 CPROTID(I)= ' ' OFFSET(I)= 1 ENDDO DO I=1,NUMRESMAX CSEQBASE(I)= ' ' CSTRBASE(I)= ' ' ACCBASE(I)= 0 VARIABILITY(I)=0 WRITENDEL(I)= 0 WRT_NINS(I)= 0 ENDDO PROTEND(0)= -1 C defaults C FILE_HSSP='/data/hssp/3b5c.hssp' C ISAFE=10 C lformula=.true. C lall=.false. LOGIPROFILE= .TRUE. LOGICONSWEIGHT= .TRUE. LOGI_INDEL= .TRUE. LSCREEN= .FALSE. C===================================================================== C======= AND HERE WE GO ============================================== C===================================================================== C CALL GETCHAR(80,OUTFILE,' output file ? ') C CALL GETINT(1,ISAFE,' HSSP-threshold + x percent ?') C CALL ASK(' including profile information?',LOGIPROFILE) C CALL ASK(' including conservation weight?',LOGICONSWEIGHT) CC CALL GETCHAR(80,PROTFILE,' protname ? ') WRITE(6,'(T2,A,T10,A,T22,A50)')'---','HSSP file',FILE_HSSP C---- calling SBR for reading CALL RS_READHSSP(KDSSP,FILE_HSSP,LERROR, + MAXRES,MAXALIGNS,MAXCORE, + PDBID,HEADER,COMPOUND,SOURCE,AUTHOR,SEQLENGTH, + NCHAIN,KCHAIN,CHAINREMARK,NALIGN, + EXCLUDEFLAG,EMBLID,STRID,IDE,SIM, + IFIR,ILAS,JFIR,JLAS,LALI,NGAP,LGAP, + LENSEQ,ACCNUM,IPROTNAME, + PDBNO,PDBSEQ,CHAINID,SECSTR,COLS,SHEETLABEL,BP1,BP2, + ACC,NOCC,VAR,ALISEQ,ALIPOINTER, + SEQPROF,NDEL,NINS,ENTROPY,RELENT,CONSWEIGHT, + LCONSERV,LOLDVERSION) C first PDBSEQ C----------------------------------------------------------------------- IF (LERROR .EQV. .TRUE.) THEN write(6,*)'xx LERROR after read hssp: ',LERROR ENDIF KRESBASE=1 IF (LERROR .EQV. .FALSE.) THEN NPROT=NPROT+1 LEN=SEQLENGTH IF (KRESBASE+LEN .GT. NUMRESMAX) THEN WRITE(6,'(T2,A,T10,A,T30,I5)')'***', + 'NUMRESMAX OVERFLOW ',KRESBASE+LEN STOP ENDIF CPROTID(NPROT)=PDBID PROTBEGIN(NPROT)=PROTEND(NPROT-1)+2 PROTEND(NPROT)=PROTBEGIN(NPROT)-1+LEN KRESBASE=PROTBEGIN(NPROT) OFFSET(NPROT)=1 WRT_NALIGN(NPROT)=NALIGN DO K=1,SEQLENGTH CSEQBASE(KRESBASE)=PDBSEQ(K) IF (PDBSEQ(K).EQ.' !')NCHAINBREAK=NCHAINBREAK+1 IF (SECSTR(K).EQ. ' ') THEN CSTRBASE(KRESBASE)='L' ELSE CSTRBASE(KRESBASE)=SECSTR(K) ENDIF ACCBASE(KRESBASE)=ACC(K) C VARIABILITY(KRESBASE)=VAR(K) IF (LOGIPROFILE .EQV. .TRUE.) THEN DO IPOS=1,MAXAA PROFILE(KRESBASE,IPOS)=SEQPROF(K,IPOS) ENDDO ENDIF IF (LOGICONSWEIGHT .EQV. .TRUE.) THEN WRT_CONSWEIGHT(KRESBASE)=CONSWEIGHT(K) END IF IF (LOGI_INDEL .EQV. .TRUE.) THEN WRITENDEL(KRESBASE)=NDEL(K) WRT_NINS(KRESBASE)=NINS(K) END IF KRESBASE=KRESBASE+1 ENDDO CALL STRPOS(FILE_HSSP,ISTART,ISTOP) C set '/' between proteins CSEQBASE(KRESBASE)='/' CSTRBASE(KRESBASE)='/' KRESBASE=KRESBASE+1 NPROTBREAK=NPROTBREAK+1 ELSE WRITE(6,'(T2,A,T10,A,T40,A)')'***', + ' ERROR READING FILE_HSSP: ',FILE_HSSP ENDIF NPROTBREAK=NPROTBREAK-1 NPROT=NPROT C.....end.loop over lifi C.................................................................... CDEBUG......... C............................................................... C write data C........................... DO I=1,NPROT PROTNAME(I)=CPROTID(I) NUMRES=PROTEND(I)-PROTBEGIN(I)+1 NUMNALIGN(I)=WRT_NALIGN(I) DO J=1,PROTEND(I) RESNAME(J)=CSEQBASE(J) RESSECSTR(J)=CSTRBASE(J) RESACC(J)=ACCBASE(J) C br 2003-08-23: save space C RESVAR(J)=VARIABILITY(J) C br 2003-08-23: end save space IF (LOGIPROFILE .EQV. .TRUE.) THEN DO K=1,MAXAA RESPROF(J,K)=PROFILE(J,K) END DO END IF IF (LOGICONSWEIGHT .EQV. .TRUE.) THEN RESCONSWEIGHT(J)=WRT_CONSWEIGHT(J) END IF IF (LOGI_INDEL .EQV. .TRUE.) THEN RESNDEL(J)=WRITENDEL(J) RESNINS(J)=WRT_NINS(J) END IF END DO END DO C changed 31-1-94 xxzz NUMNALIGN(1)=WRT_NALIGN(1) cxx WRITE(6,'(T2,A,T10,A)')'---',' RS_GETHSSP(final words) got:' WRITE(6,'(T2,A,T10,A,T25,A50)')'---','protname(50)',CPROTID(1) WRITE(6,'(T2,A,T10,A,T25,I4,T33,A,T45,I4)')'---', + 'length:',NUMRES,'N alis:',WRT_NALIGN(1) WRITE(6,'(T2,A,T10,A,T25,60A1)')'---', + 'sequence',(CSEQBASE(K),K=1,PROTEND(NPROT)) WRITE(6,'(T2,A,T10,A,T25,60A1)')'---', + 'structure',(CSTRBASE(K),K=1,PROTEND(NPROT)) WRITE(6,'(T2,A,T10,A,T25,5I10)')'---', + 'OFFSET',(OFFSET(K),K=1,NPROT) IF (LOGIPROFILE.AND.LOGICONSWEIGHT.AND.LOGI_INDEL.AND. + LSCREEN) THEN WRITE(6,'(T2,A,T10,A,T72,4A4)')'-no seq', + ' V L I M F W Y G A P S T C H R K Q E N D', + 'Cons',' Del',' Ins',' ACC' DO I=PROTBEGIN(1),PROTEND(1) WRITE(6,'(T2,I4,T8,A1,T10,20I3,T72,F4.2,2I4,I4)') + I,CSEQBASE(I), + (PROFILE(I,J),J=1,MAXAA),WRT_CONSWEIGHT(I), + WRITENDEL(I),WRT_NINS(I),RESACC(I) enddo ENDIF WRITE(6,'(T2,A,T10,A)')'---',' RS_GETHSSP END(really)' END ***** end of RS_GETHSSP ***** ------------------------------------------------------------------ ***** SUB RS_READHSSP ***** ------------------------------------------------------------------ C---- C---- NAME : RS_READHSSP C---- ARG : C---- DES : does it .. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RS_READHSSP(IUNIT,FILE_HSSP_LOC,LERROR, + MAXRES,MAXALIGNS_LOC,MAXCORE_LOC, + PDBID,HEADER,COMPOUND,SOURCE,AUTHOR,SEQLENGTH, + NCHAIN,KCHAIN,CHAINREMARK,NALIGN, + EXCLUDEFLAG,EMBLID,STRID,IDE,SIM, + IFIR,ILAS,JFIR,JLAS,LALI,NGAP,LGAP, + LENSEQ,ACCNUM,IPROTNAME, + PDBNO,PDBSEQ,CHAINID,SECSTR,COLS,SHEETLABEL,BP1,BP2, + ACC,NOCC,VAR,ALISEQ,ALIPOINTER, + SEQPROF,NDEL,NINS,ENTROPY,RELENT,CONSWEIGHT, + LCONSERV,LOLDVERSION) C---- global parameters INCLUDE 'phdParameter.f' C Reinhard Schneider 1989, BIOcomputing EMBL, D-6900 Heidelberg, FRG C please report any bug, e-mail (INTERNET): C schneider@EMBL-Heidelberg.DE C or sander@EMBL-Heidelberg.DE C======================================================================= C INCREASE THE NUMBER OF FOLLOWING THREE PARAMETER IN THE CALLING C PROGRAM IF NECESSARY C======================================================================= C maxaligns = maximal number of alignments in a HSSP-file C maxres= maximal number of residues in a PDB-protein C maxcore= maximal space for storing the alignments C======================================================================= C maxaa= 20 amino acids C nblocksize= number of alignments in one line C pdbid= Brookhaven Data Bank identifier C header,compound,source,author= informations about the PDB-protein C pdbseq= amino acid sequence of the PDB-protein C chainid= chain identifier (chain A etc.) C secstr= DSSP secondary structure summary C bp1,bp2= beta-bridge partner C cols= DSSP hydrogen bonding patterns for turns and helices, C geometrical bend, chirality, one character name of beta-ladder C and of beta-sheet C sheetlabel= chain identifier of beta bridge partner C seqlength= number of amino acids in the PDB-protein C pdbno= residue number as in PDB file C nchain= number of different chains in pdbid.DSSP data set C kchain= number of chains used in HSSP data set C nalign= number of alignments C acc= solvated residue surface area in A**2 C emblid= EMBL/SWISSPROT identifier of the alignend protein C strid= if the 3-D structure of this protein is known, then strid C (structure ID)is the Protein Data Bank identifier as taken C from the EMBL/SWISSPROT entry C iprotname= one line description of alignend protein C aliseq= sequential storage for the alignments C alipointer= points to the beginning of alignment X ( 1>= X <=nalign ) C ifir,ilas= first and last position of the alignment in the test C protein C jfir,jlas= first and last position of the alignment in the alignend C protein C lali= length of the alignment excluding insertions and deletions C ngap= number of insertions and deletions in the alignment C lgap= total length of all insertions and deletions C lenseq= length of the entire sequence of the alignend protein C ide= percentage of residue identity of the alignment C var= sequence variability as derived from the nalign alignments C seqprof= relative frequency for each of the 20 amino acids C nocc= number of alignend sequences spanning this position (including C the test sequence C ndel= number of sequences with a deletion in the test protein at this C position C nins= number of sequences with an insertion in the test protein at C this position C entropy= entropy measure of sequence variability at this position C relent= relative entropy (entropy normalized to the range 0-100) C consweight= conservation weight C======================================================================= C IMPLICIT NONE C INTEGER NBLOCKSIZE C PARAMETER (NBLOCKSIZE= 70) C INTEGER MAXRES,MAXAA C INTEGER MAXALIGNS,MAXCORE C PARAMETER (MAXAA= 20) C============================ import ================================== C CHARACTER*222 FILE_HSSP_LOC CHARACTER*(*) FILE_HSSP_LOC INTEGER IUNIT LOGICAL LERROR C attributes of sequence with known structure C CHARACTER*222 PDBID,HEADER,COMPOUND,SOURCE,AUTHOR C CHARACTER*(*) PDBID,HEADER,COMPOUND,SOURCE,AUTHOR CHARACTER*132 PDBID,HEADER,COMPOUND,SOURCE,AUTHOR CHARACTER PDBSEQ(NUMRESMAX),CHAINID(NUMRESMAX), + SECSTR(NUMRESMAX) C.......length*7 CHARACTER*7 COLS(NUMRESMAX) CHARACTER*132 CHAINREMARK C br 2003-08-23: save space C CHARACTER SHEETLABEL(NUMRESMAX) CHARACTER SHEETLABEL(1) CHARACTER SHEETLABEL_NULL C br 2003-08-23: end save space INTEGER SEQLENGTH,NCHAIN,KCHAIN,NALIGN INTEGER ACC(NUMRESMAX) C br 2003-08-23: save space C INTEGER BP1(NUMRESMAX),BP2(NUMRESMAX),PDBNO(NUMRESMAX) INTEGER BP1(1),BP2(1),PDBNO(1) INTEGER PDBNO_NULL,BP1_NULL,BP2_NULL C br 2003-08-23: end save space C attributes of alignend sequences C CHARACTER*222 EMBLID(MAXALIGNS),STRID(MAXALIGNS), C + ACCNUM(MAXALIGNS),IPROTNAME(MAXALIGNS), C + EXCLUDEFLAG(MAXALIGNS) C CHARACTER*(*) EMBLID(MAXALIGNS),STRID(MAXALIGNS), C + ACCNUM(MAXALIGNS),IPROTNAME(MAXALIGNS), C + EXCLUDEFLAG(MAXALIGNS) CHARACTER*132 EMBLID(MAXALIGNS),STRID(MAXALIGNS), + IPROTNAME(MAXALIGNS),ACCNUM(MAXALIGNS), + EXCLUDEFLAG(MAXALIGNS) INTEGER ALIPOINTER(MAXALIGNS), + IFIR(MAXALIGNS),ILAS(MAXALIGNS),JFIR(MAXALIGNS), + JLAS(MAXALIGNS),LALI(MAXALIGNS),NGAP(MAXALIGNS), + LGAP(MAXALIGNS),LENSEQ(MAXALIGNS) REAL IDE(MAXALIGNS),SIM(MAXALIGNS) C br 2003-08-23: save space C CHARACTER ALISEQ(MAXCORE) CHARACTER ALISEQ(1) CHARACTER ALISEQ_NULL C br 2003-08-23: end save space C attributes of profile INTEGER SEQPROF(NUMRESMAX,MAXAA), + NOCC(NUMRESMAX),NDEL(NUMRESMAX),NINS(NUMRESMAX) REAL CONSWEIGHT(NUMRESMAX) C br 2003-08-23: save space C INTEGER VAR(NUMRESMAX),RELENT(NUMRESMAX) C REAL ENTROPY(NUMRESMAX) INTEGER VAR(1),RELENT(1) INTEGER VAR_NULL,RELENT_NULL REAL ENTROPY(1) REAL ENTROPY_NULL C br 2003-08-23: end save space C....... LOGICAL LCONSERV,LOLDVERSION C======================================================================= C internal C INTEGER MAXALIGNS_LOC C PARAMETER (MAXALIGNS_LOC= 3000) C PARAMETER (MAXALIGNS_LOC= MAXALIGNS) C character profileseq*(maxaa) CHARACTER CTEMP*(NBLOCKSIZE),TEMPNAME*222 CHARACTER*222 LINE C CHARACTER*20 HSSPRELEASE CHARACTER CHAINSELECT LOGICAL LCHAIN,LONG_ID INTEGER ICHAINBEG,ICHAINEND,NALIGNORG, + I,J,K,IPOS,ILEN,NRES,IRES, + NBLOCK,IALIGN,IBLOCK,IALI, + IBEG,IEND,IPOINTER(MAXALIGNS) INTEGER MAXCORE_LOC,MAXALIGNS_LOC,MAXRES INTEGER ITMP LOGICAL LDEBUG_LOCAL C order of amino acid symbols in the HSSP sequence profile block C profileseq='VLIMFWYGAPSTCHRKQEND' LONG_ID=.FALSE. LERROR=.FALSE. C br 2003-08-23: avoid warnings IBEG=0 IEND=0 J= 0 C used to debug LDEBUG_LOCAL=.FALSE. C LDEBUG_LOCAL=.TRUE. NALIGN=0 CHAINREMARK=' ' DO I=1,MAXALIGNS IPOINTER(I)=0 ENDDO LCHAIN=.FALSE. TEMPNAME(1:)=FILE_HSSP_LOC I=INDEX(TEMPNAME,'_!_') IF (I.NE.0) THEN TEMPNAME(1:)=FILE_HSSP_LOC(1:I-1) LCHAIN=.TRUE. READ(FILE_HSSP_LOC(I+3:),'(A1)')CHAINSELECT WRITE(6,'(T2,A,T10,A,T50,A)')'---', + '--- RS_READHSSP: extract the chain: ',chainselect ENDIF C CALL RSLIB_OPEN_FILE(IUNIT,TEMPNAME,'OLD,READONLY',LERROR) C OPEN(IUNIT,FILE=TEMPNAME,STATUS='OLD',READONLY,ERR=99) C OPEN(IUNIT,FILE=TEMPNAME,STATUS='OLD',ERR=99) OPEN(IUNIT,FILE=TEMPNAME,ERR=99) IF (LERROR .EQV. .TRUE.) THEN WRITE(6,'(A)')'*** ERROR FOR RS_READHSSP: open problem' GOTO 99 ENDIF READ(IUNIT,'(A)',ERR=99)LINE C check if it is a HSSP-file and get the release number for format flags IF (LINE(1:4).NE.'HSSP') THEN WRITE(6,'(A)')'*** ERROR FOR RS_READHSSP: is not a HSSP-file' LERROR=.TRUE. RETURN ELSE I=INDEX(LINE,'VERSION')+7 C HSSPRELEASE=LINE(I:) LOLDVERSION=.FALSE. c if (index(hssprelease,'0.9').ne.0)loldversion=.true. ENDIF C read in PDBID etc. DO WHILE(LINE(1:6).NE.'PDBID') READ(IUNIT,'(A)',ERR=99)LINE ENDDO READ(LINE,'(11X,A)',ERR=99)PDBID DO WHILE(LINE(1:6).NE.'HEADER') READ(IUNIT,'(A)',ERR=99)LINE IF (LINE(1:23).EQ.'PARAMETER LONG-ID :YES') THEN LONG_ID=.TRUE. ENDIF ENDDO READ(LINE ,'(11X,A)',ERR=99)HEADER READ(IUNIT,'(11X,A)',ERR=99)COMPOUND READ(IUNIT,'(11X,A)',ERR=99)SOURCE READ(IUNIT,'(11X,A)',ERR=99)AUTHOR READ(IUNIT,'(11X,I4)',ERR=99)SEQLENGTH READ(IUNIT,'(11X,I4)',ERR=99)NCHAIN KCHAIN=NCHAIN READ(IUNIT,'(A)',ERR=99)LINE C IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG ',LINE IF (INDEX(LINE,'KCHAIN').NE.0) THEN READ(LINE,'(11X,I4,A)',ERR=99)KCHAIN,CHAINREMARK READ(IUNIT,'(11X,I4)',ERR=99)NALIGNORG ELSE READ(LINE,'(11X,I4)',ERR=99)NALIGNORG ENDIF C if HSSP-file contains no alignments return IF (NALIGNORG.EQ.0) THEN WRITE(6,'(T2,A,T10,A)')'---', + '--- HSSP-file contains no alignments ***' CLOSE(IUNIT) RETURN ENDIF C write(6,*)'xx before overflow, Nali=',nalignorg,' len=', C + seqlength,' kchain=',kchain,' lchain=',lchain C parameter overflow handling IF (NALIGNORG.GT.MAXALIGNS) THEN WRITE(6,'(A)')'-*- HSSP-file contains too many alignments **' WRITE(6,'(A)')'-*- INCREASE MAXALIGNS in phdParameter.f! ' WRITE(6,'(A,I8,A,I8)')'-*- is=',MAXALIGNS,' want>',NALIGNORG CLOSE(IUNIT) LERROR=.TRUE. RETURN ENDIF ITMP=SEQLENGTH+KCHAIN-1 IF (ITMP.GT.NUMRESMAX) THEN WRITE(6,'(A)')'*** PDB-sequence in HSSP-file too long ***' WRITE(6,'(A)')'*** INCREASE NUMRESMAX in phdParameter.f***' WRITE(6,'(A,I8,A,I8)')'-*- is=',NUMRESMAX,' want>',ITMP CLOSE(IUNIT) LERROR=.TRUE. RETURN ENDIF C number of sequence positions is number of residues + number of chains C chain break is indicated by a '!' NRES=SEQLENGTH+KCHAIN-1 ICHAINBEG=1 ICHAINEND=NRES IF (LCHAIN .EQV. .TRUE.) THEN C search for ALIGNMENT-block DO WHILE (LINE(1:13).NE.'## ALIGNMENTS') READ(IUNIT,'(A)',ERR=99)LINE ENDDO READ(IUNIT,'(A)',ERR=99)LINE ICHAINBEG=0 ICHAINEND=0 C read till end ; some PDB-chains have DSSP-chain breaks !! DO I=1,NRES READ(IUNIT,'(7X,I4,1X,A1)',ERR=99)PDBNO(I),CHAINID(I) IF (CHAINID(I) .EQ. CHAINSELECT) THEN IF (ICHAINBEG .EQ. 0) ICHAINBEG=I ICHAINEND=I ENDIF ENDDO WRITE(6,'(T2,A,T10,I10,I10)')'---', + ICHAINBEG,ICHAINEND REWIND(IUNIT) ENDIF SEQLENGTH=ICHAINEND-ICHAINBEG+1 C search for the PROTEINS-block LINE=' ' DO WHILE(LINE(1:11).NE.'## PROTEINS') READ(IUNIT,'(A)',ERR=99)LINE C IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG PROT=',LINE ENDDO READ(IUNIT,'(A)',ERR=99)LINE LCONSERV=.FALSE. IF (INDEX(LINE,'%WSIM').NE.0) LCONSERV= .TRUE. C READ DATA ABOUT THE ALIGNMENTS IALIGN=1 IF (LDEBUG_LOCAL .EQV. .TRUE.) + WRITE(6,'(A,I5,A,L)')'DBG NALI=',NALIGNORG,' long=',LONG_ID DO I=1,NALIGNORG C IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,'(A,I5)')'DBG iali=',I IF (LONG_ID .EQV. .TRUE.) THEN C note: read format specified below (line labelled 101) READ(IUNIT,101,ERR=99) + EXCLUDEFLAG(IALIGN),EMBLID(IALIGN)(1:),STRID(IALIGN), + IDE(IALIGN),SIM(IALIGN),IFIR(IALIGN),ILAS(IALIGN), + JFIR(IALIGN),JLAS(IALIGN),LALI(IALIGN),NGAP(IALIGN), + LGAP(IALIGN),LENSEQ(IALIGN),ACCNUM(IALIGN), + IPROTNAME(IALIGN) ELSE C note: read format specified below (line labelled 100) READ(IUNIT,100,ERR=99) + EXCLUDEFLAG(IALIGN),EMBLID(IALIGN)(1:),STRID(IALIGN), + IDE(IALIGN),SIM(IALIGN),IFIR(IALIGN),ILAS(IALIGN), + JFIR(IALIGN),JLAS(IALIGN),LALI(IALIGN),NGAP(IALIGN), + LGAP(IALIGN),LENSEQ(IALIGN),ACCNUM(IALIGN), + IPROTNAME(IALIGN) END IF IF (LDEBUG_LOCAL .EQV. .TRUE.) THEN WRITE(6,'(A,I5,A,F5.2,A,A)')'DBG PROTali(',IALIGN,') ide=', + IDE(IALIGN), + ' name=',IPROTNAME(IALIGN) END IF IF (IFIR(IALIGN) .GE. ICHAINBEG .AND. + ILAS(IALIGN) .LE. ICHAINEND) THEN IPOINTER(I)=IALIGN IALIGN=IALIGN+1 ENDIF ENDDO 100 FORMAT(5X,A1,2X,A12,A5,2X,F5.2,1X,F5.2,8(1X,I4),2X,A10,1X,A) 101 FORMAT(5X,A1,2X,A40,A5,2X,F5.2,1X,F5.2,8(1X,I4),2X,A10,1X,A) NALIGN=IALIGN-1 WRITE(6,'(T2,A,T10,A)')'---', + ' RS_READHSSP PROTEINS-block done' C init pointer ; aliseq contains the alignments (amino acid symbols) C stored in the following way ; '/' separates alignments C alignment(x) is stored from: C aliseq(alipointer(x)) to aliseq(ilas(x)-ifir(x)) C aliseq(1........46/48.........60/62....) C | | | C | | | C pointer pointer pointer C ali 1 ali 2 ali 3 C init pointer IPOS=1 DO I=1,NALIGN C br 2003-08-23 fast and slim C IF (IPOS.GE.MAXCORE) THEN C WRITE(6,'(A,I9,A)') C + ' *** LERROR: INCREASE MAXCORE to >',IPOS,'***' C STOP C ENDIF C end fast and slim br 2003-08-23 ALIPOINTER(I)=IPOS ILEN=ILAS(I)-IFIR(I)+1 IPOS=IPOS+ILEN C br 2003-08-23 fast and slim C ALISEQ(IPOS)='/' ALISEQ_NULL='/' C end fast and slim br 2003-08-23 IPOS=IPOS+1 ENDDO ALIPOINTER(NALIGN+1)=IPOS+1 C number of ALIGNMENTS-blocks IF (MOD(FLOAT(NALIGNORG),FLOAT(NBLOCKSIZE)).EQ. 0.0) THEN NBLOCK=NALIGNORG/NBLOCKSIZE ELSE NBLOCK=NALIGNORG/NBLOCKSIZE+1 ENDIF C search for ALIGNMENT-block DO WHILE (LINE(1:13).NE.'## ALIGNMENTS') READ(IUNIT,'(A)',ERR=99)LINE IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG alinot',LINE ENDDO READ(IUNIT,'(A)',ERR=99)LINE IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG ',LINE C loop over ALIGNMENTS-blocks C ....read in pdbno, chainid, secstr etc. IALIGN=0 IALI=0 DO IBLOCK=1,NBLOCK IRES=1 DO I=1,NRES C BR: 2003-08-23: save space C READ(IUNIT,200,ERR=99) C + PDBNO(IRES),CHAINID(IRES),PDBSEQ(IRES),SECSTR(IRES), C + COLS(IRES),BP1(IRES),BP2(IRES),SHEETLABEL(IRES), C + ACC(IRES),NOCC(IRES),VAR(IRES),CTEMP READ(IUNIT,200,ERR=99) + PDBNO_NULL,CHAINID(IRES),PDBSEQ(IRES),SECSTR(IRES), + COLS(IRES),BP1_NULL,BP2_NULL,SHEETLABEL_NULL, + ACC(IRES),NOCC(IRES),VAR_NULL,CTEMP C end save space br 2003-08-23 200 FORMAT(7X,I4,2(1X,A1),2X,A1,1X,A7,2(I4),A1,I4,2(1X,I4),2X,A) C.....fill up aliseq C IF (LDEBUG_LOCAL .EQV. .TRUE.) C + WRITE(6,*)'DBG IBLOCK=',IBLOCK, ' IRES=',I IF (I .GE. ICHAINBEG .AND. I .LE. ICHAINEND) THEN IRES=IRES+1 C br 2003-08-23 fast and slim C IF (PDBSEQ(I) .NE. '!') THEN C CALL STRPOS(CTEMP,IBEG,IEND) C DO IPOS=MAX(IBEG,1),MIN(NBLOCKSIZE,IEND) C IALI=IALIGN+IPOS C IF (CTEMP(IPOS:IPOS) .NE. ' ') THEN C J=ALIPOINTER(IPOINTER(IALI)) + C + (I-IFIR(IPOINTER(IALI))) C ALISEQ(J)=CTEMP(IPOS:IPOS) C ENDIF C ENDDO C ENDIF C end fast and slim br 2003-08-23 ENDIF ENDDO IALIGN=IALIGN+NBLOCKSIZE DO K=1,2 READ(IUNIT,'(A)',ERR=99)LINE IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG ',LINE ENDDO ENDDO WRITE(6,'(T2,A,T10,A)')'---', + ' RS_READHSSP ALIGNMENTS-block done' C read in sequence profile, entropy etc. IRES=1 DO I=1,NRES C BR 2003-08-23 save space C READ(IUNIT,300,ERR=99)(SEQPROF(IRES,K),K=1,MAXAA), C + NOCC(IRES),NDEL(IRES),NINS(IRES),ENTROPY(IRES), C + RELENT(IRES),CONSWEIGHT(IRES) READ(IUNIT,300,ERR=99)(SEQPROF(IRES,K),K=1,MAXAA), + NOCC(IRES),NDEL(IRES),NINS(IRES),ENTROPY_NULL, + RELENT_NULL,CONSWEIGHT(IRES) C end save space br 2003-08-23 IF (I .GE. ICHAINBEG .AND. I .LE. ICHAINEND) THEN IRES=IRES+1 ENDIF ENDDO 300 FORMAT(12X,20(I4),1X,3(1X,I4),1X,F7.3,3X,I4,2X,F4.2) WRITE(6,'(T2,A,T10,A)')'---', + ' RS_READHSSP PROFILE-block done' IF (LCHAIN .EQV. .TRUE.) THEN DO I=1,NALIGN IFIR(I)=IFIR(I)-ICHAINBEG+1 ILAS(I)=ILAS(I)-ICHAINBEG+1 ENDDO ENDIF C check if next line (last line in a HSSP-file) contains a '//' READ(IUNIT,'(A)',ERR=99)LINE IF ((LINE(1:2).EQ.'//').OR. + (LINE(1:13).EQ.'## INSERTION')) THEN WRITE(6,'(T2,A,T10,A,A50)')'---', + ' RS_READHSSP ok(cut 50): ',FILE_HSSP_LOC(1:50) GOTO 999 ELSE WRITE(6,'(T2,A,T10,A,A,A,A)')'***', + 'ERROR FOR RS_READHSSP: ',FILE_HSSP_LOC,' lastLine=', + LINE GOTO 99 ENDIF 99 WRITE(6,'(A,A)')'**** ERROR FOR RS_READHSSP: READING: ', + FILE_HSSP_LOC LERROR=.TRUE. NALIGN=0 SEQLENGTH=0 999 CLOSE(IUNIT) RETURN END ***** end of RS_READHSSP ***** ------------------------------------------------------------------ ***** SUB RSLIB_OPEN_FILE ***** ------------------------------------------------------------------ C---- C---- NAME : RSLIB_OPEN_FILE C---- ARG : C---- DES : opening file C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE RSLIB_OPEN_FILE(IUNIT,FILENAME,CSTRING,LERROR) C---- global parameters INCLUDE 'phdParameter.f' C IMPLICIT NONE C input C CSTATUS: 'old' or 'new' or 'unknown' C CACCESS: 'append' 'direct' C FORM: 'formatted' or 'unformatted' C IRECLEN: record length C NOTE: after opening a "old" or "unknown" file (no direct acess): C rewind the file, because some strange compilers put the file C pointer at the end ! CHARACTER*222 FILENAME,CSTRING INTEGER IUNIT,IRECLEN C output: lerror is true if open error LOGICAL LERROR C internal CHARACTER*200 TEMPSTRING,CTEMP CHARACTER*10 CNUMBER LOGICAL LRECLEN LOGICAL LNEW,LAPPEND,LUNKNOWN, + LUNFORMATTED,LDIRECT, + LOPENDONE,LSILENT INTEGER LENGTH,I,J,K,IEND C---- local function C INTEGER FILEN_STRING C---- br 2003-08-23: bullshit to avoid warning IEND=0 C init TEMPSTRING=' ' LNEW= .FALSE. LAPPEND= .FALSE. LRECLEN= .FALSE. LERROR= .FALSE. LUNKNOWN= .FALSE. LUNFORMATTED=.FALSE. LDIRECT= .FALSE. LOPENDONE= .FALSE. LSILENT= .FALSE. C IRECLEN=137 TEMPSTRING(1:)=CSTRING(1:) C IEND=FILEN_STRING(CSTRING) C TEMPSTRING(1:IEND)=CSTRING(1:IEND) C LENGTH=IEND TEMPSTRING(1:)=CSTRING(1:) CNUMBER='0123456789' LENGTH=LEN(TEMPSTRING) CALL RSLIB_LOWTOUP(TEMPSTRING,LENGTH) IF (INDEX(TEMPSTRING,'NEW').NE.0) THEN LNEW=.TRUE. ENDIF IF (INDEX(TEMPSTRING,'UNKNOWN').NE.0) THEN LUNKNOWN=.TRUE. ENDIF IF (INDEX(TEMPSTRING,'UNFORMATTED').NE.0) THEN LUNFORMATTED=.TRUE. ENDIF IF (INDEX(TEMPSTRING,'DIRECT').NE.0) THEN LDIRECT=.TRUE. ENDIF IF (INDEX(TEMPSTRING,'APPEND').NE.0) THEN LAPPEND=.TRUE. ENDIF IF (INDEX(TEMPSTRING,'SILENT').NE.0) THEN LSILENT=.TRUE. ENDIF IF (INDEX(TEMPSTRING,'RECL=').NE.0) THEN CTEMP=' ' K=INDEX(TEMPSTRING,'RECL=')+5 CTEMP(1:)=TEMPSTRING(K:) CALL STRPOS(CTEMP,I,J) C COMMENTED OUT 22-08, searching for problem with ALPHA C J=I C DO WHILE(INDEX(CNUMBER,CTEMP(J:J)).NE.0 ) C J=J+1 C ENDDO C J=J-1 READ(CTEMP(I:J),'(I6)')IRECLEN LRECLEN=.TRUE. ENDIF C IF (LNEW .EQV. .TRUE.) THEN IF (LNEW) THEN CALL RSLIB_DEL_OLDFILE(IUNIT,FILENAME) ENDIF IF (LNEW .AND. LUNFORMATTED .AND. LDIRECT ) THEN C IF ( (LNEW .EQV. .TRUE.) .AND. (LUNFORMATTED .EQV .TRUE.) .AND. C + (LDIRECT .EQV. .TRUE.) THEN OPEN(IUNIT,FILE=FILENAME,STATUS='NEW',FORM='UNFORMATTED', + ACCESS='DIRECT',RECL=IRECLEN,ERR=999) LOPENDONE=.TRUE. ELSE IF ((LNEW .EQV. .TRUE.) .AND. + (LUNFORMATTED .EQV. .TRUE.) ) THEN OPEN(IUNIT,FILE=FILENAME,STATUS='NEW',FORM='UNFORMATTED', + ERR=999) LOPENDONE=.TRUE. ELSE IF ((LNEW .EQV. .TRUE.) .AND. + (LUNFORMATTED .EQV. .FALSE.) .AND. + (LDIRECT .EQV. .TRUE.)) THEN OPEN(IUNIT,FILE=FILENAME,ACCESS='DIRECT',STATUS='NEW', + FORM='FORMATTED',RECL=IRECLEN,ERR=999) LOPENDONE=.TRUE. ELSE IF ((LNEW.EQV. .FALSE.) .AND. + (LUNFORMATTED .EQV. .TRUE.) .AND. + (LDIRECT .EQV. .TRUE.)) THEN OPEN(IUNIT,FILE=FILENAME,STATUS='OLD',FORM='UNFORMATTED', + ACCESS='DIRECT',RECL=IRECLEN,ERR=999) LOPENDONE=.TRUE. ELSE IF ((LNEW .EQV. .FALSE.) .AND. + (LUNFORMATTED .EQV. .FALSE.) .AND. + (LDIRECT .EQV. .TRUE.)) THEN OPEN(IUNIT,FILE=FILENAME,STATUS='OLD',FORM='FORMATTED', + ACCESS='DIRECT',RECL=IRECLEN,ERR=999) LOPENDONE=.TRUE. ELSE IF ((LNEW .EQV. .FALSE.) .AND. + (LUNFORMATTED .EQV. .TRUE.)) THEN OPEN(IUNIT,FILE=FILENAME,STATUS='OLD',FORM='UNFORMATTED', + ERR=999) REWIND(IUNIT) LOPENDONE=.TRUE. ELSE IF (LNEW .EQV. .TRUE.) THEN OPEN(IUNIT,FILE=FILENAME,STATUS='NEW',ERR=999) REWIND(IUNIT) LOPENDONE=.TRUE. C 2003-10 hack xxbr problem with IBM C ELSE IF ((LUNKNOWN .EQV..TRUE.) .AND. C + (LAPPEND .EQV. .TRUE.)) THEN C OPEN(IUNIT,FILE=FILENAME,STATUS='UNKNOWN',ACCESS='APPEND', C + ERR=999) C REWIND(IUNIT) C LOPENDONE=.TRUE. C ELSE IF ((LNEW .EQV. .FALSE.).AND. (LAPPEND .EQV. .TRUE.)) THEN C OPEN(IUNIT,FILE=FILENAME,STATUS='OLD',ACCESS='APPEND',ERR=999) C LOPENDONE=.TRUE. ELSE IF (LNEW .EQV. .FALSE.) THEN OPEN(IUNIT,FILE=FILENAME,STATUS='OLD',ERR=999) REWIND(IUNIT) LOPENDONE=.TRUE. ELSE OPEN(IUNIT,FILE=FILENAME,STATUS='UNKNOWN',ERR=999) rewind(iunit) LOPENDONE=.TRUE. ENDIF IF (LOPENDONE .EQV. .FALSE.) THEN WRITE(6,*)' ERROR in RSLIB_OPEN_FILE: file not opened' WRITE(6,*)' unknown specifier combination !' STOP ENDIF RETURN 999 IF (LSILENT .EQV. .FALSE.) THEN WRITE(6,*)' ERROR rs_gethssp: open file error for file: ' WRITE(6,*)FILENAME write(6,*)'lnew=',lnew, ' lunformatted=',lunformatted, + ' ldirect=',ldirect, ' lunknown=',lunknown, + ' lappend=',lappend write(6,*)' len=',LENGTH ENDIF LERROR=.TRUE. RETURN END ***** end of RSLIB_OPEN_FILE ***** ------------------------------------------------------------------ ***** SUB RSLIB_DEL_OLDFILE ***** ------------------------------------------------------------------ C---- C---- NAME : RSLIB_DEL_OLDFILE C---- ARG : C---- DES : deleting old file C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE RSLIB_DEL_OLDFILE(IUNIT,FILENAME) CHARACTER*222 FILENAME INTEGER IUNIT LOGICAL LEXIST,LOPEN INQUIRE(FILE=FILENAME,OPENED=LOPEN) IF (LOPEN .EQV. .TRUE.) THEN CLOSE(IUNIT) ENDIF INQUIRE(FILE=FILENAME,EXIST=LEXIST) IF (LEXIST .EQV. .TRUE.) THEN OPEN(IUNIT,FILE=FILENAME,STATUS='OLD') CLOSE(IUNIT,STATUS='DELETE') ENDIF END ***** end of RSLIB_DEL_OLDFILE ***** ------------------------------------------------------------------ ***** SUB RSLIB_LOWTOUP ***** ------------------------------------------------------------------ C---- C---- NAME : RSLIB_LOWTOUP C---- ARG : C---- DES : changing case of string. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE RSLIB_LOWTOUP(STRING,LENGTH) C changed by RS (speed up) CHARACTER*222 STRING*(*) INTEGER LENGTH DO I=1,LENGTH IF (STRING(I:I).GE.'a' .AND. STRING(I:I).LE.'z') THEN STRING(I:I)=CHAR( ICHAR(STRING(I:I))-32 ) ENDIF ENDDO RETURN END ***** end of RSLIB_LOWTOUP ***** ------------------------------------------------------------------ ***** SUB SCOUNT_HYDROPHOB ***** ------------------------------------------------------------------ C---- C---- NAME : SCOUNT_HYDROPHOB C---- ARG : C---- DES : The number of adjacent hydrophibic residues is counted. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The number of adjacent hydrophibic residues is * * -------- counted. * * in variables: KUNIT,NUMRES, RESNAME * * out variables: Potential transmembrane regions: if more than * * -------------- 15: A, V, F, P, M, I, L adjacent * * called by: DATAOT * * SBRs calling: from lib-comp.f: * * -------------- FILENSTRING * *----------------------------------------------------------------------* SUBROUTINE SCOUNT_HYDROPHOB(KUNIT) C---- include parameter files INCLUDE 'phdParameter.f' C---- local variables INTEGER HCOUNT,MUE,KUNIT,ICOUNT,ITER, + BEGSEG(1:20),ENDSEG(1:20) LOGICAL LHELP,LFOUND ******------------------------------*-----------------------------****** C---- defaults LFOUND=.FALSE. MUE=0 ICOUNT=0 DO WHILE (MUE.LT.NUMRES) HCOUNT=0 LHELP=.TRUE. DO WHILE((MUE.LT.NUMRES).AND.LHELP) MUE=MUE+1 IF ((RESNAME(MUE).EQ.'A').OR.(RESNAME(MUE).EQ.'V') + .OR.(RESNAME(MUE).EQ.'F').OR.(RESNAME(MUE).EQ.'W') + .OR.(RESNAME(MUE).EQ.'M').OR.(RESNAME(MUE).EQ.'Y') + .OR.(RESNAME(MUE).EQ.'I').OR.(RESNAME(MUE).EQ.'L')) THEN HCOUNT=HCOUNT+1 ELSE LHELP=.FALSE. END IF END DO IF (HCOUNT.GT.15) THEN ICOUNT=ICOUNT+1 LFOUND=.TRUE. BEGSEG(ICOUNT)=MUE-HCOUNT ENDSEG(ICOUNT)=MUE END IF END DO IF (LFOUND .EQV. .TRUE.) THEN WRITE(KUNIT,'(T2,A,T10,A)')'---', + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~' WRITE(KUNIT,'(T2,A)')'---' WRITE(KUNIT,'(T2,A,T10,A)')'---', + 'PHD has been trained only on few membrane proteins.' WRITE(KUNIT,'(T2,A,T10,A)')'---', + 'Consequently, the expected accuracy on these is very low.' WRITE(KUNIT,'(T2,A,T10,A)')'---', + 'The sequence you sent, seems to have transmembrane segments' WRITE(KUNIT,'(T2,A,T10,A)')'---', + '(probably helical) at the residue positions:' WRITE(KUNIT,'(T2,A)')'---' DO ITER=1,ICOUNT WRITE(KUNIT,'(T2,A,T10,A,T20,I3,T25,A,T35,I5,T42,A, + T48,I5)')'---','segment',ITER, + 'begin:',BEGSEG(ITER),'end:',ENDSEG(ITER) END DO WRITE(KUNIT,'(T2,A)')'---' WRITE(KUNIT,'(T2,A,T10,A)')'---', + 'For these positions the prediction of secondary structure as' IF (ICOUNT.GT.1) THEN WRITE(KUNIT,'(T2,A,T10,A)')'---', + 'given above might be misleading. The segments are ' WRITE(KUNIT,'(T2,A,T10,A)')'---','probably helices!' ELSE WRITE(KUNIT,'(T2,A,T10,A)')'---', + 'given above is possibly misleading. The segment is ' WRITE(KUNIT,'(T2,A,T10,A)')'---', + 'probably a helix!' END IF WRITE(KUNIT,'(T2,A)')'---' WRITE(KUNIT,'(T2,A,T10,A)')'---', + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~' WRITE(KUNIT,*) WRITE(KUNIT,*) END IF C----------------------------------------------------------------------* C---- initial check of variables passed -----* C----------------------------------------------------------------------* END ***** end of SCOUNT_HYDROPHOB ***** ------------------------------------------------------------------ ***** SUB SR_FILTER_EXP ***** ------------------------------------------------------------------ C---- C---- NAME : SR_FILTER_EXP C---- ARG : C---- DES : Computes nearest (3) neighbour averages for real input C---- DES : vector. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: computes nearest (3) neighbour averages for * * -------- real input vector * * input: OUTPUT(1:numout) * * output: OUTFIL(1:numout) * *----------------------------------------------------------------------* SUBROUTINE SR_FILTER_EXP(NUMOUTMAX,NUMOUT,OUTPUT,OUTFIL) INTEGER ITEXP,NUMOUTMAX,NUMOUT REAL OUTPUT(1:NUMOUTMAX),OUTFIL(1:NUMOUTMAX),SUM ************************************************************************ DO ITEXP=1,NUMOUT IF (ITEXP.EQ.1) THEN OUTFIL(ITEXP)=(OUTPUT(1)+OUTPUT(2))/2. ELSEIF (ITEXP.EQ.NUMOUT) THEN OUTFIL(ITEXP)=(OUTPUT(NUMOUT-1)+OUTPUT(NUMOUT))/2. ELSE SUM=0 DO IT=-1,1 SUM=SUM+OUTPUT(ITEXP+IT) END DO OUTFIL(ITEXP)=SUM/3. END IF END DO END ***** end of SR_FILTER_EXP ***** ------------------------------------------------------------------ ***** SUB TRANSAA ***** ------------------------------------------------------------------ C---- C---- NAME : TRANSAA C---- ARG : C---- DES : The 20 amino acid one letter names (+unknown+solvent C---- DES : +Asx +Glx) are 'transcribed' into a vector with C---- DES : NCODEUNT components 0,1 C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: the 20 amino acid one letter names (+unknown * * -------- +solvent+Asx+Glx) are 'transcribed' into a vector* * with NCODEUNT components 0,1 * * output variable AACODE,AABIT,AAHEX * * --------------- and: SSCODE * * external SBR: SIBIT1 (HEXNUM,BITPOW,BITVEC) * * converts the integer hexadecimal number HEXNUM into an * * integer vector BITVEC(1:(BITPOW+1)) containing 1/0 only, * * in such a way that: * * sum/j=1,(BITPOW+1) [2**(BITVEC(j-1))]=HEXNUM * * note: 2**BITPOW >= HEXNUM! * * BITVEC(1) codes 2**0! * * procedure: a one at position of CODEVECTOR means amino * * --------- acid * * 1 --> V (VAL: Valine) * * 2 --> L (LEU: Leucine) * * 3 --> I (ILE: Isoleucine) * * 4 --> M (MET: Methiomine) * * 5 --> F (PHE: Phenylalamine) * * 6 --> W (TRP: Tryptophan) * * 7 --> Y (TYR: Tyrosine) * * 8 --> G (GLY: Glycine) * * 9 --> A (ALA: Alanine) * * 10 --> P (PRO: Proline) * * 11 --> S (SER: Serine) * * 12 --> T (THR: Threonine) * * 13 --> C (CYS: Cysteine) * * 14 --> H (HIS: Histidine) * * 15 --> R (ARG: Arginine) * * 16 --> K (LYS: Lysine) * * 17 --> Q (GLN: Glutamine) * * 18 --> E (GLU: Glutamate) * * 19 --> N (ASN: Aspargine) * * 20 --> D (ASP: Aspartate) * * 21 --> U ( : Solvent 'ulterior') * * 22 --> X ( : unknown) * * 23 --> B (Asx: D or N) * * 24 --> Z (Glx: Q or E) * * SSCODE(1) --> H (helix) = H,I,G * * SSCODE(2) --> E (sheet) = E, B * * SSCODE(3) --> C (no pred.) = T, S, ' ' * * if four classes: * * SSCODE(3) --> T (turn) = T * * SSCODE(4) --> C (no pred.) = S, ' ' * * if five classes: * * SSCODE(3) --> T (turn) = T * * SSCODE(4) --> S (bend) = S * *----------------------------------------------------------------------* SUBROUTINE TRANSAA C---- parameters/global variables INCLUDE 'phdParameter.f' INTEGER ITER1,ITER2,ITEXP ******------------------------------*-----------------------------****** C AACODE(1)='A',(2)='R',(3)='N',(4)='D',(5)='C'.(6)='Q',(7)='E' C (8)='G',(9)='H',(10)='I',(11)='L',(12)='K',(13)='M',(14)='F' C (15)='P',(16)='S',(17)='T',(18)='W',(19)='Y',(20)='V',(21)='X' C (22)='U' C---- succession according to HSSP scheme AACODE(1)='V' AACODE(2)='L' AACODE(3)='I' AACODE(4)='M' AACODE(5)='F' AACODE(6)='W' AACODE(7)='Y' AACODE(8)='G' AACODE(9)='A' AACODE(10)='P' AACODE(11)='S' AACODE(12)='T' AACODE(13)='C' AACODE(14)='H' AACODE(15)='R' AACODE(16)='K' AACODE(17)='Q' AACODE(18)='E' AACODE(19)='N' AACODE(20)='D' AACODE(21)='U' AACODE24='VLIMFWYGAPSTCHRKQENDUXBZ' AACODE_LOWC='abcdefghijklmnopqrstuvwxyz' C---- C---- converting to binary vector (profile real) C---- DO ITER1=1,NBIOLOBJ DO ITER2=1,NBIOLOBJ IF (ITER1.EQ.ITER2) THEN AABIT(ITER1,ITER2)=1 ELSE AABIT(ITER1,ITER2)=0 END IF END DO END DO C---- C---- encoding the secondary structure elements, i.e. the classes of C---- secondary structure to be distinguished C---- IF (NSECEL.EQ.3) THEN SSCODE(1)='H' SSCODE(2)='E' SSCODE(3)=' ' ELSEIF (NSECEL.EQ.4) THEN SSCODE(1)='H' SSCODE(2)='E' SSCODE(3)='T' SSCODE(4)=' ' ELSEIF (NSECEL.EQ.2) THEN SSCODE(1)='H' SSCODE(2)=' ' ELSEIF (NSECEL.EQ.5) THEN SSCODE(1)='H' SSCODE(2)='E' SSCODE(3)='T' SSCODE(4)='S' SSCODE(5)=' ' ELSEIF (MODESECSTRON(1:9).EQ.'SECONDARY') THEN WRITE(6,*)' NSECEL not properly chosen: 3<=NSECEL<=5' WRITE(6,*)' stopped in TRANSAA, stop 2' STOP END IF C---- C---- coding exposure state names C---- DO ITEXP=1,10 C version real values (0-1) C IF (THREXP10ST(ITEXP).LT.THREXP3ST(2)) THEN C EXPCODE(ITEXP)='b' C ELSEIF (THREXP10ST(ITEXP).GE.THREXP3ST(3)) THEN C EXPCODE(ITEXP)='e' C ELSE C EXPCODE(ITEXP)='i' C END IF C version integer values (0-100) IF (THREXP10STI(ITEXP).LT.THREXP3STI(2)) THEN EXPCODE(ITEXP)='b' ELSEIF (THREXP10STI(ITEXP).GE.THREXP3STI(3)) THEN EXPCODE(ITEXP)='e' ELSE EXPCODE(ITEXP)='i' END IF END DO END ***** end of TRANSAA ***** ------------------------------------------------------------------ ***** SUB TRIGGER ***** ------------------------------------------------------------------ C---- C---- NAME : TRIGGER C---- ARG : C---- DES : Executes the network trigger function input --> C---- DES : output,for a particular architecture ACTCHI C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: This SBR executes the network trigger function * * -------- input --> output,for a particular architecture * * ACTCHI. * * const. passed: ACTCHI, ACTFILE, CONTROLCHAR, NUMRES, NSECEL * * var. passed: in: INPUT, out: OUTPUT * * var. read: NUMIN,NUMHID,NUMOUT,JUNCTION1ST,JUNCTION2ND * * ext. SBR: SFILEOPEN (lib-unix) * * ext. function EXP (should be available) * * called by: SBR NETWORK * * calling: SBR READARCH * *----------------------------------------------------------------------* SUBROUTINE TRIGGER C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE,ITIN,ITHID,ITOUT REAL INVABW,NEGINVABW,INTERHID ******------------------------------*-----------------------------****** * MUE,ITIN,ITHID,ITOUT: iteration variables * * INPUT (NUMHID,NUMIN+) input matrix * * is used * * INVABW =1/ABW for avoiding too high quantities * * JUNCTION1ST(j,i) connection of the first layer, i.e. between * * the input unit j and the hidden one i * * JUNCTION2ND(j,i) connection of the second layer, i.e. between * * the hidden unit j and the output one i * * LOCFIELD the local fields (abbr.: h) are defined by: * * h(I,MUE )= sum(k,{J(k,i)*s(k,mue))+b(i,mue) * * NEGINVABW =-INVABW * * NUMHID number of hidden units: 2**NUMHID > NUMOUT * * NUMIN number of input units = (WIDTH + LENGTH)*NCODEUNT* * NUMOUT number of output u. = WIDTH * LENGTH * BITACC * * OUTPUT(NUMOUT,NUMHID+) output matrix * ******------------------------------*-----------------------------****** C---- cutoffs INVABW=1./ABW NEGINVABW=(-1.)*INVABW C-------------------------------------------------- C---- loop over all residues ----- C-------------------------------------------------- DO MUE=1,NUMRES C------- compute local fields for hidden unit DO ITHID=1,NUMHID LOCFIELD1(ITHID)=0. DO ITIN=1,NUMIN IF (INPUT(ITIN,MUE).NE.0.) THEN LOCFIELD1(ITHID)=LOCFIELD1(ITHID) + +JUNCTION1ST(ITIN,ITHID)*INPUT(ITIN,MUE) END IF END DO C---------- threshold units C DO ITIN=(NUMIN+1),(NUMIN+NSECEL) DO ITIN=(NUMIN+1),(NUMIN+NUMOUT) LOCFIELD1(ITHID)=LOCFIELD1(ITHID)+JUNCTION1ST(ITIN,ITHID) END DO END DO C------- compute output DO ITOUT=1,NUMOUT LOCFIELD2(ITOUT)=0. C---------- PARALLEL C---------- DO ITHID=1,NUMHID C------------- VECTOR IF (ABS(LOCFIELD1(ITHID)).LT.INVABW) THEN INTERHID=(1./(1.+EXP (- LOCFIELD1(ITHID) ) )) LOCFIELD2(ITOUT)=LOCFIELD2(ITOUT)+ + (JUNCTION2ND(ITHID,ITOUT)*INTERHID) ELSEIF (LOCFIELD1(ITHID).LE.NEGINVABW) THEN INTERHID=0. ELSEIF (LOCFIELD1(ITHID).GE.INVABW) THEN LOCFIELD2(ITOUT)=LOCFIELD2(ITOUT) + +JUNCTION2ND(ITHID,ITOUT) INTERHID=1. ELSE WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR in SBR TRIGGER: wrong assignment for ' WRITE(6,'(T2,A,T10,A)')'***', + 'intermediate output!! Stopped at 12-10-92-1' STOP END IF C------------- END VECTOR END DO C---------- C---------- END PARALLEL C---------- threshold units C DO ITHID=(NUMHID+1),(NUMHID+NSECEL) DO ITHID=(NUMHID+1),(NUMHID+NUMOUT) LOCFIELD2(ITOUT)=LOCFIELD2(ITOUT) + +JUNCTION2ND(ITHID,ITOUT) END DO C---------- output IF ((ABS(LOCFIELD2(ITOUT)).LT.INVABW).AND. + (LOCFIELD2(ITOUT).GT.NEGINVABW)) THEN OUTPUT(ITOUT,MUE)=1./(1.+ EXP (- LOCFIELD2(ITOUT) )) ELSEIF (LOCFIELD2(ITOUT).LE.NEGINVABW) THEN OUTPUT(ITOUT,MUE)=0. ELSEIF (LOCFIELD2(ITOUT).GE.INVABW) THEN OUTPUT(ITOUT,MUE)=1. ELSE WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR in SBR TRIGGER: wrong assignment for output!' WRITE(6,'(T2,A,T10,A)')'***', + 'stopped at 12-10-92-2' STOP END IF END DO C------- end of loop over output units END DO C-------------------------------------------------- C---- end of loop over all residues ---- C-------------------------------------------------- END ***** end of TRIGGER ***** ------------------------------------------------------------------ ***** SUB TXTRES ***** ------------------------------------------------------------------ C---- C---- NAME : TXTRES C---- ARG : C---- DES : The results of the prediction are written. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The results of the prediction are written into * * -------- the output. * * control: MODESECSTRON * * input: NUMRES, NUMNETJURY * * ------ RESNAME, OUTBINCHAR, PROTNAME * * external subroutines: TIME,DATE * *----------------------------------------------------------------------* SUBROUTINE TXTRES C---- global parameters * INCLUDE 'phdParameter.f' C---- local variables INTEGER ITER LOGICAL LHELP ******------------------------------*-----------------------------****** WRITE(6,*) WRITE(6,'(T20,A)')' **************************************' WRITE(6,'(T20,A)')' ***** Data of program secstron *****' WRITE(6,'(T20,A)')' **************************************' WRITE(6,*) WRITE(6,*) WRITE(6,*) WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,80A1)')('-',ITER=1,80) WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,A)')'---' C---- call SCFDATE from external lib-syst-unix.f LHELP=.TRUE. C CALL SCFDATE(2,LHELP,STARTDATE) C---- CALL SRDTIME from external lib-syst-unix.f c$$$ CALL SRDTIME(2,LHELP) C---- writing header C ================= C CALL WRTPHDHEADER(6) C ================= C---- writing content of secondary structure and paper to referee C ================== CALL WRTCONTENT(6) C ================== WRITE(6,*) WRITE(6,*) WRITE(6,'(T10,A,T30,A50)')'Prediction for:',FILE_HSSP WRITE(6,'(T10,A)')'---------------' WRITE(6,*) WRITE(6,*) IF (MODESECSTRON(1:9).EQ.'SECONDARY') THEN C =============== CALL WRTPRED(6) C =============== ELSEIF (MODESECSTRON.EQ.'EXPOSURE') THEN C ============== CALL WRTEXP(6) C ============== END IF WRITE(6,*) WRITE(6,*) WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,A,T10,A)')'---', + 'Note: prediction has been written into file:' WRITE(6,'(T2,A,T10,A50)')'---',FILEPRED WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,70A1)')('-',ITER=1,70) WRITE(6,'(T2,A)')'---' WRITE(6,'(T2,A)')'---' END ***** end of TXTRES ***** ------------------------------------------------------------------ ***** SUB WINDIR ***** ------------------------------------------------------------------ C---- C---- NAME : WINDIR C---- ARG : C---- DES : The input and the desired output for every case are C---- DES : read and written into INPUT/DESIRED. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The input and the desired output for every case * * -------- are read and written into INPUT/DESIRED. * * control param.: MODECODEIN, FLAGTRAIN, FLAGTESTNN, * * --------------- NUMPROTTRAIN/TEST, NUMRESTRAIN/TEST * * TRAIN/TESTINGSET * * input parameter:CONTROLCHAR, * * output param.: * * input variables:RESPROF, POINTBEG, TRANSLISTTRAIN/TEST * * output variab.: INPUT,DESIRED,TSTINPUT,TSTCMPRSN * * for SBR WINCUT: PROFMAX, PROFINTERV, CASCINTERV, CASCACC * * called from: NETWORK * * SBRs calling: WINASS, WININCOMPOSITION, WININCOMPOSITION_ALL, * * -------------- WINDIRINI, WININLENGTH, WININDISTCAPS * * hierarchy: -> WINDIRINI * * -> WINASS (assign INPUT, DESIRED, + test) * * -> WININDIR * * a) -> WININAA (INPUT=CODEVECTOR for Seq.-Str.) * * -> CODEIN * * b) -> WININSTR(INPUT=CODEVECTOR for Str.-Str.) * * -> CODESTR * * -> WININCOMPOSTION_ALL * * -> WININCOMPOSTION * * -> WININLENGTH * * -> WININDISTCAPS * * procedure: For each residue R0, resp. for each object being * * --------- composed by LENGTHOBJ, NUMNEIGH neighbouring amino * acids (resp. objects) are written to both sides * * thus forming a string of 2*NUMNEIGH + 1 residues * * with residue R0 being in the centre. Each of * * these residues is encoded by a binary vector of * * dimension NCODEUNT. This final string of length * * (2*NUMNEIGH+1)*NCODEUNT represents the INPUT vec-* * tor for case R0. The corresponding output vector* * DESIRED simply contains the properties currently * * to be predicted, e.g. the secondary structure (see * commentary in parameter file for PREDICTIONTYPE) * *----------------------------------------------------------------------* SUBROUTINE WINDIR C---- global parameters INCLUDE 'phdParameter.f' C---- local parameters LOGICAL LCHECK_WRITE PARAMETER (LCHECK_WRITE=.FALSE.) C PARAMETER (LCHECK_WRITE=.TRUE.) C---- local variables INTEGER MUE,IT ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- defaults ----- C-------------------------------------------------- C ============== CALL WINDIRINI C ============== C----------------------------------------------------------------------- C---- assign INPUT/DESIRED for TESTing set------------------------------ C----------------------------------------------------------------------- C---- loop over all residues for particular protein DO MUE=1,NUMRES ACTPOS=MUE C------- case discrimination according to actual mue, i.e. the C------- position of the actual central object within the protein C------- NUMNEIGH < central position <= NUMRES-NUMNEIGH IF ((NUMNEIGH.LT.MUE).AND.(MUE.LE.(NUMRES-NUMNEIGH))) THEN CASEDISCR='MIDDLE' ACTSOLVADDBEG=0 ACTSOLVADDEND=0 ACTSOLVADDEND2=0 C------- NUMNEIGH >= central position <= NUMRES-NUMNEIGH ELSEIF ((MUE.LE.NUMNEIGH).AND.(MUE.LE.(NUMRES-NUMNEIGH))) THEN CASEDISCR='ADDBEG' ACTSOLVADDBEG=NUMNEIGH-MUE+1 ACTSOLVADDEND=0 ACTSOLVADDEND2=0 C------- NUMRES-NUMNEIGH < central position <= NUMRES ELSEIF ((NUMNEIGH.LT.MUE).AND.(MUE.GT.(NUMRES-NUMNEIGH)).AND. + (MUE.LE.NUMRES)) THEN CASEDISCR='ADDEND' ACTSOLVADDBEG=0 ACTSOLVADDEND=NUMNEIGH-(NUMRES-MUE) ACTSOLVADDEND2=0 C------- NUMRES < central position <= NUMRES ELSEIF ((NUMNEIGH.LT.MUE).AND.(MUE.GT.NUMRES)) THEN CASEDISCR='ADDEND2' ACTSOLVADDBEG=0 ACTSOLVADDEND=NUMNEIGH ACTSOLVADDEND2=-(NUMRES-MUE) C------- NUMNEIGH >= central position > NUMRES-NUMNEIGH <= NUMRES ELSEIF ((NUMNEIGH.GE.MUE).AND.(MUE.GT.(NUMRES-NUMNEIGH)).AND. + (MUE.LE.NUMRES)) THEN CASEDISCR='ADDBOTH' ACTSOLVADDBEG=NUMNEIGH-MUE+1 ACTSOLVADDEND=NUMNEIGH-(NUMRES-MUE) ACTSOLVADDEND2=0 C------- NUMNEIGH >= central position > NUMRES ELSEIF ((NUMNEIGH.GE.MUE).AND.(MUE.GT.NUMRES)) THEN CASEDISCR='ADDBOTH2' ACTSOLVADDBEG=NUMNEIGH-MUE+1 ACTSOLVADDEND=NUMNEIGH ACTSOLVADDEND2=-(NUMRES-MUE) ELSE WRITE(6,*)' fault in WINCUT, case discrimination' WRITE(6,*)' name: ',PROTNAME(1) WRITE(6,*)'length=',NUMRES,' mue=',MUE STOP END IF C------- end of case discrimination C------- assign INPUT/DESIRED IF (CASEDISCR.NE.'REJECT') THEN C =========== CALL WINASS C =========== ELSE WRITE(6,*)' Fault for casediscrimination, WINCUT' WRITE(6,*)' training set, stop 1.2' STOP END IF C-------------------------------------------------- C------- add additional unit for amino acid ------- C------- composition ------- C-------------------------------------------------- IF (LOGI_COMPOSITION .EQV. .TRUE.) THEN C---------- for N-term: compute composition of whole protein IF (MUE.EQ.1) THEN C ========================= CALL WININCOMPOSITION_ALL C ========================= END IF C---------- compute composition for current window C ===================== CALL WININCOMPOSITION C ===================== END IF C-------------------------------------------------- C------- add additional unit for protein length C-------------------------------------------------- IF (LOGI_LENGTH .EQV. .TRUE.) THEN C ================ CALL WININLENGTH C ================ END IF C-------------------------------------------------- C------- add additional units for distance to caps C-------------------------------------------------- IF (LOGI_DISTCAPS .EQV. .TRUE.) THEN C ================== CALL WININDISTCAPS C ================== END IF C-------------------------------------------------- C------- control write out! xx C-------------------------------------------------- IF (LCHECK_WRITE .EQV. .TRUE.) THEN IF (MUE.GE.17) THEN WRITE(6,*)MUE WRITE(6,'(24I3)') + (int(100*INPUT(IT,MUE)),IT=1,NUMIN) END IF IF (MUE.EQ.27) THEN WRITE(6,*)'numin=',numin,' out=',numout STOP END IF END IF END DO C---- end of loop over mue (residues of protein nue) C----------------------------------------------------------------------- C---- end of testing set------------------------------------------------ C----------------------------------------------------------------------- END ***** end of WINDIR ***** ------------------------------------------------------------------ ***** SUB WINDIRINI ***** ------------------------------------------------------------------ C---- C---- NAME : WINDIRINI C---- ARG : C---- DES : initialises some of the control variables used throughout C---- DES : programs called by WINDIR. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: initialises some of the control variables used * * -------- throughout programs called by WINDIR * * const. passed: CONTROLCHAR, MODESECSTRON, MODEASSCAS, MODEASSSTR* * var. passed: out: LOGI_REALINPUT, * * ------------ LOGI_COMPOSITION, *_LENGTH, *_DISTCAPS * * LOGI_CONS, *_INDEL, * * ACTACC, ACTINTERVALL, * * BEGUNITS_COMPOSITION, *_LENGTH, *_DISTCAPS * * PROFMAX, PROFINTERV, CASCINTERV, ACTNALIGN * * var. read: PROFACC, CASCACC, NBIOLOBJ, NUMNEIGH, NCODEUNT, * * ---------- NUMRES, RESPROF(mue), NUMNALIGN(nue=1) * * NUNITS_LENGTH, *_DISTCAPS * * called by: WINDIR * *----------------------------------------------------------------------* SUBROUTINE WINDIRINI C---- global parameters INCLUDE 'phdParameter.f' C---- local variables INTEGER ADDGLOBAL,MUE,ITPROF ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- is input real ? C-------------------------------------------------- IF ( ((CONTROLCHAR.EQ.'FST').AND. + (MODEASSCAS(ACTCHI).EQ.'PROFILE-BIN')) .OR. + ((CONTROLCHAR.EQ.'SND') .AND. + (MODEASSSTR(ACTCHI)(1:5).EQ.'REAL-')) ) THEN LOGI_REALINPUT=.FALSE. ELSE LOGI_REALINPUT=.TRUE. END IF C---- security check IF ( (MODESECSTRON.EQ.'EXPOSURE').AND.(CONTROLCHAR.EQ.'SND')) THEN WRITE(6,*)'*** WINDIRINI: check whether or not it is correct' WRITE(6,*)'*** to assume by default that 2nd archis are' WRITE(6,*)'*** not coming with real input!' STOP END IF C-------------------------------------------------- C---- any global information ? C-------------------------------------------------- LOGI_CONS=.FALSE. LOGI_INDEL=.FALSE. LOGI_COMPOSITION=.FALSE. LOGI_LENGTH=.FALSE. LOGI_DISTCAPS=.FALSE. IF (CONTROLCHAR.EQ.'FST') THEN IF ( (MODEASSCAS(ACTCHI).EQ.'PROFILE-REAL').OR. + (MODEASSCAS(ACTCHI).EQ.'ALPHABET') ) THEN LOGI_CONS=.FALSE. ELSEIF ( (MODEASSCAS(ACTCHI).EQ.'PROFILE-REAL-CONS').OR. + (MODEASSCAS(ACTCHI).EQ.'P-REAL-C') ) THEN LOGI_CONS=.TRUE. ELSEIF (MODEASSCAS(ACTCHI).EQ.'P-REAL-CONS-INDEL') THEN LOGI_CONS=.TRUE. LOGI_INDEL=.TRUE. ELSEIF ( (MODEASSCAS(ACTCHI).EQ.'P-REAL-CONS-INCOM').OR. + (MODEASSCAS(ACTCHI).EQ.'P-REAL-CIC') ) THEN LOGI_CONS=.TRUE. LOGI_INDEL=.TRUE. LOGI_COMPOSITION=.TRUE. ELSEIF ( (MODEASSCAS(ACTCHI).EQ.'P-REAL-CONS-COMPO').OR. + (MODEASSCAS(ACTCHI).EQ.'P-REAL-CC') ) THEN LOGI_CONS=.TRUE. LOGI_COMPOSITION=.TRUE. ELSEIF (MODEASSCAS(ACTCHI).EQ.'P-REAL-CCLD') THEN LOGI_CONS=.TRUE. LOGI_COMPOSITION=.TRUE. LOGI_LENGTH=.TRUE. LOGI_DISTCAPS=.TRUE. ELSEIF (MODEASSCAS(ACTCHI).EQ.'P-REAL-CICLD') THEN LOGI_CONS=.TRUE. LOGI_INDEL=.TRUE. LOGI_COMPOSITION=.TRUE. LOGI_LENGTH=.TRUE. LOGI_DISTCAPS=.TRUE. ELSE WRITE(6,'(T2,A,T10,A)')'***','WINDIRINI: trouble '// + 'initialising LOGI_* !' WRITE(6,'(T2,A,T10,A)')'***','stopped 6-3-94b' STOP END IF ELSEIF (CONTROLCHAR.EQ.'SND') THEN IF ( (MODEASSSTR(ACTCHI).EQ.'REAL-CONS').OR. + (MODEASSSTR(ACTCHI).EQ.'REAL-CONS93') ) THEN LOGI_CONS=.TRUE. ELSEIF (MODEASSSTR(ACTCHI).EQ.'REAL-CONS-INDEL') THEN LOGI_CONS=.TRUE. LOGI_INDEL=.TRUE. ELSEIF ( (MODEASSSTR(ACTCHI).EQ.'REAL-CONS-COMPO').OR. + (MODEASSSTR(ACTCHI).EQ.'REAL-CC') ) THEN LOGI_CONS=.TRUE. LOGI_COMPOSITION=.TRUE. ELSEIF (MODEASSSTR(ACTCHI).EQ.'REAL-CCLD') THEN LOGI_CONS=.TRUE. LOGI_COMPOSITION=.TRUE. LOGI_LENGTH=.TRUE. LOGI_DISTCAPS=.TRUE. ELSEIF (MODEASSSTR(ACTCHI).EQ.'RR-CCLD') THEN LOGI_CONS=.TRUE. LOGI_COMPOSITION=.TRUE. LOGI_LENGTH=.TRUE. LOGI_DISTCAPS=.TRUE. ELSEIF (MODEASSSTR(ACTCHI).NE.'REAL-OCT') THEN WRITE(6,'(T2,A,T10,A)')'***','WINDIRINI: trouble '// + 'initialising LOGI_* !' WRITE(6,'(T2,A,T10,A,T20,A1,A,A1)')'***', + 'MODEASSSTR=','|',MODEASSSTR(ACTCHI),'|' WRITE(6,'(T2,A,T10,A)')'***','stopped 6-3-94c' STOP END IF ELSE WRITE(6,'(T2,A,T10,A)')'***','ERROR in WINDIRINI '// + 'CONTROLCHAR (or MODEASSCAS/STR) wrong ! 6-2-94a' STOP END IF C-------------------------------------------------- C---- intervalls and accuracy for binary input C-------------------------------------------------- IF (LOGI_REALINPUT .EQV. .FALSE.) THEN IF (CONTROLCHAR.EQ.'FST') THEN ACTACC=PROFACC ELSE ACTACC=CASCACC END IF ACTINTERVALL=1/MAX(1.,REAL(ACTACC)) END IF C-------------------------------------------------- C---- begin of global units C-------------------------------------------------- ADDGLOBAL=0 IF (LOGI_COMPOSITION .EQV. .TRUE.) THEN BEGUNITS_COMPOSITION=(2*NUMNEIGH+1)*NCODEUNT+1 IF (LOGI_REALINPUT .EQV. .FALSE.) THEN ADDGLOBAL=NBIOLOBJ*(ACTACC-1) ELSE ADDGLOBAL=NBIOLOBJ END IF END IF IF (LOGI_LENGTH .EQV. .TRUE.) THEN BEGUNITS_LENGTH=(2*NUMNEIGH+1)*NCODEUNT+ADDGLOBAL+1 IF (LOGI_REALINPUT .EQV. .FALSE.) THEN ADDGLOBAL=ADDGLOBAL+(NUNITS_LENGTH*(ACTACC-1)) ELSE ADDGLOBAL=ADDGLOBAL+NUNITS_LENGTH END IF END IF IF (LOGI_DISTCAPS .EQV. .TRUE.) THEN BEGUNITS_DISTCAPS=(2*NUMNEIGH+1)*NCODEUNT+ADDGLOBAL+1 IF (LOGI_REALINPUT .EQV. .FALSE.) THEN ADDGLOBAL=ADDGLOBAL+(2*NUNITS_DISTCAPS*(ACTACC-1)) + ELSE ADDGLOBAL=ADDGLOBAL+2*NUNITS_DISTCAPS END IF END IF C-------------------------------------------------- C---- for the input being a profile: find out ----- C---- maximum ----- C-------------------------------------------------- PROFMAX=0 DO MUE=1,NUMRES DO ITPROF=1,(NBIOLOBJ-1) IF (RESPROF(MUE,ITPROF).GT.PROFMAX) THEN PROFMAX=RESPROF(MUE,ITPROF) END IF END DO END DO PROFINTERV=REAL(PROFMAX)/REAL(PROFACC-2) CASCINTERV=100./REAL(CASCACC-2) ACTNALIGN=NUMNALIGN(1) END ***** end of WINDIRINI ***** ------------------------------------------------------------------ ***** SUB WINASS ***** ------------------------------------------------------------------ C---- C---- NAME : WINASS C---- ARG : C---- DES : For a given window (WINCUT) the vectors for the input C---- DES : and desired output are assigned. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: For a given window (WINCUT) the vectors for the * * -------- input and desired output are assigned. * * control param.: PREDMODE, LENGTHOBJ, * * --------------- NSECEL, NCODEUNT, NUMNEIGH * * input parameter:ACTPOS, ACTPOS * * ----------------ACTSOLVADDBEG, ACTSOLVADDEND2, ACTSOLVADDEND * * output param.: ACTSTART, ACTRESIDUE, ACTCONSERV, * * -------------- ACTCONSWEIGHT, ACTPOS, ACTREGION, ACTITER, * * input variables:RESNAME, RESVAR, RESCONSWEIGHT, * * output variab.: INPUT, DESIRED, TSTCMPRSN * * called from: WINCUT * * SBRs calling: WININDIR, WINOUT * * procedure: see SBR WINDIR * *----------------------------------------------------------------------* SUBROUTINE WINASS C---- global parameters INCLUDE 'phdParameter.f' C---- local variables INTEGER ITER1,ITAA LOGICAL LHELP ******------------------------------*-----------------------------****** * MUE,IT* serve as iteration variables * * IHELP intermediately required variable * * ACTCASE0 used to memorize the actual case if entering into* * the loop over the objects * * ACTPOS0 same as ACTCASE0 for the position * ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- defaults C-------------------------------------------------- C---- set zero C ----------- CALL SISTZ1(ACTCOMPOSITION,NBIOLOBJMAX) C ----------- C-------------------------------------------------- C---- add solvents at begin ----- C-------------------------------------------------- DO ITER1=1,ACTSOLVADDBEG ACTRESIDUE='U' C------- fork to distinguish between first and second net ACTREGION='ADDBEG' ACTITER=ITER1 ACTSTART=(ITER1-1)*NCODEUNT C ============= CALL WININDIR C ============= END DO C---- sum up for input of amino acid composition IF (LOGI_COMPOSITION .EQV. .TRUE.) THEN ACTCOMPOSITION(NBIOLOBJ)=ACTSOLVADDBEG END IF C-------------------------------------------------- C---- read NUMNEIGH amino acids before central one- C-------------------------------------------------- DO ITER1=(ACTSOLVADDBEG+1),NUMNEIGH ACTRESIDUE=RESNAME(ACTPOS-(NUMNEIGH-ITER1+1)) ACTCONSWEIGHT= + RESCONSWEIGHT(ACTPOS-(NUMNEIGH-ITER1+1)) ACTNDEL=RESNDEL(ACTPOS-(NUMNEIGH-ITER1+1)) ACTNINS=RESNINS(ACTPOS-(NUMNEIGH-ITER1+1)) C------- fork to distinguish between first and second net ACTREGION='BEFORE' ACTITER=ACTPOS-(NUMNEIGH-ITER1+1) ACTSTART=(ITER1-1)*NCODEUNT C ============= CALL WININDIR C ============= C---------------------------------------- C------- sum up for input of amino acid - C------- composition - C---------------------------------------- IF (LOGI_COMPOSITION .EQV. .TRUE.) THEN LHELP=.TRUE. DO ITAA=1,(NBIOLOBJ-1) IF ((LHELP .EQV. .TRUE.) .AND. + (ACTRESIDUE.EQ.AACODE(ITAA))) THEN ACTCOMPOSITION(ITAA)=ACTCOMPOSITION(ITAA)+1 LHELP=.FALSE. END IF END DO END IF END DO C---- end of window before central ----- C-------------------------------------------------- C---------------------------------------------------------------------- C---- central 'object' which will be predicted ---- C---------------------------------------------------------------------- ACTRESIDUE=RESNAME(ACTPOS) ACTCONSWEIGHT=RESCONSWEIGHT(ACTPOS) ACTNDEL=RESNDEL(ACTPOS) ACTNINS=RESNINS(ACTPOS) C---- fork to distinguish between first and second net ACTREGION='CENTRE' ACTITER=ACTPOS ACTSTART=NUMNEIGH*NCODEUNT C ============= CALL WININDIR C ============= C---------------------------------------- C---- sum up for input of amino acid ---- C---- composition ---- C---------------------------------------- IF (LOGI_COMPOSITION .EQV. .TRUE.) THEN LHELP=.TRUE. DO ITAA=1,(NBIOLOBJ-1) IF ((LHELP .EQV. .TRUE.) .AND. + (ACTRESIDUE.EQ.AACODE(ITAA))) THEN ACTCOMPOSITION(ITAA)=ACTCOMPOSITION(ITAA)+1 LHELP=.FALSE. END IF END DO END IF C---------------------------------------------------------------------- C---- end of central objects DESIRED ----- C---------------------------------------------------------------------- C-------------------------------------------------- C---- read NUMNEIGH amino acids after central group C-------------------------------------------------- DO ITER1=1,(NUMNEIGH-ACTSOLVADDEND) ACTRESIDUE=RESNAME(ACTPOS+ITER1) ACTCONSWEIGHT=RESCONSWEIGHT(ACTPOS+ITER1) ACTNDEL=RESNDEL(ACTPOS+ITER1) ACTNINS=RESNINS(ACTPOS+ITER1) C------- fork to distinguish between first and second net ACTREGION='AFTER' ACTITER=ACTPOS+ITER1 ACTSTART=(NUMNEIGH+ITER1)*NCODEUNT C ============= CALL WININDIR C ============= C---------------------------------------- C------- sum up for input of amino acid - C------- composition - C---------------------------------------- IF (LOGI_COMPOSITION .EQV. .TRUE.) THEN LHELP=.TRUE. DO ITAA=1,(NBIOLOBJ-1) IF ((LHELP .EQV. .TRUE.) .AND. + (ACTRESIDUE.EQ.AACODE(ITAA))) THEN ACTCOMPOSITION(ITAA)=ACTCOMPOSITION(ITAA)+1 LHELP=.FALSE. END IF END DO END IF END DO C-------------------------------------------------- C---- add solvents at end ----- C-------------------------------------------------- DO ITER1=(NUMNEIGH-ACTSOLVADDEND+1),NUMNEIGH ACTRESIDUE='U' C------- fork to distinguish between first and second net ACTREGION='ADDEND' ACTITER=(ACTPOS+ITER1) ACTSTART=(NUMNEIGH+ITER1)*NCODEUNT C ============= CALL WININDIR C ============= END DO C---- sum up for input of amino acid composition IF (LOGI_COMPOSITION .EQV. .TRUE.) THEN ACTCOMPOSITION(NBIOLOBJ)=ACTCOMPOSITION(NBIOLOBJ) + +ACTSOLVADDEND END IF END ***** end of WINASS ***** ------------------------------------------------------------------ ***** SUB WININDIR ***** ------------------------------------------------------------------ C---- C---- NAME : WININDIR C---- ARG : C---- DES : For a given window position (adding spacer begin, C---- DES : before C---- DES : central, after central, adding spacer end) the input C---- DES : vector C---- DES : is assigned for exactly that region. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: For a given window position (adding spacer begin,* * -------- before central, after central, adding spacer end)* * the input vector is assigned for exactly that * * region. * * control param.: MODEASSCAS, MODEMAIN, NCODEUNT * * --------------- NBIOLOBJ, NTRAINJURY, NSECEL * * input parameter:CONTROLCHAR, ACTPOS, ACTPOS * * ----------------ACTREGION, ACTITER, ACTSTART * * input variables:RESPROF, RESNAME, RESVAR, RESCONSWEIGHT, * * ----------------INTRJ, TSTINTRJ * * from CODEIN: CODEVECTOR * * CODESTR: CODEVECTOR * * output variab.: INPUT, TSTINPUT * * for SBR CODEIN: ACTRESIDUE, CODEVECPROF, CODEVECINCASc * * called from: WINASS * * SBRs calling: CODEIN, CODESTR, WININAA, WININSTR * * procedure: see SBR WINDIR * *----------------------------------------------------------------------* SUBROUTINE WININDIR C---- global parameters INCLUDE 'phdParameter.f' C---- local variables INTEGER ITPROF,ITOUT CHARACTER*222 TMPASSCAS ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- for first network ----- C-------------------------------------------------- IF (CONTROLCHAR.EQ.'FST') THEN C---------------------------------------- C------- add solvents at begin/end ------ C---------------------------------------- IF ((ACTREGION.EQ.'ADDBEG').OR.(ACTREGION.EQ.'ADDEND')) THEN C---------- profile input? TMPASSCAS=MODEASSCAS(ACTCHI) IF ((TMPASSCAS(1:7).EQ.'PROFILE').OR. + (TMPASSCAS(1:7).EQ.'P-REAL-')) THEN DO ITPROF=1,(NBIOLOBJ-1) CODEVECPROF(ITPROF)=0 END DO CODEVECPROF(NBIOLOBJ)=PROFMAX END IF C---------- translating amino acid/profile to input vectors C =========== CALL CODEIN C =========== C---------- INPUT (resp. TSTINPUT) = CODEVECTOR C ============ CALL WININAA C ============ C---------------------------------------- C------- residues before/after/ central - C---------------------------------------- ELSEIF ((ACTREGION.EQ.'BEFORE').OR. + (ACTREGION.EQ.'CENTRE').OR. + (ACTREGION.EQ.'AFTER')) THEN C---------- profile input? TMPASSCAS=MODEASSCAS(ACTCHI) IF ((TMPASSCAS(1:7).EQ.'PROFILE').OR. + (TMPASSCAS(1:7).EQ.'P-REAL-')) THEN C change: insertion C IF ((ACTRESIDUE.EQ.'.').OR.(ACTRESIDUE.EQ.' ')) THEN IF (ACTRESIDUE.EQ.' ') THEN DO ITPROF=1,(NBIOLOBJ-1) CODEVECPROF(ITPROF)=0 END DO CODEVECPROF(NBIOLOBJ)=PROFMAX ELSE DO ITPROF=1,(NBIOLOBJ-1) CODEVECPROF(ITPROF)=RESPROF(ACTITER,ITPROF) END DO CODEVECPROF(NBIOLOBJ)=0 END IF END IF C---------- translating amino acid/profile to input vectors C =========== CALL CODEIN C =========== C---------- INPUT (resp. TSTINPUT) = CODEVECTOR C ============ CALL WININAA C ============ ELSE WRITE(6,'(T2,A,T10,A,T60,A)')'***', + 'ERROR WININDIR called with wrong ACTREGION =',ACTREGION WRITE(6,'(T2,A,T10,A,T60,A)')'***', + 'stopped at 23-10-91-1. For CONTROLCHAR=',CONTROLCHAR STOP END IF C-------------------------------------------------- C---- second network, only structure to structure - C-------------------------------------------------- ELSEIF (CONTROLCHAR.EQ.'SND') THEN C---------------------------------------- C------- add solvents at begin/end ------ C---------------------------------------- IF ((ACTREGION.EQ.'ADDBEG').OR.(ACTREGION.EQ.'ADDEND')) THEN DO ITOUT=1,NUMOUT CODEVECINCASC(ITOUT)=0 END DO CODEVECINCASC(NUMOUT+1)=100 C---------- translating secondary structure into a vector C ============ CALL CODESTR C ============ C---------- INPUT (resp. TSTINPUT) = CODEVECTOR C ============= CALL WININSTR C ============= C---------------------------------------- C------- residues before/after/central -- C---------------------------------------- ELSEIF ((ACTREGION.EQ.'BEFORE').OR.(ACTREGION.EQ.'CENTRE').OR. + (ACTREGION.EQ.'AFTER')) THEN DO ITOUT=1,NUMOUT CODEVECINCASC(ITOUT)=INT(100*OUTFST(ITOUT,ACTITER, + TRANS2FROM1(ACTCHI))) END DO CODEVECINCASC(NUMOUT+1)=0 IF (ACTPOS.LT.1) THEN WRITE(6,*)'WININDIR tries to access sample:' WRITE(6,*)ACTPOS,' stopped: 15-12-91-1' STOP END IF C---------- translating secondary structure into a vector C ============ CALL CODESTR C ============ C---------- INPUT (resp. TSTINPUT) = CODEVECTOR C ============= CALL WININSTR C ============= ELSE WRITE(6,'(T2,A,T10,A,T60,A)')'***', + 'ERROR WININDIR called with wrong ACTREGION =',ACTREGION WRITE(6,'(T2,A,T10,A,T60,A)')'***', + 'stopped at 23-10-91-2. For CONTROLCHAR=',CONTROLCHAR STOP END IF ELSE WRITE(6,'(T2,A,T10,A,T60,A)')'***', + 'ERROR WININDIR called with wrong CONTROLCHAR =',CONTROLCHAR WRITE(6,'(T2,A,T10,A,T60,A)')'***', + 'stopped at 23-10-91-3. For ACTREGION=',ACTREGION STOP END IF END ***** end of WININDIR ***** ------------------------------------------------------------------ ***** SUB WININAA ***** ------------------------------------------------------------------ C---- C---- NAME : WININAA C---- ARG : C---- DES : INPUT/TSTINPUT = CODEVECTOR for NCODEUNT units. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: INPUT/TSTINPUT = CODEVECTOR for NCODEUNT units. * * control param.: MODEMAIN,LOGICONSWEIGHT * * --------------- NCODEUNT * * input parameter:ACTSTART, ACTPOS, ACTCONSWEIGHT * * input variables:CODEVECTOR * * output variab.: INPUT,TSTINPUT * * called from: WINASS * *----------------------------------------------------------------------* SUBROUTINE WININAA C---- global parameters INCLUDE 'phdParameter.f' C---- local variables INTEGER ITER,INTERNCODEUNT ******------------------------------*-----------------------------****** C---- NCODEUNT according to MODEASSCAS: IF ((LOGI_CONS .EQV. .TRUE.) .AND. + (LOGI_INDEL .EQV. .FALSE.)) THEN INTERNCODEUNT=NCODEUNT-1 ELSEIF ((LOGI_CONS .EQV. .TRUE.) .AND. + (LOGI_INDEL.EQV. .TRUE.)) THEN INTERNCODEUNT=NCODEUNT-3 ELSE INTERNCODEUNT=NCODEUNT END IF C-------------------------------------------------- C---- for binary input ----- C-------------------------------------------------- IF ((MODEASSCAS(ACTCHI).EQ.'ALPHABET').OR. + (MODEASSCAS(ACTCHI).EQ.'PROFILE-BIN')) THEN DO ITER=1,INTERNCODEUNT INPUT((ACTSTART+ITER),ACTPOS)=INT(CODEVECTOR(ITER)) END DO C-------------------------------------------------- C---- for real input ----- C-------------------------------------------------- ELSEIF (MODEASSCAS(ACTCHI).EQ.'PROFILE-REAL') THEN DO ITER=1,INTERNCODEUNT INPUT((ACTSTART+ITER),ACTPOS)=CODEVECTOR(ITER) END DO C-------------------------------------------------- C---- for real input (with conservation weight) --- C-------------------------------------------------- ELSEIF ((LOGI_CONS .EQV. .TRUE.) .AND. + (LOGI_INDEL .EQV. .FALSE.)) THEN DO ITER=1,INTERNCODEUNT INPUT((ACTSTART+ITER),ACTPOS)=CODEVECTOR(ITER) END DO IF (ACTCONSWEIGHT.LE.2) THEN INPUT((ACTSTART+NCODEUNT),ACTPOS)=ACTCONSWEIGHT/2. ELSE INPUT((ACTSTART+NCODEUNT),ACTPOS)=0 END IF C-------------------------------------------------- C---- for real input + conservation weight + indels C-------------------------------------------------- ELSEIF ((LOGI_CONS .EQV. .TRUE.) .AND. + (LOGI_INDEL.EQV. .TRUE.)) THEN DO ITER=1,INTERNCODEUNT INPUT((ACTSTART+ITER),ACTPOS)=CODEVECTOR(ITER) END DO IF (ACTCONSWEIGHT.LE.2) THEN INPUT((ACTSTART+INTERNCODEUNT+1),ACTPOS)=ACTCONSWEIGHT/2. ELSE INPUT((ACTSTART+INTERNCODEUNT+1),ACTPOS)=0 END IF INPUT((ACTSTART+NCODEUNT-1),ACTPOS)=ACTNDEL/REAL(ACTNALIGN) INPUT((ACTSTART+NCODEUNT),ACTPOS)=ACTNINS/REAL(ACTNALIGN) ELSE WRITE(6,'(T2,A)')'***' WRITE(6,'(T2,A,T10,A)') '***','ERROR: please ask for help!' WRITE(6,'(T2,A,T10,A,A)')'***','WININAA: MODEASSCAS not in '// + 'appropriate mode! The current choice is:' WRITE(6,'(T2,A,T10,A,T40,A,T70,I3)')'***',MODEASSCAS(ACTCHI), + 'for architecture:',ACTCHI STOP END IF END ***** end of WININAA ***** ------------------------------------------------------------------ ***** SUB WININSTR ***** ------------------------------------------------------------------ C---- C---- NAME : WININSTR C---- ARG : C---- DES : INPUT/TSTINPUT = CODEVECTOR for NCODEUNT units. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: INPUT/TSTINPUT = CODEVECTOR for NCODEUNT units. * * control param.: MODEMAIN,LOGICONSWEIGHT * * --------------- NCODEUNT * * input parameter:ACTSTART, ACTPOS, ACTCONSWEIGHT * * input variables:CODEVECTOR * * output variab.: INPUT,TSTINPUT * * called from: WINASS * *----------------------------------------------------------------------* SUBROUTINE WININSTR C---- global parameters INCLUDE 'phdParameter.f' C---- local variables INTEGER ITER ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- for binary input ----- C-------------------------------------------------- IF (LOGI_REALINPUT .EQV. .FALSE.) THEN DO ITER=1,NCODEUNT INPUT((ACTSTART+ITER),ACTPOS)=INT(CODEVECTOR(ITER)) END DO ELSE DO ITER=1,NCODEUNT INPUT((ACTSTART+ITER),ACTPOS)=CODEVECTOR(ITER) END DO END IF END ***** end of WININSTR ***** ------------------------------------------------------------------ ***** SUB WININCOMPOSITION ***** ------------------------------------------------------------------ C---- C---- NAME : WININCOMPOSITION C---- ARG : C---- DES : assign the values to INPUT/TSTINPUT for the unit C---- DES : coding C---- DES : for the composition of amino acids. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: assign the values to INPUT/TSTINPUT for the unit * * -------- coding for the composition of amino acids. * * const. passed: LOGI_REALINPUT, CONTROLCHAR, * * var. passed: out: INPUT * * var. read: NUMIN, NBIOLOBJ, PROFACC, CASCACC, NUMRES, * * ---------- ACTCOMPOSITION, CODECOMPOSTION * * called by: WINDIR * *----------------------------------------------------------------------* SUBROUTINE WININCOMPOSITION C---- global parameters INCLUDE 'phdParameter.f' C---- local variables INTEGER IBEG,IBEG1,ITAA,IHELP,ITACC REAL HDIFF ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- defaults ----- C-------------------------------------------------- C---- start of coding unit IBEG=BEGUNITS_COMPOSITION-1 C-------------------------------------------------- C---- for binary input ----- C-------------------------------------------------- IF (LOGI_REALINPUT .EQV. .FALSE.) THEN DO ITAA=1,NBIOLOBJ IBEG1=IBEG+((ITAA-1)*(ACTACC-1)) IHELP=2*NUMNEIGH+1 IF (NUMRES.GT.IHELP) THEN HDIFF=(CODECOMPOSITION(ITAA)-ACTCOMPOSITION(ITAA)) + /REAL(NUMRES-IHELP) ELSE HDIFF=(CODECOMPOSITION(ITAA)-ACTCOMPOSITION(ITAA)) + /REAL(IHELP) END IF DO ITACC=1,(ACTACC-1) IF (HDIFF.GE.(ITACC*ACTINTERVALL)) THEN INPUT((IBEG1+ITACC),ACTPOS)=1 ELSE INPUT((IBEG1+ITACC),ACTPOS)=0 END IF END DO END DO C-------------------------------------------------- C---- for real input ----- C-------------------------------------------------- ELSEIF (LOGI_REALINPUT .EQV. .TRUE.) THEN IHELP=2*NUMNEIGH+1 DO ITAA=1,NBIOLOBJ IF (NUMRES.GT.IHELP) THEN HDIFF=(CODECOMPOSITION(ITAA)-ACTCOMPOSITION(ITAA)) + /REAL(NUMRES-IHELP) ELSE HDIFF=(CODECOMPOSITION(ITAA)-ACTCOMPOSITION(ITAA)) + /REAL(IHELP) END IF INPUT((IBEG+ITAA),ACTPOS)=HDIFF END DO ELSE WRITE(6,'(T2,A,T10,A)')'***','ERROR in WININCOMPOSITION'// + ' something wrong with input to SBR!' STOP END IF END ***** end of WININCOMPOSITION ***** ------------------------------------------------------------------ ***** SUB WININCOMPOSITION_ALL ***** ------------------------------------------------------------------ C---- C---- NAME : WININCOMPOSITION_ALL C---- ARG : C---- DES : Compute amino acid composittion for a particular C---- DES : protein (nue). C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Compute the amino acid composittion for a par- * * -------- ticular protein (nue). * * input: NUMRES, RESNAME, ACTPOS, * * ------ AACODE24, AACODE_LOWC, NBIOLOBJ * * output variab.: CODECOMPOSITION * * SBRs calling: SISTZ1 (from lib-comp.f) * * called by: WINDIR * *----------------------------------------------------------------------* SUBROUTINE WININCOMPOSITION_ALL C---- global parameters INCLUDE 'phdParameter.f' C---- local variables INTEGER MUE,ITAA,ITAA2,ITC CHARACTER*1 HCHAR LOGICAL LHELP,LHELP2 ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- defaults ----- C-------------------------------------------------- ITC= 0 C---- set zero C ----------- CALL SISTZ1(CODECOMPOSITION,NBIOLOBJMAX) C ----------- C---- loop over whole protein DO MUE=1,NUMRES LHELP=.TRUE. HCHAR=RESNAME(MUE) C------- check for usual amino acids DO ITAA=1,(NBIOLOBJ-1) IF (LHELP .EQV. .TRUE.) THEN IF (HCHAR.EQ.AACODE24(ITAA:ITAA)) THEN CODECOMPOSITION(ITAA)=CODECOMPOSITION(ITAA)+1 LHELP=.FALSE. END IF END IF END DO C------- check for ends, chain breaks asf IF (LHELP .EQV. .TRUE.) THEN IF ((HCHAR.EQ.'!').OR.(HCHAR.EQ.'/').OR. + (HCHAR.EQ.'U').OR.(HCHAR.EQ.'O')) THEN CODECOMPOSITION(NBIOLOBJ)=CODECOMPOSITION(NBIOLOBJ)+1 LHELP=.FALSE. END IF END IF C------- check for small caps = cysteine IF (LHELP .EQV. .TRUE.) THEN LHELP2=.TRUE. DO ITAA=1,(NBIOLOBJ-1) IF (AACODE24(ITAA:ITAA).EQ.'C') THEN ITC=ITAA LHELP2=.FALSE. END IF END DO IF (LHELP2 .EQV. .TRUE.) THEN STOP ' *** WININCOMPOSITION_ALL: NO C' END IF DO ITAA2=1,26 IF ((LHELP .EQV. .TRUE.) .AND. + (HCHAR.EQ.AACODE_LOWC(ITAA2:ITAA2))) THEN CODECOMPOSITION(ITC)=CODECOMPOSITION(ITC)+1 LHELP=.FALSE. END IF END DO END IF C------- consistency: one found? IF (LHELP .EQV. .TRUE.) THEN IF (HCHAR.NE.'.') THEN WRITE(6,'(T2,A,T10,A)')'***','ERROR in WININ'// + 'COMPOSITION_ALL of amino acids:' WRITE(6,'(T2,A,T10,A,T30,A,T35,A,T45,I4)') + '***','no match for:',HCHAR,'prot',1 END IF CODECOMPOSITION(NBIOLOBJ)=CODECOMPOSITION(NBIOLOBJ)+1 END IF END DO END ***** end of WININCOMPOSITION_ALL ***** ------------------------------------------------------------------ ***** SUB WININLENGTH ***** ------------------------------------------------------------------ C---- C---- NAME : WININLENGTH C---- ARG : C---- DES : Assign the values to INPUT/TSTINPUT for the units C---- DES : coding for C---- DES : the length of the protein. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: assign the values to INPUT/TSTINPUT for the units* * -------- coding for the length of the protein. * * const. passed: LOGI_REALINPUT, CONTROLCHAR, ACTPOS * * var. passed: out: INPUT * * var. read: SPLIT_LENGTH, BEGUNITS_LENGTH, NUNITS_LENGTH, * * ---------- NUMRES * * called by: WINDIR * *----------------------------------------------------------------------* SUBROUTINE WININLENGTH C---- global parameters INCLUDE 'phdParameter.f' C---- local variables INTEGER IBEG,IBEG1,ITLEN,ITACC,INTERV2(1:4) REAL HDIFF,HINTER LOGICAL LHELP ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- defaults ----- C-------------------------------------------------- INTERV2(1)=SPLIT_LENGTH(1) INTERV2(2)=SPLIT_LENGTH(2)-SPLIT_LENGTH(1) INTERV2(3)=SPLIT_LENGTH(3)-SPLIT_LENGTH(2) INTERV2(4)=SPLIT_LENGTH(4)-SPLIT_LENGTH(3) C---- start of coding unit IBEG=BEGUNITS_LENGTH-1 C---- checks IF (NUNITS_LENGTH.NE.4) THEN WRITE(6,'(T2,A,T10,A)')'***','ERROR in WININLENGTH: '// + 'currently only for NUNITS_LENGTH = 4 (phdParameter.f) !' WRITE(6,'(T2,A,T10,A,T40,I5,T50,A)')'***', + 'instead it is: ',NUNITS_LENGTH,'stopped 29-12-93-1.' STOP END IF C-------------------------------------------------- C---- for binary input ----- C-------------------------------------------------- IF (LOGI_REALINPUT .EQV. .FALSE.) THEN C------------------------------ C------- loop over coding units C------------------------------ LHELP=.TRUE. DO ITLEN=1,NUNITS_LENGTH IBEG1=IBEG+((ITLEN-1)*(ACTACC-1)) IF (LHELP .EQV. .TRUE.) THEN IF (NUMRES.GE.SPLIT_LENGTH(ITLEN)) THEN HDIFF=1. ELSE IF (NUMRES.GT.500) THEN HDIFF=1. ELSE HINTER=REAL(INTERV2(ITLEN) + -(SPLIT_LENGTH(ITLEN)-NUMRES)) HDIFF=HINTER/REAL(INTERV2(ITLEN)) END IF LHELP=.FALSE. END IF ELSE HDIFF=0. END IF C---------- translate reals to binary grid DO ITACC=1,(ACTACC-1) IF (HDIFF.GE.(ITACC*ACTINTERVALL)) THEN INPUT((IBEG1+ITACC),ACTPOS)=1 ELSE INPUT((IBEG1+ITACC),ACTPOS)=0 END IF END DO C---------- end translate reals to binary grid END DO C------- end loop coding units C------------------------------ C-------------------------------------------------- C---- for real input ----- C-------------------------------------------------- ELSEIF (LOGI_REALINPUT .EQV. .TRUE.) THEN LHELP=.TRUE. DO ITLEN=1,NUNITS_LENGTH IF (LHELP .EQV. .TRUE.) THEN IF (NUMRES.GE.SPLIT_LENGTH(ITLEN)) THEN HDIFF=1. ELSE IF (NUMRES.GT.500) THEN HDIFF=1. ELSE HINTER=REAL(INTERV2(ITLEN) + -(SPLIT_LENGTH(ITLEN)-NUMRES)) HDIFF=HINTER/REAL(INTERV2(ITLEN)) END IF LHELP=.FALSE. END IF ELSE HDIFF=0 END IF INPUT((IBEG+ITLEN),ACTPOS)=HDIFF END DO END IF END ***** end of WININLENGTH ***** ------------------------------------------------------------------ ***** SUB WININDISTCAPS ***** ------------------------------------------------------------------ C---- C---- NAME : WININDISTCAPS C---- ARG : C---- DES : Assign the values to INPUT/TSTINPUT for the units C---- DES : coding for C---- DES : the distance to the caps of the protein. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: Assign the values to INPUT/TSTINPUT for the units* * -------- coding for the distance to the caps of the protein * const. passed: LOGI_REALINPUT, CONTROLCHAR, ACTPOS * * var. passed: out: INPUT * * var. read: SPLIT_DISTCAPS, *_DISTCAPS, *_DISTCAPS, * * ---------- ACTACC, ACTINTERVALL, NUMRES, * called by: WINDIR * *----------------------------------------------------------------------* SUBROUTINE WININDISTCAPS C---- global parameters INCLUDE 'phdParameter.f' C---- local variables INTEGER IBEGN,IBEGC,IBEG1N,IBEG1C,ITLEN,ITACC REAL HDIFFN,HDIFFC,HINTER ******------------------------------*-----------------------------****** C-------------------------------------------------- C---- defaults ----- C-------------------------------------------------- C---- start of coding unit IBEGN=BEGUNITS_DISTCAPS-1 C---- checks IF (NUNITS_DISTCAPS.NE.4) THEN WRITE(6,'(T2,A,T10,A)')'***','ERROR in WININDISTCAPS: '// + 'currently only for NUNITS_DISTCAPS = 4 (phdParameter.f) !' WRITE(6,'(T2,A,T10,A,T40,I5,T50,A)')'***', + 'instead it is: ',NUNITS_DISTCAPS,'stopped 29-12-93-1.' STOP END IF C-------------------------------------------------- C---- for binary input ----- C-------------------------------------------------- IF (LOGI_REALINPUT .EQV. .FALSE.) THEN C------------------------------ C------- loop over coding units C------------------------------ IBEGC=BEGUNITS_DISTCAPS-1+(NUNITS_DISTCAPS*(ACTACC-1)) IBEGN=BEGUNITS_DISTCAPS-1 DO ITLEN=1,NUNITS_DISTCAPS IBEG1N=IBEGN+((ITLEN-1)*(ACTACC-1)) IBEG1C=IBEGC+((ITLEN-1)*(ACTACC-1)) C---------- N-term cap IF (ACTPOS.LE.SPLIT_DISTCAPS(ITLEN)) THEN HINTER=REAL(SPLIT_DISTCAPS(ITLEN)-ACTPOS+1) HDIFFN=MIN(1.,(HINTER/10.)) ELSE HDIFFN=0. END IF C---------- C-term cap IF ((NUMRES-ACTPOS).LE.SPLIT_DISTCAPS(ITLEN)) THEN HDIFFC=1. HINTER=REAL(SPLIT_DISTCAPS(ITLEN)-(NUMRES-ACTPOS)) HDIFFC=MIN(1.,(HINTER/10.)) ELSE HDIFFC=0. END IF C---------- translate reals to binary grid DO ITACC=1,(ACTACC-1) IF (HDIFFN.GE.(ITACC*ACTINTERVALL)) THEN INPUT((IBEG1N+ITACC),ACTPOS)=1 ELSE INPUT((IBEG1N+ITACC),ACTPOS)=0 END IF IF (HDIFFC.GE.(ITACC*ACTINTERVALL)) THEN INPUT((IBEG1C+ITACC),ACTPOS)=1 ELSE INPUT((IBEG1C+ITACC),ACTPOS)=0 END IF END DO C---------- end translate reals to binary grid END DO C------- end loop coding units C------------------------------ C-------------------------------------------------- C---- for real input ----- C-------------------------------------------------- ELSEIF (LOGI_REALINPUT .EQV. .TRUE.) THEN IBEGC=(BEGUNITS_DISTCAPS-1)+NUNITS_DISTCAPS DO ITLEN=1,NUNITS_DISTCAPS C---------- N-term cap IF (ACTPOS.LE.SPLIT_DISTCAPS(ITLEN)) THEN HINTER=REAL(SPLIT_DISTCAPS(ITLEN)-ACTPOS+1) HDIFFN=MIN(1.,(HINTER/10.)) ELSE HDIFFN=0. END IF C---------- C-term cap IF ((NUMRES-ACTPOS).LE.SPLIT_DISTCAPS(ITLEN)) THEN HDIFFC=1. HINTER=REAL(SPLIT_DISTCAPS(ITLEN)-(NUMRES-ACTPOS)) HDIFFC=MIN(1.,(HINTER/10.)) ELSE HDIFFC=0. END IF INPUT((IBEGN+ITLEN),ACTPOS)=HDIFFN INPUT((IBEGC+ITLEN),ACTPOS)=HDIFFC END DO END IF END ***** end of WININDISTCAPS ***** ------------------------------------------------------------------ ***** SUB WRTBOTHHEADER ***** ------------------------------------------------------------------ C---- C---- NAME : WRTBOTHHEADER C---- ARG : C---- DES : Write headers for prediction (sec and acc). C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTBOTHHEADER(KUNIT,VERSION,NUMNETJURY, + TXT80,IBEG,IEND) C---- local variables INTEGER KUNIT,ITER,IEND,IBEG,NUMNETJURY C CHARACTER*24 FCTIME_DATE CHARACTER*5 SBEG,SEND CHARACTER*222 INTERTXT,TXT80(1:30),VERSION ************************************************************************ C---- defaults SBEG='* ' SEND=' *' C-------------------------------------------------- C---- write header into prediction output ----- C-------------------------------------------------- CALL WRTF(KUNIT) WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' PHD output for your protein:',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(KUNIT) CALL WRTE(KUNIT) c$$$ WRITE(KUNIT,'(A3,A1,A24,T78,A3)')SBEG,' ',FCTIME_DATE(),SEND CALL WRTE(KUNIT) WRITE(KUNIT,'(A3,A11,T18,I4,T25,A35,A10,A2,T78,A3)')SBEG, + ' Jury on: ',NUMNETJURY,' different architectures '// + '(version ',VERSION,').',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG,' Note: differently trained '// + 'architectures, i.e., different versions can',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' result in different predictions.',SEND CALL WRTE(KUNIT) CALL WRTF(KUNIT) CALL WRTE(KUNIT) WRITE(KUNIT,'(A3,A,T78,A3)')SBEG,' About the protein:',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG,' ------------------',SEND CALL WRTE(KUNIT) CALL WRTE(KUNIT) IF (IBEG.LT.1) THEN WRITE(6,'(T2,A,T10,A)')'***','ERROR in WRTBOTHHEADER'// + ' Hssp file HEADER changed? ' END IF IF (IEND.GT.30) THEN WRITE(6,'(T2,A,T10,A)')'***','ERROR in WRTBOTHHEADER'// + ' Hssp file NALIGN changed? ' END IF DO ITER=IBEG,IEND INTERTXT=TXT80(ITER) WRITE(KUNIT,'(A3,T10,A60,T78,A3)')SBEG,INTERTXT,SEND IF (INTERTXT(1:6).EQ.'NALIGN') THEN WRITE(KUNIT,'(A3,T21,A,T78,A3)')SBEG, + '(=number of aligned sequences in HSSP file)',SEND END IF END DO CALL WRTE(KUNIT) CALL WRTF(KUNIT) CALL WRTE(KUNIT) END ***** end of WRTBOTHHEADER ***** ------------------------------------------------------------------ ***** SUB WRTCONTENT ***** ------------------------------------------------------------------ C---- C---- NAME : WRTCONTENT C---- ARG : C---- DES : The content in secondary structure, resp. relative percent. C---- DES : of occurrence per amino acid is written onto unit KUNIT. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The content in secondary structure, resp. relative * -------- percentage of occurrence per amino acid is * * written onto unit KUNIT. * * input variables:CONTPRED,CONTDSSP,CONTAA * * output variab.: CONTPRED,CONTDSSP,CONTAA * * called by: TXTRES, DATAOT * *----------------------------------------------------------------------* SUBROUTINE WRTCONTENT(KUNIT) C---- parameters/global variables INCLUDE 'phdParameter.f' C---- local variables INTEGER KUNIT,MUE,ITAA,ICOUNT,ITSEC, + ISORT(1:24),ITLINES,IBEG,IEND REAL HCONTAA(1:24) CHARACTER*24 TXTAA,TXTCONT CHARACTER*1 CAA(1:24),TXTSS(1:8) CHARACTER*3 SBEG,SEND ******------------------------------*-----------------------------****** C---- default TXTAA(1:24)='ABCDEFGHIKLMNPQRSTVWXYZU' SBEG='* ' SEND=' *' IF (MODESECSTRON(1:9).EQ.'SECONDARY') THEN TXTSS(1)='H' TXTSS(2)='E' IF (NSECEL.GT.3) THEN TXTSS(3)='T' END IF TXTSS(NSECEL)='L' END IF C------------------------------------------------------------- C---- secondary structure prediction ----- C------------------------------------------------------------- C---------------------------------------- C---- header C---------------------------------------- C---- paper to quote WRITE(KUNIT,'(80A)')('*',MUE=1,80) WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Publication to reference in reporting results:',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND IF (MODESECSTRON.EQ.'SECONDARY') THEN WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Rost, Burkhard; Sander, Chris: Prediction of protein '// + 'structure',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + ' at better than 70% accuracy. J. Mol. Biol., 1993, '// + '232, 584-599.',SEND END IF IF (MODESECSTRON(1:9).EQ.'SECONDARY') THEN WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Rost, Burkhard; Sander, Chris: Combining evolutionary '// + 'information',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + ' and neural networks to predict protein secondary '// + 'structure. ',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + ' Proteins, 1994, 19, 55-72.',SEND END IF IF (MODESECSTRON.EQ.'EXPOSURE') THEN WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Rost, Burkhard; Sander, Chris: Conservation and '// + 'prediction of ',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + ' solvent accessibility in protein families. Proteins, '// + '1994,',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + ' 20, 216-226.',SEND END IF IF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Rost, Burkhard; Casadio, Rita; Fariselli, Piero; '// + 'Sander, Chris: ',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + ' Prediction of helical transmembrane segments at 75% ', + SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + ' accuracy. Protein Science, 1995, 4, 521-533', + SEND END IF WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND WRITE(KUNIT,'(80A)')('*',MUE=1,80) WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)') + SBEG,'Some statistics:',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)') + SBEG,'~~~~~~~~~~~~~~~~',SEND WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Percentage of amino acids:',SEND C---------------------------------------- C---- sorting + writing the content of AA C---------------------------------------- C ============== CALL SRSORTVEC(24,24,1,CONTAA,2,ISORT,2) C ============== ICOUNT=0 DO ITAA=1,24 IF (CONTAA(ISORT(ITAA)).NE.0) THEN HCONTAA(ITAA)=CONTAA(ISORT(ITAA)) CAA(ITAA)=TXTAA(ISORT(ITAA):ISORT(ITAA)) ICOUNT=ITAA END IF END DO WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND WRITE(KUNIT,'(A3,T10,A,T26,5A9)')SBEG,'+--------------+', + ('--------+',ITAA=1,MIN(5,ICOUNT)) DO ITLINES=1,(INT((ICOUNT-0.1)/5.)+1) IBEG=(ITLINES-1)*5+1 IEND=INT(MIN(REAL(IBEG+4),REAL(ICOUNT))) WRITE(KUNIT,'(A3,T10,A,T25,A1,5(A5,A4))')SBEG, + '| AA:','|',(CAA(ITAA),' |',ITAA=IBEG,IEND) WRITE(KUNIT,'(A3,T10,A,T25,A1,5(A2,F5.1,A2))')SBEG, + '| % of AA:','|',(' ',HCONTAA(ITAA),' |',ITAA=IBEG,IEND) + WRITE(KUNIT,'(A3,T10,A,T26,5A9)')SBEG, + '+--------------+',('--------+',ITAA=IBEG,IEND) END DO C---------------------------------------- C---- writing the content of pred SS C---------------------------------------- WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND IF (MODESECSTRON(1:9).EQ.'SECONDARY') THEN IF (MODESECSTRON.EQ.'SECONDARY') THEN IF (LDSSPREAD .EQV. .FALSE.) THEN WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Percentage of secondary structure predicted:',SEND ELSE WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Percentage of secondary structure predicted/observed:',SEND END IF ELSE IF (LDSSPREAD .EQV. .FALSE.) THEN WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Percentage of helical trans-membrane predicted:',SEND ELSE WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Percentage of helical trans-membrane predicted/observed:',SEND END IF END IF WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND WRITE(KUNIT,'(A3,T10,A,T26,4A9)')SBEG, + '+--------------+',('--------+',ITSEC=1,NSECEL) WRITE(KUNIT,'(A3,T10,A,T25,A1,4(A4,A1,A4))')SBEG, + '| SecStr:','|',(' ',TXTSS(ITSEC),' |',ITSEC=1,NSECEL) WRITE(KUNIT,'(A3,T10,A,T25,A1,4(A2,F5.1,A2))')SBEG, + '| % Predicted:','|',(' ',CONTPRED(ITSEC),' |',ITSEC=1,NSECEL) END IF C---------------------------------------- C---- writing the content of obs SS -- C---------------------------------------- IF ((LDSSPREAD .EQV. .TRUE.) .AND. + (MODESECSTRON(1:9).EQ.'SECONDARY')) THEN WRITE(KUNIT,'(A3,T10,A,T26,4A9)')SBEG, + '+--------------+',('--------+',ITSEC=1,NSECEL) WRITE(KUNIT,'(A3,T10,A,T25,A1,4(A4,A1,A4))')SBEG, + '| SecStr:','|',(' ',TXTSS(ITSEC),' |',ITSEC=1,NSECEL) WRITE(KUNIT,'(A3,T10,A,T25,A1,4(A2,F5.1,A2))')SBEG, + '| % Observed:','|',(' ',CONTDSSP(ITSEC),' |',ITSEC=1,NSECEL) + END IF WRITE(KUNIT,'(A3,T10,A,T26,4A9)')SBEG, + '+--------------+',('--------+',ITSEC=1,NSECEL) C---------------------------------------- C---- assigning class to pred SS C---------------------------------------- IF (MODESECSTRON.EQ.'SECONDARY') THEN IF ((CONTPRED(1).GT.45).AND.(CONTPRED(2).LT.5)) THEN TXTCONT='all-alpha ' ELSEIF ((CONTPRED(1).LT.5).AND.(CONTPRED(2).GT.45)) THEN TXTCONT='all-beta ' ELSEIF ((CONTPRED(1).GT.30).AND.(CONTPRED(2).GT.20)) THEN TXTCONT='alpha-beta ' ELSE TXTCONT='mixed class' END IF WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'According to the following classes:',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'all-alpha: %H>45 and %E< 5; all-beta : %H<5 and %E>45',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'alpha-beta : %H>30 and %E>20; mixed: rest,',SEND WRITE(KUNIT,'(A3,T10,A,T60,A,T78,A3)')SBEG, + 'this means that the predicted class is: ',TXTCONT(1:11),SEND IF (LDSSPREAD .EQV. .TRUE.) THEN IF ((CONTDSSP(1).GT.45).AND.(CONTDSSP(2).LT.5)) THEN TXTCONT='all-alpha ' ELSEIF ((CONTDSSP(1).LT.5).AND.(CONTDSSP(2).GT.45)) THEN TXTCONT='all-beta ' ELSEIF ((CONTDSSP(1).GT.30).AND.(CONTDSSP(2).GT.20)) THEN TXTCONT='alpha-beta ' ELSE TXTCONT='mixed class' END IF WRITE(KUNIT,'(A3,T10,A,T60,A,T78,A3)')SBEG, + 'The class of the observed structure is: ',TXTCONT(1:11),SEND END IF END IF WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND WRITE(KUNIT,'(80A)')('*',MUE=1,80) WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND C---- end of content ----- C-------------------------------------------------- END ***** end of WRTCONTENT ***** ------------------------------------------------------------------ ***** SUB WRTD ***** ------------------------------------------------------------------ C---- C---- NAME : WRTD C---- ARG : C---- DES : write ending lines C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTD(K) INTEGER ITER,K WRITE(K,'(A3,T78,A3)')'* ',' *' WRITE(K,'(A3,74A1,T78,A3)')'***',('.',ITER=1,74),'***' WRITE(K,'(A3,T78,A3)')'* ',' *' END ***** end of WRTD ***** ------------------------------------------------------------------ ***** SUB WRTEXP ***** ------------------------------------------------------------------ C---- C---- NAME : WRTEXP C---- ARG : C---- DES : write solvent accessibility prediction. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTEXP(KUNIT) C---- global parameters * INCLUDE 'phdParameter.f' C---- local functions CHARACTER*222 FWRITE_STRING_NUMBERS CHARACTER*1 FC_REXP_TO_3STCHAR INTEGER FILEN_STRING C---- local variables INTEGER KUNIT,ITER,ITLINES,ITMUE,MUE,IHELP,IEND,IBEG, + OUTEXPLOC(1:80),IPOS INTEGER*2 DSSPEXPONE(1:80),PREDEXPONE(1:80) REAL REXP CHARACTER*5 SBEG,SEND CHARACTER*6 CHELP6 CHARACTER*222 INTERTXT,TXT80(1:30),VERSION,CHFILE CHARACTER*1 PREDTXT(1:80),DSSPTXT(1:80) LOGICAL LWRITE_ACC80,LWRT80 ************************************************************************ * SBRs called: WRTBOTHHEADER, WRTEXPHEADER, WRTWARN_NOALI, * * WRTPOPRED * ************************************************************************ C---- defaults LWRT80=.FALSE. SBEG='* ' SEND=' *' C-------------------------------------------------- C---- read header of HSSP file ----- C-------------------------------------------------- IEND=FILEN_STRING(FILE_HSSP_NOCHAIN) CHFILE(1:IEND)=FILE_HSSP_NOCHAIN(1:IEND) C CALL SFILEOPEN(15,CHFILE(1:IEND),'UNKNOWN',222,' ') C CALL SFILEOPEN(15,FILE_HSSP_NOCHAIN,'OLD',222,'READONLY') Cyy OPEN (15,FILE=FILE_HSSP_NOCHAIN,STATUS='OLD',READONLY) OPEN (15,FILE=FILE_HSSP_NOCHAIN,STATUS='OLD') DO ITER=1,30 READ(15,'(A80)')TXT80(ITER) END DO CLOSE(15) C---- store begin an end of text to be written DO ITER=1,30 INTERTXT=TXT80(ITER) IF (INTERTXT(1:6).EQ.'HEADER') THEN IBEG=ITER ELSEIF (INTERTXT(1:6).EQ.'NALIGN') THEN IEND=ITER END IF END DO C---------------------------------------- C---- enough residues in intervall >= 4 ? C---------------------------------------- IHELP=0 DO MUE=1,NUMRES IF (RELIND(MUE).GE.4) THEN IHELP=IHELP+1 END IF END DO IF (IHELP.GT.5) THEN LWRITE_ACC80=.TRUE. ELSE LWRITE_ACC80=.FALSE. END IF C-------------------------------------------------- C---- write header into prediction output ----- C-------------------------------------------------- VERSION=VERSION_EXP C ================== CALL WRTBOTHHEADER(KUNIT,VERSION,NUMNETJURY,TXT80,IBEG,IEND) C ================== C ================== CALL WRTEXPHEADER(KUNIT,LDSSPREAD,LWRITE_ACC80) C ================== C-------------------------------------------------- C---- write warning if too few sequences in ali --- C-------------------------------------------------- IF (NUMNALIGN(1).LE.5) THEN C ================== CALL WRTWARN_NOALI(KUNIT,MODESECSTRON) C ================== END IF C-------------------------------------------------- C---- now write the prediction for all ----- C-------------------------------------------------- C---- data WRITE(KUNIT,'(A3,T10,A,T25,A7,T40,A,T50,I5,T78,A3)')SBEG, + 'protein:',PROTNAME(1),'length',NUMRES,SEND CALL WRTE(KUNIT) WRITE(KUNIT,*) C---- strings of 60: for easy evaluation upon look DO ITLINES=1,(INT((NUMRES-1)/60.)+1) WRITE(KUNIT,'(T15,A60)')FWRITE_STRING_NUMBERS(LWRT80,ITLINES) IPOS=(ITLINES-1)*60 IEND=INT(MIN(60.,REAL(NUMRES-IPOS))) C---------------------------------------- C------- intermediate strings of lenth 60 DO ITMUE=1,INT(MIN(60.,REAL(NUMRES-IPOS))) C---------- for observed exposure IF (LDSSPREAD .EQV. .TRUE.) THEN REXP=DESEXP(IPOS+ITMUE) IF (REXP.GE.0) THEN DSSPEXPONE(ITMUE)=INT2(MIN( 9., + SQRT(100*REXP/REAL(MAXEXP)) )) C ------------------ DSSPTXT(ITMUE)= + FC_REXP_TO_3STCHAR(REXP,THREXP3ST(2),THREXP3ST(3)) C ------------------ IF ( (DSSPTXT(ITMUE).EQ.'I').OR. + (DSSPTXT(ITMUE).EQ.'i') ) THEN DSSPTXT(ITMUE)=' ' END IF ELSE WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR in WRTEXP: desired exposure < 0' WRITE(6,'(T2,A,T10,A,T30,I6,T40,A,T50,I4)')'***', + 'for itmue = ',itmue,'IPOS=',IPOS END IF END IF C---------- for predicted exposure IF (LFILTER .EQV. .TRUE.) THEN OUTEXPLOC(ITMUE)=INT(100*OUTEXPFIL(IPOS+ITMUE)) PREDTXT(ITMUE)=OUTBINCHARFIL(IPOS+ITMUE) ELSE OUTEXPLOC(ITMUE)=INT(100*OUTEXP(IPOS+ITMUE)) PREDTXT(ITMUE)=OUTBINCHAR(IPOS+ITMUE) END IF IF (OUTEXPLOC(ITMUE).GE.0) THEN PREDEXPONE(ITMUE)=INT2( MIN( 9., + SQRT(REAL(OUTEXPLOC(ITMUE))) ) ) IF ( (PREDTXT(ITMUE).EQ.'I').OR. + (PREDTXT(ITMUE).EQ.'i') ) THEN PREDTXT(ITMUE)=' ' END IF ELSE WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR in WRTEXP: predicted exposure < 0' WRITE(6,'(T2,A,T10,A,T30,I6,T40,A,T50,I4)')'***', + 'for itmue = ',itmue,'IPOS=',IPOS END IF END DO C------- end of assigning intermediate strings C---------------------------------------- C------- sequence WRITE(KUNIT,'(T10,A5,60A1,A1)')'AA |', + (RESNAME(ITMUE),ITMUE=(IPOS+1),(IPOS+IEND)),'|' C------- projection onto 3 states IF (LDSSPREAD .EQV. .TRUE.) THEN C---------- secondary structure WRITE(KUNIT,'(T10,A5,60A1,A1)')'SS |', + (CONVSECSTR(ITMUE),ITMUE=(IPOS+1),(IPOS+IEND)),'|' C---------- observed relative exposure 3states WRITE(KUNIT,'(A,T10,A5,60A1,A1)')' 3st:','O 3 |', + (DSSPTXT(ITMUE),ITMUE=1,IEND),'|' CHELP6=' ' ELSE CHELP6=' 3st:' END IF WRITE(KUNIT,'(A,T10,A5,60A1,A1)')CHELP6,'P 3 |', + (PREDTXT(ITMUE),ITMUE=1,IEND),'|' C------- detailed 10 states IF (LDSSPREAD .EQV. .TRUE.) THEN C---------- observed relative exposure WRITE(KUNIT,'(A,T10,A5,60I1,A1)')' 10st:','OBS |', + (DSSPEXPONE(ITMUE),ITMUE=1,IEND) CHELP6=' ' ELSE CHELP6=' 10st:' END IF C------- predicted relative exposure WRITE(KUNIT,'(A,T10,A5,60I1,A1)')CHELP6,'PHD |', + (PREDEXPONE(ITMUE),ITMUE=1,IEND) C------- reliability index WRITE(KUNIT,'(T10,A5,60I1,A1)') + 'Rel |',(RELIND(ITMUE),ITMUE=(IPOS+1),(IPOS+IEND)) C-------------------------------------------------- C---- now write the prediction for 81.9% ----- C-------------------------------------------------- IF (LWRITE_ACC80 .EQV. .TRUE.) THEN DO ITMUE=1,IEND IF (RELIND(IPOS+ITMUE).GE.4) THEN IF (LFILTER .EQV. .TRUE.) THEN PREDTXT(ITMUE)=OUTBINCHARFIL(IPOS+ITMUE) ELSE PREDTXT(ITMUE)=OUTBINCHAR(IPOS+ITMUE) END IF ELSE PREDTXT(ITMUE)='.' END IF END DO WRITE(KUNIT,'(T2,A,T10,A5,60A1,A1)')'subset:', + 'SUB |',(PREDTXT(ITMUE),ITMUE=1,IEND),'|' END IF WRITE(KUNIT,*) END DO C-------------------------------------------------- C---- compute accuracy if DSSP available ----- C-------------------------------------------------- IF (LDSSPREAD .EQV. .TRUE.) THEN C ============= CALL WRTPOEXP(KUNIT) C ============= END IF END ***** end of WRTEXP ***** ------------------------------------------------------------------ ***** SUB WRTEXPHEADER ***** ------------------------------------------------------------------ C---- C---- NAME : WRTEXPHEADER C---- ARG : C---- DES : write header for solvent accessibility prediction. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTEXPHEADER(KUNIT,LDSSPREAD,LWRITE_ACC80) C---- local variables INTEGER KUNIT CHARACTER*5 SBEG,SEND LOGICAL LWRITE_ACC80,LDSSPREAD ************************************************************************ C---- defaults SBEG='* ' SEND=' *' C-------------------------------------------------- C---- abbreviations used C-------------------------------------------------- WRITE(KUNIT,'(A3,A,T78,A3)')SBEG,' Abbreviations:',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG,' --------------',SEND CALL WRTE(KUNIT) WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' AA: amino acid sequence',SEND IF (LDSSPREAD .EQV. .TRUE.) THEN WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' SS: H=helix, E=extended (sheet), blank=re'// + 'st (loop)',SEND END IF WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' 3st: relative solvent accessibility (acc)'// + ' in 3 states:', SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' b = 0-9%, i = 9-36%, e = 36-100%.',SEND CALL WRTE(KUNIT) WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' PHD: Profile network prediction HeiDelberg', + SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' Rel: Reliability index of prediction (0-9)', + SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' O 3: observed relative '// + 'acc. in 3 states: B, I, E',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG,' Note: '// + 'for convenience a blank is used intermediate (i).',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' P 3: predicted rel. acc. in 3 states',SEND WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' 10st: relative solvent acc. in 10 states', + SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' = n corresponds to a relative acc.'// + ' of n*n %',SEND WRITE(KUNIT,'(A3,T78,A3)')SBEG,SEND C-------------------------------------------------- C---- subset C-------------------------------------------------- IF (LWRITE_ACC80 .EQV. .TRUE.) THEN WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' Subset: SUB: a subset of the prediction, for all '// + 'residues with',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' an expected correlation > 0.69 (tab'// + 'les in header)',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' Note: for this subset the following '// + 'symbols are used:',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' "I": is intermediate (for which above '// + '" " is used)',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' ".": means that no prediction is made '// + 'for this residue,',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' as the reliability is Rel < 4',SEND CALL WRTE(KUNIT) END IF CALL WRTF(KUNIT) END ***** end of WRTEXPHEADER ***** ------------------------------------------------------------------ ***** SUB WRTE ***** ------------------------------------------------------------------ C---- C---- NAME : WRTE C---- ARG : C---- DES : write empty line C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTE(K) INTEGER K WRITE(K,'(A3,T78,A3)')'* ',' *' END ***** end of WRTE ***** ------------------------------------------------------------------ ***** SUB WRTF ***** ------------------------------------------------------------------ C---- C---- NAME : WRTF C---- ARG : C---- DES : write final line C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTF(K) INTEGER ITER,K WRITE(K,'(A3,T78,A3)')'* ',' *' WRITE(K,'(A3,74A1,T78,A3)')'*****',('*',ITER=1,74),'*****' WRITE(K,'(A3,T78,A3)')'* ',' *' WRITE(K,'(A3,T78,A3)')'* ',' *' END ***** end of WRTF ***** ------------------------------------------------------------------ ***** SUB WRTPHDHEADER ***** ------------------------------------------------------------------ C---- C---- NAME : WRTPHDHEADER C---- ARG : C---- DES : write overall header. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTPHDHEADER(K) C---- local variables * INTEGER K C PARAMETER (KUNIT=6) CHARACTER*5 SBEG,SEND ************************************************************************ SBEG='* ' SEND=' *' ************************************************************************ C---- write header CALL WRTF(K) CALL WRTE(K) WRITE(K,'(A3,T10,A,T78,A3)')SBEG,'PredictProtein: ',SEND WRITE(K,'(A3,T10,A,T78,A3)')SBEG,'~~~~~~~~~~~~~~~ ',SEND CALL WRTE(K) WRITE(K,'(A3,T10,A,T78,A3)')SBEG, + 'Secondary structure prediction by the PHD neural network',SEND WRITE(K,'(A3,T10,A,T78,A3)')'*** ', + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(K) WRITE(K,'(A3,T10,A,T30,A,T78,A3)')SBEG,'Authors:', + 'Burkhard Rost & Chris Sander',SEND WRITE(K,'(A3,T10,A,T30,A,T78,A3)')SBEG,' ', + 'EMBL, Heidelberg, FRG',SEND WRITE(K,'(A3,T10,A,T30,A,T78,A3)')SBEG,' ', + 'Meyerhofstrasse 1, 69117 Heidelberg',SEND WRITE(K,'(A3,T10,A,T30,A,T78,A3)')SBEG,' ', + 'Internet: Predict-Help@EMBL-Heidelberg.DE',SEND CALL WRTE(K) WRITE(K,'(A3,T10,A,T30,A,T78,A3)')SBEG,'All rights reserved.', + ' ',SEND CALL WRTE(K) CALL WRTF(K) CALL WRTE(K) C---- about the prediction method CALL WRTE(K) WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + 'About the input to the network',SEND WRITE(K,'(A3,T6,A,T78,A3)')'*** ', + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'The prediction is pe', + 'rformed by a system of neural networks.',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'The input is a multi', + 'ple sequence alignment. It is taken from an HSSP ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'file (produced by th', + 'e program MaxHom: ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'Sander & Schneider (', + '1991) Proteins, Vol.9, pp. 56-68 ',SEND CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'For optimal results ', + 'the alignment should contain sequences with varying',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'degrees of sequence ', + 'similarity relative to the input protein. ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'The following is an ', + 'ideal situation:',SEND CALL WRTE(K) WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + ' +-----------------+----------------------+',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + ' | sequence: | sequence identity |',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + ' +-----------------+----------------------+',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + ' | target sequence | 100 % |',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + ' | aligned seq. 1 | 90 % |',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + ' | aligned seq. 2 | 80 % |',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + ' | ... | ... |',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + ' | aligned seq. 7 | 30 % |',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + ' +-----------------+----------------------+',SEND CALL WRTE(K) CALL WRTE(K) CALL WRTE(K) C---- results: performance accuracy CALL WRTE(K) CALL WRTF(K) WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + 'Estimated Accuracy of Prediction',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'A careful seven-fold', + ' cross validation test on some 130 protein chains ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'(about 25,000 residu', + 'es) with less than 30% pairwise sequence identity ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'gave the following r', + 'esults:',SEND CALL WRTE(K) WRITE(K,'(A3,T6,A23,A,T78,A3)')SBEG,' ++================++', + '-----------------------------------------+ ',SEND WRITE(K,'(A3,T6,A23,A,T78,A3)')SBEG,' || Qtotal = 70.8% ||', + ' ("overall three state accuracy") | ',SEND WRITE(K,'(A3,T6,A23,A,T78,A3)')SBEG,' ++================++', + '-----------------------------------------+ ',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG,' ',SEND WRITE(K,'(A3,T6,A23,A,T78,A3)')SBEG,' +------------------', + '----------+-----------------------------+ ',SEND WRITE(K,'(A3,T6,A23,A,T78,A3)')SBEG,' | Qhelix (% of obse', + 'rved)=72% | Qhelix (% of predicted)=73% | ',SEND WRITE(K,'(A3,T6,A23,A,T78,A3)')SBEG,' | Qstrand(% of obse', + 'rved)=66% | Qstrand(% of predicted)=60% | ',SEND WRITE(K,'(A3,T6,A23,A,T78,A3)')SBEG,' | Qloop (% of obse', + 'rved)=72% | Qloop (% of predicted)=74% | ',SEND WRITE(K,'(A3,T6,A23,A,T78,A3)')SBEG,' +------------------', + '----------+-----------------------------+ ',SEND CALL WRTE(K) CALL WRTE(K) C---- definitions CALL WRTD(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + 'These percentages are defined by:',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(K) CALL WRTE(K) WRITE(K,'(A3,T6,A20,A,T78,A3)')SBEG, + ' ', + 'number of correctly predicted residues ',SEND WRITE(K,'(A3,T6,A20,A,T78,A3)')SBEG, + 'Qtotal = ', + '--------------------------------------- (*100)',SEND WRITE(K,'(A3,T6,A20,A,T78,A3)')SBEG, + ' ', + ' number of all residues ',SEND CALL WRTE(K) CALL WRTE(K) WRITE(K,'(A3,T6,A20,A,T78,A3)')SBEG, + ' ', + 'no of res correctly predicted to be in helix ',SEND WRITE(K,'(A3,T6,A20,A,T78,A3)')SBEG, + 'Qhelix (% of obs) = ', + '-------------------------------------------- (*100)',SEND WRITE(K,'(A3,T6,A20,A,T78,A3)')SBEG, + ' ', + 'no of all res observed to be in helix ',SEND CALL WRTE(K) CALL WRTE(K) WRITE(K,'(A3,T6,A20,A,T78,A3)')SBEG, + ' ', + 'no of res correctly predicted to be in helix ',SEND WRITE(K,'(A3,T6,A20,A,T78,A3)')SBEG, + 'Qhelix (% of pred)= ', + '-------------------------------------------- (*100)',SEND WRITE(K,'(A3,T6,A20,A,T78,A3)')SBEG, + ' ', + 'no of all residues predicted to be in helix ',SEND CALL WRTE(K) CALL WRTE(K) C---- single protein chains CALL WRTD(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + 'Averaging over single chains',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'The most reasonable ', + 'way to compute the overall accuracies is the above ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'quoted percentage of', + ' correctly predicted residues. However, since the ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'user is mainly inter', + 'ested in the expected performance of the prediction',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'for a particular pro', + 'tein, the mean value when averaging over protein ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'chains might be of h', + 'elp as well. Computing first the three state ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'accuracy for each pr', + 'otein chain, and then averaging over 130 chains ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'yields the following', + ' average:',SEND CALL WRTE(K) WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+-------------------------------====--+',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| Qtotal/averaged over chains = 71.0% |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+-------------------------------====--+',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| standard deviation = 9.3% |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+-------------------------------------+',SEND CALL WRTE(K) CALL WRTE(K) C---- correlation coefficient CALL WRTD(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + 'Further measures of performance',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(K) CALL WRTE(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + 'Matthews correlation coefficient:',SEND CALL WRTE(K) CALL WRTE(K) WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+---------------------------------------------+',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| Chelix = 0.60, Cstrand = 0.52, Cloop = 0.51 |', + SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+---------------------------------------------+',SEND CALL WRTE(K) CALL WRTE(K) C---- length distribution CALL WRTD(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + 'Average length of predicted secondary structure segments: ', + SEND CALL WRTE(K) WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + ' +------------+----------+',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + ' | predicted | observed |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+-----------+------------+----------+',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| Lhelix = | 9.3 | 9.1 |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| Lstrand = | 5.0 | 5.1 |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| Lloop = | 6.0 | 5.8 |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+-----------+------------+----------+',SEND CALL WRTE(K) CALL WRTE(K) C---- accuracy matrix CALL WRTD(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'The accuracy matrix ', + 'in detail:',SEND CALL WRTE(K) WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+---------------------------------------+',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| number of residues with H, E, L |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+---------+------+------+------+--------+',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| |net H |net E |net L |sum obs |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+---------+------+------+------+--------+',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| obs H | 5344 | 582 | 1480 | 7406 |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| obs E | 482 | 3265 | 1231 | 4978 |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| obs L | 1445 | 1549 | 7831 | 10825 |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+---------+------+------+------+--------+',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '| sum Net | 7271 | 5396 |10542 | 23209 |',SEND WRITE(K,'(A3,T15,A,T78,A3)')SBEG, + '+---------+------+------+------+--------+',SEND CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'Note: This table is ', + 'to be read in the following manner: ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,' 5344 of all re', + 'sidues predicted to be in helix, were observed to ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,' be in helix, 4', + '82 however belong to observed strands, 1445 to ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,' observed loop ', + 'regions. The term "observed" refers to the DSSP ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,' assignment of ', + 'secondary structure calculated from 3D coordinates ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,' of experimenta', + 'lly determined structures (Dictionary of Secondary ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,' Structure of ', + 'Proteins: Kabsch & Sander (1983) Biopolymers, 22, ',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG,' 2577-2637). ',SEND CALL WRTE(K) CALL WRTE(K) C---- reliability CALL WRTE(K) CALL WRTF(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + 'Position-specific reliability index',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG, + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'The network predicts', + ' the three secondary structure types using real ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'numbers from the out', + 'put units. The prediction is assigned by choosing ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'the maximal unit ("w', + 'inner takes all"). However, the real numbers ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'contain additional i', + 'nformation. ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'E.g. the difference ', + 'between the maximal and the second largest output ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'unit can be used to ', + 'derive a "reliability index". This index is given ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'for each residue alo', + 'ng with the prediction. The index is scaled to ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'have values between ', + '0 (lowest reliability), and 9 (highest).',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'The accuracies (Qtot', + ') to be expected for residues with values above a ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'particular value of ', + 'the index are given below as well as the fraction ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'of such residues (%r', + 'es).:',SEND CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'Note: the data given', + ' in the following two tables relates to a test set ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'----- which included', + ' four chains of the membrane protein 1prc. The ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,' overall accura', + 'cy for this set is 70.2% instead of 70.8%. The ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,' differences to', + ' the set without membrane chains is marginal. ',SEND CALL WRTE(K) WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'+------', +'+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| index', +'| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| %res ', +'|100.0| 99.5| 88.6| 76.9| 65.4| 54.0| 42.1| 29.6| 15.5| 3.3|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'+------', +'+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| ', +'| | | | | | | | | | |', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| Qtot ', +'| 70.2| 70.4| 73.0| 76.0| 78.7| 81.6| 84.6| 87.3| 92.4| 95.5|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| ', +'| | | | | | | | | | |', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'+------', +'+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| H%obs', +'| 69.0| 69.3| 72.2| 76.0| 79.6| 83.4| 87.2| 91.0| 96.1| 99.2|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| E%obs', +'| 63.3| 63.5| 66.4| 69.5| 72.4| 75.9| 78.9| 81.9| 85.5| 79.0|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| ', +'| | | | | | | | | | |', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| H%prd', +'| 72.0| 72.0| 75.1| 78.3| 80.9| 84.0| 87.1| 90.2| 92.9| 94.9|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| E%prd', +'| 57.9| 58.5| 61.8| 65.6| 69.1| 73.7| 78.6| 82.6| 89.1| 98.8|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'+------', +'+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+', + SEND CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'The above table give', + 's the cumulative results, e.g. 65.4% of all ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'residues have a reli', + 'ability of at least 4. The overall three-state ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'accuracy for this su', + 'bset of about two thirds of all residues is 78.5%. ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'For this subset, e.g', + '., 79.6% of the observed helices are correctly ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'predicted, and 80.9%', + ' of all residues predicted to be in helix are ',SEND WRITE(K,'(A3,T6,A,T78,A3)')SBEG,'correct. ',SEND CALL WRTE(K) CALL WRTD(K) CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'The following table ', + 'gives the non-cumulative quantities, i.e. the ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'values per reliabili', + 'ty index range. These numbers answer the question:',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'how reliable is the ', + 'prediction for all residues labeled with the ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'particular index i.', + ' ',SEND CALL WRTE(K) CALL WRTE(K) WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'+------', +'+-----+-----+-----+-----+-----+-----+-----+-----+-----+', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| index', +'| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| %res ', +'| 10.9| 11.7| 11.5| 11.4| 11.9| 12.4| 14.1| 12.3| 3.2|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'+------', +'+-----+-----+-----+-----+-----+-----+-----+-----+-----+', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| ', +'| | | | | | | | | |', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| Qtot ', +'| 47.0| 51.2| 59.5| 62.3| 70.1| 77.5| 84.0| 91.6| 95.5|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| ', +'| | | | | | | | | |', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'+------', +'+-----+-----+-----+-----+-----+-----+-----+-----+-----+', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| H%obs', +'| 44.3| 44.9| 52.2| 58.4| 67.0| 74.8| 82.3| 94.9| 99.2|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| E%obs', +'| 44.1| 48.9| 56.4| 57.9| 66.6| 73.1| 78.6| 86.5| 79.0|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| ', +'| | | | | | | | | |', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| H%prd', +'| 45.3| 50.3| 59.0| 63.0| 69.7| 77.0| 85.2| 92.1| 94.9|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'| E%prd', +'| 38.2| 42.5| 50.3| 52.0| 60.0| 70.9| 77.1| 87.8| 98.8|', + SEND WRITE(K,'(A3,T6,A7,A,T78,A3)')SBEG,'+------', +'+-----+-----+-----+-----+-----+-----+-----+-----+-----+', + SEND CALL WRTE(K) WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'For example, for r', + 'esidues with Relindex=5 60% of all predicted beta ',SEND WRITE(K,'(A3,T6,A,T26,A,T78,A3)')SBEG,'strand residues are ', + 'correctly identified. ',SEND CALL WRTE(K) CALL WRTF(K) CALL WRTE(K) CALL WRTE(K) END ***** end of WRTPHDHEADER ***** ------------------------------------------------------------------ ***** SUB WRTPOEXP ***** ------------------------------------------------------------------ C---- C---- NAME : WRTPOEXP C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTPOEXP(KUNIT) C---- global parameters * INCLUDE 'phdParameter.f' C---- local variables INTEGER KUNIT CHARACTER*5 SBEG,SEND CHARACTER*7 INTERPROTNAME CHARACTER*222 TXT80 LOGICAL LTOPLINE ************************************************************************ * SBRs called: from library: lib-prot.f * * STABLE_EXPNOINBIN, STABLE_EXPNOINSTATES * ************************************************************************ C---- defaults SBEG='* ' SEND=' *' C-------------------------------------------------- C---- read header of HSSP file ----- C-------------------------------------------------- INTERPROTNAME(1:7)=PROTNAME(1) C---- on printer CALL WRTF(KUNIT) CALL WRTE(KUNIT) WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Performance accuracy of the prediction',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(KUNIT) CALL WRTE(KUNIT) C-------------------------------------------------- C---- table for bins C-------------------------------------------------- TXT80='full protein' C ====================== CALL STABLE_EXPNOINBIN(KUNIT,1,EXP_NOINBIN,TXT80,1) C ====================== LTOPLINE=.TRUE. C ====================== CALL STABLE_EXPSTATES(KUNIT,LTOPLINE,LTOPLINE,INTERPROTNAME,1, + EXP_NOINBIN,T2,T3A,T3B,2, + EXP_NOIN2ST,EXP_NOIN3ST,3,EXP_NOIN10ST,EXP_CORR,3) C ====================== CALL WRTE(KUNIT) CALL WRTE(KUNIT) END ***** end of WRTPOEXP ***** ------------------------------------------------------------------ ***** SUB WRTPOPRED ***** ------------------------------------------------------------------ C---- C---- NAME : WRTPOPRED C---- ARG : C---- DES : write prediction accuracy for SEC C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTPOPRED(KUNIT) C---- global parameters * INCLUDE 'phdParameter.f' C---- local variables INTEGER KUNIT,DEVNOM,NSECEL_LOC CHARACTER*5 SBEG,SEND CHARACTER*7 INTERPROTNAME LOGICAL LWRITE,LTABLE_QILS ************************************************************************ * SBRs called: from library: lib-prot.f * * STABLEPOLENFILE, SEVALINFOFILE * ************************************************************************ C---- defaults LTABLE_QILS=.TRUE. DEVNOM=50 SBEG='* ' SEND=' *' C---- blow up states for TM prediction IF (MODESECSTRON.EQ.'SECONDARY_HTM') THEN NSECEL_LOC=3 ELSE NSECEL_LOC=NSECEL END IF C-------------------------------------------------- C---- read header of HSSP file ----- C-------------------------------------------------- INTERPROTNAME(1:7)=PROTNAME(1) C---- on printer CALL WRTF(KUNIT) CALL WRTE(KUNIT) WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + 'Performance accuracy of the prediction',SEND WRITE(KUNIT,'(A3,T10,A,T78,A3)')SBEG, + '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',SEND CALL WRTE(KUNIT) CALL WRTE(KUNIT) C---- give only per-residue comparison IF (LTABLE_QILS .EQV. .FALSE.) THEN C ==================== CALL STABLEPOLENFILE(KUNIT,NSECEL_LOC,NUMOUTMAX,INTERPROTNAME, + MATNUM((NSECEL+1),(NSECEL+1)),TITLE, + MATNUM,RMATQOFDSSP,RMATQOFPRED,Q3,SQ,CORR,MATLEN) C ==================== C------- computing the information (entropy) LWRITE=.TRUE. C ================== CALL SEVALINFOFILE(KUNIT,NSECEL_LOC,NUMOUTMAX, + MATNUM,INFO,INFO_INV,LWRITE) C ================== C---- give also segment comparison ELSE C------- computing the information (entropy) LWRITE=.FALSE. C ================== CALL SEVALINFOFILE(6,NSECEL_LOC,NUMOUTMAX, + MATNUM,INFO,INFO_INV,LWRITE) C ================== C ================ CALL STABLE_QILS(KUNIT,NSECEL_LOC,NUMOUTMAX,NUMRES,1, + INTERPROTNAME,TITLE,2,MATNUM,MATLEN,3, + RMATQOFDSSP,RMATQOFPRED,Q3,SQ,CORR,INFO,INFO_INV,4, + QSOV,QFOV,DEVNOM,4) C ================ END IF CALL WRTE(KUNIT) CALL WRTE(KUNIT) END ***** end of WRTPOPRED ***** ------------------------------------------------------------------ ***** SUB WRTPRED ***** ------------------------------------------------------------------ C---- C---- NAME : WRTPRED C---- ARG : C---- DES : write secondary structure prediction. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTPRED(KUNIT) C---- global parameters * INCLUDE 'phdParameter.f' C---- local functions CHARACTER*222 FWRITE_STRING_NUMBERS INTEGER FILEN_STRING C---- local variables INTEGER KUNIT,ITER,ITLINES,MUE1,MUE2,MUE3,MUE4,IHELP, + IEND,IBEG,ITSEC,MUE5 CHARACTER*4 CHARMACH1,CHARMACH2 CHARACTER*5 SBEG,SEND CHARACTER*5 TXT(1:8) CHARACTER*222 INTERTXT,TXT80(1:30),VERSION,CHFILE,TXT_80 CHARACTER*1 INTEROUTTXT(1:80),INTERDSSPTXT(1:80) LOGICAL LWRITE_ACC80,LWRT80 ************************************************************************ * SBRs called: WRTBOTHHEADER, WRTPREDHEADER, WRTWARN_NOALI, * * WRTPOPRED * ************************************************************************ C---- br 2003-08-23: bullshit to avoid warning TXT_80=' ' C---- defaults LWRT80=.FALSE. SBEG='* ' SEND=' *' C-------------------------------------------------- C---- read header of HSSP file ----- C-------------------------------------------------- IEND=FILEN_STRING(FILE_HSSP_NOCHAIN) CHFILE(1:IEND)=FILE_HSSP_NOCHAIN(1:IEND) C CALL SFILEOPEN(15,CHFILE(1:IEND),'UNKNOWN',222,' ') C CALL SFILEOPEN(15,FILE_HSSP_NOCHAIN,'OLD',222,'READONLY') Cyy OPEN (15,FILE=FILE_HSSP_NOCHAIN,STATUS='OLD',READONLY) OPEN (15,FILE=FILE_HSSP_NOCHAIN,STATUS='OLD') DO ITER=1,30 READ(15,'(A80)')TXT80(ITER) END DO CLOSE(15) C---- store begin an end of text to be written IEND=30 DO ITER=1,30 INTERTXT=TXT80(ITER) IF (INTERTXT(1:6).EQ.'HEADER') THEN IBEG=ITER ELSEIF (INTERTXT(1:6).EQ.'NALIGN') THEN IEND=ITER END IF END DO C---------------------------------------- C---- enough residues in intervall > 5 ? C---------------------------------------- IHELP=0 DO MUE1=1,NUMRES IF (RELIND(MUE1).GE.5) THEN IHELP=IHELP+1 END IF END DO IF ( (IHELP.GT.5).AND.(MODESECSTRON.EQ.'SECONDARY') ) THEN LWRITE_ACC80=.TRUE. ELSE LWRITE_ACC80=.FALSE. END IF C-------------------------------------------------- C---- write header into prediction output ----- C-------------------------------------------------- IF (MODESECSTRON.EQ.'SECONDARY') THEN VERSION=VERSION_SEC ELSE VERSION=VERSION_HTM END IF C ================== CALL WRTBOTHHEADER(KUNIT,VERSION,NUMNETJURY,TXT80,IBEG,IEND) C ================== C ================== CALL WRTPREDHEADER(KUNIT,MODESECSTRON,LOUTBINPROB,LWRITE_ACC80) C ================== C-------------------------------------------------- C---- write warning if too few sequences in ali --- C-------------------------------------------------- IF (NUMNALIGN(1).LE.5) THEN C =================== CALL WRTWARN_NOALI(KUNIT,MODESECSTRON) C =================== END IF C-------------------------------------------------- C---- now write the prediction for all ----- C-------------------------------------------------- C---- machine readable version of strips? IF (LMACHINE_READABLE .EQV. .TRUE.) THEN CHARMACH1='# 1 ' CHARMACH2='# 2 ' ELSE CHARMACH1=' ' CHARMACH2=' ' END IF IF (LOUTBINPROB .EQV. .TRUE.) THEN TXT(1)='prH-|' TXT(2)='prE-|' TXT(NSECEL)='prL-|' IF (NSECEL.EQ.4) THEN TXT(3)='prT-|' END IF END IF C---- data WRITE(KUNIT,'(A3,T10,A,T25,A7,T40,A,T50,I5,T78,A3)')SBEG, + 'protein:',PROTNAME(1),'length',NUMRES,SEND CALL WRTE(KUNIT) WRITE(KUNIT,*) C---- strings of 80: for easy evaluation upon look MUE1=0 MUE2=0 MUE3=0 MUE4=0 DO ITLINES=1,(INT(NUMRES/60.)+1) WRITE(KUNIT,'(A4,T10,A4,T15,A60)')CHARMACH1,' ', + FWRITE_STRING_NUMBERS(LWRT80,ITLINES) IHELP=(ITLINES-1)*60 IEND=MIN(60,(NUMRES-IHELP)) WRITE(KUNIT,'(A4,T10,A5,T15,60A1,A1)')CHARMACH1,'AA |', + (RESNAME(MUE1),MUE1=(IHELP+1),(IHELP+IEND)),'|' C---------------------------------------- C------- observed secondary structure --- C---------------------------------------- IF (LDSSPREAD .EQV. .TRUE.) THEN DO MUE4=1,IEND IF ((RESSECSTR(IHELP+MUE4).EQ.'L').OR. + (RESSECSTR(IHELP+MUE4).EQ.'S').OR. + (RESSECSTR(IHELP+MUE4).EQ.'T')) THEN INTERDSSPTXT(MUE4)=' ' ELSE INTERDSSPTXT(MUE4)=RESSECSTR(IHELP+MUE4) END IF END DO WRITE(KUNIT,'(A4,T10,A5,T15,60A1,A1)')CHARMACH1,'Obs |', + (INTERDSSPTXT(MUE4),MUE4=1,IEND),'|' END IF C---------------------------------------- C------- prediction ----- C---------------------------------------- IF (LFILTER .EQV. .TRUE.) THEN DO MUE2=1,IEND IF (OUTBINCHARFIL(IHELP+MUE2).EQ.'L') THEN INTEROUTTXT(MUE2)=' ' ELSE INTEROUTTXT(MUE2)=OUTBINCHARFIL(IHELP+MUE2) END IF END DO WRITE(KUNIT,'(A4,T10,A5,T15,60A1,A1)')CHARMACH1,'PHD |', + (INTEROUTTXT(MUE4),MUE4=1,IEND),'|' ELSE WRITE(KUNIT,'(A4,T10,A5,T15,60A1,A1)')CHARMACH1,'PHD |', + (OUTBINCHAR(MUE2),MUE2=(IHELP+1),(IHELP+IEND)),'|' END IF C---------------------------------------- C------- reliability index ----- C---------------------------------------- C------- if because DEC has difficulties with the integer when <60 IF (IEND.EQ.60) THEN WRITE(KUNIT,'(A4,T10,A5,T15,60I1,A1)')CHARMACH1,'Rel |', + (RELIND(MUE3),MUE3=(IHELP+1),(IHELP+IEND)),'|' ELSE C---- br 99.01 changed C TXT_80=' ' C 110 FORMAT(I1) C DO MUE3=(IHELP+1),(IHELP+IEND) C WRITE(TXT_80(MUE3:MUE3),110,ERR=19991)RELIND(MUE3) C END DO C WRITE(KUNIT,'(A4,T10,A5,T15,A,A1)')CHARMACH1,'Rel |', C + TXT_80((IHELP+1):(IHELP+IEND)),'|' C---- br 99.03 changed again, SGI hick-up!!! WRITE(KUNIT,'(A4,T10,A5,T15,60I1)')CHARMACH1,'Rel |', + (RELIND(MUE3),MUE3=(IHELP+1),(IHELP+IEND)) 19991 CONTINUE CCC---------- for DEC CC IF (LDEC) THEN CC WRITE(KUNIT,'(A4,T10,A5,T15,60I1)')CHARMACH1,'Rel |', CC + (RELIND(MUE3),MUE3=(IHELP+1),(IHELP+IEND)) CC ELSE CCC---------- for others CC WRITE(KUNIT,'(A4,T10,A5,T15,60I1,A1)')CHARMACH1,'Rel |', CC + (RELIND(MUE3),MUE3=(IHELP+1),(IHELP+IEND)),'|' CC END IF END IF C---------------------------------------- C------- probabilities ----- C---------------------------------------- IF (LOUTBINPROB .EQV. .TRUE.) THEN WRITE(KUNIT,'(T2,A)')'detail:' DO ITSEC=1,NSECEL WRITE(KUNIT,'(A4,T10,A5,T15,60I1)')CHARMACH2,TXT(ITSEC), + (OUTBINPROB(ITSEC,MUE5),MUE5=(IHELP+1),(IHELP+IEND)) END DO END IF C-------------------------------------------------- C---- now write the prediction for 81.9% ----- C-------------------------------------------------- IF (LWRITE_ACC80 .EQV. .TRUE.) THEN DO MUE3=1,IEND IF (RELIND(IHELP+MUE3).GE.5 .AND. + (MUE3.GT.0)) THEN IF ((OUTBINCHAR(IHELP+MUE3).EQ.'H').OR. + (OUTBINCHAR(IHELP+MUE3).EQ.'E')) THEN INTEROUTTXT(MUE3)=OUTBINCHAR(IHELP+MUE3) ELSE INTEROUTTXT(MUE3)='L' END IF ELSE INTEROUTTXT(MUE3)='.' END IF END DO WRITE(KUNIT,'(T2,A,T10,A5,T15,60A1,A1)')'subset:', + 'SUB |',(INTEROUTTXT(MUE2),MUE2=1,IEND),'|' END IF WRITE(KUNIT,*) WRITE(KUNIT,*) END DO C-------------------------------------------------- C---- compute accuracy if DSSP available ----- C-------------------------------------------------- IF (LDSSPREAD .EQV. .TRUE.) THEN C ============== CALL WRTPOPRED(KUNIT) C ============== END IF END ***** end of WRTPRED ***** ------------------------------------------------------------------ ***** SUB WRTPREDHEADER ***** ------------------------------------------------------------------ C---- C---- NAME : WRTPREDHEADER C---- ARG : C---- DES : write secondary structure prediction header C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTPREDHEADER(KUNIT,MODE,LOUTBINPROB,LWRITE_ACC80) C---- local variables INTEGER KUNIT CHARACTER*5 SBEG,SEND CHARACTER*222 MODE LOGICAL LOUTBINPROB,LWRITE_ACC80 ************************************************************************ C---- defaults SBEG='* ' SEND=' *' C-------------------------------------------------- C---- abbreviations used C-------------------------------------------------- WRITE(KUNIT,'(A3,A,T78,A3)')SBEG,' Abbreviations:',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG,' --------------',SEND CALL WRTE(KUNIT) IF (MODE.EQ.'SECONDARY') THEN WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' secondary structure : H=helix, E=extended (sheet), blank=re'// + 'st (loop)',SEND ELSE WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' secondary structure : H=helical trans-membrane regions, L='// + 'rest (loop)',SEND END IF CALL WRTE(KUNIT) WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' AA: amino acid sequence',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' PHD: Profile network prediction HeiDelberg', + SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' Rel: Reliability index of prediction (0-9)', + SEND CALL WRTE(KUNIT) IF (LOUTBINPROB .EQV. .TRUE.) THEN WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' detail: ',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' prH: ''probability'' for assigning helix',SEND IF (MODE.EQ.'SECONDARY') THEN WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' prE: ''probability'' for assigning strand', + SEND END IF WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' prL: ''probability'' for assigning loop',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' note: the ''probabilites'' are scaled to the'// + ' interval 0-9, ',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' i.e. prH=5 means, that the signal at'// + ' the first',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' output node is 0.5-0.6.',SEND CALL WRTE(KUNIT) END IF IF (LWRITE_ACC80 .EQV. .TRUE.) THEN WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' subset:',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' SUB: a subset of the prediction, for all '// + 'residues with',SEND IF (MODE.EQ.'SECONDARY') THEN WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' an expected accuracy > 82% (see '// + ' tables in header)',SEND ELSE WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' an expected accuracy > 95% (see '// + ' tables in header)',SEND END IF IF (MODE.EQ.'SECONDARY') THEN WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' note: for this subset the following '// + 'symbols are used:',SEND ELSE WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' note 1: for this subset the following '// + 'symbols are used:',SEND END IF WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' L: is loop (for which above " " is used)', + SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' ".": means that no prediction is made '// + 'for this residue,',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' as the reliability is Rel < 5',SEND IF (MODE(1:13).EQ.'SECONDARY_HTM') THEN WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' note 2: the subset may contain continuous'// + ' helical segments,',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' where the row ''PHD'' has loop'// + ' loop regions. The',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' reason is that the prediction had'// + ' been filtered. ',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' In the row ''SUB'' the non-filtered'// + ' prediction is',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' given to indicate that the loop'// + ' is probably very',SEND WRITE(KUNIT,'(A3,A,T78,A3)')SBEG, + ' short!',SEND END IF CALL WRTE(KUNIT) END IF CALL WRTF(KUNIT) END ***** end of WRTPREDHEADER ***** ------------------------------------------------------------------ ***** SUB WRTWARN_NOALI ***** ------------------------------------------------------------------ C---- C---- NAME : WRTWARN_NOALI C---- ARG : C---- DES : write warning: no ali existing! C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE WRTWARN_NOALI(KUNIT,MODE) C---- global parameters * INCLUDE 'phdParameter.f' C---- local variables INTEGER KUNIT CHARACTER*5 SBEG,SEND CHARACTER*222 MODE ************************************************************************ C---- defaults SBEG='* ' SEND=' *' C-------------------------------------------------- C---- write warning if too few sequences in ali --- C-------------------------------------------------- WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG,'WARNING:',SEND WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG,'========',SEND CALL WRTE(KUNIT) IF (MODE(1:13).EQ.'SECONDARY_HTM') THEN WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'Expected accuracy is about 94% if, and only if, '// + 'the alignment contains',SEND ELSEIF (MODE(1:9).EQ.'SECONDARY') THEN WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'Expected accuracy is about 72% if, and only if, '// + 'the alignment contains',SEND ELSEIF (MODE(1:8).EQ.'EXPOSURE') THEN WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'Expected correlation is about 0.55 if, and only if, '// + 'alignment contains',SEND END IF IF (NUMNALIGN(1).EQ.1) THEN WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'sufficient information. For your sequence there '// + 'was no homologue in',SEND WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'the current version of Swissprot detected. This '// + 'implies that the',SEND IF (MODE.EQ.'SECONDARY') THEN WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'expected accuracy is about 6-10 percentage'// + ' points lower !',SEND ELSEIF (MODE.EQ.'SECONDARY_HTM') THEN WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'expected accuracy is about 2-5 percentage'// + ' points lower !',SEND ELSEIF (MODE.EQ.'EXPOSURE') THEN WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'expected correlation is about 0.1 lower!',SEND END IF ELSE WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'sufficient information. For your sequence there '// + 'were not many',SEND WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'homologues in the current version of Swissprot '// + 'detected. This ',SEND WRITE(KUNIT,'(A3,T5,A,T78,A3)')SBEG, + 'implies that the expected accuracy is some '// + 'percentage points lower !',SEND END IF CALL WRTE(KUNIT) CALL WRTF(KUNIT) CALL WRTE(KUNIT) END ***** end of WRTWARN_NOALI C vim:et:ts=2: profnet-1.0.22/src-phd/phdParameter.f0000644015075101507510000005154612021362705016703 0ustar lkajanlkajan*----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 0.2 * *----------------------------------------------------------------------* ************************************************************************ * This file contains the maximal parameters for executing multiple * * runs of secstron. The specific parameter and variables for a * * particular run are written in parsecstron resp parcollsec. * ************************************************************************ IMPLICIT NONE * **** * **** * ***PARAMETERS*** * *** * ********** * * * * ************************************************************************ C-------------------------------------------------- C---- numbers ----- C-------------------------------------------------- C---- ----- C---- ----- C---- ----- C---- architecture of network ----- C---- ----- INTEGER NUMINMAX,NUMOUTMAX,NUMHIDMAX, + NUMNEIGHMAX,NBIOLOBJMAX,NCODEUNTMAX,NHISTOMAX C---- ----- C---- units (global) ----- C---- ----- INTEGER NUNITS_LENGTH,NUNITS_DISTCAPS C---- ----- C---- reading databank ----- C---- ----- INTEGER NUMPROTMAX,NUMRESMAX C---- ----- C---- jury decision ----- C---- ----- INTEGER NUMNETMAX,NUMNETFSTMAX,NUMNETSNDMAX * * C---- ----- C---- data handling ----- C---- ----- REAL ABW * * LOGICAL LDSSP C---- protein (read hssp) INTEGER MAXALIGNS,MAXCORE * * * * C---- =================================================================* * * C---- ---------------------------------------- PARAMETER (NUMINMAX= 850) PARAMETER (NUMOUTMAX= 10) PARAMETER (NUMHIDMAX= 60) PARAMETER (NUMNEIGHMAX= 21) PARAMETER (NBIOLOBJMAX= 21) PARAMETER (NCODEUNTMAX= 63) PARAMETER (NHISTOMAX= 50) C---- ------------------------------- * * C---- ------------------------------------ PARAMETER (NUNITS_LENGTH= 4) PARAMETER (NUNITS_DISTCAPS= 4) C---- ------------------------------------ * * C---- --------------------------------------- PARAMETER (NUMPROTMAX= 2) C MAC core-dump for > 4200! C br 2003-08-23 fixed problem with core dump C PARAMETER (NUMRESMAX= 4200) C exe normal C PARAMETER (NUMRESMAX= 5000) C exe big PARAMETER (NUMRESMAX= 9999) C PARAMETER (NUMRESMAX= 10000) C---- --------------------------------------- * * C---- --------------------------------------- C for maxhom C PARAMETER (MAXALIGNS= 5000) C br 2003-08-23: no longer relevant PARAMETER (MAXCORE= 50000) C PARAMETER (MAXCORE= 1000000) C PARAMETER (MAXCORE= 3000000) INTEGER NBLOCKSIZE PARAMETER (NBLOCKSIZE= 70) INTEGER MAXAA PARAMETER (MAXAA= 20) C---- --------------------------------------- * * C---- --------------------------------------- PARAMETER (NUMNETMAX= 30) PARAMETER (NUMNETFSTMAX= 15) PARAMETER (NUMNETSNDMAX= 15) C---- --------------------------------------- * * C---- --------------------------------------- PARAMETER (ABW= 0.00001) C---- --------------------------------------- * * * * C---- --------------------------------------- PARAMETER (LDSSP=.FALSE.) C---- --------------------------------------- * * * * C---- =================================================================* ************************************************************************ * * * **** * ***VARIABLES*** * *** * ********* * * * * * * ************************************************************************ C-------------------------------------------------- C---- shared numbers ----- C-------------------------------------------------- C---- ----- C---- environment (path asf) ----- C---- ----- CHARACTER*222 PATH_PARACOM,PATH_ARCH,PATH_WORK,PATH_PRED INTEGER LENPATH_PARACOM * * * * C---- ----- C---- hssp related variables ----- C---- ----- CHARACTER*222 FILE_HSSP,FILE_HSSP_NOCHAIN CHARACTER*132 PROTNAME(1:NUMPROTMAX) * * CHARACTER*1 RESNAME(1:NUMRESMAX), + RESSECSTR(1:NUMRESMAX),CONVSECSTR(1:NUMRESMAX), + AACODE(1:NBIOLOBJMAX),SSCODE(1:7),EXPCODE(1:10) CHARACTER*24 AACODE24 CHARACTER*26 AACODE_LOWC * * C br 2003-08-23: save space C INTEGER RESVAR(1:NUMRESMAX) INTEGER RESVAR(1:1) C br 2003-08-23: end save space INTEGER RESACC(1:NUMRESMAX), + RESPROF(1:NUMRESMAX,1:NBIOLOBJMAX), + RESNDEL(1:NUMRESMAX),RESNINS(1:NUMRESMAX), + NUMNALIGN(1:NUMPROTMAX) * * REAL*4 RESCONSWEIGHT(1:NUMRESMAX) * * INTEGER POINTBEG(1:NUMPROTMAX),POINTEND(0:NUMPROTMAX), + NUMRES,AABIT(1:NBIOLOBJMAX,1:NCODEUNTMAX) * * LOGICAL LDSSPREAD * * COMMON /ENV1/PATH_PARACOM,PATH_ARCH,PATH_WORK,PATH_PRED COMMON /ENV2/LENPATH_PARACOM COMMON /DATAB1A/PROTNAME COMMON /DATAB1B/FILE_HSSP,FILE_HSSP_NOCHAIN COMMON /DATAB2/RESNAME,RESSECSTR,CONVSECSTR,AACODE,SSCODE,EXPCODE COMMON /DATAB2b/AACODE24 COMMON /DATAB2c/AACODE_LOWC COMMON /DATAB3/RESACC,RESVAR,RESPROF,RESNDEL,RESNINS,NUMNALIGN, + POINTBEG,POINTEND,NUMRES,AABIT COMMON /DATAB4/RESCONSWEIGHT COMMON /DATAB5/LDSSPREAD * * * * C---- ----- C---- Exposure related variables ----- C---- ----- INTEGER MAXEXP,T2,T3A,T3B * * REAL THREXP2ST(1:3),THREXP3ST(1:4),THREXP10ST(1:10) INTEGER THREXP2STI(1:3),THREXP3STI(1:4),THREXP10STI(1:10) * * COMMON /EXP1/MAXEXP,T2,T3A,T3B COMMON /EXP2/THREXP2ST,THREXP3ST,THREXP10ST COMMON /EXP3/THREXP2STI,THREXP3STI,THREXP10STI * * C---- ----- C---- architecture ----- C---- ----- * * INTEGER NUMIN,NUMHID,NUMOUT,NUMNEIGH,NBIOLOBJ,NCODEUNT, + NUMNETFST,NUMNETSND,NUMNETJURY,MAXVAR, + MAXACC,PROFACC,CASCACC,NSECEL INTEGER TRANS2FROM1(1:NUMNETSNDMAX) * * COMMON /COMPARA1/NUMIN,NUMHID,NUMOUT,NUMNEIGH,NBIOLOBJ,NCODEUNT, + NUMNETFST,NUMNETSND,NUMNETJURY,MAXVAR, + MAXACC,PROFACC,CASCACC,NSECEL COMMON /COMPARA2/TRANS2FROM1 * * C-------------------------------------------------- C---- characters/modes being shared ----- C-------------------------------------------------- C---- ----- C---- different modes ----- C---- ----- * * CHARACTER*222 MODEASSSTR(1:NUMNETSNDMAX), + MODEASSCAS(1:NUMNETFSTMAX),MODESECSTRON * * CHARACTER*222 FILEPRED,FILEOUTPUT,ACTFILE, + FILEARCHFST(1:NUMNETFSTMAX),FILEARCHSND(1:NUMNETSNDMAX), + FILE_ARCHLIST,FILE_RDB,FILE_WHATIF, + CHAR_ARG_READ(1:222) * * COMMON /COMPARA3/MODEASSSTR,MODEASSCAS,MODESECSTRON COMMON /COMPARA4/FILEPRED,FILEOUTPUT,ACTFILE, + FILEARCHFST,FILEARCHSND,FILE_ARCHLIST,FILE_RDB,FILE_WHATIF, + CHAR_ARG_READ C-------------------------------------------------- C---- previous parameters for particular job ----- C---- note: assigned by parset.f ----- C-------------------------------------------------- * * C---- ----- C---- junctions, biases ----- C---- ----- * * REAL JUNCTION1ST(1:(NUMINMAX+NUMOUTMAX),1:NUMHIDMAX) REAL LOCFIELD1(1:NUMHIDMAX) REAL JUNCTION2ND(1:(NUMHIDMAX+NUMOUTMAX),1:NUMOUTMAX) REAL LOCFIELD2(1:NUMOUTMAX) * * COMMON /TRIGGER3/JUNCTION1ST,JUNCTION2ND COMMON /TRIGGER4/LOCFIELD1,LOCFIELD2 * * C---- ----- C---- in/out vectors ----- C---- ----- * * REAL*4 INPUT(1:(NUMINMAX+NUMOUTMAX),1:NUMRESMAX) REAL*4 OUTPUT(1:NUMOUTMAX,1:NUMRESMAX), + OUTFIL(1:NUMOUTMAX,1:NUMRESMAX), + OUTFST(1:NUMOUTMAX,1:NUMRESMAX,1:NUMNETFSTMAX), + OUTSND(1:NUMOUTMAX,1:NUMRESMAX,1:NUMNETSNDMAX) REAL*4 OUTEXP(1:NUMRESMAX),DESEXP(1:NUMRESMAX), + OUTEXPFIL(1:NUMRESMAX) INTEGER*4 OUTBIN(1:NUMOUTMAX,1:NUMRESMAX), + OUTBINPROB(1:NUMOUTMAX,1:NUMRESMAX) * * CHARACTER*1 OUTBINCHAR(1:NUMRESMAX),OUTBINCHARFIL(1:NUMRESMAX) * * * * COMMON /EXTERN1/INPUT,OUTPUT,OUTFST,OUTSND,OUTEXP,DESEXP, + OUTFIL,OUTEXPFIL COMMON /EXTERN2/OUTBIN,OUTBINPROB COMMON /EXTERN3/OUTBINCHAR,OUTBINCHARFIL * * C---- ----- C---- reliability index ----- C---- ----- * * INTEGER NUMRELIND(0:9) INTEGER*2 RELIND(1:NUMRESMAX) INTEGER*2 DSSPVEC_I2(1:NUMRESMAX),PREDVEC_I2(1:NUMRESMAX) * * COMMON /EXTERN4a/NUMRELIND COMMON /EXTERN4b/RELIND,DSSPVEC_I2,PREDVEC_I2 * * * * C---- ----- C---- filtering stuff (exposure) ----- C---- ----- * * REAL REDUCE_MINSIZE,REDUCE_STATE0,REDUCE_STATE1 LOGICAL LREDUCE_BURRIED * * COMMON /FILTER1/REDUCE_MINSIZE,REDUCE_STATE0,REDUCE_STATE1 COMMON /FILTER2/LREDUCE_BURRIED * * C---- ----- C---- run time variables ----- C---- ----- * * CHARACTER*24 STARTDATE,ENDDATE,XDTE CHARACTER*8 STARTTIME,ENDTIME * * REAL TIMEDIFF,TIMEARRAY,TIMESTART,TIMERUN,TIMEEND * * COMMON /CLOCK1/STARTDATE,ENDDATE,XDTE,STARTTIME,ENDTIME COMMON /CLOCK2/TIMEARRAY,TIMEDIFF,TIMESTART,TIMERUN,TIMEEND * * * * C---- ----- C---- pay-off numbers ----- C---- ----- * * INTEGER MATNUM(1:(NUMOUTMAX+1),1:(NUMOUTMAX+1)), + MATLEN(1:(NUMOUTMAX+1),1:4), + MATLENDIS(1:NHISTOMAX,1:(2*NUMOUTMAX)), + NUMSEGOVERL(1:9,1:(NUMOUTMAX+1)), + COUNTSEGMAT(1:2,1:(NUMOUTMAX+1)), + EXP_NOINBIN(0:9,0:9), + EXP_NOIN2ST(1:3),EXP_NOIN3ST(1:4),EXP_NOIN10ST(1:11), + OBS_NOIN2ST(1:3),OBS_NOIN3ST(1:4),OBS_NOIN10ST(1:11) * * REAL Q3,SQ,CORR(1:NUMOUTMAX),INFO,INFO_INV, + RMATQOFDSSP(1:NUMOUTMAX,1:NUMOUTMAX), + RMATQOFPRED(1:NUMOUTMAX,1:NUMOUTMAX), + QLOV(1:2,1:(NUMOUTMAX+1)), + QSOV(1:2,1:(NUMOUTMAX+1)),QFOV(1:2,1:(NUMOUTMAX+1)), + EXP_CORR * * * * CHARACTER*132 TITLE,VERSION_SEC,VERSION_EXP,VERSION_HTM * * COMMON /PAYOFF1/MATNUM,MATLEN,MATLENDIS,NUMSEGOVERL,COUNTSEGMAT, + EXP_NOINBIN,EXP_NOIN2ST,EXP_NOIN3ST,EXP_NOIN10ST, + OBS_NOIN2ST,OBS_NOIN3ST,OBS_NOIN10ST COMMON /PAYOFF2/Q3,SQ,CORR,RMATQOFDSSP,RMATQOFPRED,INFO,INFO_INV, + QLOV,QSOV,QFOV,EXP_CORR COMMON /PAYOFF3/TITLE,VERSION_SEC,VERSION_EXP,VERSION_HTM * * * * C---- ----- C---- content, asf. ----- C---- ----- * * REAL CONTPRED(1:NUMOUTMAX),CONTDSSP(1:NUMOUTMAX),CONTAA(1:24) * * COMMON /CONT/CONTPRED,CONTDSSP,CONTAA * * C---- ----- C---- communication ----- C---- ----- * * CHARACTER*1 ACTRESIDUE CHARACTER*15 CASEDISCR,CONTROLCHAR CHARACTER*25 ACTREGION * * INTEGER ACTPOS,ACTSOLVADDBEG,ACTSOLVADDEND, + ACTSOLVADDEND2,CODEVECPROF(1:NBIOLOBJMAX),PROFMAX, + CODEVECINCASC(1:(NUMOUTMAX+1)), + CODECOMPOSITION(1:NBIOLOBJMAX), + ACTCOMPOSITION(1:NBIOLOBJMAX), + ACTCHI,ACTITER,ACTSTART,ACTNDEL,ACTNINS,ACTNALIGN,ACTACC * * INTEGER BEGUNITS_COMPOSITION, + BEGUNITS_LENGTH,BEGUNITS_DISTCAPS, + SPLIT_LENGTH(1:NUNITS_LENGTH), + SPLIT_DISTCAPS(1:(NUNITS_LENGTH+1)) * * REAL CODEVECTOR(1:NCODEUNTMAX),PROFINTERV,CASCINTERV, + ACTCONSWEIGHT,ACTINTERVALL * * LOGICAL LOGI_COMPOSITION,LOGI_LENGTH,LOGI_DISTCAPS, + LOGI_CONS,LOGI_INDEL,LOGI_REALINPUT * * COMMON /CODE1A/ACTRESIDUE COMMON /CODE1B/CASEDISCR,CONTROLCHAR COMMON /CODE1C/ACTREGION COMMON /CODE3/ACTPOS,ACTSOLVADDBEG,ACTSOLVADDEND,ACTSOLVADDEND2, + CODEVECPROF,PROFMAX,CODEVECINCASC, + CODECOMPOSITION,ACTCOMPOSITION, + ACTCHI,ACTITER,ACTSTART,ACTNDEL,ACTNINS,ACTNALIGN,ACTACC COMMON /CODE4/CODEVECTOR,PROFINTERV,CASCINTERV,ACTCONSWEIGHT, + ACTINTERVALL COMMON /CODE5/BEGUNITS_COMPOSITION, + BEGUNITS_LENGTH,BEGUNITS_DISTCAPS, + SPLIT_LENGTH,SPLIT_DISTCAPS COMMON /CODE6/LOGI_COMPOSITION,LOGI_LENGTH,LOGI_DISTCAPS, + LOGI_CONS,LOGI_INDEL,LOGI_REALINPUT * * C---- ----- C---- controls ----- C---- ----- * * LOGICAL LSERVER,LFILTER,LDEC,LOUTBINPROB, + LMACHINE_READABLE,LWHATIF,LRDB * * COMMON /CONTROL/LSERVER,LFILTER,LDEC,LOUTBINPROB, + LMACHINE_READABLE,LWHATIF,LRDB * * *----------------------------------------------------------------------* * Parmaters and Common variables for PHD * *----------------------------------------------------------------------* profnet-1.0.22/src-phd/phdParameter.f_mac0000644015075101507510000005065412021362704017521 0ustar lkajanlkajan*----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 0.2 * *----------------------------------------------------------------------* ************************************************************************ * This file contains the maximal parameters for executing multiple * * runs of secstron. The specific parameter and variables for a * * particular run are written in parsecstron resp parcollsec. * ************************************************************************ IMPLICIT NONE * **** * **** * ***PARAMETERS*** * *** * ********** * * * * ************************************************************************ C-------------------------------------------------- C---- numbers ----- C-------------------------------------------------- C---- ----- C---- ----- C---- ----- C---- architecture of network ----- C---- ----- INTEGER NUMINMAX,NUMOUTMAX,NUMHIDMAX, + NUMNEIGHMAX,NBIOLOBJMAX,NCODEUNTMAX,NHISTOMAX C---- ----- C---- units (global) ----- C---- ----- INTEGER NUNITS_LENGTH,NUNITS_DISTCAPS C---- ----- C---- reading databank ----- C---- ----- INTEGER NUMPROTMAX,NUMRESMAX C---- ----- C---- jury decision ----- C---- ----- INTEGER NUMNETMAX,NUMNETFSTMAX,NUMNETSNDMAX * * C---- ----- C---- data handling ----- C---- ----- REAL ABW * * LOGICAL LDSSP C---- protein (read hssp) INTEGER MAXALIGNS,MAXCORE * * * * C---- =================================================================* * * C---- ---------------------------------------- PARAMETER (NUMINMAX= 850) PARAMETER (NUMOUTMAX= 10) PARAMETER (NUMHIDMAX= 60) PARAMETER (NUMNEIGHMAX= 21) PARAMETER (NBIOLOBJMAX= 21) PARAMETER (NCODEUNTMAX= 63) PARAMETER (NHISTOMAX= 50) C---- ------------------------------- * * C---- ------------------------------------ PARAMETER (NUNITS_LENGTH= 4) PARAMETER (NUNITS_DISTCAPS= 4) C---- ------------------------------------ * * C---- --------------------------------------- PARAMETER (NUMPROTMAX= 2) PARAMETER (NUMRESMAX= 3000) C PARAMETER (NUMRESMAX= 5000) C PARAMETER (NUMRESMAX= 10000) C---- --------------------------------------- * * C---- --------------------------------------- C for maxhom C PARAMETER (MAXALIGNS= 3000) C PARAMETER (MAXALIGNS= 5000) PARAMETER (MAXCORE= 500000) C PARAMETER (MAXCORE= 800000) C PARAMETER (MAXCORE= 1000000) INTEGER NBLOCKSIZE PARAMETER (NBLOCKSIZE= 70) INTEGER MAXAA PARAMETER (MAXAA= 20) C---- --------------------------------------- * * C---- --------------------------------------- PARAMETER (NUMNETMAX= 30) PARAMETER (NUMNETFSTMAX= 15) PARAMETER (NUMNETSNDMAX= 15) C---- --------------------------------------- * * C---- --------------------------------------- PARAMETER (ABW= 0.00001) C---- --------------------------------------- * * * * C---- --------------------------------------- PARAMETER (LDSSP=.FALSE.) C---- --------------------------------------- * * * * C---- =================================================================* ************************************************************************ * * * **** * ***VARIABLES*** * *** * ********* * * * * * * ************************************************************************ C-------------------------------------------------- C---- shared numbers ----- C-------------------------------------------------- C---- ----- C---- environment (path asf) ----- C---- ----- CHARACTER*222 PATH_PARACOM,PATH_ARCH,PATH_WORK,PATH_PRED INTEGER LENPATH_PARACOM * * * * C---- ----- C---- hssp related variables ----- C---- ----- CHARACTER*222 FILE_HSSP,FILE_HSSP_NOCHAIN CHARACTER*132 PROTNAME(1:NUMPROTMAX) * * CHARACTER*1 RESNAME(1:NUMRESMAX), + RESSECSTR(1:NUMRESMAX),CONVSECSTR(1:NUMRESMAX), + AACODE(1:NBIOLOBJMAX),SSCODE(1:7),EXPCODE(1:10) CHARACTER*24 AACODE24 CHARACTER*26 AACODE_LOWC * * INTEGER RESACC(1:NUMRESMAX), + RESVAR(1:NUMRESMAX),RESPROF(1:NUMRESMAX,1:NBIOLOBJMAX), + RESNDEL(1:NUMRESMAX),RESNINS(1:NUMRESMAX), + NUMNALIGN(1:NUMPROTMAX) * * REAL*4 RESCONSWEIGHT(1:NUMRESMAX) * * INTEGER POINTBEG(1:NUMPROTMAX),POINTEND(0:NUMPROTMAX), + NUMRES,AABIT(1:NBIOLOBJMAX,1:NCODEUNTMAX) * * LOGICAL LDSSPREAD * * COMMON /ENV1/PATH_PARACOM,PATH_ARCH,PATH_WORK,PATH_PRED COMMON /ENV2/LENPATH_PARACOM COMMON /DATAB1A/PROTNAME COMMON /DATAB1B/FILE_HSSP,FILE_HSSP_NOCHAIN COMMON /DATAB2/RESNAME,RESSECSTR,CONVSECSTR,AACODE,SSCODE,EXPCODE COMMON /DATAB2b/AACODE24 COMMON /DATAB2c/AACODE_LOWC COMMON /DATAB3/RESACC,RESVAR,RESPROF,RESNDEL,RESNINS,NUMNALIGN, + POINTBEG,POINTEND,NUMRES,AABIT COMMON /DATAB4/RESCONSWEIGHT COMMON /DATAB5/LDSSPREAD * * * * C---- ----- C---- Exposure related variables ----- C---- ----- INTEGER MAXEXP,T2,T3A,T3B * * REAL THREXP2ST(1:3),THREXP3ST(1:4),THREXP10ST(1:10) * * COMMON /EXP1/MAXEXP,T2,T3A,T3B COMMON /EXP2/THREXP2ST,THREXP3ST,THREXP10ST * * C---- ----- C---- architecture ----- C---- ----- * * INTEGER NUMIN,NUMHID,NUMOUT,NUMNEIGH,NBIOLOBJ,NCODEUNT, + NUMNETFST,NUMNETSND,NUMNETJURY,MAXVAR, + MAXACC,PROFACC,CASCACC,NSECEL INTEGER TRANS2FROM1(1:NUMNETSNDMAX) * * COMMON /COMPARA1/NUMIN,NUMHID,NUMOUT,NUMNEIGH,NBIOLOBJ,NCODEUNT, + NUMNETFST,NUMNETSND,NUMNETJURY,MAXVAR, + MAXACC,PROFACC,CASCACC,NSECEL COMMON /COMPARA2/TRANS2FROM1 * * C-------------------------------------------------- C---- characters/modes being shared ----- C-------------------------------------------------- C---- ----- C---- different modes ----- C---- ----- * * CHARACTER*132 MODEASSSTR(1:NUMNETSNDMAX), + MODEASSCAS(1:NUMNETFSTMAX),MODESECSTRON * * CHARACTER*222 FILEPRED,FILEOUTPUT,ACTFILE, + FILEARCHFST(1:NUMNETFSTMAX),FILEARCHSND(1:NUMNETSNDMAX), + FILE_ARCHLIST,FILE_RDB,FILE_WHATIF, + CHAR_ARG_READ(1:222) * * COMMON /COMPARA3/MODEASSSTR,MODEASSCAS,MODESECSTRON COMMON /COMPARA4/FILEPRED,FILEOUTPUT,ACTFILE, + FILEARCHFST,FILEARCHSND,FILE_ARCHLIST,FILE_RDB,FILE_WHATIF, + CHAR_ARG_READ C-------------------------------------------------- C---- previous parameters for particular job ----- C---- note: assigned by parset.f ----- C-------------------------------------------------- * * C---- ----- C---- junctions, biases ----- C---- ----- * * REAL JUNCTION1ST(1:(NUMINMAX+NUMOUTMAX),1:NUMHIDMAX) REAL LOCFIELD1(1:NUMHIDMAX) REAL JUNCTION2ND(1:(NUMHIDMAX+NUMOUTMAX),1:NUMOUTMAX) REAL LOCFIELD2(1:NUMOUTMAX) * * COMMON /TRIGGER3/JUNCTION1ST,JUNCTION2ND COMMON /TRIGGER4/LOCFIELD1,LOCFIELD2 * * C---- ----- C---- in/out vectors ----- C---- ----- * * REAL*4 INPUT(1:(NUMINMAX+NUMOUTMAX),1:NUMRESMAX) REAL*4 OUTPUT(1:NUMOUTMAX,1:NUMRESMAX), + OUTFIL(1:NUMOUTMAX,1:NUMRESMAX), + OUTFST(1:NUMOUTMAX,1:NUMRESMAX,1:NUMNETFSTMAX), + OUTSND(1:NUMOUTMAX,1:NUMRESMAX,1:NUMNETSNDMAX) REAL*4 OUTEXP(1:NUMRESMAX),DESEXP(1:NUMRESMAX), + OUTEXPFIL(1:NUMRESMAX) INTEGER*4 OUTBIN(1:NUMOUTMAX,1:NUMRESMAX), + OUTBINPROB(1:NUMOUTMAX,1:NUMRESMAX) * * CHARACTER*1 OUTBINCHAR(1:NUMRESMAX),OUTBINCHARFIL(1:NUMRESMAX) * * * * COMMON /EXTERN1/INPUT,OUTPUT,OUTFST,OUTSND,OUTEXP,DESEXP, + OUTFIL,OUTEXPFIL COMMON /EXTERN2/OUTBIN,OUTBINPROB COMMON /EXTERN3/OUTBINCHAR,OUTBINCHARFIL * * C---- ----- C---- reliability index ----- C---- ----- * * INTEGER NUMRELIND(0:9) INTEGER*2 RELIND(1:NUMRESMAX) INTEGER*2 DSSPVEC_I2(1:NUMRESMAX),PREDVEC_I2(1:NUMRESMAX) * * COMMON /EXTERN4a/NUMRELIND COMMON /EXTERN4b/RELIND,DSSPVEC_I2,PREDVEC_I2 * * * * C---- ----- C---- filtering stuff (exposure) ----- C---- ----- * * REAL REDUCE_MINSIZE,REDUCE_STATE0,REDUCE_STATE1 LOGICAL LREDUCE_BURRIED * * COMMON /FILTER1/REDUCE_MINSIZE,REDUCE_STATE0,REDUCE_STATE1 COMMON /FILTER2/LREDUCE_BURRIED * * C---- ----- C---- run time variables ----- C---- ----- * * CHARACTER*24 STARTDATE,ENDDATE,XDTE CHARACTER*8 STARTTIME,ENDTIME * * REAL TIMEDIFF,TIMEARRAY,TIMESTART,TIMERUN,TIMEEND * * COMMON /CLOCK1/STARTDATE,ENDDATE,XDTE,STARTTIME,ENDTIME COMMON /CLOCK2/TIMEARRAY,TIMEDIFF,TIMESTART,TIMERUN,TIMEEND * * * * C---- ----- C---- pay-off numbers ----- C---- ----- * * INTEGER MATNUM(1:(NUMOUTMAX+1),1:(NUMOUTMAX+1)), + MATLEN(1:(NUMOUTMAX+1),1:4), + MATLENDIS(1:NHISTOMAX,1:(2*NUMOUTMAX)), + NUMSEGOVERL(1:9,1:(NUMOUTMAX+1)), + COUNTSEGMAT(1:2,1:(NUMOUTMAX+1)), + EXP_NOINBIN(0:9,0:9), + EXP_NOIN2ST(1:3),EXP_NOIN3ST(1:4),EXP_NOIN10ST(1:11), + OBS_NOIN2ST(1:3),OBS_NOIN3ST(1:4),OBS_NOIN10ST(1:11) * * REAL Q3,SQ,CORR(1:NUMOUTMAX),INFO,INFO_INV, + RMATQOFDSSP(1:NUMOUTMAX,1:NUMOUTMAX), + RMATQOFPRED(1:NUMOUTMAX,1:NUMOUTMAX), + QLOV(1:2,1:(NUMOUTMAX+1)), + QSOV(1:2,1:(NUMOUTMAX+1)),QFOV(1:2,1:(NUMOUTMAX+1)), + EXP_CORR * * * * CHARACTER*132 TITLE,VERSION_SEC,VERSION_EXP,VERSION_HTM * * COMMON /PAYOFF1/MATNUM,MATLEN,MATLENDIS,NUMSEGOVERL,COUNTSEGMAT, + EXP_NOINBIN,EXP_NOIN2ST,EXP_NOIN3ST,EXP_NOIN10ST, + OBS_NOIN2ST,OBS_NOIN3ST,OBS_NOIN10ST COMMON /PAYOFF2/Q3,SQ,CORR,RMATQOFDSSP,RMATQOFPRED,INFO,INFO_INV, + QLOV,QSOV,QFOV,EXP_CORR COMMON /PAYOFF3/TITLE,VERSION_SEC,VERSION_EXP,VERSION_HTM * * * * C---- ----- C---- content, asf. ----- C---- ----- * * REAL CONTPRED(1:NUMOUTMAX),CONTDSSP(1:NUMOUTMAX),CONTAA(1:24) * * COMMON /CONT/CONTPRED,CONTDSSP,CONTAA * * C---- ----- C---- communication ----- C---- ----- * * CHARACTER*1 ACTRESIDUE CHARACTER*15 CASEDISCR,CONTROLCHAR CHARACTER*25 ACTREGION * * INTEGER ACTPOS,ACTSOLVADDBEG,ACTSOLVADDEND, + ACTSOLVADDEND2,CODEVECPROF(1:NBIOLOBJMAX),PROFMAX, + CODEVECINCASC(1:(NUMOUTMAX+1)), + CODECOMPOSITION(1:NBIOLOBJMAX), + ACTCOMPOSITION(1:NBIOLOBJMAX), + ACTCHI,ACTITER,ACTSTART,ACTNDEL,ACTNINS,ACTNALIGN,ACTACC * * INTEGER BEGUNITS_COMPOSITION, + BEGUNITS_LENGTH,BEGUNITS_DISTCAPS, + SPLIT_LENGTH(1:NUNITS_LENGTH), + SPLIT_DISTCAPS(1:(NUNITS_LENGTH+1)) * * REAL CODEVECTOR(1:NCODEUNTMAX),PROFINTERV,CASCINTERV, + ACTCONSWEIGHT,ACTINTERVALL * * LOGICAL LOGI_COMPOSITION,LOGI_LENGTH,LOGI_DISTCAPS, + LOGI_CONS,LOGI_INDEL,LOGI_REALINPUT * * COMMON /CODE1A/ACTRESIDUE COMMON /CODE1B/CASEDISCR,CONTROLCHAR COMMON /CODE1C/ACTREGION COMMON /CODE3/ACTPOS,ACTSOLVADDBEG,ACTSOLVADDEND,ACTSOLVADDEND2, + CODEVECPROF,PROFMAX,CODEVECINCASC, + CODECOMPOSITION,ACTCOMPOSITION, + ACTCHI,ACTITER,ACTSTART,ACTNDEL,ACTNINS,ACTNALIGN,ACTACC COMMON /CODE4/CODEVECTOR,PROFINTERV,CASCINTERV,ACTCONSWEIGHT, + ACTINTERVALL COMMON /CODE5/BEGUNITS_COMPOSITION, + BEGUNITS_LENGTH,BEGUNITS_DISTCAPS, + SPLIT_LENGTH,SPLIT_DISTCAPS COMMON /CODE6/LOGI_COMPOSITION,LOGI_LENGTH,LOGI_DISTCAPS, + LOGI_CONS,LOGI_INDEL,LOGI_REALINPUT * * C---- ----- C---- controls ----- C---- ----- * * LOGICAL LSERVER,LFILTER,LDEC,LOUTBINPROB, + LMACHINE_READABLE,LWHATIF,LRDB * * COMMON /CONTROL/LSERVER,LFILTER,LDEC,LOUTBINPROB, + LMACHINE_READABLE,LWHATIF,LRDB * * *----------------------------------------------------------------------* * Parmaters and Common variables for PHD * *----------------------------------------------------------------------* profnet-1.0.22/src-phd/save-para.f0000644015075101507510000004716012021362705016143 0ustar lkajanlkajan*----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 0.2 * *----------------------------------------------------------------------* ************************************************************************ * This file contains the maximal parameters for executing multiple * * runs of secstron. The specific parameter and variables for a * * particular run are written in parsecstron resp parcollsec. * ************************************************************************ IMPLICIT NONE * **** * **** * ***PARAMETERS*** * *** * ********** * * * * ************************************************************************ C-------------------------------------------------- C---- numbers ----- C-------------------------------------------------- C---- ----- C---- ----- C---- ----- C---- architecture of network ----- C---- ----- INTEGER NUMINMAX,NUMOUTMAX,NUMHIDMAX, + NUMNEIGHMAX,NBIOLOBJMAX,NCODEUNTMAX,NHISTOMAX C---- ----- C---- units (global) ----- C---- ----- INTEGER NUNITS_LENGTH,NUNITS_DISTCAPS C---- ----- C---- reading databank ----- C---- ----- INTEGER NUMPROTMAX,NUMRESMAX C---- ----- C---- jury decision ----- C---- ----- INTEGER NUMNETMAX,NUMNETFSTMAX,NUMNETSNDMAX * * C---- ----- C---- data handling ----- C---- ----- REAL ABW * * LOGICAL LDSSP * * * * C---- =================================================================* * * C---- ---------------------------------------- PARAMETER (NUMINMAX= 1000) PARAMETER (NUMOUTMAX= 10) PARAMETER (NUMHIDMAX= 60) PARAMETER (NUMNEIGHMAX= 21) PARAMETER (NBIOLOBJMAX= 21) PARAMETER (NCODEUNTMAX= 63) PARAMETER (NHISTOMAX= 50) C---- ------------------------------- * * C---- ------------------------------------ PARAMETER (NUNITS_LENGTH= 4) PARAMETER (NUNITS_DISTCAPS= 4) C---- ------------------------------------ * * C---- --------------------------------------- PARAMETER (NUMPROTMAX= 1) PARAMETER (NUMRESMAX= 10000) C---- --------------------------------------- * * C---- --------------------------------------- PARAMETER (NUMNETMAX= 30) PARAMETER (NUMNETFSTMAX= 15) PARAMETER (NUMNETSNDMAX= 15) C---- --------------------------------------- * * C---- --------------------------------------- PARAMETER (ABW= 0.00001) C---- --------------------------------------- * * * * C---- --------------------------------------- PARAMETER (LDSSP=.FALSE.) C---- --------------------------------------- * * * * C---- =================================================================* ************************************************************************ * * * **** * ***VARIABLES*** * *** * ********* * * * * * * ************************************************************************ C-------------------------------------------------- C---- shared numbers ----- C-------------------------------------------------- C---- ----- C---- environment (path asf) ----- C---- ----- CHARACTER*132 PATH_PARACOM,PATH_ARCH,PATH_WORK,PATH_PRED INTEGER LENPATH_PARACOM * * * * C---- ----- C---- hssp related variables ----- C---- ----- CHARACTER*132 FILE_HSSP,FILE_HSSP_NOCHAIN CHARACTER*132 PROTNAME(1:NUMPROTMAX) * * CHARACTER*1 RESNAME(1:NUMRESMAX), + RESSECSTR(1:NUMRESMAX),CONVSECSTR(1:NUMRESMAX), + AACODE(1:NBIOLOBJMAX),SSCODE(1:7),EXPCODE(1:10) CHARACTER*24 AACODE24 CHARACTER*26 AACODE_LOWC * * INTEGER RESACC(1:NUMRESMAX), + RESVAR(1:NUMRESMAX),RESPROF(1:NUMRESMAX,1:NBIOLOBJMAX), + RESNDEL(1:NUMRESMAX),RESNINS(1:NUMRESMAX), + NUMNALIGN(1:NUMPROTMAX) * * REAL*4 RESCONSWEIGHT(1:NUMRESMAX) * * INTEGER POINTBEG(1:NUMPROTMAX),POINTEND(0:NUMPROTMAX), + NUMRES,AABIT(1:NBIOLOBJMAX,1:NCODEUNTMAX) * * LOGICAL LDSSPREAD * * COMMON /ENV1/PATH_PARACOM,PATH_ARCH,PATH_WORK,PATH_PRED COMMON /ENV2/LENPATH_PARACOM COMMON /DATAB1A/PROTNAME COMMON /DATAB1B/FILE_HSSP,FILE_HSSP_NOCHAIN COMMON /DATAB2/RESNAME,RESSECSTR,CONVSECSTR,AACODE,SSCODE,EXPCODE COMMON /DATAB2b/AACODE24 COMMON /DATAB2c/AACODE_LOWC COMMON /DATAB3/RESACC,RESVAR,RESPROF,RESNDEL,RESNINS,NUMNALIGN, + POINTBEG,POINTEND,NUMRES,AABIT COMMON /DATAB4/RESCONSWEIGHT COMMON /DATAB5/LDSSPREAD * * * * C---- ----- C---- Exposure related variables ----- C---- ----- INTEGER MAXEXP,T2,T3A,T3B * * REAL THREXP2ST(1:3),THREXP3ST(1:4),THREXP10ST(1:10) * * COMMON /EXP1/MAXEXP,T2,T3A,T3B COMMON /EXP2/THREXP2ST,THREXP3ST,THREXP10ST * * C---- ----- C---- architecture ----- C---- ----- * * INTEGER NUMIN,NUMHID,NUMOUT,NUMNEIGH,NBIOLOBJ,NCODEUNT, + NUMNETFST,NUMNETSND,NUMNETJURY,MAXVAR, + MAXACC,PROFACC,CASCACC,NSECEL INTEGER TRANS2FROM1(1:NUMNETSNDMAX) * * COMMON /COMPARA1/NUMIN,NUMHID,NUMOUT,NUMNEIGH,NBIOLOBJ,NCODEUNT, + NUMNETFST,NUMNETSND,NUMNETJURY,MAXVAR, + MAXACC,PROFACC,CASCACC,NSECEL COMMON /COMPARA2/TRANS2FROM1 * * C-------------------------------------------------- C---- characters/modes being shared ----- C-------------------------------------------------- C---- ----- C---- different modes ----- C---- ----- * * CHARACTER*132 MODEASSSTR(1:NUMNETSNDMAX), + MODEASSCAS(1:NUMNETFSTMAX),MODESECSTRON * * CHARACTER*132 FILEPRED,FILEOUTPUT,ACTFILE, + FILEARCHFST(1:NUMNETFSTMAX),FILEARCHSND(1:NUMNETSNDMAX), + FILE_ARCHLIST,FILE_RDB,FILE_WHATIF, + CHAR_ARG_READ(1:100) * * COMMON /COMPARA3/MODEASSSTR,MODEASSCAS,MODESECSTRON COMMON /COMPARA4/FILEPRED,FILEOUTPUT,ACTFILE, + FILEARCHFST,FILEARCHSND,FILE_ARCHLIST,FILE_RDB,FILE_WHATIF, + CHAR_ARG_READ C-------------------------------------------------- C---- previous parameters for particular job ----- C---- note: assigned by parset.f ----- C-------------------------------------------------- * * C---- ----- C---- junctions, biases ----- C---- ----- * * REAL JUNCTION1ST(1:(NUMINMAX+NUMOUTMAX),1:NUMHIDMAX) REAL LOCFIELD1(1:NUMHIDMAX) REAL JUNCTION2ND(1:(NUMHIDMAX+NUMOUTMAX),1:NUMOUTMAX) REAL LOCFIELD2(1:NUMOUTMAX) * * COMMON /TRIGGER3/JUNCTION1ST,JUNCTION2ND COMMON /TRIGGER4/LOCFIELD1,LOCFIELD2 * * C---- ----- C---- in/out vectors ----- C---- ----- * * REAL*4 INPUT(1:(NUMINMAX+NUMOUTMAX),1:NUMRESMAX) REAL*4 OUTPUT(1:NUMOUTMAX,1:NUMRESMAX), + OUTFIL(1:NUMOUTMAX,1:NUMRESMAX), + OUTFST(1:NUMOUTMAX,1:NUMRESMAX,1:NUMNETFSTMAX), + OUTSND(1:NUMOUTMAX,1:NUMRESMAX,1:NUMNETSNDMAX) REAL*4 OUTEXP(1:NUMRESMAX),DESEXP(1:NUMRESMAX), + OUTEXPFIL(1:NUMRESMAX) INTEGER*4 OUTBIN(1:NUMOUTMAX,1:NUMRESMAX), + OUTBINPROB(1:NUMOUTMAX,1:NUMRESMAX) * * CHARACTER*1 OUTBINCHAR(1:NUMRESMAX),OUTBINCHARFIL(1:NUMRESMAX) * * * * COMMON /EXTERN1/INPUT,OUTPUT,OUTFST,OUTSND,OUTEXP,DESEXP, + OUTFIL,OUTEXPFIL COMMON /EXTERN2/OUTBIN,OUTBINPROB COMMON /EXTERN3/OUTBINCHAR,OUTBINCHARFIL * * C---- ----- C---- reliability index ----- C---- ----- * * INTEGER NUMRELIND(0:9) INTEGER*2 RELIND(1:NUMRESMAX) INTEGER*2 DSSPVEC_I2(1:NUMRESMAX),PREDVEC_I2(1:NUMRESMAX) * * COMMON /EXTERN4a/NUMRELIND COMMON /EXTERN4b/RELIND,DSSPVEC_I2,PREDVEC_I2 * * * * C---- ----- C---- filtering stuff (exposure) ----- C---- ----- * * REAL REDUCE_MINSIZE,REDUCE_STATE0,REDUCE_STATE1 LOGICAL LREDUCE_BURRIED * * COMMON /FILTER1/REDUCE_MINSIZE,REDUCE_STATE0,REDUCE_STATE1 COMMON /FILTER2/LREDUCE_BURRIED * * C---- ----- C---- run time variables ----- C---- ----- * * CHARACTER*24 STARTDATE,ENDDATE,XDTE CHARACTER*8 STARTTIME,ENDTIME * * REAL TIMEDIFF,TIMEARRAY,TIMESTART,TIMERUN,TIMEEND * * COMMON /CLOCK1/STARTDATE,ENDDATE,XDTE,STARTTIME,ENDTIME COMMON /CLOCK2/TIMEARRAY,TIMEDIFF,TIMESTART,TIMERUN,TIMEEND * * * * C---- ----- C---- pay-off numbers ----- C---- ----- * * INTEGER MATNUM(1:(NUMOUTMAX+1),1:(NUMOUTMAX+1)), + MATLEN(1:(NUMOUTMAX+1),1:4), + MATLENDIS(1:NHISTOMAX,1:(2*NUMOUTMAX)), + NUMSEGOVERL(1:9,1:(NUMOUTMAX+1)), + COUNTSEGMAT(1:2,1:(NUMOUTMAX+1)), + EXP_NOINBIN(0:9,0:9), + EXP_NOIN2ST(1:3),EXP_NOIN3ST(1:4),EXP_NOIN10ST(1:11), + OBS_NOIN2ST(1:3),OBS_NOIN3ST(1:4),OBS_NOIN10ST(1:11) * * REAL Q3,SQ,CORR(1:NUMOUTMAX),INFO,INFO_INV, + RMATQOFDSSP(1:NUMOUTMAX,1:NUMOUTMAX), + RMATQOFPRED(1:NUMOUTMAX,1:NUMOUTMAX), + QLOV(1:2,1:(NUMOUTMAX+1)), + QSOV(1:2,1:(NUMOUTMAX+1)),QFOV(1:2,1:(NUMOUTMAX+1)), + EXP_CORR * * * * CHARACTER*132 TITLE,VERSION_SEC,VERSION_EXP,VERSION_HTM * * COMMON /PAYOFF1/MATNUM,MATLEN,MATLENDIS,NUMSEGOVERL,COUNTSEGMAT, + EXP_NOINBIN,EXP_NOIN2ST,EXP_NOIN3ST,EXP_NOIN10ST, + OBS_NOIN2ST,OBS_NOIN3ST,OBS_NOIN10ST COMMON /PAYOFF2/Q3,SQ,CORR,RMATQOFDSSP,RMATQOFPRED,INFO,INFO_INV, + QLOV,QSOV,QFOV,EXP_CORR COMMON /PAYOFF3/TITLE,VERSION_SEC,VERSION_EXP,VERSION_HTM * * * * C---- ----- C---- content, asf. ----- C---- ----- * * REAL CONTPRED(1:NUMOUTMAX),CONTDSSP(1:NUMOUTMAX),CONTAA(1:24) * * COMMON /CONT/CONTPRED,CONTDSSP,CONTAA * * C---- ----- C---- communication ----- C---- ----- * * CHARACTER*1 ACTRESIDUE CHARACTER*15 CASEDISCR,CONTROLCHAR CHARACTER*25 ACTREGION * * INTEGER ACTPOS,ACTSOLVADDBEG,ACTSOLVADDEND, + ACTSOLVADDEND2,CODEVECPROF(1:NBIOLOBJMAX),PROFMAX, + CODEVECINCASC(1:(NUMOUTMAX+1)), + CODECOMPOSITION(1:NBIOLOBJMAX), + ACTCOMPOSITION(1:NBIOLOBJMAX), + ACTCHI,ACTITER,ACTSTART,ACTNDEL,ACTNINS,ACTNALIGN,ACTACC * * INTEGER BEGUNITS_COMPOSITION, + BEGUNITS_LENGTH,BEGUNITS_DISTCAPS, + SPLIT_LENGTH(1:NUNITS_LENGTH), + SPLIT_DISTCAPS(1:(NUNITS_LENGTH+1)) * * REAL CODEVECTOR(1:NCODEUNTMAX),PROFINTERV,CASCINTERV, + ACTCONSWEIGHT,ACTINTERVALL * * LOGICAL LOGI_COMPOSITION,LOGI_LENGTH,LOGI_DISTCAPS, + LOGI_CONS,LOGI_INDEL,LOGI_REALINPUT * * COMMON /CODE1A/ACTRESIDUE COMMON /CODE1B/CASEDISCR,CONTROLCHAR COMMON /CODE1C/ACTREGION COMMON /CODE3/ACTPOS,ACTSOLVADDBEG,ACTSOLVADDEND,ACTSOLVADDEND2, + CODEVECPROF,PROFMAX,CODEVECINCASC, + CODECOMPOSITION,ACTCOMPOSITION, + ACTCHI,ACTITER,ACTSTART,ACTNDEL,ACTNINS,ACTNALIGN,ACTACC COMMON /CODE4/CODEVECTOR,PROFINTERV,CASCINTERV,ACTCONSWEIGHT, + ACTINTERVALL COMMON /CODE5/BEGUNITS_COMPOSITION, + BEGUNITS_LENGTH,BEGUNITS_DISTCAPS, + SPLIT_LENGTH,SPLIT_DISTCAPS COMMON /CODE6/LOGI_COMPOSITION,LOGI_LENGTH,LOGI_DISTCAPS, + LOGI_CONS,LOGI_INDEL,LOGI_REALINPUT * * C---- ----- C---- controls ----- C---- ----- * * LOGICAL LSERVER,LFILTER,LDEC,LOUTBINPROB, + LMACHINE_READABLE,LWHATIF,LRDB * * COMMON /CONTROL/LSERVER,LFILTER,LDEC,LOUTBINPROB, + LMACHINE_READABLE,LWHATIF,LRDB * * *----------------------------------------------------------------------* * Parmaters and Common variables for PHD * *----------------------------------------------------------------------* profnet-1.0.22/src-phd/tmp.f0000644015075101507510000000155512021362704015061 0ustar lkajanlkajan program test CHARACTER*24 FCTIME_DATE CHARACTER*24 CTEMP write(6,*)'xx =',FCTIME_DATE() END CHARACTER*24 FUNCTION FCTIME_DATE() IMPLICIT NONE C---- variables passed from/to SBR calling CHARACTER*24 CTEMP,CTEMP2 ******------------------------------*-----------------------------****** * execution of function * CTEMP=' ' CALL DATE_AND_TIME(CTEMP,CTEMP2) FCTIME_DATE= ' ' FCTIME_DATE(1:4)= CTEMP(1:4) FCTIME_DATE(5:5)= '_' FCTIME_DATE(6:7)= CTEMP(5:6) FCTIME_DATE(8:8)= '_' FCTIME_DATE(9:10)= CTEMP(7:8) FCTIME_DATE(11:13)=' - ' FCTIME_DATE(14:15)=CTEMP2(1:2) FCTIME_DATE(16:16)=':' FCTIME_DATE(17:18)=CTEMP2(3:4) FCTIME_DATE(19:19)=':' FCTIME_DATE(20:21)=CTEMP2(5:6) END profnet-1.0.22/src-phd/tmp2.f0000644015075101507510000004536512021362705015153 0ustar lkajanlkajan*----------------------------------------------------------------------* SUBROUTINE RS_READHSSPx(IUNIT,FILE_HSSP_LOC,LERROR, + MAXRES,MAXALIGNS_LOC,MAXCORE_LOC, + PDBID,HEADER,COMPOUND,SOURCE,AUTHOR,SEQLENGTH, + NCHAIN,KCHAIN,CHAINREMARK,NALIGN, + EXCLUDEFLAG,EMBLID,STRID,IDE,SIM, + IFIR,ILAS,JFIR,JLAS,LALI,NGAP,LGAP, + LENSEQ,ACCNUM,IPROTNAME, + PDBNO,PDBSEQ,CHAINID,SECSTR,COLS,SHEETLABEL,BP1,BP2, + ACC,NOCC,VAR,ALISEQ,ALIPOINTER, + SEQPROF,NDEL,NINS,ENTROPY,RELENT,CONSWEIGHT, + LCONSERV,LOLDVERSION) C---- global parameters INCLUDE 'phdParameter.f' C Reinhard Schneider 1989, BIOcomputing EMBL, D-6900 Heidelberg, FRG C please report any bug, e-mail (INTERNET): C schneider@EMBL-Heidelberg.DE C or sander@EMBL-Heidelberg.DE C======================================================================= C INCREASE THE NUMBER OF FOLLOWING THREE PARAMETER IN THE CALLING C PROGRAM IF NECESSARY C======================================================================= C maxaligns = maximal number of alignments in a HSSP-file C maxres= maximal number of residues in a PDB-protein C maxcore= maximal space for storing the alignments C======================================================================= C maxaa= 20 amino acids C nblocksize= number of alignments in one line C pdbid= Brookhaven Data Bank identifier C header,compound,source,author= informations about the PDB-protein C pdbseq= amino acid sequence of the PDB-protein C chainid= chain identifier (chain A etc.) C secstr= DSSP secondary structure summary C bp1,bp2= beta-bridge partner C cols= DSSP hydrogen bonding patterns for turns and helices, C geometrical bend, chirality, one character name of beta-ladder C and of beta-sheet C sheetlabel= chain identifier of beta bridge partner C seqlength= number of amino acids in the PDB-protein C pdbno= residue number as in PDB file C nchain= number of different chains in pdbid.DSSP data set C kchain= number of chains used in HSSP data set C nalign= number of alignments C acc= solvated residue surface area in A**2 C emblid= EMBL/SWISSPROT identifier of the alignend protein C strid= if the 3-D structure of this protein is known, then strid C (structure ID)is the Protein Data Bank identifier as taken C from the EMBL/SWISSPROT entry C iprotname= one line description of alignend protein C aliseq= sequential storage for the alignments C alipointer= points to the beginning of alignment X ( 1>= X <=nalign ) C ifir,ilas= first and last position of the alignment in the test C protein C jfir,jlas= first and last position of the alignment in the alignend C protein C lali= length of the alignment excluding insertions and deletions C ngap= number of insertions and deletions in the alignment C lgap= total length of all insertions and deletions C lenseq= length of the entire sequence of the alignend protein C ide= percentage of residue identity of the alignment C var= sequence variability as derived from the nalign alignments C seqprof= relative frequency for each of the 20 amino acids C nocc= number of alignend sequences spanning this position (including C the test sequence C ndel= number of sequences with a deletion in the test protein at this C position C nins= number of sequences with an insertion in the test protein at C this position C entropy= entropy measure of sequence variability at this position C relent= relative entropy (entropy normalized to the range 0-100) C consweight= conservation weight C======================================================================= C IMPLICIT NONE C INTEGER NBLOCKSIZE C PARAMETER (NBLOCKSIZE= 70) C INTEGER MAXRES,MAXAA C INTEGER MAXALIGNS,MAXCORE C PARAMETER (MAXAA= 20) C============================ import ================================== C CHARACTER*222 FILE_HSSP_LOC CHARACTER*(*) FILE_HSSP_LOC INTEGER IUNIT LOGICAL LERROR C attributes of sequence with known structure C CHARACTER*222 PDBID,HEADER,COMPOUND,SOURCE,AUTHOR C CHARACTER*(*) PDBID,HEADER,COMPOUND,SOURCE,AUTHOR CHARACTER*132 PDBID,HEADER,COMPOUND,SOURCE,AUTHOR CHARACTER PDBSEQ(NUMRESMAX),CHAINID(NUMRESMAX), + SECSTR(NUMRESMAX) C.......length*7 CHARACTER*7 COLS(NUMRESMAX) CHARACTER*132 CHAINREMARK C br 2003-08-23: save space C CHARACTER SHEETLABEL(NUMRESMAX) CHARACTER SHEETLABEL(1) CHARACTER SHEETLABEL_NULL C br 2003-08-23: end save space INTEGER SEQLENGTH,NCHAIN,KCHAIN,NALIGN INTEGER ACC(NUMRESMAX) C br 2003-08-23: save space C INTEGER BP1(NUMRESMAX),BP2(NUMRESMAX),PDBNO(NUMRESMAX) INTEGER BP1(1),BP2(1),PDBNO(1) INTEGER PDBNO_NULL,BP1_NULL,BP2_NULL C br 2003-08-23: end save space C attributes of alignend sequences C CHARACTER*222 EMBLID(MAXALIGNS),STRID(MAXALIGNS), C + ACCNUM(MAXALIGNS),IPROTNAME(MAXALIGNS), C + EXCLUDEFLAG(MAXALIGNS) C CHARACTER*(*) EMBLID(MAXALIGNS),STRID(MAXALIGNS), C + ACCNUM(MAXALIGNS),IPROTNAME(MAXALIGNS), C + EXCLUDEFLAG(MAXALIGNS) CHARACTER*132 EMBLID(MAXALIGNS),STRID(MAXALIGNS), + IPROTNAME(MAXALIGNS),ACCNUM(MAXALIGNS), + EXCLUDEFLAG(MAXALIGNS) INTEGER ALIPOINTER(MAXALIGNS), + IFIR(MAXALIGNS),ILAS(MAXALIGNS),JFIR(MAXALIGNS), + JLAS(MAXALIGNS),LALI(MAXALIGNS),NGAP(MAXALIGNS), + LGAP(MAXALIGNS),LENSEQ(MAXALIGNS) REAL IDE(MAXALIGNS),SIM(MAXALIGNS) C br 2003-08-23: save space C CHARACTER ALISEQ(MAXCORE) CHARACTER ALISEQ(1) CHARACTER ALISEQ_NULL C br 2003-08-23: end save space C attributes of profile INTEGER SEQPROF(NUMRESMAX,MAXAA), + NOCC(NUMRESMAX),NDEL(NUMRESMAX),NINS(NUMRESMAX) REAL CONSWEIGHT(NUMRESMAX) C br 2003-08-23: save space C INTEGER VAR(NUMRESMAX),RELENT(NUMRESMAX) C REAL ENTROPY(NUMRESMAX) INTEGER VAR(1),RELENT(1) INTEGER VAR_NULL,RELENT_NULL REAL ENTROPY(1) REAL ENTROPY_NULL C br 2003-08-23: end save space C....... LOGICAL LCONSERV,LOLDVERSION C======================================================================= C internal C INTEGER MAXALIGNS_LOC C PARAMETER (MAXALIGNS_LOC= 3000) C PARAMETER (MAXALIGNS_LOC= MAXALIGNS) C character profileseq*(maxaa) CHARACTER CTEMP*(NBLOCKSIZE),TEMPNAME*222 CHARACTER*222 LINE C CHARACTER*20 HSSPRELEASE CHARACTER CHAINSELECT LOGICAL LCHAIN,LONG_ID INTEGER ICHAINBEG,ICHAINEND,NALIGNORG, + I,J,K,IPOS,ILEN,NRES,IRES, + NBLOCK,IALIGN,IBLOCK,IALI, + IBEG,IEND,IPOINTER(MAXALIGNS) INTEGER MAXCORE_LOC,MAXALIGNS_LOC,MAXRES INTEGER ITMP LOGICAL LDEBUG_LOCAL C order of amino acid symbols in the HSSP sequence profile block C profileseq='VLIMFWYGAPSTCHRKQEND' LERROR=.FALSE. C br 2003-08-23: avoid warnings IBEG=0 IEND=0 J= 0 C used to debug C LDEBUG_LOCAL=.FALSE. LDEBUG_LOCAL=.TRUE. C BR 2007/08/22: not sure this is right, was not initialized LONG_ID=.FALSE. NALIGN=0 CHAINREMARK=' ' DO I=1,MAXALIGNS IPOINTER(I)=0 ENDDO LCHAIN=.FALSE. TEMPNAME(1:)=FILE_HSSP_LOC I=INDEX(TEMPNAME,'_!_') IF (I.NE.0) THEN TEMPNAME(1:)=FILE_HSSP_LOC(1:I-1) LCHAIN=.TRUE. READ(FILE_HSSP_LOC(I+3:),'(A1)')CHAINSELECT WRITE(6,'(T2,A,T10,A,T50,A)')'---', + '--- RS_READHSSP: extract the chain: ',chainselect ENDIF C CALL RSLIB_OPEN_FILE(IUNIT,TEMPNAME,'OLD,READONLY',LERROR) C OPEN(IUNIT,FILE=TEMPNAME,STATUS='OLD',READONLY,ERR=99) C OPEN(IUNIT,FILE=TEMPNAME,STATUS='OLD',ERR=99) OPEN(IUNIT,FILE=TEMPNAME,ERR=99) IF (LERROR .EQV. .TRUE.) THEN WRITE(6,'(A)')'*** ERROR FOR RS_READHSSP: open problem' GOTO 99 ENDIF READ(IUNIT,'(A)',ERR=99)LINE C check if it is a HSSP-file and get the release number for format flags IF (LINE(1:4).NE.'HSSP') THEN WRITE(6,'(A)')'*** ERROR FOR RS_READHSSP: is not a HSSP-file' LERROR=.TRUE. RETURN ELSE I=INDEX(LINE,'VERSION')+7 C HSSPRELEASE=LINE(I:) LOLDVERSION=.FALSE. c if (index(hssprelease,'0.9').ne.0)loldversion=.true. ENDIF C read in PDBID etc. DO WHILE(LINE(1:6).NE.'PDBID') READ(IUNIT,'(A)',ERR=99)LINE ENDDO READ(LINE,'(11X,A)',ERR=99)PDBID DO WHILE(LINE(1:6).NE.'HEADER') READ(IUNIT,'(A)',ERR=99)LINE IF (LINE(1:23).EQ.'PARAMETER LONG-ID :YES') THEN LONG_ID=.TRUE. IF (LDEBUG_LOCAL .EQV. .TRUE.) + WRITE(6,'(A,A)')'DBG longid LINE=',LINE(1:23) ENDIF ENDDO READ(LINE ,'(11X,A)',ERR=99)HEADER READ(IUNIT,'(11X,A)',ERR=99)COMPOUND READ(IUNIT,'(11X,A)',ERR=99)SOURCE READ(IUNIT,'(11X,A)',ERR=99)AUTHOR READ(IUNIT,'(11X,I4)',ERR=99)SEQLENGTH READ(IUNIT,'(11X,I4)',ERR=99)NCHAIN KCHAIN=NCHAIN READ(IUNIT,'(A)',ERR=99)LINE C IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG ',LINE IF (INDEX(LINE,'KCHAIN').NE.0) THEN READ(LINE,'(11X,I4,A)',ERR=99)KCHAIN,CHAINREMARK READ(IUNIT,'(11X,I4)',ERR=99)NALIGNORG ELSE READ(LINE,'(11X,I4)',ERR=99)NALIGNORG ENDIF C if HSSP-file contains no alignments return IF (NALIGNORG.EQ.0) THEN WRITE(6,'(T2,A,T10,A)')'---', + '--- HSSP-file contains no alignments ***' CLOSE(IUNIT) RETURN ENDIF C write(6,*)'xx before overflow, Nali=',nalignorg,' len=', C + seqlength,' kchain=',kchain,' lchain=',lchain C parameter overflow handling IF (NALIGNORG.GT.MAXALIGNS) THEN WRITE(6,'(A)')'-*- HSSP-file contains too many alignments **' WRITE(6,'(A)')'-*- INCREASE MAXALIGNS in phdParameter.f! ' WRITE(6,'(A,I8,A,I8)')'-*- is=',MAXALIGNS,' want>',NALIGNORG CLOSE(IUNIT) LERROR=.TRUE. RETURN ENDIF ITMP=SEQLENGTH+KCHAIN-1 IF (ITMP.GT.NUMRESMAX) THEN WRITE(6,'(A)')'*** PDB-sequence in HSSP-file too long ***' WRITE(6,'(A)')'*** INCREASE NUMRESMAX in phdParameter.f***' WRITE(6,'(A,I8,A,I8)')'-*- is=',NUMRESMAX,' want>',ITMP CLOSE(IUNIT) LERROR=.TRUE. RETURN ENDIF C number of sequence positions is number of residues + number of chains C chain break is indicated by a '!' NRES=SEQLENGTH+KCHAIN-1 ICHAINBEG=1 ICHAINEND=NRES IF (LCHAIN .EQV. .TRUE.) THEN C search for ALIGNMENT-block DO WHILE (LINE(1:13).NE.'## ALIGNMENTS') READ(IUNIT,'(A)',ERR=99)LINE ENDDO READ(IUNIT,'(A)',ERR=99)LINE ICHAINBEG=0 ICHAINEND=0 C read till end ; some PDB-chains have DSSP-chain breaks !! DO I=1,NRES READ(IUNIT,'(7X,I4,1X,A1)',ERR=99)PDBNO(I),CHAINID(I) IF (CHAINID(I) .EQ. CHAINSELECT) THEN IF (ICHAINBEG .EQ. 0) ICHAINBEG=I ICHAINEND=I ENDIF ENDDO WRITE(6,'(T2,A,T10,I10,I10)')'---', + ICHAINBEG,ICHAINEND REWIND(IUNIT) ENDIF SEQLENGTH=ICHAINEND-ICHAINBEG+1 C search for the PROTEINS-block LINE=' ' DO WHILE(LINE(1:11).NE.'## PROTEINS') READ(IUNIT,'(A)',ERR=99)LINE C IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG PROT=',LINE ENDDO READ(IUNIT,'(A)',ERR=99)LINE LCONSERV=.FALSE. IF (INDEX(LINE,'%WSIM').NE.0) LCONSERV= .TRUE. C READ DATA ABOUT THE ALIGNMENTS IALIGN=1 IF (LDEBUG_LOCAL .EQV. .TRUE.) + WRITE(6,'(A,I5,A,A)')'DBG NALI=',NALIGNORG,' longid=',LONG_ID DO I=1,NALIGNORG IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,'(A,I5)')'DBG iali=',I IF (LONG_ID .EQV. .TRUE.) THEN C note: read format specified below (line labelled 101) write(6,*)'xxok in long' READ(IUNIT,101,ERR=99) + EXCLUDEFLAG(IALIGN),EMBLID(IALIGN)(1:),STRID(IALIGN), + IDE(IALIGN),SIM(IALIGN),IFIR(IALIGN),ILAS(IALIGN), + JFIR(IALIGN),JLAS(IALIGN),LALI(IALIGN),NGAP(IALIGN), + LGAP(IALIGN),LENSEQ(IALIGN),ACCNUM(IALIGN), + IPROTNAME(IALIGN) write(6,*)'xxok in long after i=',i ELSE write(6,*)'xxok in short' C note: read format specified below (line labelled 100) READ(IUNIT,100,ERR=99) + EXCLUDEFLAG(IALIGN),EMBLID(IALIGN)(1:),STRID(IALIGN), + IDE(IALIGN),SIM(IALIGN),IFIR(IALIGN),ILAS(IALIGN), + JFIR(IALIGN),JLAS(IALIGN),LALI(IALIGN),NGAP(IALIGN), + LGAP(IALIGN),LENSEQ(IALIGN),ACCNUM(IALIGN), + IPROTNAME(IALIGN) END IF write(6,*)'xxok after endif' IF (LDEBUG_LOCAL .EQV. .TRUE.) THEN WRITE(6,'(A,I5,A,F5.2,A,A)')'DBG PROTali(',IALIGN,') ide=', + IDE(IALIGN), + ' name=',IPROTNAME(IALIGN) END IF IF (IFIR(IALIGN) .GE. ICHAINBEG .AND. + ILAS(IALIGN) .LE. ICHAINEND) THEN IPOINTER(I)=IALIGN IALIGN=IALIGN+1 ENDIF ENDDO write(6,*)' xxok after loop' 100 FORMAT(5X,A1,2X,A12,A5,2X,F5.2,1X,F5.2,8(1X,I4),2X,A10,1X,A) 101 FORMAT(5X,A1,2X,A40,A5,2X,F5.2,1X,F5.2,8(1X,I4),2X,A10,1X,A) NALIGN=IALIGN-1 WRITE(6,'(T2,A,T10,A)')'---', + ' RS_READHSSP PROTEINS-block done' C init pointer ; aliseq contains the alignments (amino acid symbols) C stored in the following way ; '/' separates alignments C alignment(x) is stored from: C aliseq(alipointer(x)) to aliseq(ilas(x)-ifir(x)) C aliseq(1........46/48.........60/62....) C | | | C | | | C pointer pointer pointer C ali 1 ali 2 ali 3 C init pointer IPOS=1 DO I=1,NALIGN C br 2003-08-23 fast and slim C IF (IPOS.GE.MAXCORE) THEN C WRITE(6,'(A,I9,A)') C + ' *** LERROR: INCREASE MAXCORE to >',IPOS,'***' C STOP C ENDIF C end fast and slim br 2003-08-23 ALIPOINTER(I)=IPOS ILEN=ILAS(I)-IFIR(I)+1 IPOS=IPOS+ILEN C br 2003-08-23 fast and slim C ALISEQ(IPOS)='/' ALISEQ_NULL='/' C end fast and slim br 2003-08-23 IPOS=IPOS+1 ENDDO ALIPOINTER(NALIGN+1)=IPOS+1 C number of ALIGNMENTS-blocks IF (MOD(FLOAT(NALIGNORG),FLOAT(NBLOCKSIZE)).EQ. 0.0) THEN NBLOCK=NALIGNORG/NBLOCKSIZE ELSE NBLOCK=NALIGNORG/NBLOCKSIZE+1 ENDIF C search for ALIGNMENT-block DO WHILE (LINE(1:13).NE.'## ALIGNMENTS') READ(IUNIT,'(A)',ERR=99)LINE IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG alinot',LINE ENDDO READ(IUNIT,'(A)',ERR=99)LINE IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG ',LINE C loop over ALIGNMENTS-blocks C ....read in pdbno, chainid, secstr etc. IALIGN=0 IALI=0 DO IBLOCK=1,NBLOCK IRES=1 DO I=1,NRES C BR: 2003-08-23: save space C READ(IUNIT,200,ERR=99) C + PDBNO(IRES),CHAINID(IRES),PDBSEQ(IRES),SECSTR(IRES), C + COLS(IRES),BP1(IRES),BP2(IRES),SHEETLABEL(IRES), C + ACC(IRES),NOCC(IRES),VAR(IRES),CTEMP READ(IUNIT,200,ERR=99) + PDBNO_NULL,CHAINID(IRES),PDBSEQ(IRES),SECSTR(IRES), + COLS(IRES),BP1_NULL,BP2_NULL,SHEETLABEL_NULL, + ACC(IRES),NOCC(IRES),VAR_NULL,CTEMP C end save space br 2003-08-23 200 FORMAT(7X,I4,2(1X,A1),2X,A1,1X,A7,2(I4),A1,I4,2(1X,I4),2X,A) C.....fill up aliseq C IF (LDEBUG_LOCAL .EQV. .TRUE.) C + WRITE(6,*)'DBG IBLOCK=',IBLOCK, ' IRES=',I IF (I .GE. ICHAINBEG .AND. I .LE. ICHAINEND) THEN IRES=IRES+1 C br 2003-08-23 fast and slim C IF (PDBSEQ(I) .NE. '!') THEN C CALL STRPOS(CTEMP,IBEG,IEND) C DO IPOS=MAX(IBEG,1),MIN(NBLOCKSIZE,IEND) C IALI=IALIGN+IPOS C IF (CTEMP(IPOS:IPOS) .NE. ' ') THEN C J=ALIPOINTER(IPOINTER(IALI)) + C + (I-IFIR(IPOINTER(IALI))) C ALISEQ(J)=CTEMP(IPOS:IPOS) C ENDIF C ENDDO C ENDIF C end fast and slim br 2003-08-23 ENDIF ENDDO IALIGN=IALIGN+NBLOCKSIZE DO K=1,2 READ(IUNIT,'(A)',ERR=99)LINE IF (LDEBUG_LOCAL .EQV. .TRUE.) WRITE(6,*)'DBG ',LINE ENDDO ENDDO WRITE(6,'(T2,A,T10,A)')'---', + ' RS_READHSSP ALIGNMENTS-block done' C read in sequence profile, entropy etc. IRES=1 DO I=1,NRES C BR 2003-08-23 save space C READ(IUNIT,300,ERR=99)(SEQPROF(IRES,K),K=1,MAXAA), C + NOCC(IRES),NDEL(IRES),NINS(IRES),ENTROPY(IRES), C + RELENT(IRES),CONSWEIGHT(IRES) READ(IUNIT,300,ERR=99)(SEQPROF(IRES,K),K=1,MAXAA), + NOCC(IRES),NDEL(IRES),NINS(IRES),ENTROPY_NULL, + RELENT_NULL,CONSWEIGHT(IRES) C end save space br 2003-08-23 IF (I .GE. ICHAINBEG .AND. I .LE. ICHAINEND) THEN IRES=IRES+1 ENDIF ENDDO 300 FORMAT(12X,20(I4),1X,3(1X,I4),1X,F7.3,3X,I4,2X,F4.2) WRITE(6,'(T2,A,T10,A)')'---', + ' RS_READHSSP PROFILE-block done' IF (LCHAIN .EQV. .TRUE.) THEN DO I=1,NALIGN IFIR(I)=IFIR(I)-ICHAINBEG+1 ILAS(I)=ILAS(I)-ICHAINBEG+1 ENDDO ENDIF C check if next line (last line in a HSSP-file) contains a '//' READ(IUNIT,'(A)',ERR=99)LINE IF ((LINE(1:2).EQ.'//').OR. + (LINE(1:13).EQ.'## INSERTION')) THEN WRITE(6,'(T2,A,T10,A,A50)')'---', + ' RS_READHSSP ok(cut 50): ',FILE_HSSP_LOC(1:50) GOTO 999 ELSE WRITE(6,'(T2,A,T10,A,A,A,A)')'***', + 'ERROR FOR RS_READHSSP: ',FILE_HSSP_LOC,' lastLine=', + LINE GOTO 99 ENDIF 99 WRITE(6,'(A,A)')'**** ERROR FOR RS_READHSSP: READING: ', + FILE_HSSP_LOC LERROR=.TRUE. NALIGN=0 SEQLENGTH=0 999 CLOSE(IUNIT) RETURN END ***** end of RS_READHSSP profnet-1.0.22/src-phd/x.f0000644015075101507510000000064012021362704014522 0ustar lkajanlkajan LOGICAL LCONSERV,LOLDVERSION C Compiler bug patch C write data in loop, because the SUN4 compiler has a limit stacksize of C 4096 (before it was 8192 MURKS) in a routine(do_u_out, rwrite or w4cp) C integer NPACK C parameter (NPACK=1000) C...... LOGICAL LSCREEN INTEGER MAXALIGNS_LOC,MAXRES C======================================================================= profnet-1.0.22/src/0000755015075101507510000000000012021365335013336 5ustar lkajanlkajanprofnet-1.0.22/src/Doc-lib-nn0000644015075101507510000000000012021362711015124 0ustar lkajanlkajanprofnet-1.0.22/src/Doc-nn.txt0000644015075101507510000001455212021362711015217 0ustar lkajanlkajan* ----------------------------------------------------------------------* * * organisation and dependence of program, functions, and subroutines * for nn.f * * ------------------------------ * keywords: * ------------------------------ * * nn internal subroutines: * nn external subroutines: * lib-nn internal subroutines: * lib-nn external subroutines: * lib-SGI64 internal subroutines: * * ------------------------------ * notations: * ------------------------------ * * '-> x' means is calling the following * '.. self content' means: no subroutine called * * * ----------------------------------------------------------------------* * --------------------- * nn internal subroutines: * --------------------- * * MAIN -> GET_ARG_NUMBER,GET_ARGUMENT,SRDTIME, * -> SCFDATE,ININN,RDPAR,RDIN,RDOUT,RDSAM, * -> RDJCT, * -> INIJCT, * -> INITHRUNT, * -> NETOUT, * -> WRTOUT, * -> WRTJCT, * -> TRAIN, * -> WRTSCR, * -> WRTERR, * -> WRTYEAH * TRG1ST .. self-content * TRG2ND .. self-content * TRGNORM .. self-content * ININN -> INIPAR_CON,INIPAR_DEFAULT,INIPAR_ASK, * -> INIPAR_SWITCH * INIPAR_ASK -> GETCHAR,GETINT * INIPAR_CON .. self-content * INIPAR_DEFAULT .. self-content * INIPAR_SWITCH -> SCHAR_TO_INT * INITHRUNT .. self-content * RDJCT -> SFILEOPEN,RDJCT_HEAD,RDJCT_JCT1, * -> RDJCT_JCT2,RDJCT_WRT * RDJCT_HEAD -> RDJCT_CHECK * RDJCT_JCT1 .. self-content * RDJCT_JCT2 .. self-content * RDJCT_CHECK .. self-content * RDJCT_WRT .. self-content * RDIN -> SFILEOPEN,RDIN_HEAD,RDIN_DATA,RDIN_WRT * RDIN_HEAD .. self-content * RDIN_DATA .. self-content * RDIN_WRT .. self-content * RDOUT -> SFILEOPEN,RDOUT_HEAD,RDOUT_DATA, * -> RDOUT_WRT * RDOUT_HEAD .. self-content * RDOUT_DATA .. self-content * RDOUT_WRT .. self-content * RDPAR -> SFILEOPEN,RDPAR_I,RDPAR_F,RDPAR_A, * -> RDPAR_WRT * RDPAR_I -> RDPAR_ERR * RDPAR_F .. self-content * RDPAR_A .. self-content * RDPAR_ERR .. self-content * RDPAR_WRT .. self-content * RDSAM -> SFILEOPEN * NETOUT -> NETOUT_MUE,NETOUT_BIN,NETOUT_ERR * NETOUT_MUE .. self-content * NETOUT_BIN .. self-content * NETOUT_ERR .. self-content * TRAIN -> NETOUT,TRAIN_STOP,TRAIN_WRT, * -> TRAIN_INISWP,TRAIN_INIMUE, * -> TRAIN_BACKPROP, * -> WRTOUT, * -> WRTJCT * TRAIN_BACKPROP .. self-content * TRAIN_INIMUE -> SRSTE2,SRSTZ2,NETOUT_MUE * TRAIN_INISWP -> SRSTZ2 * TRAIN_STOP .. self-content * TRAIN_WRT .. self-content * WRTJCT -> SFILEOPEN,WRTHEAD * WRTOUT -> WRTHEAD,NETOUT_MUE * WRTERR -> SFILEOPEN * WRTHEAD -> WRTHEAD_GEN,WRTHEAD_JOB * WRTHEAD_GEN .. self-content * WRTHEAD_JOB .. self-content * WRTSCR -> WRTERR * WRTYEAH -> SFILEOPEN * * ----------------------------------------------------------------------* * --------------------- * nn external subroutines: * --------------------- * * call from missing: * GETCHAR * GETINT * GET_ARGUMENT * GET_ARG_NUMBER * INIJCT * SCFDATE * SCHAR_TO_INT * SFILEOPEN * SRDTIME * SRSTE2 * SRSTZ2 # * * ----------------------------------------------------------------------* * --------------------- * lib-nn internal subroutines: * --------------------- * * EMPTYSTRING .. self-content * FILEN_STRING .. self-content * FILENSTRING .. self-content * FILENSTRING_ALPHANUMSEN .. self-content * FRMAX1 .. self-content * FRMAX2 .. self-content * GETCHAR -> WRITELINES * GETINT -> WRITELINES,STRPOS,GETTOKEN,RIGHTADJUST * GETTOKEN .. self-content * GET_ARGUMENT -> GETARG * GET_ARG_NUMBER .. self-content * RIGHTADJUST .. self-content * SCFDATE .. self-content * SFILEOPEN .. self-content * SCHAR_TO_INT -> SILEN_STRING * SILEN_STRING .. self-content * SRSTE2 .. self-content * SRSTZ2 .. self-content * STRPOS .. self-content * WRITELINES -> STRPOS * * ----------------------------------------------------------------------* * --------------------- * lib-nn external subroutines: * --------------------- * * call from missing: * GETARG # * * ----------------------------------------------------------------------* * --------------------- * lib-SGI64 internal subroutines: * --------------------- * * INIJCT .. self-content * SRDTIME .. self-content * * ----------------------------------------------------------------------* # profnet-1.0.22/src/Makefile0000755015075101507510000000165412021363230014777 0ustar lkajanlkajan#===================================================================== F77 = gfortran BIN = profnet_prof #===================================================================== ARCH = LINUX FFLAGS := $(FFLAGS) -O2 -Wuninitialized FFLAGS := $(FFLAGS) -Wall -Wno-unused #===================================================================== NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f SOURCES := $(NN_OBJS) profPar.f #===================================================================== all: $(BIN) #===================================================================== # Make Neural Network #===================================================================== $(BIN): $(SOURCES) @echo --- making $(BIN) $(F77) $(CPPFLAGS) $(FFLAGS) $(LDFLAGS) -o $@ $(NN_OBJS) clean: rm -f *.o $(BIN) install: mkdir -p $(DESTDIR)$(prefix)/bin && \ cp $(BIN) $(DESTDIR)$(prefix)/bin/ .PHONY: all clean install profnet-1.0.22/src/PROFin.dat0000644015075101507510000032362312021362712015132 0ustar lkajanlkajan* NNin_in file for FORTRAN NN.f (input vectors) * ----------------------------------------------------------------- * Parameter input for neural network (nn) * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Burkhard Rost, CUBIC NYC / LION Heidelberg * fax: +1-212-305 3773 * email: rost@columbia.edu * www: http://cubic.bioc.columbia.edu * date: May 8, 2002 * acc * 1st,unb * 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ITSAM: 40 0 0 92 0 0 0 0 0 0 0 0 4 0 4 0 0 0 0 0 0 0 39 0 0 4 12 81 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 38 0 0 0 0 0 0 0 0 0 0 0 12 77 8 0 0 0 0 0 0 0 4 0 31 0 0 12 0 0 0 0 0 0 62 8 0 12 4 0 0 0 0 0 0 0 4 0 25 0 0 0 0 0 0 0 0 0 15 12 15 27 31 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 0 4 0 0 0 50 0 0 0 35 4 0 8 0 0 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 0 92 0 0 0 0 0 4 0 0 0 4 0 42 0 0 0 0 0 0 0 0 0 12 4 32 36 0 0 0 12 0 0 0 4 0 0 16 0 0 0 0 0 0 0 0 0 28 0 4 4 0 0 0 0 0 0 0 8 56 0 28 0 0 0 8 0 0 0 4 84 0 0 0 0 0 0 4 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 0 0 0 14 68 0 5 0 0 0 0 0 9 0 5 0 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 67 0 0 17 0 0 22 0 0 4 2 10 0 2 0 4 8 10 10 4 13 13 0 4 0 0 2 6 2 76 0 0 0 100 100 100 90 60 0 0 0 85 100 85 100 70 11 44 26 58 40 55 30 52 90 70 11 44 26 19 0 78 64 58 40 31 15 59 46 66 0 0 0 0 0 0 0 0 0 0 0 0 ITSAM: 41 4 12 81 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 38 0 0 0 0 0 0 0 0 0 0 0 12 77 8 0 0 0 0 0 0 0 4 0 31 0 0 12 0 0 0 0 0 0 62 8 0 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0 0 0 0 0 0 0 // profnet-1.0.22/src/RUN-special0000644015075101507510000000010212021362711015327 0ustar lkajanlkajanprof.SGI64 switch 385 55 10 46 100 PROFin.dat PROFacc_tst.jct noneprofnet-1.0.22/src/ReadMe-mac0000644015075101507510000000033112021362711015144 0ustar lkajanlkajan# gnu g77 -o prof.MAC -O3 prof.f lib-prof.f lib-sys-MAC.f /usr/local/bin -o prof.MACINTEL -O3 prof.f lib-prof.f lib-sys-LINUX.f # ibm /opt/ibmcmp/xlf/8.1/bin/f77 -o prof.IBM -O3 prof.f lib-prof.f lib-sys-MACIBM.f profnet-1.0.22/src/compile_macintel.csh0000755015075101507510000000043312021362711017337 0ustar lkajanlkajan# gnu gfortran compiler - only on INTEL MAC echo "--- now PROF: " echo "/usr/local/bin -o prof.MACINTEL -O3 prof.f lib-prof.f lib-sys-LINUX.f" #/usr/local/bin -o prof.MACINTEL -O3 prof.f lib-prof.f lib-sys-LINUX.f /usr/bin/f77 -o prof.MACINTEL -O3 prof.f lib-prof.f lib-sys-LINUX.f profnet-1.0.22/src/lib-LINUX.f0000644015075101507510000002202112021362711015140 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** FCT FCTIME_DATE ***** ------------------------------------------------------------------ C---- C---- NAME : FCTIME_DATE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns date * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: char*8 YYYYMMDD * * input : NOM, DEN * *----------------------------------------------------------------------* CHARACTER*24 FUNCTION FCTIME_DATE() IMPLICIT NONE ******------------------------------*-----------------------------****** * execution of function * C FCTIME_DATE=FDATE() FCTIME_DATE='' END ***** end of FCTIME_DATE ***** ------------------------------------------------------------------ ***** FCT FRTIME_SECNDS ***** ------------------------------------------------------------------ C---- C---- NAME : FRTIME_SECNDS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns CPU time seconds * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: cputime * * input : NOM, DEN * *----------------------------------------------------------------------* REAL FUNCTION FRTIME_SECNDS(T1) IMPLICIT NONE C---- variables passed from/to SBR calling REAL T1 ******------------------------------*-----------------------------****** * execution of function * FRTIME_SECNDS=SECNDS(T1) END ***** end of FRTIME_SECNDS ***** ------------------------------------------------------------------ ***** SUB INIJCT ***** ------------------------------------------------------------------ C---- C---- NAME : INIJCT C---- ARG : C---- DES : Generation of the initial couplings and biases of C---- DES : the network. Options: C---- DES : RANDOM : locfield (i,j,TIMEST=0) = [-/+diceintervall] C---- DES : with equal distribution C---- IN p: NUMSAM,NUMIN,NUMHID,NUMOUT, DICESEED C---- IN v: JCT1ST,JCT2ND,BIAS1ST,BIAS2ND C---- OUT : setting of JCT1ST, JCT2ND C---- FROM : MAIN C---- CALL2: C---- LIB : RAN(SEED), creates random numbers between 0 and * C---- LIB+ : 1 (1 excluded, 0 included), it is called by com-* C---- LIB+ : piling with -lV77, each call initializes next * C---- LIB+ : seed, according to: seed=6909*seed+mod(2**32) * C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIJCT C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER I,J,NUMHIDFIRST,NUMHIDLAST Cunix C REAL RAN,DICE1,DICE2,DICEINTERVX Clinux REAL RAND,DICE1,DICE2,DICEINTERVX ******------------------------------*-----------------------------****** * I,J serve as iteration variables * * DICE1,2 =RAN(DICESEED1),i.e. random number between 0,1* * NUMHIDFIRST number of units in the first hidden layer * * NUMHIDLAST number of units in the last hidden layer * ******------------------------------*-----------------------------****** DICEINTERVX=DICEITRVL C---- ------------------------------------------------------------------ C---- first layer junctions C---- ------------------------------------------------------------------ DICESEED1=DICESEED+DICESEED_ADDJCT IF (NUMLAYERS.EQ.1) THEN NUMHIDFIRST=NUMOUT NUMHIDLAST=0 ELSE NUMHIDFIRST=NUMHID NUMHIDLAST=NUMHID END IF C---- loop over hidden units DO I=1,NUMHIDFIRST C------- junctions (loop over input units) DO J=1,NUMIN C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST(J,I)= (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST(J,I)= DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST((NUMIN+1),I)= + (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST((NUMIN+1),I)=DICEINTERVX*DICE2 END IF END DO C---- ------------------------------------------------------------------ C---- last layer junctions C---- ------------------------------------------------------------------ DO I=1,NUMOUT C------- junctions DO J=1,NUMHIDLAST C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND(J,I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND(J,I)=DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND((NUMHID+1),I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND((NUMHID+1),I)=DICEINTERVX*DICE2 END IF END DO END ***** end of INIJCT ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix C REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME INTEGER ITER LOGICAL LOGIWRITE Cunix C TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) Clinux TIMEDIFF=DTIME(TIMEARRAYM) C TIMEDIFF= TIMEDIFFX(1) IF (LOGIWRITE) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src/lib-prof.f0000755015075101507510000011334312021362712015223 0ustar lkajanlkajan ***** ------------------------------------------------------------------ ***** FCT EMPTYSTRING ***** ------------------------------------------------------------------ C---- C---- NAME : EMPTYSTRING C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* FUNCTION EMPTYSTRING(STRING) LOGICAL EMPTYSTRING CHARACTER STRING*(*) EMPTYSTRING=.TRUE. DO I=1,LEN(STRING) IF(STRING(I:I).NE.' ') THEN EMPTYSTRING=.FALSE. RETURN ENDIF ENDDO RETURN END ***** end of EMPTYSTRING ***** ------------------------------------------------------------------ ***** FCT FILEN_STRING ***** ------------------------------------------------------------------ C---- C---- NAME : FILEN_STRING C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1993 version 0.1 * * changed: Oct, 1994 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The length of a given character string is returned * input: STRING string of character*80 * * output: LEN length of string without blanks * *----------------------------------------------------------------------* INTEGER FUNCTION FILEN_STRING(STRING) C---- variables passing CHARACTER STRING*(*) C---- local variables INTEGER ITER,ITER2,COUNT,COUNTBEF,NCHAR CHARACTER*456 CHECK LOGICAL LHELP,LHELP2 ******------------------------------*-----------------------------****** C---- defaults CHECK(1:52)= + 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz' CHECK(53:73)='1234567890-._/+=:!~*,' NCHAR=73 LHELP=.TRUE. COUNT=0 COUNTBEF=0 DO ITER=1,456 IF (LHELP) THEN LHELP2=.FALSE. DO ITER2=1,NCHAR IF ((.NOT.LHELP2).AND. + STRING(ITER:ITER).EQ.CHECK(ITER2:ITER2)) THEN LHELP2=.TRUE. COUNT=COUNT+1 END IF END DO IF (.NOT.LHELP2) THEN IF ( (COUNT.EQ.0).AND.(STRING(ITER:ITER).eq.' ') ) THEN COUNTBEF=COUNTBEF+1 ELSE LHELP=.FALSE. FILEN_STRING=ITER-1-COUNTBEF END IF END IF END IF END DO IF (COUNT.NE.FILEN_STRING) THEN WRITE(6,'(T2,A)')'-!-' WRITE(6,'(T2,A,T10,A)')'-!-','WARNING FILEN_STRING:'// + 'two different results.' WRITE(6,'(T2,A,T10,A,T20,I5,T30,A,T40,I5,T50,A,T60,A1,A,A1)') + '-!-','first = ',FILEN_STRING, + 'count: ',count,'for: ','|',STRING(1:COUNT),'|' WRITE(6,'(T2,A)')'-!-' END IF FILEN_STRING=COUNT END ***** end of FILEN_STRING ***** ------------------------------------------------------------------ ***** FCT FILENSTRING ***** ------------------------------------------------------------------ C---- C---- NAME : FILENSTRING C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The length of a given character string is returned * input: STRING string of character*80 * * output: LEN length of string without blanks * *----------------------------------------------------------------------* INTEGER FUNCTION FILENSTRING(STRING) C---- variables passing CHARACTER STRING*(*) C CHARACTER*(*) STRING C CHARACTER*456 STRING C---- local variables INTEGER ICOUNT,ITER LOGICAL LHELP ******------------------------------*-----------------------------****** C---- defaults ICOUNT=0 LHELP=.TRUE. DO ITER=1,80 IF (LHELP.AND.(STRING(ITER:ITER).NE.' ')) THEN ICOUNT=ICOUNT+1 ELSE LHELP=.FALSE. END IF END DO FILENSTRING=ICOUNT END ***** end of FILENSTRING ***** ------------------------------------------------------------------ ***** FCT FILENSTRING_ALPHANUMSEN ***** ------------------------------------------------------------------ C---- C---- NAME : FILENSTRING_ALPHANUMSEN C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The length of a given character string is returned * -------- (only numbers 0-9, letters a-z, A-Z, and the fol-* * lowing symbols are allowed: '.','-','_'. * * input: STRING string of character*80 * * output: LEN length of string without blanks * *----------------------------------------------------------------------* INTEGER FUNCTION FILENSTRING_ALPHANUMSEN(STRING) C---- variables passing CHARACTER STRING*(*) C---- local variables INTEGER ICOUNT,ITER LOGICAL LHELP,LLETTER,LREST ******------------------------------*-----------------------------****** C---- defaults ICOUNT=0 LHELP=.TRUE. DO ITER=1,80 IF (LHELP) THEN LLETTER=.FALSE. LREST=.FALSE. IF ((STRING(ITER:ITER).EQ.'A').OR. + (STRING(ITER:ITER).EQ.'B').OR. + (STRING(ITER:ITER).EQ.'C').OR. + (STRING(ITER:ITER).EQ.'D').OR. + (STRING(ITER:ITER).EQ.'E').OR. + (STRING(ITER:ITER).EQ.'F').OR. + (STRING(ITER:ITER).EQ.'G').OR. + (STRING(ITER:ITER).EQ.'H').OR. + (STRING(ITER:ITER).EQ.'I').OR. + (STRING(ITER:ITER).EQ.'J').OR. + (STRING(ITER:ITER).EQ.'K').OR. + (STRING(ITER:ITER).EQ.'L').OR. + (STRING(ITER:ITER).EQ.'M').OR. + (STRING(ITER:ITER).EQ.'N').OR. + (STRING(ITER:ITER).EQ.'O').OR. + (STRING(ITER:ITER).EQ.'P').OR. + (STRING(ITER:ITER).EQ.'Q').OR. + (STRING(ITER:ITER).EQ.'R').OR. + (STRING(ITER:ITER).EQ.'S').OR. + (STRING(ITER:ITER).EQ.'T')) THEN LLETTER=.TRUE. END IF IF (.NOT.LLETTER) THEN IF ((STRING(ITER:ITER).EQ.'U').OR. + (STRING(ITER:ITER).EQ.'V').OR. + (STRING(ITER:ITER).EQ.'W').OR. + (STRING(ITER:ITER).EQ.'X').OR. + (STRING(ITER:ITER).EQ.'Y').OR. + (STRING(ITER:ITER).EQ.'Z').OR. + (STRING(ITER:ITER).EQ.'a').OR. + (STRING(ITER:ITER).EQ.'b').OR. + (STRING(ITER:ITER).EQ.'c').OR. + (STRING(ITER:ITER).EQ.'d').OR. + (STRING(ITER:ITER).EQ.'e').OR. + (STRING(ITER:ITER).EQ.'f').OR. + (STRING(ITER:ITER).EQ.'g').OR. + (STRING(ITER:ITER).EQ.'h').OR. + (STRING(ITER:ITER).EQ.'i').OR. + (STRING(ITER:ITER).EQ.'j')) THEN LLETTER=.TRUE. END IF END IF IF (.NOT.LLETTER) THEN IF ((STRING(ITER:ITER).EQ.'k').OR. + (STRING(ITER:ITER).EQ.'l').OR. + (STRING(ITER:ITER).EQ.'m').OR. + (STRING(ITER:ITER).EQ.'n').OR. + (STRING(ITER:ITER).EQ.'o').OR. + (STRING(ITER:ITER).EQ.'p').OR. + (STRING(ITER:ITER).EQ.'q').OR. + (STRING(ITER:ITER).EQ.'r').OR. + (STRING(ITER:ITER).EQ.'s').OR. + (STRING(ITER:ITER).EQ.'t').OR. + (STRING(ITER:ITER).EQ.'u').OR. + (STRING(ITER:ITER).EQ.'v').OR. + (STRING(ITER:ITER).EQ.'w').OR. + (STRING(ITER:ITER).EQ.'x').OR. + (STRING(ITER:ITER).EQ.'y').OR. + (STRING(ITER:ITER).EQ.'z')) THEN LLETTER=.TRUE. END IF END IF IF (.NOT.LLETTER) THEN IF ((STRING(ITER:ITER).EQ.'1').OR. + (STRING(ITER:ITER).EQ.'2').OR. + (STRING(ITER:ITER).EQ.'3').OR. + (STRING(ITER:ITER).EQ.'4').OR. + (STRING(ITER:ITER).EQ.'5').OR. + (STRING(ITER:ITER).EQ.'6').OR. + (STRING(ITER:ITER).EQ.'7').OR. + (STRING(ITER:ITER).EQ.'8').OR. + (STRING(ITER:ITER).EQ.'9').OR. + (STRING(ITER:ITER).EQ.'0').OR. + (STRING(ITER:ITER).EQ.'.').OR. + (STRING(ITER:ITER).EQ.'-').OR. + (STRING(ITER:ITER).EQ.'_').OR. + (STRING(ITER:ITER).EQ.'*')) THEN LREST=.TRUE. END IF END IF IF (LLETTER.OR.LREST) THEN ICOUNT=ICOUNT+1 ELSE LHELP=.FALSE. END IF END IF END DO FILENSTRING_ALPHANUMSEN=ICOUNT END ***** end of FILENSTRING_ALPHANUMSEN ***** ------------------------------------------------------------------ ***** FCT FRMAX1 ***** ------------------------------------------------------------------ C---- C---- NAME : FRMAX1 C---- ARG : RVEC,IROW C---- DES : computes the maximal value of all elements of the real C---- DES : vector RVEC(IROW): C---- DES : result = max/i [RVEC(i)] C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: May, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: computation of maximal value of the elements of * * a real vector * * input parameter:IROW * * input variables:RVEC * * output: result = max/j [ RVEC1(j)] * C----------------------------------------------------------------------- C----------------------------------------------------------------------- *----------------------------------------------------------------------* REAL FUNCTION FRMAX1(RVEC,IROW) INTEGER IROW REAL RESULT REAL RVEC(1:IROW) RESULT=0. DO ITER=1,IROW RESULT=MAX(RESULT,RVEC(ITER)) END DO FRMAX1=RESULT END ***** end of FRMAX1 ***** ------------------------------------------------------------------ ***** FCT FRMAX2 ***** ------------------------------------------------------------------ C---- C---- NAME : FRMAX2 C---- ARG : RMAT,IROW,ICOL C---- DES : computes the maximal value of all elements of the real C---- DES : matrix RMAT(IROW,ICOL): C---- DES : result = max/i,j [RVEC(i,j)] C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: computation of maximal value of the elements of * * a real matrix * * input parameter:IROW, ICOL * * input variables:RMAT * * output: result = max/i,j [ RMAT(i,j)] * *----------------------------------------------------------------------* REAL FUNCTION FRMAX2(RMAT,IROW,ICOL) INTEGER IROW,ICOL,ITROW,ITCOL REAL RESULT,MAX REAL RMAT(1:IROW,1:ICOL) RESULT=0. DO ITCOL=1,ICOL DO ITROW=1,IROW RESULT=MAX(RESULT,RMAT(ITROW,ITCOL)) END DO END DO FRMAX2=RESULT END ***** end of FRMAX2 ***** ------------------------------------------------------------------ ***** SUB GETCHAR ***** ------------------------------------------------------------------ C---- C---- NAME : GETCHAR C---- ARG : C---- DES : prompts for printable (keyboard) characters C---- DES : Caution: line with '$!' is truncated as comment C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE GETCHAR(KCHAR,CHARARR,CTEXT) LOGICAL EMPTYSTRING CHARACTER*80 LINE CHARACTER*(*) CTEXT CHARACTER CHARARR*(*) WRITE(*,*) WRITE(*,*)'================================================='// + '==============================' CALL WRITELINES(CTEXT) IF(KCHAR.LT.1)THEN WRITE(*,*)'*** CHARPROMPT: illegal KCHAR',KCHAR RETURN ENDIF 10 CONTINUE WRITE(*,*) IF(KCHAR.GT.1) THEN WRITE(*,'(2X,''Enter letter string of length <'',I3)')KCHAR ELSE WRITE(*,'(2X,''Enter one letter !'')') ENDIF WRITE(*,'(2X,''[CR=default]: '')') WRITE(*, '(2X,''Default: '',80A1)' ) (CHARARR(K:K),K=1,KCHAR) LINE=' ' READ(*,'(A80)',ERR=10,END=11) LINE IF(.NOT.EMPTYSTRING(LINE)) THEN C ! assuming default values were set outside .... C...remove comments ( 34535345 !$ comment ) KCOMMENT=INDEX(LINE,'!$') IF(KCOMMENT.NE.0) LINE(KCOMMENT:80)=' ' DO I=1,80 ***** ------------------------------------------------------------------ IF (INDEX(' ABCDEFGHIJKLMNOPQRSTUVWXYZ',LINE(I:I)).EQ. + 0) THEN IF (INDEX(' abcdefghijklmnopqrstuvwxyz',LINE(I:I)).EQ. + 0) THEN C IF (INDEX('~!@#$%^&*()_+=-{}[]:""|\;,' ,LINE(I:I)).EQ. IF (INDEX('~!@#$%^&*()_+=-{}[]:""|;,' ,LINE(I:I)).EQ. + 0) THEN IF (INDEX('.?/><1234567890 ',LINE(I:I)). + EQ.0) THEN WRITE(*, + '(2X,''*** characters only, not: '',A40)') + LINE(1:40) GO TO 10 ENDIF ENDIF ENDIF ENDIF ENDDO READ(LINE,'(80A1)',ERR=10,END=99) (CHARARR(K:K),K=1,KCHAR) ENDIF 11 WRITE(*,'(2X,A7,60A1)') ' echo: ', (CHARARR(K:K),K=1,KCHAR) RETURN 99 WRITE(*,*)' CHARPROMPT: END OF LINE DURING READ - check format!' END ***** end of GETCHAR ***** ------------------------------------------------------------------ ***** SUB GETINT ***** ------------------------------------------------------------------ C---- C---- NAME : GETINT C---- ARG : C---- DES : For interactive use via terminal. C---- DES : Prompts for KINT integers from input unit *. C---- DES : Returns new values in INTNUM. C---- DES : Offers previous values as default. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *----------------------------------------------------------------------* SUBROUTINE GETINT(KINT,INTNUM,CTEXT) INTEGER LINELEN PARAMETER(LINELEN=80) CHARACTER*(LINELEN) LINE CHARACTER*(*) CTEXT INTEGER INTNUM LOGICAL EMPTYSTRING INTEGER NUMSTART CHARACTER*20 CTEMP WRITE(*,*) WRITE(*,*)'===================================================='// + '===========================' CALL WRITELINES(CTEXT) IF(KINT.LT.1.OR.KINT.GT.100) THEN WRITE(*,*)'*** INTPROMPT: KINT no good',KINT RETURN ENDIF 10 WRITE(*,*) WRITE(*,'(2X,''Default: '',I10)') INTNUM IF(KINT.GT.1) THEN WRITE(*,'(2X,''Enter'',I3,'' integers [CR=default]: '')')KINT ELSE WRITE(*,'(2X,''Enter one integer [CR=default]: '')') ENDIF LINE=' ' READ(*,'(A80)',ERR=10,END=11) LINE IF(.NOT.EMPTYSTRING(LINE)) THEN C...remove comments ( 34535345 !$ comment ) KCOMMENT=INDEX(LINE,' !$') IF(KCOMMENT.NE.0) LINE(KCOMMENT:linelen)=' ' C.. check for legal string DO I=1,linelen IF(INDEX(' ,+-0123456789',LINE(I:I)).EQ.0) THEN WRITE(*,'(2X,''*** not an integer: '',A40)') LINE(1:40) GO TO 10 ENDIF ENDDO CALL StrPos(LINE,IStart,IStop) C terminate line by comma for ND-100 C LINE=LINE(1:IStop)//',' CUG READ(LINE(IStart:IStop),'(i)',ERR=10,END=11) Cug + (INTNUM(K),K=1,KINT) CUG CALL GETTOKEN(LINE,LINELEN,1,NUMSTART,CTEMP) CALL RIGHTADJUST(CTEMP,20) READ(CTEMP,'(I20)') INTNUM ENDIF 11 WRITE(*,'(2X,'' echo:'',I10)') INTNUM RETURN END ***** end of GETINT ***** ------------------------------------------------------------------ ***** SUB GETTOKEN ***** ------------------------------------------------------------------ C---- C---- NAME : GETTOKEN C---- ARG : C---- DES : returns the itokens token of cstring in ctoken. firstpos is C---- DES : position in cstring at which substring ctoken starts C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE GETTOKEN(CSTRING,LEN,ITOKEN,FIRSTPOS,CTOKEN) c Implicit None C Import INTEGER LEN, ITOKEN CHARACTER*(*) CSTRING C Export INTEGER FIRSTPOS CHARACTER*(*) CTOKEN C Internal INTEGER IPOS, THISTOKEN, TPOS LOGICAL FINISHED, INSIDE CTOKEN = ' ' TPOS = 0 FINISHED = .FALSE. IF ( CSTRING(1:1) .EQ. ' ' ) THEN THISTOKEN = 0 INSIDE = .FALSE. ELSE THISTOKEN = 1 INSIDE = .TRUE. FIRSTPOS = 1 IF ( THISTOKEN .EQ. ITOKEN ) THEN TPOS = TPOS + 1 CTOKEN(TPOS:TPOS) = CSTRING(1:1) ENDIF ENDIF IPOS = 2 DO WHILE ( IPOS .LE. LEN .AND. .NOT. FINISHED ) IF ( CSTRING(IPOS:IPOS) .EQ. ' ' ) THEN IF ( INSIDE ) THEN INSIDE = .FALSE. IF ( THISTOKEN .EQ. ITOKEN ) FINISHED = .TRUE. ENDIF ELSE IF ( .NOT. INSIDE ) THEN INSIDE = .TRUE. FIRSTPOS = IPOS THISTOKEN = THISTOKEN + 1 ENDIF IF ( THISTOKEN .EQ. ITOKEN ) THEN TPOS = TPOS + 1 CTOKEN(TPOS:TPOS) = CSTRING(IPOS:IPOS) ENDIF ENDIF IPOS = IPOS + 1 ENDDO RETURN END ***** end of GETTOKEN ***** ------------------------------------------------------------------ ***** SUB GET_ARGUMENT ***** ------------------------------------------------------------------ C---- C---- NAME : GET_ARGUMENT C---- ARG : NUMBER,ARGUMENT C---- DES : returns the content of x-th argument C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE GET_ARGUMENT(INUMBER,ARGUMENT) CHARACTER*(*) ARGUMENT INTEGER INUMBER CALL GETARG(INUMBER,ARGUMENT) RETURN END ***** end of GET_ARGUMENT ***** ------------------------------------------------------------------ ***** SUB GET_ARG_NUMBER ***** ------------------------------------------------------------------ C---- C---- NAME : GET_ARG_NUMBER C---- ARG : INUMBER C---- DES : returns number of arguments C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE GET_ARG_NUMBER(INUMBER) INTEGER INUMBER,IARGC INUMBER=0 INUMBER=IARGC() RETURN END ***** end of GET_ARG_NUMBER ***** ------------------------------------------------------------------ ***** SUB RightADJUST ***** ------------------------------------------------------------------ C---- C---- NAME : RightADJUST C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RightADJUST(STRING,NLEN) CHARACTER*(*) STRING INTEGER NLEN C...find position of last non-blank IF (NLEN.LT.1) RETURN L=NLEN DO WHILE(STRING(L:L).EQ.' '.AND.L.GT.1) L=L-1 ENDDO IF (L.LT.NLEN) THEN C..L is position of last non-blank STRING(NLEN-L+1:NLEN)=STRING(1:L) C.C..fill rest with blanks from 1 to NLEN-L DO IL=1,NLEN-L STRING(IL:IL)=' ' ENDDO ENDIF RETURN END ***** end of RIGHTADJUST ***** ------------------------------------------------------------------ ***** SUB SCFDATE ***** ------------------------------------------------------------------ C---- C---- NAME : SCFDATE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE SCFDATE(CALL,LOGIWRITE,DATEOLD) IMPLICIT NONE CHARACTER*24 ACTDATE,DATEOLD INTEGER CALL,ITER LOGICAL LOGIWRITE C ACTDATE=FDATE() ACTDATE='' IF (LOGIWRITE) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) IF (CALL.EQ.2) THEN WRITE(6,'(T10,A11,A24)')'started: ',DATEOLD WRITE(6,'(T10,A11,A24)')' ended: ',ACTDATE ELSE WRITE(6,'(T10,A11,A24)')' time: ',ACTDATE END IF WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF IF (CALL.EQ.1) THEN DATEOLD=ACTDATE END IF END ***** end of SCFDATE ***** ------------------------------------------------------------------ ***** SUB SFILEOPEN ***** ------------------------------------------------------------------ C---- C---- NAME : SFILEOPEN C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE SFILEOPEN(UNIT,FILENAME,ACTSTATUS,LENGTH,ACTTASK) IMPLICIT NONE C---- local function INTEGER FILEN_STRING C---- local variables INTEGER UNIT,LENGTH,IEND CHARACTER*(*) FILENAME,ACTSTATUS,ACTTASK CHARACTER*456 CHFILE ******------------------------------*-----------------------------****** C purge blanks from file name IEND=FILEN_STRING(FILENAME) CHFILE(1:IEND)=FILENAME(1:IEND) C OPEN(UNIT,FILE=FILENAME,STATUS=ACTSTATUS) OPEN(UNIT,FILE=CHFILE(1:IEND),STATUS=ACTSTATUS) C---- bullshit to avoid warnings IF (ACTTASK.EQ.'XX') THEN CONTINUE END IF IF (LENGTH.LT.1) THEN CONTINUE END IF RETURN END ***** end of SFILEOPEN ***** ------------------------------------------------------------------ ***** SUB SCHAR_TO_INT ***** ------------------------------------------------------------------ C---- C---- NAME : SCHAR_TO_INT C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1993 version 0.1 * * changed: Apr, 1993 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The character CHAR is converted to an integer. * * in variables: CHAR * * out variables: INUM * * SBRs calling: from lib-comp.f: * * -------------- SILEN_STRING(STRING,IBEG,IEND) * * procedure: be careful '-1' or 'a1' might produce errors * * ---------- *----------------------------------------------------------------------* SUBROUTINE SCHAR_TO_INT(CHAR,INUM) IMPLICIT NONE C---- variables passed INTEGER INUM CHARACTER CHAR*(*) C---- local variables * INTEGER ITER,ITER2,IBEG,IEND,ILEN,SUM,PROD ******------------------------------*-----------------------------****** C---- defaults C---- determine non-blank length of character CHAR C ================= CALL SILEN_STRING(CHAR,IBEG,IEND) C ================= ILEN=IEND-IBEG+1 C---- loop over length: SUM=0 DO ITER=1,ILEN PROD=1 DO ITER2=1,(ILEN-ITER) PROD=10*PROD END DO IF (CHAR(ITER:ITER).EQ.'1') THEN SUM=SUM+PROD ELSEIF (CHAR(ITER:ITER).EQ.'2') THEN SUM=SUM+PROD*2 ELSEIF (CHAR(ITER:ITER).EQ.'3') THEN SUM=SUM+PROD*3 ELSEIF (CHAR(ITER:ITER).EQ.'4') THEN SUM=SUM+PROD*4 ELSEIF (CHAR(ITER:ITER).EQ.'5') THEN SUM=SUM+PROD*5 ELSEIF (CHAR(ITER:ITER).EQ.'6') THEN SUM=SUM+PROD*6 ELSEIF (CHAR(ITER:ITER).EQ.'7') THEN SUM=SUM+PROD*7 ELSEIF (CHAR(ITER:ITER).EQ.'8') THEN SUM=SUM+PROD*8 ELSEIF (CHAR(ITER:ITER).EQ.'9') THEN SUM=SUM+PROD*9 END IF END DO INUM=SUM END ***** end of SCHAR_TO_INT ***** ------------------------------------------------------------------ ***** SUB SILEN_STRING ***** ------------------------------------------------------------------ C---- C---- NAME : SILEN_STRING C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Feb, 1993 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* * purpose: The length of a given character string is returned * -------- resp. non-blank begin (ibeg) and end (iend) * * input: STRING string of character*80 * * output: ibeg,iend * *----------------------------------------------------------------------* SUBROUTINE SILEN_STRING(STRING,IBEG,IEND) C---- variables passing CHARACTER STRING*(*) C---- local variables INTEGER ICOUNT,ITER,IBEG,IEND CHARACTER*80 HSTRING LOGICAL LHELP ******------------------------------*-----------------------------****** C---- defaults HSTRING=STRING ICOUNT=0 LHELP=.TRUE. DO ITER=1,80 IF (LHELP) THEN IF (HSTRING(ITER:ITER).NE.' ') THEN IF (ICOUNT.EQ.0) THEN IBEG=ITER END IF ICOUNT=ICOUNT+1 ELSE IF (ICOUNT.NE.0) THEN IEND=ITER-1 LHELP=.FALSE. END IF END IF END IF END DO IF (ICOUNT.EQ.0) THEN WRITE(6,'(T2,A,T10,A,A1,A,A1)')'***', + 'ERROR: Sbr SILEN_STRING: empty string:','|',STRING,'|' END IF END ***** end of SILEN_STRING ***** ------------------------------------------------------------------ ***** SUB SRSTE2 ***** ------------------------------------------------------------------ C---- C---- NAME : SRSTE2 C---- ARG : RMAT1,RMAT2,IROW,ICOL C---- DES : sets real matrix RMAT1(IROW,ICOL)= C---- DES : real matrix RMAT2(IROW,ICOL) C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: the 2-dimensional real matrix RMAT1(rows,columns) is set* C equal to the 2-D real one RMAT2 * C input parameter: IROW,ICOL * C input variables: RMAT1(real matrix) , RMAT2 * C output variables: RMAT1(i,j)=RMAT2(i,j) for all i,j * *----------------------------------------------------------------------* SUBROUTINE SRSTE2(RMAT1,RMAT2,IROW,ICOL) REAL RMAT1(1:IROW,1:ICOL) REAL RMAT2(1:IROW,1:ICOL) DO ITER2=1,ICOL DO ITER1=1,IROW RMAT1(ITER1,ITER2)=RMAT2(ITER1,ITER2) END DO END DO END ***** end of SRSTE2 ***** ------------------------------------------------------------------ ***** SUB SRSTZ2 ***** ------------------------------------------------------------------ C---- C---- NAME : SRSTZ2 C---- ARG : RMAT,IROW,ICOL C---- DES : Sets zero a 2-dimensional real matrix with the C---- DES : row-length C---- DES : IROW, the column-length ICOL :RMAT(IROW,ICOL) C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Mar, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* C purpose: a real two dimensional matrix RMAT(rows,columns) is set * C to zero * C input parameter: IROW,ICOL * C input variables: RMAT(real matrix) * C output variables: RMAT=0. for all elements * *----------------------------------------------------------------------* SUBROUTINE SRSTZ2(RMAT,IROW,ICOL) REAL RMAT(1:IROW,1:ICOL) DO ITER2=1,ICOL DO ITER1=1,IROW RMAT(ITER1,ITER2)=0. END DO END DO END ***** end of SRSTZ2 ***** ------------------------------------------------------------------ ***** SUB StrPos ***** ------------------------------------------------------------------ C---- C---- NAME : StrPos C---- ARG : C---- DES : StrPos(Source,IStart,IStop): Finds the positions of the C---- DES : first and last non-blank/non-TAB in Source. C---- DES : IStart=IStop=0 for empty Source C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE StrPos(Source,IStart,IStop) CHARACTER*(*) Source INTEGER ISTART,ISTOP ISTART=0 ISTOP=0 DO J=1,LEN(SOURCE) IF(SOURCE(J:J).NE.' ')THEN ISTART=J GOTO 20 ENDIF ENDDO RETURN 20 DO J=LEN(SOURCE),1,-1 IF(SOURCE(J:J).NE.' ')THEN ISTOP=J RETURN ENDIF ENDDO ISTART=0 ISTOP=0 RETURN END ***** end of STRPOS ***** ------------------------------------------------------------------ ***** SUB WRITELINES ***** ------------------------------------------------------------------ C---- C---- NAME : WRITELINES C---- ARG : C---- DES : if 'cstring' contains '/n' (new line) this routine writes C---- DES : cstring line by line on screen; called by GETINT,GETREAL.. C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRITELINES(CSTRING) CHARACTER*(*) CSTRING INTEGER ICUTBEGIN(10),ICUTEND(10) CALL StrPos(CSTRING,ISTART,ISTOP) ILINE=1 ICUTBEGIN(ILINE)=1 ICUTEND(ILINE)=ISTOP DO I=1,ISTOP-1 IF(CSTRING(I:I+1).EQ.'/n')THEN ILINE=ILINE+1 ICUTBEGIN(ILINE)=I+2 ICUTEND(ILINE-1)=I-1 ICUTEND(ILINE)=ISTOP ENDIF ENDDO DO I=1,ILINE WRITE(*,*)CSTRING(ICUTBEGIN(I):ICUTEND(I)) ENDDO RETURN END ***** end of WRITELINES profnet-1.0.22/src/lib-sys-ALPHA.f0000644015075101507510000002175512021362711015717 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** FCT FCTIME_DATE ***** ------------------------------------------------------------------ C---- C---- NAME : FCTIME_DATE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns date * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: char*8 YYYYMMDD * * input : NOM, DEN * *----------------------------------------------------------------------* CHARACTER*24 FUNCTION FCTIME_DATE() IMPLICIT NONE ******------------------------------*-----------------------------****** * execution of function * C FCTIME_DATE=FDATE() FCTIME_DATE='' END ***** end of FCTIME_DATE ***** ------------------------------------------------------------------ ***** FCT FRTIME_SECNDS ***** ------------------------------------------------------------------ C---- C---- NAME : FRTIME_SECNDS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns CPU time seconds * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: cputime * * input : NOM, DEN * *----------------------------------------------------------------------* REAL FUNCTION FRTIME_SECNDS(T1) IMPLICIT NONE C---- variables passed from/to SBR calling REAL T1 ******------------------------------*-----------------------------****** * execution of function * FRTIME_SECNDS=SECNDS(T1) END ***** end of FRTIME_SECNDS ***** ------------------------------------------------------------------ ***** SUB INIJCT ***** ------------------------------------------------------------------ C---- C---- NAME : INIJCT C---- ARG : C---- DES : Generation of the initial couplings and biases of C---- DES : the network. Options: C---- DES : RANDOM : locfield (i,j,TIMEST=0) = [-/+diceintervall] C---- DES : with equal distribution C---- IN p: NUMSAM,NUMIN,NUMHID,NUMOUT, DICESEED C---- IN v: JCT1ST,JCT2ND,BIAS1ST,BIAS2ND C---- OUT : setting of JCT1ST, JCT2ND C---- FROM : MAIN C---- CALL2: C---- LIB : RAN(SEED), creates random numbers between 0 and * C---- LIB+ : 1 (1 excluded, 0 included), it is called by com-* C---- LIB+ : piling with -lV77, each call initializes next * C---- LIB+ : seed, according to: seed=6909*seed+mod(2**32) * C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIJCT C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER I,J,NUMHIDFIRST,NUMHIDLAST Cunix REAL RAN,DICE1,DICE2,DICEINTERVX Clinux C REAL RAND,DICE1,DICE2,DICEINTERVX ******------------------------------*-----------------------------****** * I,J serve as iteration variables * * DICE1,2 =RAN(DICESEED1),i.e. random number between 0,1* * NUMHIDFIRST number of units in the first hidden layer * * NUMHIDLAST number of units in the last hidden layer * ******------------------------------*-----------------------------****** DICEINTERVX=DICEITRVL C---- ------------------------------------------------------------------ C---- first layer junctions C---- ------------------------------------------------------------------ DICESEED1=DICESEED+DICESEED_ADDJCT IF (NUMLAYERS.EQ.1) THEN NUMHIDFIRST=NUMOUT NUMHIDLAST=0 ELSE NUMHIDFIRST=NUMHID NUMHIDLAST=NUMHID END IF C---- loop over hidden units DO I=1,NUMHIDFIRST C------- junctions (loop over input units) DO J=1,NUMIN C---------- generating random numbers from [0,1) Cunix DICE1= RAN(DICESEED1) DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST(J,I)= (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST(J,I)= DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix DICE1= RAN(DICESEED1) DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST((NUMIN+1),I)= + (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST((NUMIN+1),I)=DICEINTERVX*DICE2 END IF END DO C---- ------------------------------------------------------------------ C---- last layer junctions C---- ------------------------------------------------------------------ DO I=1,NUMOUT C------- junctions DO J=1,NUMHIDLAST C---------- generating random numbers from [0,1) Cunix DICE1= RAN(DICESEED1) DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND(J,I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND(J,I)=DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix DICE1= RAN(DICESEED1) DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND((NUMHID+1),I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND((NUMHID+1),I)=DICEINTERVX*DICE2 END IF END DO END ***** end of INIJCT ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux C REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME INTEGER ITER LOGICAL LOGIWRITE Cunix TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) Clinux C TIMEDIFF=DTIME(TIMEARRAYM) IF (LOGIWRITE) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src/lib-sys-LINUX.f0000755015075101507510000001432212021362712015765 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** SUB INIJCT ***** ------------------------------------------------------------------ C---- C---- NAME : INIJCT C---- ARG : C---- DES : Generation of the initial couplings and biases of C---- DES : the network. Options: C---- DES : RANDOM : locfield (i,j,TIMEST=0) = [-/+diceintervall] C---- DES : with equal distribution C---- IN p: NUMSAM,NUMIN,NUMHID,NUMOUT, DICESEED C---- IN v: JCT1ST,JCT2ND,BIAS1ST,BIAS2ND C---- OUT : setting of JCT1ST, JCT2ND C---- FROM : MAIN C---- CALL2: C---- LIB : RAN(SEED), creates random numbers between 0 and * C---- LIB+ : 1 (1 excluded, 0 included), it is called by com-* C---- LIB+ : piling with -lV77, each call initializes next * C---- LIB+ : seed, according to: seed=6909*seed+mod(2**32) * C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIJCT C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER I,J,NUMHIDFIRST,NUMHIDLAST Cunix C REAL RAN,DICE1,DICE2,DICEINTERVX Clinux REAL RAND,DICE1,DICE2,DICEINTERVX ******------------------------------*-----------------------------****** * I,J serve as iteration variables * * DICE1,2 =RAN(DICESEED1),i.e. random number between 0,1* * NUMHIDFIRST number of units in the first hidden layer * * NUMHIDLAST number of units in the last hidden layer * ******------------------------------*-----------------------------****** DICEINTERVX=DICEITRVL C---- ------------------------------------------------------------------ C---- first layer junctions C---- ------------------------------------------------------------------ DICESEED1=DICESEED+DICESEED_ADDJCT IF (NUMLAYERS.EQ.1) THEN NUMHIDFIRST=NUMOUT NUMHIDLAST=0 ELSE NUMHIDFIRST=NUMHID NUMHIDLAST=NUMHID END IF C---- loop over hidden units DO I=1,NUMHIDFIRST C------- junctions (loop over input units) DO J=1,NUMIN C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST(J,I)= (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST(J,I)= DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST((NUMIN+1),I)= + (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST((NUMIN+1),I)=DICEINTERVX*DICE2 END IF END DO C---- ------------------------------------------------------------------ C---- last layer junctions C---- ------------------------------------------------------------------ DO I=1,NUMOUT C------- junctions DO J=1,NUMHIDLAST C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND(J,I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND(J,I)=DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND((NUMHID+1),I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND((NUMHID+1),I)=DICEINTERVX*DICE2 END IF END DO END ***** end of INIJCT ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix C REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME INTEGER ITER LOGICAL LOGIWRITE Cunix C TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) Clinux TIMEDIFF=DTIME(TIMEARRAYM) C TIMEDIFF= TIMEDIFFX(1) IF (LOGIWRITE) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src/lib-sys-MAC.f0000644015075101507510000001432212021362712015463 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** SUB INIJCT ***** ------------------------------------------------------------------ C---- C---- NAME : INIJCT C---- ARG : C---- DES : Generation of the initial couplings and biases of C---- DES : the network. Options: C---- DES : RANDOM : locfield (i,j,TIMEST=0) = [-/+diceintervall] C---- DES : with equal distribution C---- IN p: NUMSAM,NUMIN,NUMHID,NUMOUT, DICESEED C---- IN v: JCT1ST,JCT2ND,BIAS1ST,BIAS2ND C---- OUT : setting of JCT1ST, JCT2ND C---- FROM : MAIN C---- CALL2: C---- LIB : RAN(SEED), creates random numbers between 0 and * C---- LIB+ : 1 (1 excluded, 0 included), it is called by com-* C---- LIB+ : piling with -lV77, each call initializes next * C---- LIB+ : seed, according to: seed=6909*seed+mod(2**32) * C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIJCT C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER I,J,NUMHIDFIRST,NUMHIDLAST Cunix C REAL RAN,DICE1,DICE2,DICEINTERVX Clinux REAL RAND,DICE1,DICE2,DICEINTERVX ******------------------------------*-----------------------------****** * I,J serve as iteration variables * * DICE1,2 =RAN(DICESEED1),i.e. random number between 0,1* * NUMHIDFIRST number of units in the first hidden layer * * NUMHIDLAST number of units in the last hidden layer * ******------------------------------*-----------------------------****** DICEINTERVX=DICEITRVL C---- ------------------------------------------------------------------ C---- first layer junctions C---- ------------------------------------------------------------------ DICESEED1=DICESEED+DICESEED_ADDJCT IF (NUMLAYERS.EQ.1) THEN NUMHIDFIRST=NUMOUT NUMHIDLAST=0 ELSE NUMHIDFIRST=NUMHID NUMHIDLAST=NUMHID END IF C---- loop over hidden units DO I=1,NUMHIDFIRST C------- junctions (loop over input units) DO J=1,NUMIN C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST(J,I)= (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST(J,I)= DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST((NUMIN+1),I)= + (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST((NUMIN+1),I)=DICEINTERVX*DICE2 END IF END DO C---- ------------------------------------------------------------------ C---- last layer junctions C---- ------------------------------------------------------------------ DO I=1,NUMOUT C------- junctions DO J=1,NUMHIDLAST C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND(J,I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND(J,I)=DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND((NUMHID+1),I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND((NUMHID+1),I)=DICEINTERVX*DICE2 END IF END DO END ***** end of INIJCT ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix C REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME INTEGER ITER LOGICAL LOGIWRITE Cunix C TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) Clinux TIMEDIFF=DTIME(TIMEARRAYM) C TIMEDIFF= TIMEDIFFX(1) IF (LOGIWRITE) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src/lib-sys-MACIBM.f0000644015075101507510000002363512021362711016021 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** FCT FCTIME_DATE ***** ------------------------------------------------------------------ C---- C---- NAME : FCTIME_DATE C---- ARG : C---- DES : C---- OUT : character*24 'YYYY_MM_DD - hh:mm:ss' C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns date * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: char*8 YYYYMMDD * * input : NOM, DEN * *----------------------------------------------------------------------* CHARACTER*24 FUNCTION FCTIME_DATE() IMPLICIT NONE C---- variables passed from/to SBR calling CHARACTER*24 CTEMP,CTEMP2 ******------------------------------*-----------------------------****** * execution of function * CTEMP=' ' CALL DATE_AND_TIME(CTEMP) FCTIME_DATE= ' ' FCTIME_DATE(1:4)= CTEMP(1:4) FCTIME_DATE(5:5)= '_' FCTIME_DATE(6:7)= CTEMP(5:6) FCTIME_DATE(8:8)= '_' FCTIME_DATE(9:10)= CTEMP(7:8) FCTIME_DATE(11:13)=' - ' FCTIME_DATE(14:15)=CTEMP2(1:2) FCTIME_DATE(16:16)=':' FCTIME_DATE(17:18)=CTEMP2(3:4) FCTIME_DATE(19:19)=':' FCTIME_DATE(20:21)=CTEMP2(5:6) END ***** end of FCTIME_DATE ***** ------------------------------------------------------------------ ***** FCT FRTIME_SECNDS ***** ------------------------------------------------------------------ C---- C---- NAME : FRTIME_SECNDS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns CPU time seconds * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: cputime * * input : T1: time to start (from previous call for unix) * *----------------------------------------------------------------------* REAL FUNCTION FRTIME_SECNDS(T1) IMPLICIT NONE C---- variables passed from/to SBR calling REAL T1 ******------------------------------*-----------------------------****** * execution of function * CALL CPU_TIME(T1) FRTIME_SECNDS=T1 END ***** end of FRTIME_SECNDS ***** ------------------------------------------------------------------ ***** SUB INIJCT ***** ------------------------------------------------------------------ C---- C---- NAME : INIJCT C---- ARG : C---- DES : Generation of the initial couplings and biases of C---- DES : the network. Options: C---- DES : RANDOM : locfield (i,j,TIMEST=0) = [-/+diceintervall] C---- DES : with equal distribution C---- IN p: NUMSAM,NUMIN,NUMHID,NUMOUT, DICESEED C---- IN v: JCT1ST,JCT2ND,BIAS1ST,BIAS2ND C---- OUT : setting of JCT1ST, JCT2ND C---- FROM : MAIN C---- CALL2: C---- LIB : RAN(SEED), creates random numbers between 0 and * C---- LIB+ : 1 (1 excluded, 0 included), it is called by com-* C---- LIB+ : piling with -lV77, each call initializes next * C---- LIB+ : seed, according to: seed=6909*seed+mod(2**32) * C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIJCT C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER I,J,NUMHIDFIRST,NUMHIDLAST Cunix C REAL RAN,DICE1,DICE2,DICEINTERVX Clinux REAL RAND,DICE1,DICE2,DICEINTERVX ******------------------------------*-----------------------------****** * I,J serve as iteration variables * * DICE1,2 =RAN(DICESEED1),i.e. random number between 0,1* * NUMHIDFIRST number of units in the first hidden layer * * NUMHIDLAST number of units in the last hidden layer * ******------------------------------*-----------------------------****** DICEINTERVX=DICEITRVL C---- ------------------------------------------------------------------ C---- first layer junctions C---- ------------------------------------------------------------------ DICESEED1=DICESEED+DICESEED_ADDJCT IF (NUMLAYERS.EQ.1) THEN NUMHIDFIRST=NUMOUT NUMHIDLAST=0 ELSE NUMHIDFIRST=NUMHID NUMHIDLAST=NUMHID END IF C---- loop over hidden units DO I=1,NUMHIDFIRST C------- junctions (loop over input units) DO J=1,NUMIN C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) Cibm CALL RANDOM_NUMBER(DICE1) CALL RANDOM_NUMBER(DICE2) IF (DICE1.LT.0.5) THEN JCT1ST(J,I)= (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST(J,I)= DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) Cibm CALL RANDOM_NUMBER(DICE1) CALL RANDOM_NUMBER(DICE2) IF (DICE1.LT.0.5) THEN JCT1ST((NUMIN+1),I)= + (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST((NUMIN+1),I)=DICEINTERVX*DICE2 END IF END DO C---- ------------------------------------------------------------------ C---- last layer junctions C---- ------------------------------------------------------------------ DO I=1,NUMOUT C------- junctions DO J=1,NUMHIDLAST C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) Cibm CALL RANDOM_NUMBER(DICE1) CALL RANDOM_NUMBER(DICE2) IF (DICE1.LT.0.5) THEN JCT2ND(J,I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND(J,I)=DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) Cibm CALL RANDOM_NUMBER(DICE1) CALL RANDOM_NUMBER(DICE2) IF (DICE1.LT.0.5) THEN JCT2ND((NUMHID+1),I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND((NUMHID+1),I)=DICEINTERVX*DICE2 END IF END DO END ***** end of INIJCT ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix C REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME,TIME_TMP INTEGER ITER LOGICAL LOGIWRITE Cunix C TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) Clinux CC TIMEDIFF= TIMEDIFFX(1) C TIMEDIFF=DTIME(TIMEARRAYM) Cibm CALL CPU_TIME(TIMEDIFF) IF (LOGIWRITE) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src/lib-sys-MACINTEL.f0000644015075101507510000001432212021362712016257 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** SUB INIJCT ***** ------------------------------------------------------------------ C---- C---- NAME : INIJCT C---- ARG : C---- DES : Generation of the initial couplings and biases of C---- DES : the network. Options: C---- DES : RANDOM : locfield (i,j,TIMEST=0) = [-/+diceintervall] C---- DES : with equal distribution C---- IN p: NUMSAM,NUMIN,NUMHID,NUMOUT, DICESEED C---- IN v: JCT1ST,JCT2ND,BIAS1ST,BIAS2ND C---- OUT : setting of JCT1ST, JCT2ND C---- FROM : MAIN C---- CALL2: C---- LIB : RAN(SEED), creates random numbers between 0 and * C---- LIB+ : 1 (1 excluded, 0 included), it is called by com-* C---- LIB+ : piling with -lV77, each call initializes next * C---- LIB+ : seed, according to: seed=6909*seed+mod(2**32) * C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIJCT C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER I,J,NUMHIDFIRST,NUMHIDLAST Cunix C REAL RAN,DICE1,DICE2,DICEINTERVX Clinux REAL RAND,DICE1,DICE2,DICEINTERVX ******------------------------------*-----------------------------****** * I,J serve as iteration variables * * DICE1,2 =RAN(DICESEED1),i.e. random number between 0,1* * NUMHIDFIRST number of units in the first hidden layer * * NUMHIDLAST number of units in the last hidden layer * ******------------------------------*-----------------------------****** DICEINTERVX=DICEITRVL C---- ------------------------------------------------------------------ C---- first layer junctions C---- ------------------------------------------------------------------ DICESEED1=DICESEED+DICESEED_ADDJCT IF (NUMLAYERS.EQ.1) THEN NUMHIDFIRST=NUMOUT NUMHIDLAST=0 ELSE NUMHIDFIRST=NUMHID NUMHIDLAST=NUMHID END IF C---- loop over hidden units DO I=1,NUMHIDFIRST C------- junctions (loop over input units) DO J=1,NUMIN C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST(J,I)= (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST(J,I)= DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST((NUMIN+1),I)= + (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST((NUMIN+1),I)=DICEINTERVX*DICE2 END IF END DO C---- ------------------------------------------------------------------ C---- last layer junctions C---- ------------------------------------------------------------------ DO I=1,NUMOUT C------- junctions DO J=1,NUMHIDLAST C---------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND(J,I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND(J,I)=DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix C DICE1= RAN(DICESEED1) C DICE2= RAN(DICESEED1) Clinux DICE1= RAND(DICESEED1) DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND((NUMHID+1),I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND((NUMHID+1),I)=DICEINTERVX*DICE2 END IF END DO END ***** end of INIJCT ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix C REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME INTEGER ITER LOGICAL LOGIWRITE Cunix C TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) Clinux TIMEDIFF=DTIME(TIMEARRAYM) C TIMEDIFF= TIMEDIFFX(1) IF (LOGIWRITE) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src/lib-sys-SGI64.f0000644015075101507510000002175512021362712015667 0ustar lkajanlkajan***** ------------------------------------------------------------------ ***** FCT FCTIME_DATE ***** ------------------------------------------------------------------ C---- C---- NAME : FCTIME_DATE C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns date * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: char*8 YYYYMMDD * * input : NOM, DEN * *----------------------------------------------------------------------* CHARACTER*24 FUNCTION FCTIME_DATE() IMPLICIT NONE ******------------------------------*-----------------------------****** * execution of function * C FCTIME_DATE=FDATE() FCTIME_DATE='' END ***** end of FCTIME_DATE ***** ------------------------------------------------------------------ ***** FCT FRTIME_SECNDS ***** ------------------------------------------------------------------ C---- C---- NAME : FRTIME_SECNDS C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 2003 version 1.0 * * EMBL/LION http://www.predictprotein.org/ * * D-69012 Heidelberg rost@columbia.edu * * changed: Aug, 2003 version 1.0 * *----------------------------------------------------------------------* * purpose: returns CPU time seconds * * note: machine type dependent: * * SGI, UNIX, LINUX: absolute unix time * * IBM: cputime * * input : NOM, DEN * *----------------------------------------------------------------------* REAL FUNCTION FRTIME_SECNDS(T1) IMPLICIT NONE C---- variables passed from/to SBR calling REAL T1 ******------------------------------*-----------------------------****** * execution of function * FRTIME_SECNDS=SECNDS(T1) END ***** end of FRTIME_SECNDS ***** ------------------------------------------------------------------ ***** SUB INIJCT ***** ------------------------------------------------------------------ C---- C---- NAME : INIJCT C---- ARG : C---- DES : Generation of the initial couplings and biases of C---- DES : the network. Options: C---- DES : RANDOM : locfield (i,j,TIMEST=0) = [-/+diceintervall] C---- DES : with equal distribution C---- IN p: NUMSAM,NUMIN,NUMHID,NUMOUT, DICESEED C---- IN v: JCT1ST,JCT2ND,BIAS1ST,BIAS2ND C---- OUT : setting of JCT1ST, JCT2ND C---- FROM : MAIN C---- CALL2: C---- LIB : RAN(SEED), creates random numbers between 0 and * C---- LIB+ : 1 (1 excluded, 0 included), it is called by com-* C---- LIB+ : piling with -lV77, each call initializes next * C---- LIB+ : seed, according to: seed=6909*seed+mod(2**32) * C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIJCT C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER I,J,NUMHIDFIRST,NUMHIDLAST Cunix REAL RAN,DICE1,DICE2,DICEINTERVX Clinux C REAL RAND,DICE1,DICE2,DICEINTERVX ******------------------------------*-----------------------------****** * I,J serve as iteration variables * * DICE1,2 =RAN(DICESEED1),i.e. random number between 0,1* * NUMHIDFIRST number of units in the first hidden layer * * NUMHIDLAST number of units in the last hidden layer * ******------------------------------*-----------------------------****** DICEINTERVX=DICEITRVL C---- ------------------------------------------------------------------ C---- first layer junctions C---- ------------------------------------------------------------------ DICESEED1=DICESEED+DICESEED_ADDJCT IF (NUMLAYERS.EQ.1) THEN NUMHIDFIRST=NUMOUT NUMHIDLAST=0 ELSE NUMHIDFIRST=NUMHID NUMHIDLAST=NUMHID END IF C---- loop over hidden units DO I=1,NUMHIDFIRST C------- junctions (loop over input units) DO J=1,NUMIN C---------- generating random numbers from [0,1) Cunix DICE1= RAN(DICESEED1) DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST(J,I)= (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST(J,I)= DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix DICE1= RAN(DICESEED1) DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT1ST((NUMIN+1),I)= + (-1.)*DICEINTERVX*DICE2 ELSE JCT1ST((NUMIN+1),I)=DICEINTERVX*DICE2 END IF END DO C---- ------------------------------------------------------------------ C---- last layer junctions C---- ------------------------------------------------------------------ DO I=1,NUMOUT C------- junctions DO J=1,NUMHIDLAST C---------- generating random numbers from [0,1) Cunix DICE1= RAN(DICESEED1) DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND(J,I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND(J,I)=DICEINTERVX*DICE2 END IF END DO C------- thresholds (resp. biases) C------- generating random numbers from [0,1) Cunix DICE1= RAN(DICESEED1) DICE2= RAN(DICESEED1) Clinux C DICE1= RAND(DICESEED1) C DICE2= RAND(DICESEED1) IF (DICE1.LT.0.5) THEN JCT2ND((NUMHID+1),I)=(-1.)*DICEINTERVX*DICE2 ELSE JCT2ND((NUMHID+1),I)=DICEINTERVX*DICE2 END IF END DO END ***** end of INIJCT ***** ------------------------------------------------------------------ ***** SUB SRDTIME ***** ------------------------------------------------------------------ C---- C---- NAME : SRDTIME C---- ARG : C---- DES : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: Dec, 1991 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* *** *** *** *** *** SUBROUTINE SRDTIME *** *** *** *** *** *----------------------------------------------------------------------* SUBROUTINE SRDTIME(LOGIWRITE) IMPLICIT NONE Cunix REAL TIMEARRAYM,TIMEDIFF,DTIME,TIME_TMP Clinux C REAL TIMEARRAYM(1:2),TIMEDIFF,DTIME INTEGER ITER LOGICAL LOGIWRITE Cunix TIMEDIFF=DTIME(TIMEARRAYM,TIME_TMP) Clinux C TIMEDIFF=DTIME(TIMEARRAYM) IF (LOGIWRITE) THEN WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) WRITE (6,'(T10,A12,T25,F9.3,A5)') + 'total time: ',TIMEDIFF,' sec' WRITE(6,*) WRITE(6,'(T10,7A5)')('-----',ITER=1,7) WRITE(6,*) END IF END ***** end of SRDTIME profnet-1.0.22/src/make.ALPHA0000644015075101507510000000063712021362712015024 0ustar lkajanlkajan#HOME-PATH = /home/rost ARCH = ALPHA EXE = prof.$(ARCH) #===================================================================== LDFLAGS = -O3 -C FFLAGS = -O4 #===================================================================== O= prof.o lib-prof.o lib-sys-$(ARCH).o $(EXE): $O f77 $(FFLAGS) -o $(EXE) ${LDFLAGS} $O prof.o: profPar.f profnet-1.0.22/src/make.LINUX0000644015075101507510000000126512021362710015072 0ustar lkajanlkajanHOME-PATH = /home/rost #===================================================================== EXENAME = prof.$(ARCH) F77 = f77 #F77 = /usr/pub/pgi/linux86/bin/pgf77 CC = cc #LDFLAGS = #===================================================================== #LIB-PROF = lib-prof #LIB-SYS = lib-$(ARCH) #===================================================================== FFLAGS = -O3 -C #LIB-FLAGS = -O3 -c #===================================================================== O= prof.o lib-prof.o lib-sys-$(ARCH).o $(EXENAME): $O $(OLIBS) $(F77) -o $(EXENAME) ${FFLAGS} $O prof.o : profPar.f profnet-1.0.22/src/make.LINUX-pgi0000644015075101507510000000150212021362711015642 0ustar lkajanlkajanHOME-PATH = /home/rost #===================================================================== EXENAME = prof.$(ARCH) #F77 = f77 F77 = /usr/pub/pgi/linux86/bin/pgf77 CC = cc LDFLAGS = #===================================================================== LIB-PROF = lib-prof LIB-SYS = lib-$(ARCH) #===================================================================== OLIBS = $(LIB-PROF).o \ $(LIB-SYS).o #===================================================================== #FFLAGS=-C -g3 FFLAGS = -O3 LIB-FLAGS = -O3 -c #===================================================================== O= prof.f lib-prof.f lib-sys-$(ARCH).f $(EXENAME): $O $(F77) -o $(EXENAME) ${FFLAGS} $O prof.o : profPar.f profnet-1.0.22/src/make.MAC0000644015075101507510000000133212021362710014566 0ustar lkajanlkajanHOME-PATH = /home/rost #===================================================================== EXENAME = prof.$(ARCH) F77 = g77 #F77 = /usr/local/bin/g77 #F77 = /usr/pub/pgi/linux86/bin/pgf77 CC = cc #LDFLAGS = #===================================================================== #LIB-PROF = lib-prof #LIB-SYS = lib-sys-$(ARCH) #===================================================================== FFLAGS = -O3 -C #LIB-FLAGS = -O3 -c #===================================================================== O= prof.o lib-prof.o lib-sys-$(ARCH).o $(EXENAME): $O $(OLIBS) $(F77) -o $(EXENAME) ${FFLAGS} $O prof.o : profPar.f profnet-1.0.22/src/make.MACIBM0000644015075101507510000000140412021362712015120 0ustar lkajanlkajanHOME-PATH = /home/rost #===================================================================== EXENAME = prof.$(ARCH) F77 = /opt/ibmcmp/xlf/8.1/bin/f77 #F77 = g77 #F77 = /usr/local/bin/g77 #F77 = /usr/pub/pgi/linux86/bin/pgf77 CC = cc #LDFLAGS = #===================================================================== #LIB-PROF = lib-prof #LIB-SYS = lib-sys-$(ARCH) #===================================================================== FFLAGS = -O3 -C #LIB-FLAGS = -O3 -c #===================================================================== O= prof.o lib-prof.o lib-sys-$(ARCH).o $(EXENAME): $O $(OLIBS) $(F77) -o $(EXENAME) ${FFLAGS} $O prof.o : profPar.f profnet-1.0.22/src/make.MACINTEL0000644015075101507510000000133312021362710015363 0ustar lkajanlkajanHOME-PATH = /home/rost #===================================================================== EXENAME = prof.$(ARCH) #F77 = g77 F77 = /usr/local/bin/g77 #F77 = /usr/pub/pgi/linux86/bin/pgf77 #CC = cc #LDFLAGS = #===================================================================== #LIB-PROF = lib-prof #LIB-SYS = lib-sys-$(ARCH) #===================================================================== FFLAGS = -O3 -C #LIB-FLAGS = -O3 -c #===================================================================== O= prof.o lib-prof.o lib-sys-$(ARCH).o $(EXENAME): $O $(OLIBS) $(F77) -o $(EXENAME) ${FFLAGS} $O prof.o : profPar.f profnet-1.0.22/src/make.SGI320000644015075101507510000000273112021362712014763 0ustar lkajanlkajan#!/usr/sbin/smake # HOME-PATH = /home/rost #===================================================================== EXENAME = prof.$(ARCH) F77 = f77 CC = cc LDFLAGS = #===================================================================== LIB-PROF = lib-prof LIB-SYS = lib-$(ARCH) #===================================================================== OLIBS = $(LIB-PROF).o \ $(LIB-SYS).o #===================================================================== #FFLAGS=-C -O3 -c -extend_source -nocpp -Olimit=4000 #FFLAGS=-C -g3 -Olimit 2000 #FFLAGS=-C -temp=/usr/tmp/ FFLAGS=-C -O2 -Olimit 4000 LIB-FLAGS = -O2 -c -extend_source -nocpp -Olimit 15000 #===================================================================== O= prof.o lib-prof.o lib-sys-$(ARCH).o $(EXENAME): $O $(OLIBS) $(F77) -o $(EXENAME) ${FFLAGS} $O prof.o : profPar.f lib-$(ARCH).o : profPar.f #======================================================================== # old #libs: $(OLIBS) #$(LIBDIR)/$(LIB-UNIX).o: $(LIBPATH)/$(LIB-UNIX).f # $(F77) $(LIB-FLAGS) $(LIBPATH)/$(LIB-UNIX).f # \mv $(LIB-UNIX).o $(LIBDIR)/$(LIB-UNIX).o # #$(LIBDIR)/$(LIB-COMP).o: $(LIBPATH)/$(LIB-COMP).f # $(F77) $(LIB-FLAGS) $(LIBPATH)/$(LIB-COMP).f # \mv $(LIB-COMP).o $(LIBDIR)/$(LIB-COMP).o # #$(LIBDIR)/$(LIB-PROT).o: $(LIBPATH)/$(LIB-PROT).f # $(F77) $(LIB-FLAGS) $(LIBPATH)/$(LIB-PROT).f # \mv $(LIB-PROT).o $(LIBDIR)/$(LIB-PROT).o profnet-1.0.22/src/make.SGI640000644015075101507510000000167712021362710014776 0ustar lkajanlkajan#!/usr/sbin/smake # #HOME-PATH = /home/rost #===================================================================== ARCH = SGI64 EXENAME = prof.$(ARCH) F77 = f77 #CC = cc #LDFLAGS = #===================================================================== LIB-PROF = lib-prof LIB-SYS = lib-$(ARCH) #===================================================================== OLIBS = $(LIB-PROF).o \ $(LIB-SYS).o #===================================================================== #FFLAGS=-C -O3 -c -extend_source -nocpp #FFLAGS=-C -g3 #FFLAGS=-C -temp=/usr/tmp/ #FFLAGS=-C -O2 FFLAGS = -O3 -C -64 LIB-FLAGS = -O3 -c -64 #===================================================================== O= prof.o lib-prof.o lib-sys-$(ARCH).o $(EXENAME): $O $(OLIBS) $(F77) -o $(EXENAME) ${FFLAGS} $O prof.o : profPar.f lib-$(ARCH).o : profPar.f profnet-1.0.22/src/make.SGI64_no640000644015075101507510000000124412021362711015633 0ustar lkajanlkajan#!/usr/sbin/smake # #HOME-PATH = /home/rost #===================================================================== ARCH = SGI64 EXENAME = prof.$(ARCH) F77 = f77 LDFLAGS = #===================================================================== #FFLAGS=-C -O3 -c -extend_source -nocpp #FFLAGS=-C -g3 #FFLAGS=-C -temp=/usr/tmp/ #FFLAGS=-C -O2 FFLAGS = -O3 -C LIB-FLAGS = -O3 -c #===================================================================== O= prof.o lib-prof.o lib-sys-$(ARCH).o $(EXENAME): $O $(OLIBS) $(F77) $(FFLAGS) -o $(EXENAME) ${LIB-FLAGS} $O nn.o : profPar.f lib-$(ARCH).o : profPar.f profnet-1.0.22/src/prof.f0000755015075101507510000042071312021362711014460 0ustar lkajanlkajan*----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * *----------------------------------------------------------------------* ***** ------------------------------------------------------------------ ***** internal navigation: ***** ***** MAIN PROF ***** -> main program ***** FUNCTIONS fff ***** -> sorted alphabetically ***** SUBROUTINES sss ***** -> sorted alphabetically ***** ***** for further details: Doc-prof.txt ***** ***** ------------------------------------------------------------------ ***** ------------------------------------------------------------------ ***** MAIN PROF ***** ------------------------------------------------------------------ PROGRAM PROF C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER ITER,STPTMP INTEGER FILEN_STRING C REAL TIME0 REAL SECNDS,FRTIME_SECNDS C CHARACTER*80 INTERFILEBANK CHARACTER*456 HC LOGICAL LWRITE,LERR,LBIN ******------------------------------*-----------------------------****** * LWRITE controls whether calls of time and date are written* * into the printer * * SECNDS external function returning seconds elapsed since * * midnight * ******------------------------------*-----------------------------****** C---- ------------------------------------------------------------------ C---- input (getting started) C---- ------------------------------------------------------------------ C---- C---- command line C---- C get number of command line argumentss CALL GET_ARG_NUMBER(NUMARGUMENTS) C too many arguments? IF (NUMARGUMENTS.GT.NUMARG_MAX) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'ERROR: PROF too many cmd line args' STOP END IF C get command line arguments DO ITER=1,NUMARGUMENTS CALL GET_ARGUMENT(ITER,PASSED_ARGC(ITER)) END DO * * C---- C---- general stuff for CPU time C---- C run time TIMEFLAG=.FALSE. C call SRDTIME(LWRITE) from personal lib-syst.f LWRITE=.FALSE. CALL SRDTIME(LWRITE) C call SCFDATE(1,LWRITE) from personal lib-syst.f LWRITE=.FALSE. CALL SCFDATE(1,LWRITE,STARTDATE) C elapsed time: real: seconds since midnight-supplied arg C TIME0=0.0 C TIMESTART=SECNDS(TIME0) C--- commented out 2007_08_22 (BR problem with MAC intel g77) C TIMESTART= FRTIME_SECNDS(TIME0) LERR=.TRUE. LBIN=.TRUE. C---- C---- initialise parameters and read command line C---- CALL INIPROF C---- C---- read files C---- C read parameters IF (LOGI_RDPAR) THEN CALL RDPAR END IF C read input vectors IF (LOGI_RDIN) THEN CALL RDIN END IF C read output vectors IF (LOGI_RDOUT) THEN CALL RDOUT END IF C read succession of training IF (STPSWPMAX.GT.0) THEN CALL RDSAM END IF C read junctions (only if training from tabula rasa) IF (FILEIN_JCT(1:3).NE.'NEW') THEN CALL RDJCT ELSE CALL INIJCT C CALL WRTJCT(10,FILEOUT_JCT(1)) END IF C ini threshold units CALL INITHRUNT C security IF (BITACC.EQ.0) THEN WRITE(6,'(A)')'*** ERROR MAIN BITACC MAY NOT be zero' STOP '*** ERROR MAIN BITACC not set' END IF C---- ------------------------------------------------------------------ C---- network training, or triggering C---- ------------------------------------------------------------------ C---- ------------------------------ C---- network switch only IF (STPSWPMAX.EQ.0) THEN C---- 1st: Lerr, 2nd: Lbin, 3rd: stp IF (LOGI_SWITCH) THEN LERR=.FALSE. LBIN=.FALSE. ELSE LERR=.TRUE. LBIN=.TRUE. END IF CALL NETOUT(LERR,LBIN,1) C---- stp=1 for all CALL WRTOUT(10,FILEOUT_OUT(1),1,1) IF (.NOT.LOGI_SWITCH) THEN CALL WRTJCT(10,FILEOUT_JCT(1)) END IF C---- ------------------------------ C---- training ELSE C------- optimized online training IF (NUMLAYERS.EQ.2) THEN C ********** CALL TRAIN C ********** ELSE WRITE(6,*)'*** TRAINPERC not yet implemented' STOP C ************** C CALL TRAINPERC C ************** END IF END IF C---- ------------------------------------------------------------------ C---- output C---- ------------------------------------------------------------------ * * C---- write results onto printer IF (.NOT.LOGI_SWITCH) THEN IF (STPSWPMAX.EQ.0) STPTMP=1 IF (STPSWPMAX.GT.0) STPTMP=STPINFCNT CALL WRTSCR(STPTMP) CALL WRTERR(10,FILEOUT_ERR,STPTMP) CALL WRTYEAH(10,FILEOUT_YEAH) ELSEIF (LOGI_DEBUG .AND. + FILEOUT_OUT(1)(1:4).NE.'none') THEN WRITE(6,'(A,A)') + '--- PROF finished fine! FILEOUT=', + FILEOUT_OUT(1)(1:FILEN_STRING(FILEOUT_OUT(1))) END IF END ***** end of PROF ***** ------------------------------------------------------------------ ***** FUNCTIONS fff ***** ------------------------------------------------------------------ ***** ------------------------------------------------------------------ ***** FCT TRG1ST ***** ------------------------------------------------------------------ C---- C---- NAME : TRG1ST C---- ARG : x C---- DES : This sigmoid function works as a trigger generating in C---- DES : layer l an output between 0 and 1 from the input (local C---- DES : filed) of the previous layer (l-1). Thus TRG1ST C---- DES : determins the state of the 'neurons' in layer l. C---- DES : C---- DES : The particular choice (any monotonically increasing C---- DES : function that can be differentiated will do) is: C---- DES : TRG1ST (x) = 1./ (1.+exp(-x)) C---- DES : the derivation is given by: C---- DES : f''(x)=f(x)*( 1-f(x) ) ] C---- IN : input parameters are the 'local fields' C---- FROM : C---- *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* REAL FUNCTION TRG1ST (X) IF (X.LT.-50) THEN TRG1ST=0. ELSEIF (X.GT.50) THEN TRG1ST=1. ELSE TRG1ST = 1./ ( 1. + EXP (-X) ) END IF END ***** end of TRG1ST ***** ------------------------------------------------------------------ ***** SUB TRG2ND ***** ------------------------------------------------------------------ C---- C---- NAME : TRG2ND C---- ARG : X C---- DES : see TRG1ST C---- * procedure: *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* REAL FUNCTION TRG2ND (X) IF (X.LT.-50) THEN TRG2ND=0. ELSEIF (X.GT.50) THEN TRG2ND=1. ELSE TRG2ND = 1./ ( 1. + EXP (-X) ) END IF END ***** end of TRG2ND ***** ------------------------------------------------------------------ ***** FCT TRGNORM ***** ------------------------------------------------------------------ C---- C---- NAME : TRGNORM C---- ARG : C---- DES : The normal trigger function f(h(i)) with df/dh(j) C---- DES : =0 is substituted by a function containing the sum C---- DES : over all output fields as a normalization C---- C---- NOTE : f''(h)=f(h)( 1-f(h) ) C---- NOTE : i.e., the same as for TRG1ST, and TRG2ND C---- * procedure: *----------------------------------------------------------------------* * Burkhard Rost Aug, 1998 version 1.0 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: Mar, 1994 version 0.1 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* REAL FUNCTION TRGNORM (X) INCLUDE 'profPar.f' INTEGER ITOUT REAL X,HELPSUM HELPSUM=0. IF (NUMLAYERS.EQ.1) THEN DO ITOUT=1,NUMOUT HELPSUM=EXP(FLD1ST(ITOUT)) END DO ELSE WRITE(6,*)' NUMLAYERS>1 not yet implemented for TRGNORM' STOP END IF TRGNORM=(1./HELPSUM)*EXP(X) END ***** end of TRGNORM ***** ------------------------------------------------------------------ ***** SUBROUTINES sss ***** ------------------------------------------------------------------ ***** ------------------------------------------------------------------ ***** SUB INIPROF ***** ------------------------------------------------------------------ C---- C---- NAME : INIPROF C---- ARG : C---- DES : Parameters (numbers, characters, flags) for executing a C---- DES : particular PROF job are initially assigned. C---- IN : PASSED_ARGC (common) C---- OUT : setting of initial defaults C---- FROM : MAIN C---- CALL2: INIPAR_CON, INIPAR_DEFAULT, INIPAR_ASK C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIPROF C---- include parameter files INCLUDE 'profPar.f' C---- local functions C INTEGER FILEN_STRING C---- local variables INTEGER IT C LOGICAL LTEST,LTESTTRN LOGICAL LHELP,LERROR CHARACTER*456 ARG1,ARG2 ******------------------------------*-----------------------------****** C---- get help? LHELP=.FALSE. LERROR=.FALSE. IF (NUMARGUMENTS.LT.1) THEN LERROR=.TRUE. ELSEIF ((NUMARGUMENTS.EQ.1).AND. + (INDEX(PASSED_ARGC(1),'help').NE.0)) THEN LHELP=.TRUE. END IF IF (LERROR) THEN WRITE(6,'(A,T5,A)')'---','start program with:' WRITE(6,'(A,T5,A)')'---',' exe [help]' WRITE(6,'(A,T5,A)')'---','or: exe fPar' WRITE(6,'(A,T5,A)')'---','or: exe [inter] ' WRITE(6,'(A,T5,A)')'---',' (will bring up dialog)' STOP ELSEIF (LHELP) THEN WRITE(6,'(A,T5,A)')'---','start the program with:' WRITE(6,'(A,T5,A)')'---',' exe [inter] ' WRITE(6,'(A,T5,A)')'---',' (will bring up dialog)' WRITE(6,'(A,T5,A)')'---',' ' WRITE(6,'(A,T5,A)')'---','or: exe filePar ' WRITE(6,'(A,T5,A)')'---',' filePar = file with input'// + ' parameters (also gives fileIn, fileOut)' WRITE(6,'(A,T5,A)')'---',' ' WRITE(6,'(A,T5,A)')'---','or: exe switch AND_following_args' WRITE(6,'(A,T5,A)')'---',' ' WRITE(6,'(A,T5,A)')'---',' 1: "switch"' WRITE(6,'(A,T5,A)')'---',' 2: number of input units' WRITE(6,'(A,T5,A)')'---',' 3: number of hidden units' WRITE(6,'(A,T5,A)')'---',' 4: number of output units' WRITE(6,'(A,T5,A)')'---',' 5: number of samples' WRITE(6,'(A,T5,A)')'---',' 6: bitacc (typically 100)' WRITE(6,'(A,T5,A)')'---',' 7: file with input vectors' WRITE(6,'(A,T5,A)')'---',' 8: file with junctions' WRITE(6,'(A,T5,A)')'---',' 9: file with output of PROF' WRITE(6,'(A,T5,A)')'---',' ="none" -> no file written' WRITE(6,'(A,T5,A)')'---',' 10: optional=dbg' WRITE(6,'(A,T5,A)')'---',' NOTES:' WRITE(6,'(A,T5,A)')'---',' - 1st MUST be "switch"!' WRITE(6,'(A,T5,A)')'---',' - tested only with 2 layers!' WRITE(6,'(A,T5,A)')'---',' ' WRITE(6,'(A,T5,A)')'---','SORRY no further help, yet!' STOP END IF C---- usually untouched constants CALL INIPAR_CON C---- handle the arguments passed to program DO IT=(NUMARGUMENTS+1),NUMARG_MAX PASSED_ARGC(IT)='UNK' END DO C---- -------------------------------------------------- C---- initialising according to input read ARG1=PASSED_ARGC(1) IF (NUMARGUMENTS.GT.1) ARG2=PASSED_ARGC(1) C---- ask for input IF ((ARG1(1:5).EQ.'INTER').OR.(ARG1(1:5).EQ.'inter')) THEN CALL INIPAR_DEFAULT LOGI_INTERACTIVE=.TRUE. CALL INIPAR_ASK C---- ask for input ELSE IF ((ARG1(1:6).EQ.'switch').OR.(ARG1(1:6).EQ.'switch')) THEN CALL INIPAR_DEFAULT LOGI_SWITCH= .TRUE. CALL INIPAR_SWITCH C---- read input from files ELSE FILEIN_PAR= ARG1 LOGI_RDPAR= .TRUE. LOGI_RDIN= .TRUE. LOGI_RDOUT= .TRUE. IF (NUMARGUMENTS.GT.1 .AND. ARG2(1:3).EQ.'dbg') THEN LOGI_DEBUG= .TRUE. END IF END IF C---- end of initialising the main stuff C---- -------------------------------------------------- * * END ***** end of INIPROF ***** ------------------------------------------------------------------ ***** SUB INIPAR_ASK ***** ------------------------------------------------------------------ C---- C---- NAME : INIPAR_ASK C---- ARG : C---- DES : Asking for input parameters C---- DES : C---- IN : C---- FROM : INIPROF C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIPAR_ASK C---- include parameter files INCLUDE 'profPar.f' INTEGER IH(1:2) CHARACTER*456 FILETMP ******------------------------------*-----------------------------****** CALL GETCHAR(80,PATH_ARCH,' path of architectures ? ') CALL GETCHAR(80,FILEIN_PAR,' parameter file? (`i` if interactive') IF ((INDEX(FILEIN_PAR,'i').NE.0) .OR. + (INDEX(FILEIN_PAR,'I').NE.0) ) THEN LOGI_RDPAR= .TRUE. ELSE WRITE(6,*)'*** missing ini.f: ask for parameters' STOP END IF CALL GETCHAR(80,FILETMP,' input file? (`i` if interactive') IF ((FILETMP(1:1).EQ.'i').OR.(FILETMP(1:1).EQ.'I')) THEN LOGI_RDIN= .TRUE. ELSE WRITE(6,*)'*** missing ini.f: ask for input data' STOP END IF CALL GETCHAR(80,FILETMP,' output file? (`i` if interactive') IF ((FILETMP(1:1).EQ.'i').OR.(FILETMP(1:1).EQ.'I')) THEN LOGI_RDOUT= .TRUE. ELSE WRITE(6,*)'*** missing ini.f: ask for parameters' STOP END IF C CALL ASK(' realinput ? ',LOGI_REALINPUT) C IH(1)=INT(MAXQ3*100) C CALL GETINT(1,IH(1),' 100 * MAXQ3 (i.e. for 0.95 give 95) ') IH(1)=STPINF CALL GETINT(1,IH(1),' STPINF ') STPINF=IH(1) IH(1)=STPMAX CALL GETINT(1,IH(1),' STPMAX ') STPMAX=IH(1) IH(1)=STPSWPMAX CALL GETINT(1,IH(1),' STPSWPMAX ') STPSWPMAX=IH(1) IH(1)=INT(EPSILON*100) CALL GETINT(1,IH(1),' 100 * EPSILON ') EPSILON=IH(1)/100. IH(1)=INT(ALPHA*100) CALL GETINT(1,IH(1),' 100 * ALPHA ') ALPHA=IH(1)/100. IH(1)=INT(TEMPERATURE*100) CALL GETINT(1,IH(1),' 100 * TEMPERATURE ') TEMPERATURE=INT(IH(1)/100.) END ***** end of INIPAR_ASK ***** ------------------------------------------------------------------ ***** SUB INIPAR_CON ***** ------------------------------------------------------------------ C---- C---- NAME : INIPAR_CON C---- ARG : C---- DES : Initialising constants that are usually not touched C---- IN : C---- FROM : INIPROF C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIPAR_CON C---- include parameter files INCLUDE 'profPar.f' ******------------------------------*-----------------------------****** C---- -------------------------------------------------- * Various numerical constants C---- number of layers NUMLAYERS= 2 C---- grids ... BITACC= 1 C (if out outbin=0) ERRBINACC= 0.2 C---- end, bias asf. ERRBIAS= 0.0 C ERRBIAS= 0.05 ERRSTOP= 0.005 ERRBINSTOP= 0.95 THRESHOUT= 0.5 DICEITRVL= 0.1 C---- random number generation DICESEED= 100025 DICESEED_ADDJCT= 0 DICESEED_ADDTRN= 0 ABW= 10E-10 C ABW= 0.00001 MAXCPUTIME= 1000000. TIMEOUT= 300. C---- -------------------------------------------------- * Various flags and names C---- modes TRGTYPE= '1/(1+EXP(-X))' TRNTYPE= 'ONLINE' ERRTYPE= 'DELTASQ' C ERRTYPE= 'LN(1-DELTASQ)' C---- temporary output LOGI_TMPWRTOUT= .FALSE. LOGI_TMPWRTJB= .FALSE. C---- LOGI_TRANSLATE(0)=.FALSE. LOGI_TRANSLATE(1)=.TRUE. C---- ------------------------------ C ------------ C alternatives C ------------ C TRGTYPE='EXP(X(I))/SUM(J,EXP(X(J)))' C TRNTYPE='BATCH' C ERRTYPE='LN(1-DELTASQ)' C---- --------------------------------------------------- * * END ***** end of INIPAR_CON ***** ------------------------------------------------------------------ ***** SUB INIPAR_DEFAULT ***** ------------------------------------------------------------------ C---- C---- NAME : INIPAR_DEFAULT C---- ARG : C---- DES : Initialising constants C---- IN : C---- FROM : INIPROF C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIPAR_DEFAULT C---- include parameter files INCLUDE 'profPar.f' C---- local functions C INTEGER FILEN_STRING ******------------------------------*-----------------------------****** C---- -------------------------------------------------- C---- set path for architecture files PATH_ARCH=' ' LENPATH_ARCH= 1 C---- -------------------------------------------------- C---- architecture C---- number of hidden units NUMHID= 15 C---- number of layers (now <= 2) NUMLAYERS= 2 C---- -------------------------------------------------- C---- end, cycles asf C---- cycles and info per cycle C G M T C---- number of steps before write STPINF= 40000 C---- maximal number of steps STPMAX= 200000 C---- maximal number of sweeps C---- STPMAX < NPATTERN*STSWPMAX STPSWPMAX= 200 C---- -------------------------------------------------- C---- speed C---- learning speed EPSILON= 0.05 C---- momentum ALPHA= 0.20 C---- speed reduction TEMPERATURE= 1.00 C---- -------------------------------------------------- C---- flags LOGI_INTERACTIVE= .FALSE. LOGI_SWITCH= .FALSE. LOGI_DEBUG= .FALSE. C input files LOGI_RDPAR= .FALSE. LOGI_RDIN= .FALSE. LOGI_RDOUT= .FALSE. END ***** end of INIPAR_DEFAULT ***** ------------------------------------------------------------------ ***** SUB INIPAR_SWITCH ***** ------------------------------------------------------------------ C---- C---- NAME : INIPAR_SWITCH C---- ARG : C---- DES : switch mode: input to fortran script MUST be: C---- DES : arg 1= "switch" keyword! C---- DES : arg 2= number of input units C---- DES : arg 3= number of hidden units C---- DES : arg 4= number of output units C---- DES : arg 5= number of samples C---- DES : arg 6= bitacc (is typically 100) C---- DES : arg 7= file with input vectors C---- DES : arg 8= file with junctions C---- DES : arg 9= file with output of PROF C---- DES : if = 'none' no output file written C---- DES : arg 10= optional if set: debug mode C---- DES : C---- IN : PASSED_ARGC(it) GLOBAL (profPar.f) C---- FROM : INIPROF C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Dec, 1999 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INIPAR_SWITCH C---- include parameter files INCLUDE 'profPar.f' INTEGER FILEN_STRING INTEGER IT,IH(1:10),CTNUM CHARACTER*456 FILETMP,VARIN CHARACTER*20 CTMP ******------------------------------*-----------------------------****** C---- C---- set defaults for SWITCH mode (1) C---- NUMFILEIN_IN= 1 NUMFILEIN_OUT= 0 NUMFILEOUT_OUT=1 C STPSWPMAX= 0 C LOGI_RDPAR= .FALSE. LOGI_RDIN= .TRUE. LOGI_RDOUT= .FALSE. LOGI_RDINWRT= .FALSE. LOGI_RDJCTWRT= .FALSE. C BITACC= 100 C---- C---- get integers (argument 2-5) C---- DO IT=2,6 CALL SCHAR_TO_INT(PASSED_ARGC(IT),IH(IT)) END DO NUMIN= IH(2) NUMHID=IH(3) NUMOUT=IH(4) NUMSAM=IH(5) BITACC=IH(6) C---- C---- set dependent defaults for SWITCH mode (2) C---- NUMLAYERS= 2 IF (NUMHID.EQ.0) NUMLAYERS=1 C---- C---- get file names C---- CTNUM=6 VARIN= PASSED_ARGC(CTNUM+1) FILEIN_IN(1)= VARIN(1:FILEN_STRING(VARIN)) VARIN= PASSED_ARGC(CTNUM+2) FILEIN_JCT= VARIN(1:FILEN_STRING(VARIN)) VARIN= PASSED_ARGC(CTNUM+3) FILEOUT_OUT(1)= VARIN(1:FILEN_STRING(VARIN)) C---- C---- debug mode? C---- IF (NUMARGUMENTS.GE.(CTNUM+4)) THEN LOGI_DEBUG= .TRUE. END IF C---- ------------------------------------------------------------------ C---- write what we got C---- ------------------------------------------------------------------ IF (LOGI_DEBUG) THEN CTMP=' ' CTMP='--- INIPAR_SWITCH: ' WRITE(6,'(A,T20,A,T35,I8)')CTMP,'NUMIN', NUMIN WRITE(6,'(A,T20,A,T35,I8)')CTMP,'NUMHID', NUMHID WRITE(6,'(A,T20,A,T35,I8)')CTMP,'NUMOUT', NUMOUT WRITE(6,'(A,T20,A,T35,I8)')CTMP,'NUMLAYERS',NUMLAYERS C---- WRITE(6,'(A,T20,A,T35,I8)')CTMP,'NUMSAM', NUMSAM C---- WRITE(6,'(A,T20,A,T35,I8)')CTMP,'NUMFILEIN_IN', NUMFILEIN_IN WRITE(6,'(A,T20,A,T35,I8)')CTMP,'NUMFILEIN_OUT', NUMFILEIN_OUT WRITE(6,'(A,T20,A,T35,I8)')CTMP,'NUMFILEOUT_OUT',NUMFILEOUT_OUT WRITE(6,'(A,T20,A,T35,I8)')CTMP,'NUMFILEOUT_JCT',NUMFILEOUT_JCT C---- DO IT=1,NUMFILEIN_IN WRITE(6,'(A,T20,A,T35,I4,A1,A)')CTMP,'FILEIN_IN',IT,' ', + FILEIN_IN(IT)(1:FILEN_STRING(FILEIN_IN(IT))) END DO WRITE(6,'(A,T20,A,T40,A)')CTMP, + 'FILEIN_JCT',FILEIN_JCT(1:FILEN_STRING(FILEIN_JCT)) DO IT=1,NUMFILEOUT_OUT WRITE(6,'(A,T20,A,T35,I4,A1,A)')CTMP,'FILEOUT_OUT',IT,' ', + FILEOUT_OUT(IT)(1:FILEN_STRING(FILEOUT_OUT(IT))) END DO END IF END ***** end of INIPAR_SWITCH ***** ------------------------------------------------------------------ ***** SUB INITHRUNT ***** ------------------------------------------------------------------ C---- C---- NAME : INITHRUNT C---- ARG : C---- DES : the additional input/hidden units for writing the C---- DES : thresholds/biases as parts of the junctions. C---- IN : NUMSAM,NUMIN,NUMHID/1,NUMSAM C---- OUT : INPUT(NUMIN+1,MUE), C---- OUT : OUTHID(HID+1,MUE),OUTHID1(HID1+1,MUE) C---- FROM : MAIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE INITHRUNT C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER MUE ******------------------------------*-----------------------------****** C---- NUMLAYERS=1 ----- IF (NUMLAYERS.EQ.1) THEN DO MUE=1,NUMSAM INPUT((NUMIN+1),MUE)=INT2(BITACC) END DO C---- NUMLAYERS=2 ----- ELSEIF (NUMLAYERS.EQ.2) THEN DO MUE=1,NUMSAM INPUT((NUMIN+1),MUE)=INT2(BITACC) OUTHID((NUMHID+1))=1. END DO END IF END ***** end of INITHRUNT ***** ------------------------------------------------------------------ ***** SUB RDJCT ***** ------------------------------------------------------------------ C---- C---- NAME : RDJCT C---- ARG : C---- DES : Architecture read from file C---- IN : C---- FROM : MAIN C---- CALL2: RDJCT_HEAD, RDJCT_JCT1, RDJCT_JCT2, RDJCT_WRT C---- LIB : SFILEOPEN C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDJCT C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables * CHARACTER*80 HC,MREAD LOGICAL LDONE,LREAD ******------------------------------*-----------------------------****** C message onto screen C WRITE(6,'(A)')'--- ' IF (.NOT. LOGI_SWITCH .OR. LOGI_DEBUG) THEN WRITE(6,'(A,T16,A)')'--- RDjct file=', + FILEIN_JCT(1:FILEN_STRING(FILEIN_JCT)) END IF C---- C---- read file with junctions C---- CALL SFILEOPEN(10,FILEIN_JCT,'OLD',456,'READONLY') LDONE=.FALSE. DO WHILE (.NOT.LDONE) LREAD=.FALSE. READ(10,'(A9)',END=2057)HC C---- terminate reading IF (HC(1:2).EQ.'//') THEN LDONE=.TRUE. LREAD=.FALSE. ELSEIF (HC(1:9).EQ.'* overall') THEN LREAD=.FALSE. MREAD='H' ELSEIF (HC(1:9).EQ.'* jct 1st') THEN LREAD=.FALSE. MREAD='1' ELSEIF (HC(1:9).EQ.'* jct 2nd') THEN LREAD=.FALSE. MREAD='2' ELSEIF (HC(1:1).NE.'*') THEN BACKSPACE 10 LREAD=.TRUE. ELSE LREAD=.FALSE. END IF C---- C header (numin,numsam,numsamfile) C---- IF (LREAD.AND.(MREAD.EQ.'H')) THEN CALL RDJCT_HEAD ELSEIF (LREAD.AND.(MREAD.EQ.'1')) THEN CALL RDJCT_JCT1 ELSEIF (LREAD.AND.(MREAD.EQ.'2')) THEN CALL RDJCT_JCT2 ELSEIF (LREAD) THEN WRITE(6,'(A,T10,A,A,A)')'***', + 'ERROR RDJCT MREAD not recognised:',MREAD,':' STOP '*** RDJCT: left due to error in reading inJct' END IF END DO 2057 CONTINUE CLOSE(10) C---- C header (numin,numsam,numsamfile) C---- C control write IF (LOGI_RDJCTWRT) THEN CALL RDJCT_WRT END IF END ***** end of RDJCT ***** ------------------------------------------------------------------ ***** SUB RDJCT_HEAD ***** ------------------------------------------------------------------ C---- C---- NAME : RDJCT_HEAD C---- ARG : C---- DES : reading and checking header of file with input vec C---- IN : C---- FROM : RDJCT C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDJCT_HEAD C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER VARIN,IT,NUMINLOC,NUMHIDLOC,NUMOUTLOC CHARACTER*80 HC,VARINC,MODEPREDLOC,MODENETLOC,MODEJOBLOC, + MODEINLOC,MODEOUTLOC LOGICAL LERROR ******------------------------------*-----------------------------****** LERROR=.FALSE. C---- C---- loop over 3 INTEGERS: NUMIN, NUMHID, NUMOUT C---- DO IT=1,3 READ(10,'(A20,T25,I8)')HC,VARIN IF (HC(1:5).EQ.'NUMIN') THEN NUMINLOC=VARIN ELSEIF (HC(1:6).EQ.'NUMHID') THEN NUMHIDLOC=VARIN ELSEIF (HC(1:6).EQ.'NUMOUT') THEN NUMOUTLOC=VARIN ELSE WRITE(6,'(T2,A,T10,A,A,A)')'***', + 'ERROR RDJCT_HEAD I HC not recognised:',HC,':' LERROR=.TRUE. END IF END DO C---- C---- loop over modes: MODEPRED, MODENET, MODEJOB, MODEIN, C---- DO IT=1,5 READ(10,'(A20,T25,A)')HC,VARINC IF (INDEX(HC,'MODEPRED').NE.0) THEN MODEPREDLOC=VARINC(1:FILEN_STRING(VARINC)) ELSEIF (INDEX(HC,'MODENET') .NE.0) THEN MODENETLOC=VARINC(1:FILEN_STRING(VARINC)) ELSEIF (INDEX(HC,'MODEJOB') .NE.0) THEN MODEJOBLOC=VARINC(1:FILEN_STRING(VARINC)) ELSEIF (INDEX(HC,'MODEIN') .NE.0) THEN MODEINLOC=VARINC(1:FILEN_STRING(VARINC)) ELSEIF (INDEX(HC,'MODEOUT') .NE.0) THEN MODEOUTLOC=VARINC(1:FILEN_STRING(VARINC)) ELSE WRITE(6,'(T2,A,T10,A,A,A)')'***', + 'ERROR RDJCT_HEAD A HC not recognised:',HC,':' LERROR=.TRUE. END IF END DO C---- C---- error check (consistency with file.para) C---- CALL RDJCT_CHECK(NUMINLOC,NUMHIDLOC,NUMOUTLOC, + MODEPREDLOC,MODENETLOC,MODEJOBLOC,MODEINLOC,MODEOUTLOC) C---- C error -> back C---- IF (LERROR) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'RDJCT_HEAD: reading header of input vectors' STOP '*** RDJCT_HEAD: left due to error in reading inJct' END IF END ***** end of RDJCT_HEAD ***** ------------------------------------------------------------------ ***** SUB RDJCT_JCT1 ***** ------------------------------------------------------------------ C---- C---- NAME : RDJCT_JCT1 C---- ARG : C---- DES : reading and checking JCT1 of architecture C---- IN : C---- FROM : RDJCT C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDJCT_JCT1 C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER ITHID,ITIN ******------------------------------*-----------------------------****** DO ITHID=1,NUMHID C---- WRITE(6,'(I4,A,I4,A,I4)')ITHID,' OF ',NUMHID,' 1:',(NUMIN+1) READ(10,'(10F10.4)') + (JCT1ST(ITIN,ITHID),ITIN=1,(NUMIN+1)) END DO END ***** end of RDJCT_JCT1 ***** ------------------------------------------------------------------ ***** SUB RDJCT_JCT2 ***** ------------------------------------------------------------------ C---- C---- NAME : RDJCT_JCT2 C---- ARG : C---- DES : reading and checking JCT2 of architecture C---- IN : C---- FROM : RDJCT C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDJCT_JCT2 C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER ITHID,ITOUT ******------------------------------*-----------------------------****** DO ITHID=1,(NUMHID+1) READ(10,'(10F10.4)')(JCT2ND(ITHID,ITOUT),ITOUT=1,NUMOUT) END DO END ***** end of RDJCT_JCT2 ***** ------------------------------------------------------------------ ***** SUB RDJCT_CHECK ***** ------------------------------------------------------------------ C---- C---- NAME : RDJCT_CHECK C---- ARG : C---- DES : compares parameters read from JCT and PAR C---- IN : C---- FROM : RDJCT_HEAD C---- *----------------------------------------------------------------------* * Burkhard Rost Oct, 1998 version 1.0 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: Oct, 1998 version 0.1 * *----------------------------------------------------------------------* SUBROUTINE RDJCT_CHECK(NUMINLOC,NUMHIDLOC,NUMOUTLOC, + MODEPREDLOC,MODENETLOC,MODEJOBLOC,MODEINLOC,MODEOUTLOC) C---- include parameter files INCLUDE 'profPar.f' C---- variables passed INTEGER NUMINLOC,NUMHIDLOC,NUMOUTLOC CHARACTER*80 MODEPREDLOC,MODENETLOC,MODEJOBLOC, + MODEINLOC,MODEOUTLOC C---- local variables * LOGICAL LERROR,LWARN ******------------------------------*-----------------------------****** LERROR= .FALSE. LWARN= .FALSE. C---- C---- archictecture (NUMIN,NUMHID,NUMOUT) C---- IF (NUMINLOC.NE.NUMIN) THEN WRITE(6,'(T2,A,T10,A,I6,A,I6)')'***', + 'ERROR RDJCT_CHECK: NUMIN para=', + NUMIN,' file_jct=',NUMINLOC LERROR=.TRUE. END IF IF (NUMHIDLOC.NE.NUMHID) THEN WRITE(6,'(T2,A,T10,A,I6,A,I6)')'***', + 'ERROR RDJCT_CHECK: NUMHID para=', + NUMHID,' file_jct=',NUMHIDLOC LERROR=.TRUE. END IF IF (NUMOUTLOC.NE.NUMOUT) THEN WRITE(6,'(T2,A,T10,A,I6,A,I6)')'***', + 'ERROR RDJCT_CHECK: NUMOUT para=', + NUMOUT,' file_jct=',NUMOUTLOC LERROR=.TRUE. END IF C---- C---- modes C---- IF (LOGI_SWITCH.EQV..FALSE.) THEN IF (MODEPREDLOC.NE.MODEPRED) THEN WRITE(6,'(T2,A,T10,A,A,A,A)')'***', + 'ERROR RDJCT_CHECK: MODEPRED para=', + MODEPRED,' file_jct=',MODEPREDLOC LERROR=.TRUE. END IF IF (MODENETLOC .NE.MODENET) THEN WRITE(6,'(T2,A,T10,A,A,A,A)')'***', + 'ERROR RDJCT_CHECK: MODENET para=', + MODENET,' file_jct=',MODENETLOC LERROR=.TRUE. END IF IF (MODEJOBLOC .NE.MODEJOB) THEN WRITE(6,'(T2,A,T10,A,A,A,A)')'***', + 'ERROR RDJCT_CHECK: MODEJOB para=', + MODEJOB,' file_jct=',MODEJOBLOC LERROR=.TRUE. END IF IF (MODEINLOC .NE.MODEIN) THEN WRITE(6,'(T2,A,T10,A,A,A,A)')'***', + 'ERROR RDJCT_CHECK: MODEIN para=', + MODEIN,' file_jct=',MODEINLOC LERROR=.TRUE. END IF IF (MODEOUTLOC .NE.MODEOUT) THEN WRITE(6,'(T2,A,T10,A,A,A,A)')'***', + 'ERROR RDJCT_CHECK: MODEOUT para=', + MODEOUT,' file_jct=',MODEOUTLOC LERROR=.TRUE. END IF END IF C---- C error -> back C---- IF (LERROR) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'RDJCT_CHECK: reading header of input vectors' STOP '*** RDJCT_HEAD: left due to error in reading inJct' END IF END ***** end of RDJCT_CHECK ***** ------------------------------------------------------------------ ***** SUB RDJCT_WRT ***** ------------------------------------------------------------------ C---- C---- NAME : RDJCT_WRT C---- ARG : C---- DES : writes the architecture read C---- IN : C---- FROM : RDJCT C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDJCT_WRT C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER ITIN,ITHID,ITOUT,KUNIT CHARACTER*80 CTMP,CTMP2 ******------------------------------*-----------------------------****** C---- C WRITE(6,'(A)')'--- ' KUNIT=6 CTMP='--- RDjct: ' CTMP2='--------------------------------------------------' WRITE(KUNIT,'(A,T16,A50)')CTMP,CTMP2 WRITE(KUNIT,'(A,T16,A)')CTMP,'Architecture vectors read:' C---- C---- 1st layer C---- WRITE(KUNIT,'(A,T16,A)')CTMP,' ' WRITE(KUNIT,'(A,T16,A,I8)')CTMP,'JCT1: col=1..NUMHID =',NUMHID WRITE(KUNIT,'(A,T16,A,I8)')CTMP,'JCT1: row=1..NUMIN+ =',(NUMIN+1) DO ITHID=1,NUMHID WRITE(KUNIT,'(10F10.4)')(JCT1ST(ITIN,ITHID),ITIN=1,(NUMIN+1)) END DO C---- C---- 2nd layer C---- WRITE(KUNIT,'(A,T16,A)')CTMP,' ' WRITE(KUNIT,'(A,T16,A,I8)')CTMP,'JCT2: col=1..NUMHID+=',(NUMHID+1) WRITE(KUNIT,'(A,T16,A,I8)')CTMP,'JCT2: row=1..NUMHID =',NUMOUT DO ITHID=1,(NUMHID+1) WRITE(KUNIT,'(10F10.4)')(JCT2ND(ITHID,ITOUT),ITOUT=1,NUMOUT) END DO WRITE(KUNIT,'(A,T16,A,T35)')CTMP,'end of reading architecture' IF (KUNIT.NE.6) THEN CLOSE(KUNIT) END IF END ***** end of RDJCT_WRT ***** ------------------------------------------------------------------ ***** SUB RDIN ***** ------------------------------------------------------------------ C---- C---- NAME : RDIN C---- ARG : C---- DES : Reads the protein input from file C---- IN : C---- FROM : MAIN C---- CALL2: RDIN_HEAD, RDIN_DATA, RDIN_WRT C---- LIB : SFILEOPEN C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDIN C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER ITFILE,CNTTOT,CNTRD,NUMINLOC,NUMSAMLOC CHARACTER*80 HC,MREAD LOGICAL LDONE,LREAD ******------------------------------*-----------------------------****** C message onto screen C WRITE(6,'(A)')'--- ' CNTTOT=0 C---- C---- loop over input files C---- DO ITFILE=1,NUMFILEIN_IN C message onto screen IF (.NOT. LOGI_SWITCH .OR. LOGI_DEBUG) THEN C WRITE(6,'(A,T16,A)')'--- RDin file=', C + FILEIN_IN(ITFILE)(1:FILEN_STRING(FILEIN_IN(ITFILE))) WRITE(6,'(A,T16,A)')'--- RDin', + FILEIN_IN(ITFILE)(1:FILEN_STRING(FILEIN_IN(ITFILE))) END IF C read CALL SFILEOPEN(10,FILEIN_IN(ITFILE),'OLD',456,'READONLY') LDONE=.FALSE. DO WHILE (.NOT.LDONE) LREAD=.FALSE. READ(10,'(A9)',END=4057)HC C terminate reading IF (HC(1:2).EQ.'//') THEN LDONE=.TRUE. LREAD=.FALSE. ELSEIF (HC(1:9).EQ.'* overall') THEN LREAD=.FALSE. MREAD='H' ELSEIF (HC(1:9).EQ.'* samples') THEN LREAD=.FALSE. MREAD='D' ELSEIF (HC(1:1).NE.'*') THEN BACKSPACE 10 LREAD=.TRUE. ELSE LREAD=.FALSE. END IF C---- C header (numin,numsam,numsamfile) C---- IF (LREAD.AND.(MREAD.EQ.'H')) THEN CALL RDIN_HEAD(NUMINLOC,NUMSAMLOC) ELSEIF (LREAD.AND.(MREAD.EQ.'D')) THEN CALL RDIN_DATA(CNTRD,NUMINLOC) CNTTOT=CNTTOT+CNTRD IF (CNTTOT.GT.NUMSAM) THEN WRITE(6,'(A,T10,A,A,I8,A,I8)')'***','ERROR RDIN ', + ' NUMSAM=',NUMSAM,' already CNTTOT=',CNTTOT STOP '*** RDIN: left due to error in reading inIn' END IF ELSEIF (LREAD) THEN WRITE(6,'(A,T10,A,A,A)')'***', + 'ERROR RDIN MREAD not recognised:',MREAD,':' STOP '*** RDIN: left due to error in reading inIn' END IF END DO 4057 CONTINUE CLOSE(10) END DO C end of loop over input files C---- ------------------------------ C---- C number of samples ok? C---- IF (CNTTOT.NE.NUMSAM) THEN WRITE(6,'(A,T10,A,I6,A,I6)')'***', + 'ERROR RDin: NUMSAM (from para)=',NUMSAM, + ' NUMSAM read (from filein)=',CNTTOT STOP '*** RDIN: left due to error in read inIn' END IF C---- C control write C---- IF (LOGI_RDINWRT) THEN CALL RDIN_WRT END IF END ***** end of RDIN ***** ------------------------------------------------------------------ ***** SUB RDIN_HEAD(NUMINLOC,NUMSAMLOC) ***** ------------------------------------------------------------------ C---- C---- NAME : RDIN_HEAD(NUMINLOC,NUMSAMLOC) C---- ARG : C---- DES : reading and checking header of file with input vec C---- IN : C---- FROM : RDIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDIN_HEAD(NUMINLOC,NUMSAMLOC) C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER VARIN,NUMINLOC,NUMSAMLOC,IT CHARACTER*80 HC LOGICAL LERROR ******------------------------------*-----------------------------****** LERROR=.FALSE. C loop over 3 variables DO IT=1,2 READ(10,'(A20,T25,I8)')HC,VARIN IF (HC(1:5) .EQ.'NUMIN') THEN NUMINLOC=VARIN ELSEIF (HC(1:10).EQ.'NUMSAMFILE') THEN NUMSAMFILE=VARIN ELSE WRITE(6,'(A,T10,A,A,A)')'***', + 'ERROR RDIN_HEAD HC not recognised:',HC,':' LERROR=.TRUE. END IF END DO C---- C---- check C---- IF (NUMIN.NE.NUMINLOC) THEN WRITE(6,'(A,T10,A,A,I8,A,I8)')'***','ERROR RDIN_HEAD ', + ' NUMIN=',NUMIN,' NUMINLOC=',NUMINLOC LERROR=.TRUE. END IF C IF (NUMSAM.NE.NUMSAMLOC) THEN C WRITE(6,'(A,T10,A,A,I8,A,I8)')'***','ERROR RDIN_HEAD ', C + ' NUMSAM=',NUMSAM,' NUMSAMLOC=',NUMSAMLOC C LERROR=.TRUE. C END IF IF (LERROR) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'RDIN_HEAD: reading header of input vectors' STOP '*** RDIN_HEAD: left due to error in reading inIn' END IF END ***** end of RDIN_HEAD ***** ------------------------------------------------------------------ ***** SUB RDIN_DATA(CNTRD,NUMINLOC) ***** ------------------------------------------------------------------ C---- C---- NAME : RDIN_DATA(CNTRD,NUMINLOC) C---- ARG : C---- DES : reading and checking DATA of file with input vec C---- IN : C---- FROM : RDIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDIN_DATA(CNTRD,NUMINLOC) C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER ITSAMRD,ITSAM,ITIN,CNTRD,NUMINLOC CHARACTER*80 HC ******------------------------------*-----------------------------****** CNTRD=0 C---- loop over all samples in local file DO ITSAM=1,NUMSAMFILE READ(10,'(A8,I8)')HC,ITSAMRD READ(10,'(25I6)')(INPUT(ITIN,ITSAMRD),ITIN=1,NUMINLOC) CNTRD=CNTRD+1 END DO END ***** end of RDIN_DATA ***** ------------------------------------------------------------------ ***** SUB RDIN_WRT ***** ------------------------------------------------------------------ C---- C---- NAME : RDIN_WRT C---- ARG : C---- DES : writes the input vectors read C---- IN : C---- FROM : RDIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDIN_WRT C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER ITSAM,ITIN CHARACTER*80 CTMP,CTMP2 ******------------------------------*-----------------------------****** C---- C WRITE(6,'(A)')'--- ' CTMP='--- RDin: ' CTMP2='--------------------------------------------------' WRITE(6,'(A,T16,A50)')CTMP,CTMP2 WRITE(6,'(A,T16,A)')CTMP,'Input vectors read:' C---- C---- integers C---- WRITE(6,'(A,T16,A)')CTMP,' ' WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMIN',NUMIN WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMSAM',NUMSAM C---- C---- vectors C---- WRITE(6,'(A,T16,A)')CTMP,' ' DO ITSAM=1,NUMSAM WRITE(6,'(A,T16,A10,I6,A3)')CTMP,'ITSAM=',ITSAM,' : ' WRITE(6,'(25I4)')(INPUT(ITIN,ITSAM),ITIN=1,NUMIN) END DO WRITE(6,'(A,T16,A,T35)')CTMP,'end of reading input vectors' END ***** end of RDIN_WRT ***** ------------------------------------------------------------------ ***** SUB RDOUT ***** ------------------------------------------------------------------ C---- C---- NAME : RDOUT C---- ARG : C---- DES : Reads the protein input from file C---- IN : C---- FROM : MAIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDOUT C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables * INTEGER ITFILE,CNTTOT,CNTRD Cxx INTEGER COUNT_CLASS(1:10),ITOUT,ITSAM Cxx CHARACTER*80 HC,MREAD LOGICAL LDONE,LREAD ******------------------------------*-----------------------------****** C message onto screen C WRITE(6,'(A)')'--- ' CNTTOT=0 C---- C---- loop over input files C---- DO ITFILE=1,NUMFILEIN_OUT C message onto screen C WRITE(6,'(A,T16,A)')'--- RDout file=', C + FILEIN_OUT(ITFILE)(1:FILEN_STRING(FILEIN_OUT(ITFILE))) WRITE(6,'(A,T16,A)')'--- RDout', + FILEIN_OUT(ITFILE)(1:FILEN_STRING(FILEIN_OUT(ITFILE))) C read CALL SFILEOPEN(10,FILEIN_OUT(ITFILE),'OLD',456,'READONLY') LDONE=.FALSE. DO WHILE (.NOT.LDONE) LREAD=.FALSE. READ(10,'(A9)',END=3057)HC C terminate reading IF (HC(1:2).EQ.'//') THEN LDONE=.TRUE. LREAD=.FALSE. ELSEIF (HC(1:9).EQ.'* overall') THEN LREAD=.FALSE. MREAD='H' ELSEIF (HC(1:9).EQ.'* samples') THEN LREAD=.FALSE. MREAD='D' ELSEIF (HC(1:1).NE.'*') THEN BACKSPACE 10 LREAD=.TRUE. ELSE LREAD=.FALSE. END IF C---- C header (numin,numsam,numsamfile) C---- IF (LREAD.AND.(MREAD.EQ.'H')) THEN CALL RDOUT_HEAD ELSEIF (LREAD.AND.(MREAD.EQ.'D')) THEN CALL RDOUT_DATA(CNTRD) CNTTOT=CNTTOT+CNTRD IF (CNTTOT.GT.NUMSAM) THEN WRITE(6,'(A,T10,A,A,I8,A,I8)')'***','ERROR RDOUT ', + ' NUMSAM=',NUMSAM,' already CNTTOT=',CNTTOT STOP '*** RDOUT: left due to error in reading inOut' END IF ELSEIF (LREAD) THEN WRITE(6,'(A,T10,A,A,A)')'***', + 'ERROR RDOUT MREAD not recognised:',MREAD,':' STOP '*** RDOUT: left due to error in reading inOut' END IF END DO 3057 CONTINUE CLOSE(10) END DO C end of loop over input files C---- ------------------------------ C---- write stat DO ITOUT=1,NUMOUT COUNT_CLASS(ITOUT)=0 END DO DO ITSAM=1,NUMSAM DO ITOUT=1,NUMOUT IF (OUTDES(ITOUT,ITSAM).GT.0) THEN COUNT_CLASS(ITOUT)=COUNT_CLASS(ITOUT)+1 END IF END DO END DO IF (.FALSE.) THEN WRITE(6,*)'xx stat on class' DO ITOUT=1,NUMOUT WRITE(6,'(A,I8,A,F6.1,A,I8)') + 'xx stat i=',ITOUT, + ' perc=',(100*COUNT_CLASS(ITOUT))/REAL(NUMSAM), + ' num=', COUNT_CLASS(ITOUT) END DO END IF C control write IF (LOGI_RDOUTWRT) THEN CALL RDOUT_WRT END IF END ***** end of RDOUT ***** ------------------------------------------------------------------ ***** SUB RDOUT_HEAD ***** ------------------------------------------------------------------ C---- C---- NAME : RDOUT_HEAD C---- ARG : C---- DES : reading and checking header of file with input vec C---- IN : C---- FROM : RDOUT C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDOUT_HEAD C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER VARIN,NUMOUTLOC,NUMSAMLOC,IT CHARACTER*80 HC LOGICAL LERROR ******------------------------------*-----------------------------****** LERROR=.FALSE. C loop over 3 variables DO IT=1,2 READ(10,'(A20,T25,I8)')HC,VARIN IF (HC(1:6) .EQ.'NUMOUT') THEN NUMOUTLOC=VARIN ELSEIF (HC(1:10).EQ.'NUMSAMFILE') THEN NUMSAMFILE=VARIN ELSE WRITE(6,'(T2,A,T10,A,A,A)')'***', + 'ERROR RDOUT_HEAD HC not recognised:',HC,':' LERROR=.TRUE. END IF END DO C---- C---- check DATA read C---- IF (NUMOUT.NE.NUMOUTLOC) THEN WRITE(6,'(A,T10,A,A,I8,A,I8)')'***','ERROR RDOUT_HEAD ', + ' NUMOUT=',NUMOUT,' NUMOUTLOC=',NUMOUTLOC LERROR=.TRUE. END IF C IF (NUMSAM.NE.NUMSAMLOC) THEN C WRITE(6,'(A,T10,A,A,I8,A,I8)')'***','ERROR RDOUT_HEAD ', C + ' NUMSAM=',NUMSAM,' NUMSAMLOC=',NUMSAMLOC C LERROR=.TRUE. C END IF IF (LERROR) THEN WRITE(6,'(T2,A,T10,A)')'***', + 'RDOUT_HEAD: reading header of input vectors' STOP '*** RDOUT_HEAD: left due to error in reading inIn' END IF END ***** end of RDOUT_HEAD ***** ------------------------------------------------------------------ ***** SUB RDOUT_DATA(CNTRD) ***** ------------------------------------------------------------------ C---- C---- NAME : RDOUT_DATA(CNTRD) C---- ARG : C---- DES : reading and checking DATA of file with input vec C---- IN : C---- FROM : RDOUT C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDOUT_DATA(CNTRD) C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER ITSAMRD,ITSAM,ITOUT,CNTRD CHARACTER*80 HC ******------------------------------*-----------------------------****** CNTRD=0 C---- loop over all samples in local file DO ITSAM=1,NUMSAMFILE READ(10,'(I8,A1,25I6)')ITSAMRD,HC, + (OUTDES(ITOUT,ITSAMRD),ITOUT=1,NUMOUT) CNTRD=CNTRD+1 END DO END ***** end of RDOUT_DATA ***** ------------------------------------------------------------------ ***** SUB RDOUT_WRT ***** ------------------------------------------------------------------ C---- C---- NAME : RDOUT_WRT C---- ARG : C---- DES : writes the input vectors read C---- IN : C---- FROM : RDOUT C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDOUT_WRT C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER ITSAM,ITOUT CHARACTER*80 CTMP,CTMP2 ******------------------------------*-----------------------------****** C---- C WRITE(6,'(A)')'--- ' CTMP='--- RDout: ' CTMP2='--------------------------------------------------' WRITE(6,'(A,T16,A50)')CTMP,CTMP2 WRITE(6,'(A,T16,A)')CTMP,'Output vectors read:' C---- C---- integers C---- WRITE(6,'(A,T16,A)')CTMP,' ' WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMOUT',NUMOUT WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMSAM',NUMSAM C---- C---- vectors C---- WRITE(6,'(A,T16,A)')CTMP,' ' DO ITSAM=1,NUMSAM WRITE(6,'(A,T16,I8,A3,25I4)')CTMP,ITSAM,' : ', + (OUTDES(ITOUT,ITSAM),ITOUT=1,NUMOUT) END DO WRITE(6,'(A,T16,A,T35)')CTMP,'end of reading output vectors' END ***** end of RDOUT_WRT ***** ------------------------------------------------------------------ ***** SUB RDPAR ***** ------------------------------------------------------------------ C---- C---- NAME : RDPAR C---- ARG : C---- DES : Reads the architecture specifica parameters from C---- DES : perl (profWrt.pl) generated file C---- IN : C---- FROM : MAIN C---- CALL2: RDPAR_WRT, RDPAR_I,_F,_A C---- LIB : SFILEOPEN C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDPAR C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables CHARACTER*456 HC,MREAD LOGICAL LDONE,LREAD ******------------------------------*-----------------------------****** C message onto screen C WRITE(6,'(A)')'--- ' WRITE(6,'(A,T16,A)')'--- RDpar file=', + FILEIN_PAR(1:FILEN_STRING(FILEIN_PAR)) C---- read parameters from file PROF_InPar CALL SFILEOPEN(10,FILEIN_PAR,'OLD',456,'READONLY') LDONE=.FALSE. DO WHILE (.NOT.LDONE) LREAD=.FALSE. C>>>>>>> GOTO END READ(10,'(A3)',END=15047)HC C------- terminate reading IF (HC(1:2).EQ.'//') THEN LDONE=.TRUE. LREAD=.FALSE. ELSEIF (HC(1:3).EQ.'* I') THEN LREAD=.FALSE. MREAD='I' ELSEIF (HC(1:3).EQ.'* F') THEN LREAD=.FALSE. MREAD='F' ELSEIF (HC(1:3).EQ.'* A') THEN LREAD=.FALSE. MREAD='A' ELSEIF (HC(1:1).NE.'*') THEN BACKSPACE 10 LREAD=.TRUE. ELSE LREAD=.FALSE. END IF IF (LREAD) THEN IF (MREAD.EQ.'I') THEN CALL RDPAR_I ELSEIF (MREAD.EQ.'F') THEN CALL RDPAR_F ELSEIF (MREAD.EQ.'A') THEN CALL RDPAR_A ELSE WRITE(6,'(A,T10,A,A,A)')'***', + 'ERROR RDPAR MREAD not recognised:',MREAD,':' STOP '*** RDPAR: left due to error in reading inPar' END IF END IF END DO 15047 CONTINUE CLOSE(10) * * C---- control write IF (LOGI_RDPARWRT) THEN CALL RDPAR_WRT END IF END ***** end of RDPAR ***** ------------------------------------------------------------------ ***** SUB RDPAR_I ***** ------------------------------------------------------------------ C---- C---- NAME : RDPAR_I C---- ARG : C---- DES : reading and interpreting one line with I8 input C---- IN : C---- FROM : C---- CALL2: RDPAR C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDPAR_I C---- include parameter files INCLUDE 'profPar.f' C---- local variables INTEGER VARIN CHARACTER*80 HC CHARACTER*456 CHAR_RD ******------------------------------*-----------------------------****** C---- read READ(10,'(A20,T25,I8)')HC,VARIN C---- ------------------------------ C---- interpret IF (HC(1:5) .EQ.'NUMIN') THEN NUMIN=VARIN CALL RDPAR_ERR('NUMIN ',VARIN) ELSEIF (HC(1:6) .EQ.'NUMHID') THEN NUMHID=VARIN CALL RDPAR_ERR('NUMHID ',VARIN) ELSEIF (HC(1:6) .EQ.'NUMOUT') THEN NUMOUT=VARIN CALL RDPAR_ERR('NUMOUT ',VARIN) ELSEIF (HC(1:9) .EQ.'NUMLAYERS') THEN NUMLAYERS=VARIN ELSEIF (HC(1:6) .EQ.'NUMSAM') THEN NUMSAM=VARIN CALL RDPAR_ERR('NUMSAM ',VARIN) C---- C---- number of files C---- ELSEIF (HC(1:12).EQ.'NUMFILEIN_IN') THEN NUMFILEIN_IN=VARIN CALL RDPAR_ERR(HC // ' ',VARIN) ELSEIF (HC(1:13).EQ.'NUMFILEIN_OUT') THEN NUMFILEIN_OUT=VARIN CALL RDPAR_ERR(HC // ' ',VARIN) ELSEIF (HC(1:14).EQ.'NUMFILEOUT_OUT') THEN NUMFILEOUT_OUT=VARIN CALL RDPAR_ERR(HC // ' ',VARIN) ELSEIF (HC(1:14).EQ.'NUMFILEOUT_JCT') THEN NUMFILEOUT_JCT=VARIN CALL RDPAR_ERR(HC // ' ',VARIN) C---- C---- training times C---- ELSEIF (HC(1:9) .EQ.'STPSWPMAX') THEN STPSWPMAX=VARIN CALL RDPAR_ERR('STPSWPMAX ',VARIN) ELSEIF (HC(1:6) .EQ.'STPMAX') THEN STPMAX=VARIN CALL RDPAR_ERR('STPMAX ',VARIN) ELSEIF (HC(1:6) .EQ.'STPINF') THEN STPINF=VARIN CALL RDPAR_ERR('STPINF ',VARIN) ELSEIF (HC(1:6) .EQ.'BITACC') THEN BITACC=VARIN ELSEIF (HC(1:10).EQ.'ERRBINSTOP') THEN ERRBINSTOP=VARIN C---- C---- miscellaneous C---- ELSEIF (HC(1:8) .EQ.'DICESEED') THEN DICESEED=VARIN ELSEIF (HC(1:15).EQ.'DICESEED_ADDJCT') THEN DICESEED_ADDJCT=VARIN ELSEIF (HC(1:15).EQ.'DICESEED_ADDTRN') THEN DICESEED_ADDTRN=VARIN C---- C---- logicals C---- ELSEIF (HC(1:13) .EQ.'LOGI_RDPARWRT') THEN LOGI_RDPARWRT=LOGI_TRANSLATE(VARIN) ELSEIF (HC(1:13) .EQ.'LOGI_RDINWRT') THEN LOGI_RDINWRT=LOGI_TRANSLATE(VARIN) ELSEIF (HC(1:13) .EQ.'LOGI_RDOUTWRT') THEN LOGI_RDOUTWRT=LOGI_TRANSLATE(VARIN) ELSEIF (HC(1:13) .EQ.'LOGI_RDJCTWRT') THEN LOGI_RDJCTWRT=LOGI_TRANSLATE(VARIN) C---- C---- unrecognised C---- ELSE WRITE(6,'(A,T10,A,A,I8)')'***', + 'RDPAR_I: no interpretation of',HC,VARIN STOP '*** RDPAR_I: left due to error in reading inPar' END IF END ***** end of RDPAR_I ***** ------------------------------------------------------------------ ***** SUB RDPAR_F ***** ------------------------------------------------------------------ C---- C---- NAME : RDPAR_F C---- ARG : C---- DES : reading and interpreting one line with F12.3 input C---- IN : C---- FROM : C---- CALL2: RDPAR C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * *----------------------------------------------------------------------* SUBROUTINE RDPAR_F C---- include parameter files INCLUDE 'profPar.f' C---- local variables REAL VARIN CHARACTER*80 HC ******------------------------------*-----------------------------****** C---- read READ(10,'(A20,T25,F15.6)')HC,VARIN C---- ------------------------------ C---- interpret IF (HC(1:7) .EQ.'EPSILON') THEN EPSILON=VARIN ELSEIF (HC(1:5) .EQ.'ALPHA') THEN ALPHA=VARIN ELSEIF (HC(1:11).EQ.'TEMPERATURE') THEN TEMPERATURE=VARIN C---- ELSEIF (HC(1:7) .EQ.'ERRSTOP') THEN ERRSTOP=VARIN ELSEIF (HC(1:7) .EQ.'ERRBIAS') THEN ERRBIAS=VARIN ELSEIF (HC(1:10).EQ.'ERRBINACC') THEN ERRBINACC=VARIN C---- ELSEIF (HC(1:10).EQ.'THRESHOUT') THEN THRESHOUT=VARIN ELSEIF (HC(1:10).EQ.'DICEITRVL') THEN DICEITRVL=VARIN C---- C---- unrecognised C---- ELSE WRITE(6,'(A,T10,A,A,I8)')'***', + '*** RDPAR_F: no interpretation of',HC,VARIN STOP '*** RDPAR_F: left due to error in reading inPar' END IF END ***** end of RDPAR_F ***** ------------------------------------------------------------------ ***** SUB RDPAR_A ***** ------------------------------------------------------------------ C---- C---- NAME : RDPAR_A C---- ARG : C---- DES : reading and interpreting one line with A456 input C---- DES : C---- IN : C---- FROM : RDPAR C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * *----------------------------------------------------------------------* SUBROUTINE RDPAR_A C---- include parameter files INCLUDE 'profPar.f' C---- local function C CHARACTER*80 FCUT_SPACES INTEGER FILEN_STRING C---- local variables INTEGER IT CHARACTER*456 VARIN,HC2 CHARACTER*80 HC LOGICAL LERROR ******------------------------------*-----------------------------****** LERROR=.FALSE. C---- read READ(10,'(A20,T25,A)')HC,VARIN HC2=VARIN(1:FILEN_STRING(VARIN)) VARIN=' ' VARIN=HC2 C---- ------------------------------ C---- interpret C---- C---- modes IF (HC(1:7) .EQ.'TRNTYPE') THEN TRNTYPE=VARIN(1:FILEN_STRING(VARIN)) IF ((TRNTYPE.NE.'BATCH').AND.(TRNTYPE.NE.'ONLINE')) THEN WRITE(6,'(A,T10,A,A)')'***', + 'RDPAR_A: TRNTYPE=[BATCH|ONLINE], is=',VARIN LERROR=.TRUE. END IF ELSEIF (HC(1:7) .EQ.'TRGTYPE') THEN TRGTYPE=VARIN(1:FILEN_STRING(VARIN)) IF ((TRGTYPE.NE.'SIG').AND.(TRGTYPE.NE.'LOG')) THEN WRITE(6,'(A,T10,A,A)')'***', + 'RDPAR_A: TRGTYPE=[SIG|LOG], is=',VARIN LERROR=.TRUE. END IF ELSEIF (HC(1:7) .EQ.'ERRTYPE') THEN ERRTYPE=VARIN IF ( (ERRTYPE(1:7) .NE.'DELTASQ').AND. + (ERRTYPE(1:12).NE.'LN_1-DELTASQ')) THEN WRITE(6,'(A,T10,A,A)')'***', + 'RDPAR_A: ERRTYPE=[DELTASQ|LN_1-DELTASQ], is=', + VARIN LERROR=.TRUE. END IF ELSEIF (HC(1:8) .EQ.'MODEPRED') THEN MODEPRED=VARIN(1:FILEN_STRING(VARIN)) ELSEIF (HC(1:7) .EQ.'MODENET') THEN MODENET=VARIN(1:FILEN_STRING(VARIN)) ELSEIF (HC(1:6) .EQ.'MODEIN') THEN MODEIN=VARIN(1:FILEN_STRING(VARIN)) ELSEIF (HC(1:7) .EQ.'MODEOUT') THEN MODEOUT=VARIN(1:FILEN_STRING(VARIN)) ELSEIF (HC(1:7) .EQ.'MODEJOB') THEN MODEJOB=VARIN(1:FILEN_STRING(VARIN)) C---- C---- input files C---- ELSEIF (HC(1:9) .EQ.'FILEIN_IN') THEN FILEIN_IN(1)=VARIN(1:FILEN_STRING(VARIN)) DO IT=2,NUMFILEIN_IN C---------- read again READ(10,'(A20,T25,A)')HC,FILEIN_IN(IT) IF (HC(1:9).NE.'FILEIN_IN') THEN WRITE(6,'(A,T10,A,A,A,A)')'***', + 'RDPAR_A:loop read filein_in, is', + HC,' V=',VARIN LERROR=.TRUE. END IF END DO ELSEIF (HC(1:10).EQ.'FILEIN_OUT') THEN FILEIN_OUT(1)=VARIN(1:FILEN_STRING(VARIN)) DO IT=2,NUMFILEIN_OUT C---------- read again READ(10,'(A20,T25,A)')HC,FILEIN_OUT(IT) IF (HC(1:10).NE.'FILEIN_OUT') THEN WRITE(6,'(A,T10,A,A,A,A)')'***', + 'RDPAR_A:loop read filein_OUT, is', + HC,' V=',VARIN LERROR=.TRUE. END IF END DO ELSEIF (HC(1:10).EQ.'FILEIN_JCT') THEN FILEIN_JCT=VARIN(1:FILEN_STRING(VARIN)) ELSEIF (HC(1:10).EQ.'FILEIN_SAM') THEN FILEIN_SAM=VARIN(1:FILEN_STRING(VARIN)) C---- C---- output files C---- ELSEIF (HC(1:11).EQ.'FILEOUT_OUT') THEN FILEOUT_OUT(1)=VARIN DO IT=2,NUMFILEOUT_OUT C---------- read again READ(10,'(A20,T25,A)')HC,FILEOUT_OUT(IT) IF (HC(1:11).NE.'FILEOUT_OUT') THEN WRITE(6,'(A,T10,A,A,A,A)')'***', + 'RDPAR_A:loop read FILEOUT_OUT, is', + HC,' V=',VARIN LERROR=.TRUE. END IF END DO ELSEIF (HC(1:11).EQ.'FILEOUT_JCT') THEN FILEOUT_JCT(1)=VARIN DO IT=2,NUMFILEOUT_JCT C---------- read again READ(10,'(A20,T25,A)')HC,FILEOUT_JCT(IT) IF (HC(1:11).NE.'FILEOUT_JCT') THEN WRITE(6,'(A,T10,A,A,A,A)')'***', + 'RDPAR_A:loop read FILEOUT_JCT, is', + HC,' V=',VARIN LERROR=.TRUE. END IF END DO ELSEIF (HC(1:11).EQ.'FILEOUT_ERR') THEN FILEOUT_ERR=VARIN(1:FILEN_STRING(VARIN)) ELSEIF (HC(1:12).EQ.'FILEOUT_YEAH') THEN FILEOUT_YEAH=VARIN(1:FILEN_STRING(VARIN)) C---- C---- unrecognised C---- ELSE WRITE(6,'(A,T10,A,A,A,A)')'***', + 'RDPAR_A: no interpretation of: hc= (',HC, + '), var=(',VARIN,')' STOP '*** RDPAR_A: left due to error in reading inPar' END IF * * C---- -------------------------------------------------- C---- error while reading? IF (LERROR) THEN WRITE(6,'(A,T10,A)')'***', + 'RDPAR_A: succession of parameters wrong' STOP '*** RDPAR_A: left due to error in reading inPar' END IF END ***** end of RDPAR_A ***** ------------------------------------------------------------------ ***** SUB RDPAR_ERR ***** ------------------------------------------------------------------ C---- C---- NAME : RDPAR_ERR C---- ARG : CHAR,VARIN C---- DES : checks some typical errors of the parameter file read C---- * purpose: T * in: character indicating which variable is currently * in: treated * out: * called by: READPAR_I,READPAR_F,READPAR_A * calling: * lib: * procedure: *----------------------------------------------------------------------* * Burkhard Rost Sep, 1999 version 1.0 * * CUBIC http://www.columbia.edu * * New York rost@columbia.edu * * changed: Sep, 1999 version 0.1 * *----------------------------------------------------------------------* SUBROUTINE RDPAR_ERR(CHAR_RD,VARIN) C---- include parameter files INCLUDE 'profPar.f' C---- variables passed CHARACTER*456 CHAR_RD INTEGER VARIN C---- local parameters C---- local variables * ******------------------------------*-----------------------------****** * * ******------------------------------*-----------------------------****** C---- ------------------------------------------------------------------ C---- C---- ------------------------------------------------------------------ IF (CHAR_RD(1:6) .EQ. 'NUMIN ' .AND. + NUMIN .GT. NUMIN_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMIN read=',NUMIN,' NUMIN_MAX=',NUMIN_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' ELSEIF (CHAR_RD(1:7) .EQ. 'NUMHID ' .AND. + NUMHID .GT. NUMHID_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMHID read=',NUMHID,' NUMHID_MAX=',NUMHID_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' ELSEIF (CHAR_RD(1:7) .EQ. 'NUMOUT ' .AND. + NUMOUT .GT. NUMOUT_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMOUT read=',NUMOUT,' NUMOUT_MAX=',NUMOUT_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' ELSEIF (CHAR_RD(1:7) .EQ. 'NUMSAM ' .AND. + NUMSAM .GT. NUMSAM_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMSAM read=',NUMSAM,' NUMSAM_MAX=',NUMSAM_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' ELSEIF (CHAR_RD(1:7) .EQ. 'NUMFILE' .AND. + VARIN .GT. NUMFILES_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMFILE* read=',VARIN,' NUMFILE_MAX=', + NUMFILES_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' ELSEIF (CHAR_RD(1:9) .EQ. 'STPSWPMAX' .AND. + VARIN .GT. STPSWPMAX_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: STPSWPMAX read=',VARIN,' STPSWPMAX_MAX=', + STPSWPMAX_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' ELSEIF (CHAR_RD(1:6) .EQ. 'STPMAX' .AND. + VARIN .GT. STPMAX_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: STPMAX read=',VARIN,' STPMAX_MAX=', + STPMAX_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' ELSEIF (CHAR_RD(1:6) .EQ. 'STPINF' .AND. + VARIN .GT. STPMAX_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: STPINF read=',VARIN,' STPMAX_MAX=', + STPMAX_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' END IF END ***** end of RDPAR_ERR ***** ------------------------------------------------------------------ ***** SUB RDPAR_WRT ***** ------------------------------------------------------------------ C---- C---- NAME : RDPAR_WRT C---- ARG : C---- DES : reading and interpreting one line with F12.3 input C---- IN : C---- FROM : RDPAR C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDPAR_WRT C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER IT CHARACTER*80 CTMP,CTMP2 ******------------------------------*-----------------------------****** C---- CTMP='--- RDpar: ' CTMP2='--------------------------------------------------' C WRITE(6,'(A)')'--- ' WRITE(6,'(A,T16,A50)')CTMP,CTMP2 WRITE(6,'(A,T16,A)')CTMP,'Parameters read:' C---- C---- integers C---- WRITE(6,'(A,T16,A)')CTMP,' ' WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMIN',NUMIN WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMHID',NUMHID WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMOUT',NUMOUT WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMLAYERS',NUMLAYERS C---- WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMSAM',NUMSAM C---- WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMFILEIN_IN',NUMFILEIN_IN WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMFILEIN_OUT',NUMFILEIN_OUT WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMFILEOUT_OUT',NUMFILEOUT_OUT WRITE(6,'(A,T16,A,T35,I8)')CTMP,'NUMFILEOUT_JCT',NUMFILEOUT_JCT C---- WRITE(6,'(A,T16,A,T35,I8)')CTMP,'STPSWPMAX',STPSWPMAX WRITE(6,'(A,T16,A,T35,I8)')CTMP,'STPMAX',STPMAX WRITE(6,'(A,T16,A,T35,I8)')CTMP,'STPINF',STPINF WRITE(6,'(A,T16,A,T35,I8)')CTMP,'ERRBINSTOP',ERRBINSTOP C---- C---- reals C---- WRITE(6,'(A,T16,A)')CTMP,' ' WRITE(6,'(A,T16,A,T35,F15.6)')CTMP,'EPSILON',EPSILON WRITE(6,'(A,T16,A,T35,F15.6)')CTMP,'ALPHA',ALPHA WRITE(6,'(A,T16,A,T35,F15.6)')CTMP,'TEMPERATURE',TEMPERATURE C---- WRITE(6,'(A,T16,A,T35,F15.6)')CTMP,'ERRSTOP',ERRSTOP WRITE(6,'(A,T16,A,T35,F15.6)')CTMP,'ERRBIAS',ERRBIAS C---- C---- characters C---- WRITE(6,'(A,T16,A)')CTMP,' ' WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'TRNTYPE',TRNTYPE(1:FILEN_STRING(TRNTYPE)) WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'TRGTYPE',TRGTYPE(1:FILEN_STRING(TRGTYPE)) WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'ERRTYPE',ERRTYPE(1:FILEN_STRING(ERRTYPE)) WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'MODEPRED',MODEPRED(1:FILEN_STRING(MODEPRED)) WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'MODENET',MODENET(1:FILEN_STRING(MODENET)) WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'MODEIN',MODEIN(1:FILEN_STRING(MODEIN)) WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'MODEJOB',MODEJOB(1:FILEN_STRING(MODEJOB)) C---- C---- files C---- DO IT=1,NUMFILEIN_IN WRITE(6,'(A,T16,A,T30,I4,A1,A)')CTMP,'FILEIN_IN',IT,' ', + FILEIN_IN(IT)(1:FILEN_STRING(FILEIN_IN(IT))) END DO DO IT=1,NUMFILEIN_OUT WRITE(6,'(A,T16,A,T30,I4,A1,A)')CTMP,'FILEIN_OUT',IT,' ', + FILEIN_OUT(IT)(1:FILEN_STRING(FILEIN_OUT(IT))) END DO WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'FILEIN_JCT',FILEIN_JCT(1:FILEN_STRING(FILEIN_JCT)) WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'FILEIN_SAM',FILEIN_SAM(1:FILEN_STRING(FILEIN_SAM)) DO IT=1,NUMFILEOUT_OUT WRITE(6,'(A,T16,A,T30,I4,A1,A)')CTMP,'FILEOUT_OUT',IT,' ', + FILEOUT_OUT(IT)(1:FILEN_STRING(FILEOUT_OUT(IT))) END DO DO IT=1,NUMFILEOUT_JCT WRITE(6,'(A,T16,A,T30,I4,A1,A)')CTMP,'FILEOUT_JCT',IT,' ', + FILEOUT_JCT(IT)(1:FILEN_STRING(FILEOUT_JCT(IT))) END DO WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'FILEOUT_ERR',FILEOUT_ERR(1:FILEN_STRING(FILEOUT_ERR)) WRITE(6,'(A,T16,A,T35,A)')CTMP, + 'FILEOUT_YEAH',FILEOUT_YEAH(1:FILEN_STRING(FILEOUT_YEAH)) WRITE(6,'(A,T16,A,T35)')CTMP,'end of reading parameters' END ***** end of RDPAR_WRT ***** ------------------------------------------------------------------ ***** SUB RDSAM ***** ------------------------------------------------------------------ C---- C---- NAME : RDSAM C---- ARG : C---- DES : reads the succession of samples C---- IN : C---- FROM : MAIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE RDSAM C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables * INTEGER IT,STPMAXLOC,VARIN CHARACTER*80 HC,MREAD LOGICAL LDONE,LREAD ******------------------------------*-----------------------------****** C message onto screen C WRITE(6,'(A)')'--- ' WRITE(6,'(A,T16,A)')'--- RDsam file=', + FILEIN_SAM(1:FILEN_STRING(FILEIN_SAM)) C---- read parameters from file PROF_InPar CALL SFILEOPEN(10,FILEIN_SAM,'OLD',456,'READONLY') LDONE=.FALSE. DO WHILE (.NOT.LDONE) LREAD=.FALSE. READ(10,'(A3)',END=6067)HC C------- terminate reading IF (HC(1:2).EQ.'//') THEN LDONE=.TRUE. LREAD=.FALSE. ELSEIF (HC(1:3).EQ.'* o') THEN LREAD=.FALSE. MREAD='H' ELSEIF (HC(1:3).EQ.'* p') THEN LREAD=.FALSE. MREAD='D' ELSEIF (HC(1:1).NE.'*') THEN BACKSPACE 10 LREAD=.TRUE. ELSE LREAD=.FALSE. END IF IF (LREAD) THEN IF (MREAD.EQ.'H') THEN READ(10,'(A20,T25,I8)',END=6067)HC,VARIN STPMAXLOC=VARIN IF (HC(1:6).NE.'STPMAX') THEN WRITE(6,'(A,T10,A,A)')'***', + 'ERROR RDSAM not NUMSAM:',HC STOP '*** RDSAM: left due to error in reading inSam' ELSEIF (STPMAXLOC.LT.STPMAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'ERROR RDSAM STPMAXLOC=',STPMAXLOC, + ' STPMAX=',STPMAX Cxx STOP '*** RDPAR: left due to error in reading inSam' END IF ELSEIF (MREAD.EQ.'D') THEN READ(10,'(25I8)',END=6067)(PICKSAM(IT),IT=1,STPMAXLOC) Cxx READ(10,'(25I8)',END=6067)(PICKSAM(IT),IT=1,STPMAX) LDONE=.TRUE. ELSE WRITE(6,'(A,T10,A,A,A)')'***', + 'ERROR RDSAM MREAD not recognised:',MREAD,':' STOP '*** RDPAR: left due to error in reading inPar' END IF END IF END DO 6067 CONTINUE CLOSE(10) END ***** end of RDSAM ***** ------------------------------------------------------------------ ***** SUB NETOUT(LERR,LBIN,STP) ***** ------------------------------------------------------------------ C---- C---- NAME : NETOUT C---- ARG : LERR,LBIN,STP C---- DES : executes network NETOUT function input --> output C---- IN : logicals : do error? do error bin?, current step C---- FROM : MAIN, TRAIN C---- CALL2: NETOUT_MUE, NETOUT_BIN, NETOUT_ERR C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE NETOUT(LERR,LBIN,STP) C---- parameters/global variables INCLUDE 'profPar.f' C---- local variables INTEGER MUE,STP,ITOUT LOGICAL LBIN,LERR ******------------------------------*-----------------------------****** * INPUT (NUMHID,NUMIN+) input matrix * * is used * * INVABW =1/ABW for avoiding too high quantities * * FLD the local fields (abbr.: h) are defined by: * * h(I,MUE )= sum(k,{J(k,i)*s(k,mue))+b(i,mue) * * NEGINVABW =-INVABW * ******------------------------------*-----------------------------****** C---- cutoffs INVABW=1./ABW NEGINVABW=(-1.)*INVABW * * C---- -------------------------------------------------- C---- loop over all samples (residues) C---- -------------------------------------------------- DO MUE=1,NUMSAM C---- C---- this burns CPU! network input-> output C---- CALL NETOUT_MUE(MUE) C WRITE(6,'(A,I5,A,3I4,A,3I4)')'dbg: NETOUT mue=',MUE, C + ' out=',(INT(100*OUTPUT(ITOUT)),ITOUT=1,NUMOUT), C + ' des=',(OUTDES(ITOUT,MUE),ITOUT=1,NUMOUT) C WRITE(6,'(A,I5,A,3I4)')'dbg: NETOUT mue=',MUE, C + ' out=',(INT(100*OUTPUT(ITOUT)),ITOUT=1,NUMOUT) C---- C---- this HAS burned CPU! network input-> output C---- C winner-take-all decision IF (LBIN) THEN CALL NETOUT_BIN(MUE) END IF C compile network error IF (LERR) THEN CALL NETOUT_ERR(MUE,STP) END IF END DO C WRITE(6,*)'yy err=',err(stp),' bin=',errbin(stp) END ***** end of NETOUT ***** ------------------------------------------------------------------ ***** SUB NETOUT_MUE ***** ------------------------------------------------------------------ C---- C---- NAME : NETOUT_MUE C---- ARG : MUE C---- DES : executes network NETOUT function input --> output C---- DES : for one pattern C---- IN : number of current pattern C---- FROM : NETOUT, TRAIN, WRTOUT C---- CALL2: C---- C---- IN GLOBAL : INPUT, JCT1st, JCT2ND, NUMHID,*IN,*OUT,BITACC, C---- OUT GLOBAL : OUTPUT, FLD1st, FLD2nd C---- C---- ********************* C---- NOTE : heavy in terms of CPU C---- ********************* C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE NETOUT_MUE(MUE) C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables * INTEGER MUE,ITHID,ITIN,ITOUT ******------------------------------*-----------------------------****** C---- C---- compute local fields for hidden unit C---- DO ITHID=1,NUMHID FLD1ST(ITHID)=0. DO ITIN=1,NUMIN IF (INPUT(ITIN,MUE).NE.0.) THEN FLD1ST(ITHID)=FLD1ST(ITHID) + +JCT1ST(ITIN,ITHID)*INPUT(ITIN,MUE) END IF END DO C rescale with BITACC FLD1ST(ITHID)=FLD1ST(ITHID)/REAL(BITACC) C threshold units FLD1ST(ITHID)=FLD1ST(ITHID)+JCT1ST((NUMIN+1),ITHID) END DO C---- C---- compute value of hidden units C---- C VECTOR DO ITHID=1,NUMHID IF ( ABS(FLD1ST(ITHID)).LT.INVABW) THEN OUTHID(ITHID)=(1./(1.+EXP (- FLD1ST(ITHID) ) )) ELSEIF (FLD1ST(ITHID).LE.NEGINVABW) THEN OUTHID(ITHID)=0. ELSEIF (FLD1ST(ITHID).GE.INVABW) THEN OUTHID(ITHID)=1. ELSE WRITE(6,'(T2,A,T10,A,I8)')'***', + 'ERROR in NETOUT_MUE: wrong assignment MUE=',MUE WRITE(6,'(T2,A,T10,A)')'***', + 'intermediate output!! Stopped at 12-10-92-1' STOP '*** NETOUT_MUE: left due to error (FLD1ST wrong)' END IF END DO C END VECTOR C---- C---- compute local field for second layer C---- DO ITOUT=1,NUMOUT FLD2ND(ITOUT)=0. C PARALLEL DO ITHID=1,NUMHID IF (OUTHID(ITHID).GT.ABW) THEN FLD2ND(ITOUT)=FLD2ND(ITOUT)+ + (JCT2ND(ITHID,ITOUT)*OUTHID(ITHID)) END IF END DO C END PARALLEL C threshold unit FLD2ND(ITOUT)=FLD2ND(ITOUT)+JCT2ND((NUMHID+1),ITOUT) END DO C---- C---- compute output C---- DO ITOUT=1,NUMOUT IF ((ABS(FLD2ND(ITOUT)).LT.INVABW).AND. + (FLD2ND(ITOUT).GT.NEGINVABW)) THEN OUTPUT(ITOUT)=1./(1.+ EXP (- FLD2ND(ITOUT) )) ELSEIF (FLD2ND(ITOUT).LE.NEGINVABW) THEN OUTPUT(ITOUT)=0. ELSEIF (FLD2ND(ITOUT).GE.INVABW) THEN OUTPUT(ITOUT)=1. ELSE WRITE(6,'(T2,A,T10,A,I8)')'***', + 'ERROR in NETOUT_MUE: output wrong assigned, MUE=',MUE WRITE(6,'(T2,A,T10,A)')'***','stopped at 12-10-92-2' STOP '*** NETOUT_OUT: left due to error (FLD2ND wrong)' END IF END DO END ***** end of NETOUT_MUE ***** ------------------------------------------------------------------ ***** SUB NETOUT_BIN ***** ------------------------------------------------------------------ C---- C---- NAME : NETOUT_BIN C---- ARG : MUE C---- DES : winner-take-all decision, only maximal unit will be C---- DES : set to 1 C---- IN : number of current pattern C---- FROM : NETOUT, TRAIN C---- CALL2: C---- LIB : FRMAX1 C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE NETOUT_BIN(MUE) C---- global parameters and variables INCLUDE 'profPar.f' C---- local functions REAL FRMAX1 C---- local variables INTEGER MUE,ITOUT REAL HELPMAX ******------------------------------*-----------------------------****** C---- C---- the winner takes it all C---- OUTWIN(MUE)=0 IF (NUMOUT.EQ.1) THEN IF (OUTPUT(1).GT.THRESHOUT) THEN OUTWIN(MUE)=1 END IF ELSE C security: set zero DO ITOUT=(NUMOUT+1),NUMOUT_MAX OUTPUT(ITOUT)=0 END DO C find max HELPMAX=FRMAX1(OUTPUT,NUMOUT_MAX) C which unit DO ITOUT=1,NUMOUT IF (OUTPUT(ITOUT).EQ.HELPMAX) THEN OUTWIN(MUE)=INT2(ITOUT) END IF END DO END IF * * C---- C---- at least one bin = 1 ? C---- IF ((OUTWIN(MUE).EQ.0).AND.(NUMOUT.GT.1)) THEN WRITE(6,'(T2,A,T10,A,I8)')'***', + 'ERROR NETOUT_BIN no winner, mue=',mue WRITE(6,'(T2,A,T10,10F5.2)')'***', + (OUTPUT(ITOUT),ITOUT=1,NUMOUT) STOP '*** NETOUT_BIN: left due to error (no winner)' END IF END ***** end of NETOUT_BIN ***** ------------------------------------------------------------------ ***** SUB NETOUT_ERR ***** ------------------------------------------------------------------ C---- C---- NAME : NETOUT_ERR C---- ARG : MUE,STP C---- DES : compiles the current error committed by the NN C---- IN : number of current pattern, number of current step C---- OUT : ERR(STP), OKBIN(STP), ERRBIN(STP) C---- note : additive, initialised for first pattern C---- C---- FROM : NETOUT, TRAIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE NETOUT_ERR(MUE,STP) C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables * INTEGER ITOUT,MUE,STP REAL DELTA,RHELP ******------------------------------*-----------------------------****** C---- C---- setting zero for first pattern C---- IF (MUE.EQ.1) THEN ERR(STP)=0. OKBIN(STP)=0 ERRBIN(STP)=100 END IF C---- C---- error per sample C---- C real error RHELP=0.0 DO ITOUT=1,NUMOUT DELTA=OUTPUT(ITOUT)-(OUTDES(ITOUT,MUE)/BITACC) IF ( ABS(DELTA).GT.ABW) THEN RHELP=RHELP+(DELTA)**2 END IF END DO C binary error IF (NUMOUT.EQ.1) THEN IF (((OUTDES(1,MUE).EQ.0).AND. + (OUTPUT(1).LT.ERRBINACC)).OR. + ((OUTDES(1,MUE).EQ.BITACC).AND. + (OUTPUT(1).GT.(1-ERRBINACC)))) THEN OKBIN(STP)=OKBIN(STP)+1 END IF ELSE POSWIN=OUTWIN(MUE) IF (((OUTPUT(POSWIN).LT.ERRBINACC).AND. + (OUTDES(POSWIN,MUE).EQ.0)).OR. + ((OUTPUT(POSWIN).GT.(1-ERRBINACC)).AND. + (OUTDES(POSWIN,MUE).EQ.BITACC))) THEN OKBIN(STP)=OKBIN(STP)+1 END IF END IF C total error ERR(STP)=ERR(STP)+RHELP C---- C---- scaling error for last sample C---- IF (MUE.EQ.NUMSAM) THEN C ERR(STP)=(1./REAL(NUMSAM))*(1./REAL(NUMOUT))*ERR(STP) ERR(STP)=(1./REAL(NUMSAM))*(1./REAL(NUMOUT))*ERR(STP) ERRBIN(STP)=100*(1.-(OKBIN(STP)/REAL(NUMSAM))) END IF END ***** end of NETOUT_ERR ***** ------------------------------------------------------------------ ***** SUB TRAIN ***** ------------------------------------------------------------------ C---- C---- NAME : TRAIN C---- ARG : C---- DES : optimized version of error back-prop training C---- IN : C---- FROM : MAIN C---- CALL2: TRAIN_BACKPROP C---- CALL2: TRAIN_INIMUE -> NETOUT_MUE, lib: SRSTE2, SRSTZ2 C---- CALL2: TRAIN_INISWP -> lib: STRSTZ2 C---- CALL2: TRAIN_STOP C---- CALL2: TRAIN_WRT C---- CALL2: NETOUT -> NETOUT_MUE|BIN|ERR C---- CALL2: WRTJCT -> lib: SFILEOPEN, WRTHEAD C---- CALL2: WRTOUT -> NETOUT_MUE, WRTHEAD, lib: SFILEOPEN C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE TRAIN C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER MUE,ITIN,ITHID,ITOUT REAL DELTA(1:NUMOUT_MAX),FACDELTA(1:NUMOUT_MAX) REAL*4 RHELP,VECSUM CHARACTER*80 CTMP,CTMP2 LOGICAL LERR,LBIN,LSTOP,LCONT ******------------------------------*-----------------------------****** LERR=.TRUE. LBIN=.TRUE. CTMP='--- TRAIN: ' CTMP2='--------------------------------------------------' C writing into header (arrived at OTRNON asf) WRITE(6,'(A15,A50)')CTMP,CTMP2 WRITE(6,'(A15)')CTMP WRITE(6,'(A15,A)')CTMP,'----------------' WRITE(6,'(A15,A)')CTMP,'arrived in TRAIN' WRITE(6,'(A15,A)')CTMP,'----------------' WRITE(6,'(A15)')CTMP C initialise 1: check training accuracy asf. CALL NETOUT(LERR,LBIN,STPNOW) CALL TRAIN_STOP(LSTOP,STPNOW,CTMP) CALL TRAIN_WRT(CTMP,0,0) IF (LSTOP) THEN C never enter the while ! LCONT= .FALSE. ELSE C ini for first sweep (stpswp) LCONT= .TRUE. STPSWPNOW=1 STPNOW= 0 END IF C----------------------------------------------------------------------- C---- THE LOOP: by intrinsic time scale: STPNOW C---- intrinsic time scale given by training set C----------------------------------------------------------------------- DO WHILE ((STPSWPNOW.LE.STPSWPMAX) .AND. + (STPNOW.LE.STPMAX) .AND. LCONT) C---- (0) PDJCT1ST,PDJCT2ND,DJCT1ST,DJCT1ST == 0 C---- (n) count up (STPNOW,STPSWPNOW,STPINFNOW) CALL TRAIN_INISWP(CTMP) C---- end learning after STPMAX steps IF (STPNOW.GT.STPMAX) THEN STPSWPNOW=STPSWPMAX STPNOW= STPNOW-1 LCONT= .FALSE. ELSE MUE=PICKSAM(STPNOW) IF (MUE .EQ.0) THEN WRITE(6,*)'*** ERROR TRAIN: (MUE=0) STPNOW=',STPNOW STOP ENDIF C---- set OUTPUT for current MUE CALL TRAIN_INIMUE(MUE) C---- here goes THE thing CALL TRAIN_BACKPROP(MUE) END IF C------- write info about how far things have come IF (STPINFNOW.EQ.STPINF) THEN STPINFNOW=0 STPINFCNT=STPINFCNT+1 C---------- network input -> output CALL NETOUT(LERR,LBIN,STPINFCNT) C---------- write onto screen CALL TRAIN_WRT(CTMP,STPINFCNT,STPNOW) C---------- write the current output into file CALL WRTOUT(10,FILEOUT_OUT(STPINFCNT),STPINFCNT,STPNOW) C---------- write current junctions into file CALL WRTJCT(10,FILEOUT_JCT(STPINFCNT)) C---------- error low enough? CALL TRAIN_STOP(LSTOP,STPNOW,CTMP) C---------- terminate! IF (LSTOP) THEN LCONT= .FALSE. END IF END IF C------- end of one back-prop step END DO C---- end of loop over STPSWP (i.e. all samples) C----------------------------------------------------------------------- IF (STPSWPNOW.GE.STPSWPMAX) THEN WRITE(6,'(A15,A,I8,A,I8)')CTMP,'end reached for STSWPNOW=', + STPSWPNOW,' >= STPSWPMAX=',STPSWPMAX END IF IF (STPNOW.GE.STPMAX) THEN WRITE(6,'(A15,A,I8,A,I8)')CTMP,'end reached for STNOW=', + STPNOW,' >= STPMAX=',STPMAX END IF END ***** end of TRAIN ***** ------------------------------------------------------------------ ***** SUB TRAIN_BACKPROP ***** ------------------------------------------------------------------ C---- C---- NAME : TRAIN_BACKPROP C---- ARG : MUE C---- DES : optimized version of error back-prop training C---- IN : current pattern MUE C---- FROM : TRAIN C---- CALL2: C---- * procedure: back-prop algorithm * * d(i) = desired output for unit i (1..numout=N2) * o(i) = output for unit i (1..numout=N2) * h(j) = hidden output for unit j (1..numhid=N1) * s(k) = input for unit k (1..numin=N0) * * J1 : junction between hidden and input * J2 : junction between output and hidden * * f(x) = 1 / (1 + e^(-x)) sigmoid * df/dx = f ( 1 - f) (df/dx) * * * N1+1 * o(i) = f ( SUM J2(ij)* f ( h(j) ) ) * j * * N0+1 * h(j) = f ( SUM J1(jk) * s(k) ) * k * N2 * E = SUM ( o(i) - d(i) ) **2 * i * * DELTA(i) = o(i) - d(i) * * +--- is f' ---+ * dE | | * ------- = DELTA(i) * o(i)*(1-o(i)) * h(j) * dJ2(ij) * +--- is f' ---+ * dE | | * ------- = s(k) * h(j)*(1-h(j)) * VECSUM(j) * dJ1(jk) * N2 * VECSUM(j) = SUM J2(ij) * o(i)*(1-o(i)) * DELTA(i) * i * dE DELTA(i) * E -> ln ( 1 - E ) => ---- -> ----------------- * dJ 1 - DELTA(i)**2 * *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE TRAIN_BACKPROP(MUE) C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables * INTEGER MUE,ITIN,ITHID,ITOUT REAL DELTA(1:NUMOUT_MAX),FACDELTA(1:NUMOUT_MAX),DIFF REAL*4 RHELP,VECSUM CHARACTER*80 CTMP,CTMP2 LOGICAL LERR,LBIN,LSTOP,LCONT * * ******------------------------------*-----------------------------****** * FACDELTA the factor of 'all deltas', i.e.: * * FACDELTA= f''(out)*(out-des), or corresponding * * quantity for algorithms other than sigmoid * * MOMENTUM intermediately required variable storing the * * 'momentum' = alpha * olddeljunc * * STPINFCNT counts the steps of learning up to each STPINFth * * one and is set zero then * * DELTA for particular i,mue: output(i,mue)-desired(i,mue) * * PDELJCT1st/2nd stores the changes from the last TIME * ******------------------------------*-----------------------------****** C---- ------------------------------------------------------------------ C---- prefactors for changing junctions C---- C---- i=1,numout: C---- DELTA(i)= [ OUT(i) - OUTDES(i) ] C---- FACDELTA(i)= DELTA(i) * OUT(i) * (1-OUT(i)) C---- where: C---- OUT*(1-OUT)= derivative of sigmoid! C---- ------------------------------------------------------------------ DO ITOUT=1,NUMOUT IF (ERRBIAS.EQ.0.) THEN DELTA(ITOUT)=OUTPUT(ITOUT)-(OUTDES(ITOUT,MUE)/REAL(BITACC)) ELSE IF (OUTDES(ITOUT,MUE).EQ.BITACC) THEN DELTA(ITOUT)= ERRBIAS+OUTPUT(ITOUT)-1. ELSE DELTA(ITOUT)=-ERRBIAS + +OUTPUT(ITOUT)-(OUTDES(ITOUT,MUE)/REAL(BITACC)) END IF END IF C------- different for E = ln (1 -deltasq) C---- note: not activated to speed up!! Csleep IF (ERRTYPE(1:12).EQ.'LN_1-DELTASQ') THEN DIFF= 1 - ( DELTA(ITOUT)*DELTA(ITOUT) ) C IF (ABS(DIFF).LT.10E-8) THEN IF (ABS(DIFF).LT.ABW) THEN DELTA(ITOUT)=1. ELSE DELTA(ITOUT)=DELTA(ITOUT)/DIFF END IF Csleep END IF C------- final factors FACDELTA(ITOUT)= + DELTA(ITOUT) * OUTPUT(ITOUT)*(1.-(OUTPUT(ITOUT))) C------- setting FACDELTA to zero, if below threshold ABW C IF (ABS(FACDELTA(ITOUT)).LT.10E-10) THEN IF (ABS(FACDELTA(ITOUT)).LT.ABW) THEN FACDELTA(ITOUT)=0. END IF END DO C---- end of prefactors for output units C---- ------------------------------------------------------------------ C---- changes for last layer C---- C---- i=1,numout; k=1,numhid+1 C---- DJ2(k,i)=-1 * epsilon * FACDELTA(i) * OUTHID(k) C---- + alpha * previousDJ2(k,i) C---- ------------------------------------------------------------------ DO ITOUT=1,NUMOUT RHELP=(-1) * EPSILON * FACDELTA(ITOUT) DO ITHID=1,(NUMHID+1) C---------- momentum IF ( (ALPHA.GT.0).AND. + (ABS(PDJCT2ND(ITHID,ITOUT)).GT.ABW)) THEN DJCT2ND(ITHID,ITOUT)=RHELP*OUTHID(ITHID) + + ALPHA*PDJCT2ND(ITHID,ITOUT) ELSE DJCT2ND(ITHID,ITOUT)=RHELP*OUTHID(ITHID) END IF END DO END DO C---- ------------------------------------------------------------------ C---- changes for first layer C---- C---- k=1,numhid; m=1,numin+1 C---- DJ1(m,k)=-1 * epsilon * J2(k,i) * FACDELTA(i) C---- * OUTHID(k) * (1-OUTHID(k)) * INPUT(m) C---- + alpha * previousDJ1(k,m) C---- C---- C---- ------------------------------------------------------------------ DO ITHID=1,NUMHID VECSUM=0. DO ITOUT=1,NUMOUT IF (FACDELTA(ITOUT).NE.0.) THEN VECSUM=VECSUM+(JCT2ND(ITHID,ITOUT)*FACDELTA(ITOUT)) END IF END DO VECSUM=VECSUM*(-1)*EPSILON*OUTHID(ITHID)*(1.-OUTHID(ITHID)) DO ITIN=1,(NUMIN+1) C---------- momentum IF ( (ALPHA.GT.0).AND. + (ABS(PDJCT1ST(ITIN,ITHID)).GT.ABW)) THEN DJCT1ST(ITIN,ITHID)= + VECSUM*(INPUT(ITIN,MUE)/REAL(BITACC)) + + ALPHA*PDJCT1ST(ITIN,ITHID) ELSE DJCT1ST(ITIN,ITHID)= + VECSUM*(INPUT(ITIN,MUE)/REAL(BITACC)) END IF END DO END DO C---- ------------------------------ C---- update junctions for MUE C---- ------------------------------ C first layer DO ITHID=1,NUMHID DO ITIN=1,(NUMIN+1) IF (ABS(DJCT1ST(ITIN,ITHID)).GT.ABW) THEN JCT1ST(ITIN,ITHID)= + JCT1ST(ITIN,ITHID)+DJCT1ST(ITIN,ITHID) END IF END DO END DO C second layer DO ITOUT=1,NUMOUT DO ITHID=1,(NUMHID+1) IF (ABS(DJCT1ST(ITHID,ITOUT)).GT.ABW) THEN JCT2ND(ITHID,ITOUT)= + JCT2ND(ITHID,ITOUT)+DJCT2ND(ITHID,ITOUT) END IF END DO END DO C---- ------------------------------------------------------------------ C---- end of back-propagation for SAMPLE MUE C---- ------------------------------------------------------------------ END ***** end of TRAIN_BACKPROP ***** ------------------------------------------------------------------ ***** SUB TRAIN_INIMUE ***** ------------------------------------------------------------------ C---- C---- NAME : TRAIN_INIMUE C---- ARG : MUE C---- DES : initialises DJ1, DJ2, C---- IN : C---- FROM : TRAIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE TRAIN_INIMUE(MUE) C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables * INTEGER MUE ******------------------------------*-----------------------------****** C---- setting previous changes to olddel IF ((ALPHA.GT.0).AND.((EPSILON/ALPHA).LE.10)) THEN CALL SRSTE2(PDJCT1ST,DJCT1ST,(NUMIN_MAX+1),NUMHID_MAX) CALL SRSTE2(PDJCT2ND,DJCT1ST,(NUMHID_MAX+1),NUMOUT_MAX) END IF C---- setting deltaJ to 0 IF (STPNOW.GT.1) THEN CALL SRSTZ2(DJCT1ST,(NUMIN_MAX+1),NUMHID_MAX) CALL SRSTZ2(DJCT1ST,(NUMHID_MAX+1),NUMOUT_MAX) END IF C---- call trigger CALL NETOUT_MUE(MUE) END ***** end of TRAIN_INIMUE ***** ------------------------------------------------------------------ ***** SUB TRAIN_INISWP ***** ------------------------------------------------------------------ C---- C---- NAME : TRAIN_INISWP C---- ARG : CTMP C---- DES : C---- IN : C---- FROM : C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE TRAIN_INISWP(CTMP) C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables * CHARACTER*80 CTMP ******------------------------------*-----------------------------****** C---- for first step set deltaJ and previous deltaJ to zero IF (STPNOW.EQ.0) THEN CALL SRSTZ2(PDJCT1ST,(NUMIN_MAX+1),NUMHID_MAX) CALL SRSTZ2(PDJCT2ND,(NUMHID_MAX+1),NUMOUT_MAX) CALL SRSTZ2(DJCT1ST,(NUMIN_MAX+1),NUMHID_MAX) CALL SRSTZ2(DJCT1ST,(NUMHID_MAX+1),NUMOUT_MAX) WRITE(6,'(A15,A)')CTMP,'First cycle PDJ, DJ: all set to zero' END IF C---- count up STPNOW= STPNOW+1 STPINFNOW= STPINFNOW+1 C---- count up STPSWPNOW ? IF (STPSWPNOW*NUMSAM .LE. STPNOW) THEN STPSWPNOW=STPSWPNOW+1 END IF END ***** end of TRAIN_INISWP ***** ------------------------------------------------------------------ ***** SUB TRAIN_STOP(LSTOP,STPLOC,CTMP) ***** ------------------------------------------------------------------ C---- C---- NAME : TRAIN_STOP(LSTOP,STPLOC,CTMP) C---- ARG : C---- DES : checks whether stop condition reached C---- IN : C---- FROM : TRAIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE TRAIN_STOP(LSTOP,STPLOC,CTMP) C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER STPLOC,ITER CHARACTER*80 CTMP LOGICAL LSTOP ******------------------------------*-----------------------------****** LSTOP=.FALSE. IF ( (ERR(STPINFCNT).LE.ERRSTOP).OR. + (ERRBIN(STPINFCNT).LE.ERRBINSTOP) ) THEN WRITE(6,'(A15)')CTMP WRITE(6,'(A15,60A1)')CTMP,('-',ITER=1,60) WRITE(6,'(A15,A,I8)')CTMP, + 'stop condition reached in stpinfcnt=',STPINFCNT IF (ERR(STPINFCNT).LE.ERRSTOP) THEN WRITE(6,'(A15,A,F10.4,A,F10.4)')CTMP, + 'REAL ERROR:',ERR(STPINFCNT),' < ',ERRSTOP ELSE WRITE(6,'(A15,A,F8.2,A,F8.2)')CTMP, + 'BIN ERROR:',ERRBIN(STPINFCNT),' < ',ERRBINSTOP END IF WRITE(6,'(A15,A6,A2,I8,A,A2,F10.4,A,F10.4)')CTMP, + 'STP ',': ',STPLOC, ' ERR ',': ',ERR(STPINFCNT), + ' ERRSTOP :',ERRSTOP WRITE(6,'(A15,A6,A2,I8,A,A2,F8.2,A,F8.2)')CTMP, + 'STPINF',': ',STPINFCNT,' ERRBIN',': ',ERRBIN(STPINFCNT), + ' ERRBINSTOP:',ERRBINSTOP LSTOP=.TRUE. END IF END ***** end of TRAIN_STOP ***** ------------------------------------------------------------------ ***** SUB TRAIN_WRT(CTMP,STPINFLOC,STPLOC,STPMAX,STPSWPNOW,STPSWPMAX) ***** ------------------------------------------------------------------ C---- C---- NAME : TRAIN_WRT(CTMP,STPINF,STPNOW,STPMAX,STPSWPNOW,STPSWPMAX) C---- ARG : C---- DES : write current accuracy onto screen C---- IN : CTMP begin of line to write C---- IN : STPINF number of times all information about accuracy C---- IN : has been written so far (including current step) C---- IN : STPNOW current step C---- IN : STPMAX maximal number of steps allowed (then stop!) C---- IN : STPSWPNOW number of sweeps (one sweep = once through C---- IN : ALL patterns) C---- IN : STPSWPMAX maximal number of sweeps allowed (then stop!) C---- IN : C---- FROM : TRAIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * * changed: Sep, 1999 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE TRAIN_WRT(CTMP,STPINFLOC,STPLOC) C---- global parameters and variables INCLUDE 'profPar.f' C---- local variables INTEGER STPINFLOC,STPLOC,STPINFMAXLOC, + STPSWPNOWLOC,STPSWPMAXLOC CHARACTER*(*) CTMP ******------------------------------*-----------------------------****** C---- C---- current accuracy (err,errbin, asf) C---- WRITE(6,'(A15,A)')CTMP,'--------------------' WRITE(6,'(A15,A)')CTMP,'accuracy: ' C WRITE(6,'(A15,4(A,I8))')CTMP, C + 'STPSWP',STPSWPNOWLOC,' max=',STPSWPMAXLOC, C + 'STPINF',STPINFLOC,' max=',STPMAXLOC WRITE(6,'(A15,A6,A2,I8,A,A2,F10.4)')CTMP, + 'STP ',': ',STPLOC, ' ERR ',': ',ERR(STPINFLOC) WRITE(6,'(A15,A6,A2,I8,A,A2,F8.2)')CTMP, + 'STPINF',': ',STPINFLOC,' ERRBIN',': ',ERRBIN(STPINFLOC) END ***** end of TRAIN_WRT ***** ------------------------------------------------------------------ ***** SUB WRTJCT(KUNIT,FILE) ***** ------------------------------------------------------------------ C---- C---- NAME : WRTJCT(KUNIT,FILE) C---- ARG : C---- DES : writes the current architecture C---- IN : C---- FROM : MAIN C---- CALL2: WRTHEAD C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTJCT(KUNIT,FILE) C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER ITIN,ITHID,ITOUT,KUNIT CHARACTER*(*) FILE ******------------------------------*-----------------------------****** C---- open file IF (KUNIT.NE.6) THEN CALL SFILEOPEN(KUNIT,FILE,'UNKNOWN',456,' ') END IF C---- C---- header tag C---- WRITE(KUNIT,'(A2,A20,A)')'* ', + 'PROFout_jct ', + 'file from FORTRAN PROF.f (junctions)' C---- C---- header blabla C---- CALL WRTHEAD(KUNIT) C---- C---- header numbers C---- WRITE(KUNIT,'(A2,A)')'* ','--------------------' WRITE(KUNIT,'(A2,A)')'* ','overall: (A,T25,I8)' WRITE(KUNIT,'(A,A2,T25,I8)')'NUMIN',': ',NUMIN WRITE(KUNIT,'(A,A2,T25,I8)')'NUMHID',': ',NUMHID WRITE(KUNIT,'(A,A2,T25,I8)')'NUMOUT',': ',NUMOUT C---- WRITE(KUNIT,'(A,A2,T25,A)') + 'MODEPRED',': ',MODEPRED(1:FILEN_STRING(MODEPRED)) WRITE(KUNIT,'(A,A2,T25,A)') + 'MODENET',': ', MODENET(1:FILEN_STRING(MODENET)) WRITE(KUNIT,'(A,A2,T25,A)') + 'MODEJOB',': ', MODEJOB(1:FILEN_STRING(MODEJOB)) WRITE(KUNIT,'(A,A2,T25,A)') + 'MODEIN',': ', MODEIN(1:FILEN_STRING(MODEIN)) WRITE(KUNIT,'(A,A2,T25,A)') + 'MODEOUT',': ', MODEOUT(1:FILEN_STRING(MODEOUT)) C---- C---- 1st layer C---- WRITE(KUNIT,'(A2,A)')'* ','--------------------' WRITE(KUNIT,'(A2,A)')'* ', + 'jct 1st layer: row=numhid (10F10.4), col=(numin+1)' C jct1st DO ITHID=1,NUMHID WRITE(KUNIT,'(10F10.4)') + (JCT1ST(ITIN,ITHID),ITIN=1,(NUMIN+1)) END DO C---- C---- 2nd layer C---- WRITE(KUNIT,'(A2,A)')'* ','--------------------' WRITE(KUNIT,'(A2,A)')'* ', + 'jct 2nd layer: row=numhid+1 (10F10.4), col=numout' C jct2nd DO ITHID=1,(NUMHID+1) WRITE(KUNIT,'(10F10.4)')(JCT2ND(ITHID,ITOUT),ITOUT=1,NUMOUT) END DO C---- C---- control end C---- IF (KUNIT.NE.6) THEN WRITE(KUNIT,'(A2)')'//' CLOSE(KUNIT) END IF END ***** end of WRTJCT ***** ------------------------------------------------------------------ ***** SUB WRTOUT(KUNIT,FILE,STPINFLOC,STPLOC) ***** ------------------------------------------------------------------ C---- C---- NAME : WRTOUT(KUNIT,FILE,STPINFLOC,STPLOC) C---- ARG : C---- DES : writes the input vectors read C---- IN : C---- FROM : TRAIN, MAIN C---- CALL2: WRTHEAD, NETOUT_MUE C---- LIB : SFILEOPEN C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTOUT(KUNIT,FILE,STPINFLOC,STPLOC) C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER ITSAM,ITOUT,KUNIT,STPINFLOC,STPLOC,KUNITX CHARACTER*(*) FILE CHARACTER*80 CTMP LOGICAL LOGI_WRTFILE ******------------------------------*-----------------------------****** LOGI_WRTFILE= .TRUE. KUNITX= KUNIT C---- C---- write to screen if FILE='none' C---- IF (FILE(1:4).EQ.'none'.OR.FILE(1:4).EQ.'NONE') THEN LOGI_WRTFILE= .FALSE. KUNITX=6 END IF C---- open file IF (KUNITX.NE.6) THEN OPEN(KUNITX,FILE=FILE(1:FILEN_STRING(FILE))) END IF CTMP='--- WRTOUT: ' C---- C---- header tag C---- IF (LOGI_WRTFILE .EQV. .TRUE. ) THEN WRITE(KUNITX,'(A2,A20,A)')'* ', + 'PROFout_out ', + 'file from FORTRAN PROF.f (output)' ELSE WRITE(KUNITX,'(A2,A)')'* ', + 'Copyright: Burkhard Rost rost@columbia.edu' WRITE(KUNITX,'(A2,A)')'* ','NEURAL NETWORK output syntax: ' WRITE(KUNITX,'(A2,A,A)')'* ', + 'residue_number(I8) SPACE(A1) output values (100I4)' END IF C---- C---- header blabla C---- IF (LOGI_WRTFILE) THEN CALL WRTHEAD(KUNITX) END IF C---- C---- header numbers C---- IF (LOGI_WRTFILE) THEN WRITE(KUNITX,'(A2,A)')'* ','--------------------' WRITE(KUNITX,'(A2,A)')'* ','overall: (A,T25,I8)' WRITE(KUNITX,'(A,A2,T25,I8)')'NUMOUT', ': ',NUMOUT WRITE(KUNITX,'(A,A2,T25,I8)')'NUMSAM', ': ',NUMSAM C---- WRITE(KUNITX,'(A,A2,T25,A)') + 'MODEPRED',': ',MODEPRED(1:FILEN_STRING(MODEPRED)) WRITE(KUNITX,'(A,A2,T25,A)') + 'MODENET',': ',MODENET(1:FILEN_STRING(MODENET)) WRITE(KUNITX,'(A,A2,T25,A)') + 'MODEIN',': ',MODEIN(1:FILEN_STRING(MODEIN)) WRITE(KUNITX,'(A,A2,T25,A)') + 'MODEJOB',': ',MODEJOB(1:FILEN_STRING(MODEJOB)) C---- C---- current accuracy (err,errbin, asf) C---- WRITE(KUNITX,'(A2,A)')'* ','--------------------' WRITE(KUNITX,'(A2,A)')'* ','accuracy: (A,T25,I8)' WRITE(KUNITX,'(A,A2,T25,I8)') 'STPINF',': ',STPINFLOC WRITE(KUNITX,'(A,A2,T25,I8)') 'STP', ': ',STPLOC WRITE(KUNITX,'(A,A2,T25,F8.4)')'ERRBIN',': ',ERRBIN(STPINFLOC) WRITE(KUNITX,'(A,A2,T25,F8.4)')'ERR', ': ',ERR(STPINFLOC) C---- C---- output vectors C---- WRITE(KUNITX,'(A2,A)')'* ','--------------------' WRITE(KUNITX,'(A2,A)')'* ','out vec: (I8,A1,100I4)' END IF C---- yy tmp beg C IF (KUNITX.NE.6) THEN C WRITE(6,'(A15,A8,10(I2,A3,A3))')CTMP,'yy mue', C + (ITOUT,'o ',' d',ITOUT=1,NUMOUT) C END IF C---- yy tmp end DO ITSAM=1,NUMSAM CALL NETOUT_MUE(ITSAM) WRITE(KUNITX,'(I8,A1,100I4)')ITSAM,' ', + (INT(BITACC*OUTPUT(ITOUT)),ITOUT=1,NUMOUT) C---- yy tmp beg C WRITE(6,'(A15,I8,10(I4,I4))')CTMP,ITSAM, C + (INT(BITACC*OUTPUT(ITOUT)),OUTDES(ITOUT,ITSAM), C + ITOUT=1,NUMOUT) C---- yy tmp end END DO IF (KUNITX.NE.6) THEN CLOSE(KUNITX) END IF END ***** end of WRTOUT ***** ------------------------------------------------------------------ ***** SUB WRTERR ***** ------------------------------------------------------------------ C---- C---- NAME : WRTERR C---- ARG : KUNIT,FILE,STPTMP C---- DES : writes the history of the error propagation C---- IN : unit, file-to-write, last step C---- FROM : MAIN, WRTSCR C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTERR(KUNIT,FILE,STPTMP) C---- include parameter files INCLUDE 'profPar.f' C---- local variables * INTEGER IT,KUNIT,STPTMP CHARACTER*(*) FILE CHARACTER XC,CTAB ******------------------------------*-----------------------------****** C---- spacer CTAB=CHAR(9) XC=CTAB C---- open file IF (KUNIT.NE.6) THEN CALL SFILEOPEN(KUNIT,FILE,'UNKNOWN',456,' ') END IF C---- C---- header IF (KUNIT.NE.6) THEN C---- header tag WRITE(KUNIT,'(A)')'# Perl-RDB' WRITE(KUNIT,'(A2,A,T25,A)')'# ', + 'PROFout_err','file from FORTRAN PROF.f (error)' C---- number of steps executed WRITE(KUNIT,'(A2,A,T25,I5)')'# ','PARA: STPINF =',STPTMP END IF C---- names WRITE(KUNIT,'(A5,A,A8,A,A8,A,A8)') + 'NO',XC,'STEP',XC,'ERROR',XC,'ERRBIN' C---- formats IF (KUNIT.NE.6) THEN WRITE(KUNIT,'(A5,A,A8,A,A8,A,A8)') + '5N',XC,'8N',XC,'8.4F',XC,'8.4F' END IF C---- C---- data (history of error) C---- IF (STPTMP.EQ.0) THEN WRITE(KUNIT,'(I5,A,I8,A,F8.4,A,F8.4)') + 0,XC,(0),XC,ERR(0),XC,ERRBIN(0) ELSE DO IT=1,STPTMP WRITE(KUNIT,'(I5,A,I8,A,F8.4,A,F8.4)') + IT,XC,(IT*STPINF),XC,ERR(IT),XC,ERRBIN(IT) END DO END IF IF (KUNIT.NE.6) THEN CLOSE(KUNIT) END IF END ***** end of WRTERR ***** ------------------------------------------------------------------ ***** SUB WRTHEAD ***** ------------------------------------------------------------------ C---- C---- NAME : WRTHEAD C---- ARG : KUNIT C---- DES : write header for files C---- IN : C---- FROM : MAIN, WRTOUT, WRTJCT, WRTSCREEN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTHEAD(KUNIT) C---- include parameter files INCLUDE 'profPar.f' C---- local variables * INTEGER KUNIT ******------------------------------*-----------------------------****** * * C general information (address asf) CALL WRTHEAD_GEN(KUNIT) C specific information CALL WRTHEAD_JOB(KUNIT) END ***** end of WRTHEAD ***** ------------------------------------------------------------------ ***** SUB WRTHEAD_GEN ***** ------------------------------------------------------------------ C---- C---- NAME : WRTHEAD_GEN C---- ARG : KUNIT C---- DES : writes address asf onto KUNIT C---- IN : C---- FROM : WRTHEAD C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTHEAD_GEN(KUNIT) C---- local function C---- local variables INTEGER KUNIT CHARACTER*80 CTMP ******------------------------------*-----------------------------****** CTMP='* ' C header WRITE(KUNIT,'(A5)')CTMP C title WRITE(KUNIT,'(A5,A)')CTMP,'-------------------------------' WRITE(KUNIT,'(A5,A)')CTMP,'Output from neural network (PROF)' WRITE(KUNIT,'(A5,A)')CTMP,'-------------------------------' WRITE(KUNIT,'(A5,A)')CTMP,' ' C address WRITE(KUNIT,'(A5,A)')CTMP, + 'author: Burkhard Rost, Columbia Univ NYC / LION Heidelberg' WRITE(KUNIT,'(A5,A)')CTMP,'fax: +1-212-305-7932' WRITE(KUNIT,'(A5,A)')CTMP,'email: rost@columbia.edu' WRITE(KUNIT,'(A5,A)')CTMP, + 'www: http://cubic.bioc.columbia.edu/' WRITE(KUNIT,'(A5,A)')CTMP,' ' WRITE(KUNIT,'(A5,A)')CTMP,'All rights reserved.' WRITE(KUNIT,'(A5,A)')CTMP,' ' C date C WRITE(KUNIT,'(A5,A7,A24)')CTMP,'date: ',FDATE() WRITE(KUNIT,'(A5,A7,A24)')CTMP,'date: ','' WRITE(KUNIT,'(A5)')CTMP END ***** end of WRTHEAD_GEN ***** ------------------------------------------------------------------ ***** SUB WRTHEAD_JOB ***** ------------------------------------------------------------------ C---- C---- NAME : WRTHEAD_JOB C---- ARG : KUNIT C---- DES : writes specific details about current job C---- IN : C---- FROM : WRTHEAD C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTHEAD_JOB(KUNIT) C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER KUNIT CHARACTER*80 CTMP ******------------------------------*-----------------------------****** CTMP='* ' WRITE(KUNIT,'(A5)')CTMP C modes WRITE(KUNIT,'(A5,A,T35,A)')CTMP, + 'MODEPRED',MODEPRED(1:FILEN_STRING(MODEPRED)) WRITE(KUNIT,'(A5,A,T35,A)')CTMP, + 'MODENET',MODENET(1:FILEN_STRING(MODENET)) WRITE(KUNIT,'(A5,A,T35,A)')CTMP, + 'MODEIN',MODEIN(1:FILEN_STRING(MODEIN)) WRITE(KUNIT,'(A5,A,T35,A)')CTMP, + 'MODEJOB',MODEJOB(1:FILEN_STRING(MODEJOB)) C training, trigger, and error type WRITE(KUNIT,'(A5,A,T35,3(A10,A1))')CTMP,'TRN-, TRG-, ERRTYPE', + TRNTYPE(1:FILEN_STRING(TRNTYPE)),',', + TRGTYPE(1:FILEN_STRING(TRGTYPE)),',', + ERRTYPE(1:FILEN_STRING(ERRTYPE)),' ' C architecture WRITE(KUNIT,'(A5,A,T35,3(I8,A1))')CTMP,'NUMIN, -HID, -OUT', + NUMIN,',',NUMHID,',',NUMOUT,' ' C samples asf WRITE(KUNIT,'(A5,A,T35,I8)')CTMP,'NUMSAM',NUMSAM WRITE(KUNIT,'(A5,A,T35,3(I8,A1))')CTMP,'STPSWPMAX, -MAX, -INF', + STPSWPMAX,',',STPMAX,',',STPINF,' ' WRITE(KUNIT,'(A5,A,T35,I8,A1,F8.4)')CTMP,'ERRBINSTOP, -STOP', + ERRBINSTOP,',',ERRSTOP C training WRITE(KUNIT,'(A5,A,T35,3(F8.4,A1))')CTMP,'EPSILON, ALPHA, TEMP', + EPSILON,',',ALPHA,',',TEMPERATURE,' ' WRITE(KUNIT,'(A5)')CTMP END ***** end of WRTHEAD_JOB ***** ------------------------------------------------------------------ ***** SUB WRTSCR ***** ------------------------------------------------------------------ C---- C---- NAME : WRTSCR C---- ARG : STPTMP C---- DES : writes control output onto screen C---- IN : last step C---- FROM : MAIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTSCR(STPTMP) C---- include parameter files INCLUDE 'profPar.f' C---- params INTEGER STPTMP C---- local function INTEGER FILEN_STRING C---- local variables INTEGER IT CHARACTER*80 CTMP,CTMP2 ******------------------------------*-----------------------------****** CTMP= '--- WRTscr: ' CTMP2='--------------------------------------------------' WRITE(6,'(A15,A50)') CTMP,CTMP2 WRITE(6,'(A15)') CTMP WRITE(6,'(A15,A)') CTMP,'Final results of PROF' WRITE(6,'(A15,A)') CTMP,'-------------------' WRITE(6,'(A15)') CTMP C WRITE(6,'(A15,A24)') CTMP,FDATE() WRITE(6,'(A15,A24)') CTMP,'' WRITE(6,'(A15)') CTMP C---- C---- header numbers C---- WRITE(6,'(A15,A)') CTMP,'--------------------' WRITE(6,'(A15,A)') CTMP,'overall: (A,T25,I8)' WRITE(6,'(A15,A,T35,I8)') CTMP,'NUMIN', NUMIN WRITE(6,'(A15,A,T35,I8)') CTMP,'NUMHID', NUMHID WRITE(6,'(A15,A,T35,I8)') CTMP,'NUMOUT', NUMOUT WRITE(6,'(A15,A,T35,I8)') CTMP,'NUMSAM', NUMSAM WRITE(6,'(A15)') CTMP C---- WRITE(6,'(A15,A,T35,I8)') CTMP,'STPSWPMAX',STPSWPMAX WRITE(6,'(A15,A,T35,I8)') CTMP,'STPMAX', STPMAX WRITE(6,'(A15,A,T35,I8)') CTMP,'STPINF', STPINF WRITE(6,'(A15)') CTMP C---- C---- reals C---- WRITE(6,'(A15,A)') CTMP,' ' WRITE(6,'(A15,A,T35,F15.6)')CTMP,'EPSILON', EPSILON WRITE(6,'(A15,A,T35,F15.6)')CTMP,'ALPHA', ALPHA WRITE(6,'(A15,A,T35,F15.6)')CTMP,'TEMPERATURE',TEMPERATURE WRITE(6,'(A15)') CTMP C---- WRITE(6,'(A15,A,T35,I8)') CTMP,'ERRBINSTOP', ERRBINSTOP WRITE(6,'(A15,A,T35,F15.6)')CTMP,'ERRSTOP', ERRSTOP WRITE(6,'(A15)') CTMP C---- C---- characters C---- WRITE(6,'(A15,A)') CTMP,' ' WRITE(6,'(A15,A,T35,A)') CTMP,'TRNTYPE', + TRNTYPE(1:FILEN_STRING(TRNTYPE)) WRITE(6,'(A15,A,T35,A)') CTMP,'TRGTYPE', + TRGTYPE(1:FILEN_STRING(TRGTYPE)) WRITE(6,'(A15,A,T35,A)') CTMP,'ERRTYPE', + ERRTYPE(1:FILEN_STRING(ERRTYPE)) WRITE(6,'(A15)') CTMP WRITE(6,'(A15,A,T35,A)') CTMP,'MODEPRED', + MODEPRED(1:FILEN_STRING(MODEPRED)) WRITE(6,'(A15,A,T35,A)') CTMP,'MODENET', + MODENET(1:FILEN_STRING(MODENET)) WRITE(6,'(A15,A,T35,A)') CTMP,'MODEIN', + MODEIN(1:FILEN_STRING(MODEIN)) WRITE(6,'(A15,A,T35,A)') CTMP,'MODEJOB', + MODEJOB(1:FILEN_STRING(MODEJOB)) C---- C---- files C---- DO IT=1,NUMFILEIN_IN WRITE(6,'(A15,A,T30,I4,A1,A)')CTMP,'FILEIN_IN',IT,' ', + FILEIN_IN(IT)(1:FILEN_STRING(FILEIN_IN(IT))) END DO DO IT=1,NUMFILEIN_OUT WRITE(6,'(A15,A,T30,I4,A1,A)')CTMP,'FILEIN_OUT',IT,' ', + FILEIN_OUT(IT)(1:FILEN_STRING(FILEIN_OUT(IT))) END DO WRITE(6,'(A15,A,T35,A)')CTMP, + 'FILEIN_JCT',FILEIN_JCT(1:FILEN_STRING(FILEOUT_JCT)) C DO IT=1,NUMFILEOUT_OUT DO IT=1,STPTMP WRITE(6,'(A15,A,T30,I4,A1,A)')CTMP,'FILEOUT_OUT',IT,' ', + FILEOUT_OUT(IT)(1:FILEN_STRING(FILEOUT_OUT(IT))) END DO C DO IT=1,NUMFILEOUT_JCT DO IT=1,STPTMP WRITE(6,'(A15,A,T30,I4,A1,A)')CTMP,'FILEOUT_JCT',IT,' ', + FILEOUT_JCT(IT)(1:FILEN_STRING(FILEOUT_JCT(IT))) END DO WRITE(6,'(A15,A,T35)')CTMP,'end of reading parameters' C---- C---- error history C---- CALL WRTERR(6,'STDOUT',STPTMP) C---- C---- current accuracy (err,errbin, asf) C---- WRITE(6,'(A15,A)') CTMP,'--------------------' WRITE(6,'(A15,A)') CTMP,'accuracy: ' WRITE(6,'(A15,A6,A2,I8,A,A2,F8.4)')CTMP, + 'STP ',': ',STPNOW, ' ERR ',': ',ERR(STPINFCNT) WRITE(6,'(A15,A6,A2,I8,A,A2,F8.4)')CTMP, + 'STPINF',': ',STPINFCNT,' ERRBIN',': ',ERRBIN(STPINFCNT) C---- WRITE(6,'(A15)') CTMP WRITE(6,'(A15,A50)') CTMP,CTMP2 END ***** end of WRTSCR ***** ------------------------------------------------------------------ ***** SUB WRTYEAH ***** ------------------------------------------------------------------ C---- C---- NAME : WRTYEAH C---- ARG : KUNIT,FILE C---- DES : writes specific details about current job C---- IN : C---- FROM : MAIN C---- CALL2: C---- *----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * CUBIC/LION http://cubic.bioc.columbia.edu * * Columbia University rost@columbia.edu * * changed: June, 1998 version 0.2 * * changed: Aug, 1998 version 1.0 * *----------------------------------------------------------------------* SUBROUTINE WRTYEAH(KUNIT,FILE) C---- include parameter files INCLUDE 'profPar.f' C---- local function INTEGER FILEN_STRING C---- local variables INTEGER KUNIT CHARACTER*(*) FILE CHARACTER*80 CTMP ******------------------------------*-----------------------------****** C---- open file IF (KUNIT.NE.6) THEN CALL SFILEOPEN(KUNIT,FILE,'UNKNOWN',456,' ') END IF C---- write CTMP='--- WRTYEAH ' WRITE(KUNIT,'(A5)')CTMP WRITE(KUNIT,'(A,T16,A)')CTMP,'everything seems fine! HAPPY??' C---- close file IF (KUNIT.NE.6) THEN CLOSE(KUNIT) END IF END ***** end of WRTYEAH C---- vim:et: profnet-1.0.22/src/profPar.f0000644015075101507510000002165512021362711015122 0ustar lkajanlkajan*----------------------------------------------------------------------* * Burkhard Rost May, 1998 version 0.1 * * EMBL/LION http://www.embl-heidelberg.de/~rost/ * * D-69012 Heidelberg rost@embl-heidelberg.de * * changed: June, 1998 version 0.2 * *----------------------------------------------------------------------* ***** ------------------------------------------------------------------ ***** nnPar.f ***** ------------------------------------------------------------------ * This file contains the parameters and variables for a particular * * run of program nn.f * C---- ------------------------------------------------------------------ IMPLICIT NONE C---- ------------------------------------------------------------------ C---- PARAMETERS C---- ------------------------------------------------------------------ C---- number of command line arguments INTEGER NUMARG_MAX C---- architecture of network INTEGER NUMIN_MAX,NUMOUT_MAX,NUMHID_MAX C---- I/O-vectors (maximal number of sam) INTEGER NUMSAM_MAX C---- error-back-propagation steps INTEGER STPSWPMAX_MAX,STPMAX_MAX C---- number of input/output files INTEGER NUMFILES_MAX *---- ------------------------------------------------- * C G M T C lkajan: Tune these to the particular network in question - understand C lkajan: what it needs. C lkajan: The below numbers are the values used by prof as in C lkajan: prof{sec,acc}: PARAMETER (NUMIN_MAX= 800) C lkajan: The below number of 10000 is suitable for a method that C lkajan: presents a sample for each amino acids of a protein because C lkajan: we do not encounter a protein longer than 10000AA very often. PARAMETER (NUMSAM_MAX= 10000) PARAMETER (NUMHID_MAX= 100) PARAMETER (NUMOUT_MAX= 10) PARAMETER (NUMFILES_MAX= 2) PARAMETER (STPSWPMAX_MAX= 5) C lkajan: STPMAX_MAX somehow controls the number of input vectors that can C lkajan: be evaluated in one go. There is a simple integer array that gets C lkajan: allocated to STPMAX_MAX size. PARAMETER (STPMAX_MAX= 5) PARAMETER (NUMARG_MAX= 500) C G M T *---- ------------------------------------------------- * C---- tab C CHARACTER CTAB C PARAMETER (CTAB=CHAR(9)) C---- ------------------------------------------------------------------ C---- CONSTANTS C---- ------------------------------------------------------------------ C---- architecture INTEGER NUMLAYERS,NUMIN,NUMOUT,NUMHID,JCT_MAX,BITACC C---- back-propagation INTEGER STPSWPMAX,STPMAX,STPINF,ERRBINSTOP REAL TEMPERATURE,EPSILON,ALPHA, + ERRBIAS,DICEITRVL,ERRSTOP,ERRBINACC CHARACTER*456 TRNTYPE,ERRTYPE,TRGTYPE C---- data handling INTEGER DICESEED,DICESEED1,DICESEED_ADDJCT,DICESEED_ADDTRN REAL ABW,INVABW,NEGINVABW,MAXCPUTIME,TIMEOUT C---- input/output LOGICAL LOGI_RDPAR,LOGI_RDIN,LOGI_RDOUT,LOGI_SCREEN, + LOGI_RDPARWRT,LOGI_RDINWRT,LOGI_RDOUTWRT, + LOGI_RDJCTWRT,LOGI_TMPWRTOUT,LOGI_TMPWRTJB C---- general LOGICAL LOGI_TRANSLATE(0:1) C for information, only! CHARACTER*80 MODEPRED,MODENET,MODEIN,MODEOUT,MODEJOB *---- ------------------------------------------------- * COMMON /CON_ARCH/NUMLAYERS,NUMIN,NUMOUT,NUMHID,JCT_MAX,BITACC COMMON /CON_PROP1/TEMPERATURE,EPSILON,ALPHA, + ERRBIAS,DICEITRVL,ERRSTOP,ERRBINACC COMMON /CON_PROP2/TRNTYPE,ERRTYPE,TRGTYPE COMMON /CON_PROP3/STPSWPMAX,STPMAX,STPINF,ERRBINSTOP COMMON /CON_DATA1/DICESEED,DICESEED1, + DICESEED_ADDJCT,DICESEED_ADDTRN COMMON /CON_DATA2/ABW,INVABW,NEGINVABW,MAXCPUTIME,TIMEOUT COMMON /CON_IO1/LOGI_RDPAR,LOGI_RDIN,LOGI_RDOUT,LOGI_SCREEN, + LOGI_RDPARWRT,LOGI_RDINWRT,LOGI_RDOUTWRT, + LOGI_RDJCTWRT,LOGI_TMPWRTOUT,LOGI_TMPWRTJB COMMON /CON_GEN1/LOGI_TRANSLATE COMMON /CON_GEN2/MODEPRED,MODENET,MODEIN,MODEOUT,MODEJOB C---- ------------------------------------------------------------------ C---- VARIABLES C---- ------------------------------------------------------------------ C---- main program INTEGER LENPATH_ARCH CHARACTER*456 PATH_ARCH COMMON /MAIN1/LENPATH_ARCH COMMON /MAIN2/PATH_ARCH C---- managing command line input INTEGER NUMARGUMENTS CHARACTER*456 PASSED_ARGC(1:NUMARG_MAX) LOGICAL LOGI_INTERACTIVE,LOGI_SWITCH,LOGI_DEBUG COMMON /INUMARGC/PASSED_ARGC COMMON /INUMARGI/NUMARGUMENTS COMMON /INUMARGL/LOGI_INTERACTIVE,LOGI_SWITCH,LOGI_DEBUG C---- input files INTEGER NUMFILEIN_IN,NUMFILEIN_OUT CHARACTER*456 FILEIN_PAR,FILEIN_JCT,FILEIN_SAM, + FILEIN_IN(1:NUMFILES_MAX),FILEIN_OUT(1:NUMFILES_MAX) C---- output files INTEGER NUMFILEOUT_JCT,NUMFILEOUT_OUT CHARACTER*456 FILEOUT_OUT(1:NUMFILES_MAX), + FILEOUT_JCT(1:NUMFILES_MAX), + FILEOUT_ERR,FILEOUT_YEAH COMMON /FILE1/FILEIN_PAR,FILEIN_IN,FILEIN_OUT,FILEIN_JCT, + FILEIN_SAM,FILEOUT_OUT,FILEOUT_JCT, + FILEOUT_ERR,FILEOUT_YEAH COMMON /FILE2/NUMFILEIN_IN,NUMFILEIN_OUT, + NUMFILEOUT_JCT,NUMFILEOUT_OUT *---- ------------------------------------------------- * C---- input vectors INTEGER NUMSAM,NUMSAMFILE,MAXINPUT,POSWIN INTEGER*2 INPUT(1:(NUMIN_MAX+1),1:NUMSAM_MAX), + OUTDES(1:NUMOUT_MAX,1:NUMSAM_MAX), + OUTWIN(1:NUMSAM_MAX) REAL*4 OUTPUT(1:NUMOUT_MAX) COMMON /INVEC1/NUMSAM,NUMSAMFILE,MAXINPUT,POSWIN COMMON /INVEC2/INPUT,OUTDES,OUTWIN COMMON /INVEC3/OUTPUT *---- ------------------------------------------------- * C---- junctions C---- for NUMLAYERS=1 C REAL JCT1ST(1:(NUMIN_MAX+1),1:NUMOUT_MAX), C + DJCT1ST(1:(NUMIN_MAX+1),1:NUMOUT_MAX), C + PDJCT1ST(1:(NUMIN_MAX+1),1:NUMOUT_MAX), C + FLD1ST(1:NUMOUT_MAX) C---- for NUMLAYERS=2 REAL JCT1ST(1:(NUMIN_MAX+1),1:NUMHID_MAX), + DJCT1ST(1:(NUMIN_MAX+1),1:NUMHID_MAX), + PDJCT1ST(1:(NUMIN_MAX+1),1:NUMHID_MAX), + FLD1ST(1:NUMHID_MAX) REAL OUTHID(1:(NUMHID_MAX+1)), + JCT2ND(1:(NUMHID_MAX+1),1:NUMOUT_MAX), + DJCT2ND(1:(NUMHID_MAX+1),1:NUMOUT_MAX), + PDJCT2ND(1:(NUMHID_MAX+1),1:NUMOUT_MAX), + FLD2ND(1:NUMOUT_MAX) COMMON /ARCHJ/JCT1ST,DJCT1ST,PDJCT1ST,FLD1ST,OUTHID, + JCT2ND,DJCT2ND,PDJCT2ND,FLD2ND *---- ------------------------------------------------- * C---- back-propagation INTEGER STPSWPNOW,STPNOW,STPINFNOW,STPINFCNT, + PICKSAM(1:STPMAX_MAX),OKBIN(0:(STPSWPMAX_MAX+1)) REAL ERR(0:(STPSWPMAX_MAX+1)), + ERRBIN(0:(STPSWPMAX_MAX+1)) COMMON /PROP4/STPSWPNOW,STPNOW,STPINFNOW,STPINFCNT,PICKSAM,OKBIN COMMON /PROP5/ERR,ERRBIN *---- ------------------------------------------------- * C---- interpretations REAL THRESHOUT COMMON /MEANING1/THRESHOUT *---- ------------------------------------------------- * C---- time CHARACTER*24 STARTDATE,ENDDATE CHARACTER*8 STARTTIME,ENDTIME REAL TIMEDIFF,TIMEARRAY,TIMESTART,TIMERUN,TIMEEND LOGICAL TIMEFLAG COMMON /CLOCK1/STARTDATE,ENDDATE,STARTTIME,ENDTIME COMMON /CLOCK2/TIMEARRAY,TIMEDIFF,TIMESTART,TIMERUN,TIMEEND COMMON /CLOCK3/TIMEFLAG * * *---- ------------------------------------------------- * C---- garbage variables in order to spare memory space (eqUIVALENCE..) LOGICAL GARBAGEFLAG(1:(NUMSAM_MAX+100)) COMMON /FLAG1/GARBAGEFLAG C---- ------------------------------------------------------------------ ***** end of nnPar profnet-1.0.22/src/tmp.f0000644015075101507510000000057512021362711014307 0ustar lkajanlkajan program tmp character*24 actdate,fdate INTEGER DATE_TIME character*10 big(3) C ACTDATE=FDATE() ACTDATE='' write(6,*)'xx act=',actdate call DATE_and_time(big(1),big(2),big(3),date_time) write(6,*)'xx 1=',big(1) write(6,*)'xx 2=',big(2) write(6,*)'xx 3=',big(3) write(6,*)'xx d=',date_time end profnet-1.0.22/AUTHORS0000644015075101507510000000105412021362710013611 0ustar lkajanlkajanAuthors: Burkhard Rost Bug fixes and enhancements by Laszlo Kajan and Guy Yachdav Copyright: Copyright 1998-2011 by Burkhard Rost EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE) Copyright 2009-2011 by Laszlo Kajan Technical University Munich (Munich, DE) Copyright 2009-2011 by Guy Yachdav CUBIC (Columbia University, NY, USA) and Technical University Munich (Munich, DE) profnet-1.0.22/COPYING0000644015075101507510000010451312021362710013600 0ustar lkajanlkajan GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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But first, please read . profnet-1.0.22/ChangeLog0000644015075101507510000000757012021415647014334 0ustar lkajanlkajanprofnet (1.0.22) unstable; urgency=low * Removed -fbounds-check from all Makefiles in order to fix the 'Actual string length is shorter than the declared one' issue. -- Laszlo Kajan Tue, 04 Sep 2012 14:06:13 +0200 profnet (1.0.21) unstable; urgency=low * fixed ERRBINSTOP REAL issue -- Laszlo Kajan Tue, 21 Jun 2011 16:14:12 +0200 profnet (1.0.20) * enhanced man page * added GPL v3 as COPYING * fixed unused LOGIUNK issue * removed -Werror gfortran argument * fixed INTEGER(4) to INTEGER(2) warnings, mostly with INT2() conversion -- Laszlo Kajan Tue, 14 Jun 2011 12:49:12 +0200 profnet (1.0.19) * added profnet_chop -- Laszlo Kajan Wed, 12 May 2010 19:57:07 +0200 profnet (1.0.18) * corrected NUMIN-comment for norsnet * added metadisorder (MD) -- Laszlo Kajan Wed, 17 Mar 2010 14:50:50 +0100 profnet (1.0.17) * added profnet_isis -- Laszlo Kajan Fri, 26 Feb 2010 11:23:20 +0100 profnet (1.0.16) * added 'patch' target * added profnet_con network for profcon -- Laszlo Kajan Tue, 23 Feb 2010 10:51:46 +0100 profnet (1.0.15) * prof for norsnet is the same as for bval - there should be only one. Now at least both are the same here. -- Laszlo Kajan Wed, 17 Feb 2010 11:41:07 +0100 profnet (1.0.14) * Burkhard recommended to change RDATE to a simple empty (initialized) string '' -- Laszlo Kajan Thu, 11 Feb 2010 12:25:05 +0100 profnet (1.0.13) * Increased STPMAX_MAX to 100000 for profnet_snapfun * Corrected FDATE calls for phd * Removed src-phd/mat * Replaced uninitialized string FDATE with call to FDATE() funtion -- Laszlo Kajan Wed, 10 Feb 2010 13:21:15 +0100 profnet (1.0.12) * added phd1994 man page * initialized variables instead of -finit-local-zero -- Laszlo Kajan Tue, 05 Jan 2010 18:04:58 +0100 profnet (1.0.11) * norsnet added * prof added (profsec, profacc). Notably phd is a different source unrelated to this set. * many updates incorporated from profphd's prof_nn sources * renamed sources nn* to prof* -- Laszlo Kajan Fri, 18 Dec 2009 13:56:10 +0100 profnet (1.0.10) * profnet_bval magic understood: broken code that checked if NUMIN was <= NUMIN_MAX allowed Avner to get away with loading 209 input nodes to a space for 194 * NUMIN_MAX bug fixed in common source but that fix breaks profbval so that one is still made with required bug in place. Attempts to get profbval perform with the fixed code failed, a retraining of the network is recommended. -- Laszlo Kajan Thu, 17 Dec 2009 18:14:45 +0100 profnet (1.0.8) * snap -> snapfun (Yana suggested new name) -- Laszlo Kajan Thu, 10 Dec 2009 14:20:29 +0100 profnet (1.0.7) * added profnet_snap -- Guy Yachdav Thu, 10 Dec 2009 09:04:30 +0100 profnet (1.0.5) * commited new version of source files that make profnet produce the correct predictions -- Guy Yachdav Tue, 08 Dec 2009 16:12:16 +0100 profnet (1.0.4) * commited new version of source files that make profnet produce the correct predictions -- Guy Yachdav Tue, 08 Dec 2009 16:12:16 +0100 profnet (1.0.3) * man page change to include command line options. -- Guy Yachdav Wed, 02 Dec 2009 11:58:14 +0100 profnet (1.0.2) * man page change to include command line options. -- Guy Yachdav Sun, 29 Nov 2009 18:14:50 +0100 profnet (1.0.1) * Compiles cleanly -- Guy Yachdav Mon, 30 Nov 2009 16:00:19 +0100 profnet (1.0.0) * Initial version. -- Guy Yachdav Sun, 29 Nov 2009 18:14:50 +0100 profnet-1.0.22/Makefile0000644015075101507510000000735212021367476014226 0ustar lkajanlkajanPACKAGE := profnet VERSION := 1.0.22 DISTDIR := $(PACKAGE)-$(VERSION) SRCDIR := src NET := bval chop con isis md norsnet prof snapfun NETDIR := $(addsuffix _dir,$(NET)) NETDIFF := $(addprefix diff-,$(NET)) NETPATCH := $(NET:%=%_dir/patch_stamp) NETPATCHNEW := $(addsuffix .patch.new,$(NET)) NETDISTCLEAN := $(addprefix distclean-,$(NET)) NETINSTALL := $(addprefix install-,$(NET)) MAN1POD := profnet.pod MAN1GZ := $(MAN1POD:%.pod=%.1.gz) all: net man phd net: $(NET) diff: $(NETDIFF) $(NETDIFF) : diff-% : %.patch.new $(NETPATCHNEW): %.patch.new : if [ -d $*_dir ]; then \ diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src $*_dir > $@ || true; \ fi $(NETDIR) : %_dir : mkdir -p $@ && rsync -avC src/. ./$@/. %_dir/patch_stamp: | %_dir patch -p 1 -E -d $*_dir < $*.patch && touch $@ patch: $(NETPATCH) $(NET) : % : | %_dir/patch_stamp $(MAKE) -C $@_dir $(NETINSTALL) : install-% : mkdir -p $(DESTDIR)$(prefix)/bin && \ cp -a $*_dir/profnet_$* \ $(DESTDIR)$(prefix)/bin/ mkdir -p $(DESTDIR)$(prefix)/share/man/man1 && cp $(MAN1GZ) $(DESTDIR)$(prefix)/share/man/man1/profnet_$*.1.gz phd: $(MAKE) -C src-phd install-phd: $(MAKE) -C src-phd install mkdir -p $(DESTDIR)$(prefix)/share/man/man1 && cp $(MAN1GZ) $(DESTDIR)$(prefix)/share/man/man1/profphd_net.1.gz rm -f $(DESTDIR)$(prefix)/share/man/man1/phd1994.1.gz && ln -s profphd_net.1.gz $(DESTDIR)$(prefix)/share/man/man1/phd1994.1.gz install: $(NETINSTALL) install-phd man: $(MAN1GZ) $(MAN3:%.pod=%.3.gz) $(MAN1GZ) : %.1.gz : %.pod pod2man -c 'User Commands' -r "$(VERSION)-$(RGVERSION)" $< | gzip -c > $@ help: @echo "Rules:" @echo "all* - build all" @echo "net - make all network binaries" @echo "$(NET) -" @echo " make a specific network binary" @echo "diff - prepare patch files for profnet varieties" @echo "$(NETDIFF) -" @echo " make a specific network variety patch" @echo " A diff is run between the src dir - the base network - and the" @echo " variety given. This prepares a patch file with .patch.new extension" @echo " that can me renamed to .patch. Network varieties are obtained by" @echo " applying the appropriate .patch file to the base network in src." @echo " Importantly only these patch files are distributed with this package," @echo " the network variety directories (e.g. snapfun_dir) are used only for" @echo " building the binary. Preserve your updates to the base version" @echo " by preparing and updating the appropriate patch file." @echo "$(NETDISTCLEAN) -" @echo " distclean a specific network variety" @echo "clean" @echo "dist" @echo "distclean" @echo "man - make all manual pages" @echo "install - install all" @echo "$(NETINSTALL) -" @echo " install a specific variety to \$$DESTDIR\$$prefix" @echo "install-phd - install profphd_net" @echo "patch - patch and prepare all for compilation" @echo "phd - make profphd_net" @echo @echo "Variables:" @echo " Meaning and purpose not clear any more." @echo "DESTDIR - install to DESTDIR" @echo "prefix - common installation prefix for all files" @echo " use prefix=$$HOME to build for personal use" distclean: clean $(NETDISTCLEAN) rm -rf\ $(DISTDIR) \ $(DISTDIR).tar.gz $(NETDISTCLEAN) : distclean-% : rm -rf $*_dir dist: $(DISTDIR) tar -ch -f - "$(DISTDIR)" | gzip -c >$(DISTDIR).tar.gz rm -rf $(DISTDIR) $(DISTDIR): distclean rm -rf $(DISTDIR) && mkdir -p $(DISTDIR) && \ rsync -avC \ --exclude /*-stamp \ --exclude .*.swp \ --exclude debian \ AUTHORS \ ChangeLog \ COPYING \ Makefile \ $(PACKAGE).spec \ src \ src-phd \ *.patch \ *.pod \ $(DISTDIR)/; clean: $(MAKE) -C src clean $(MAKE) -C src-phd clean rm -f *.[0123456789].gz .PHONY: all clean diff install-phd man net patch phd $(NET) $(NETDIFF) $(NETDISTCLEAN) $(NETPATCHNEW) # vim:ai: profnet-1.0.22/bval.patch0000644015075101507510000001352312021363354014517 0ustar lkajanlkajandiff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile bval_dir/Makefile --- src/Makefile 2010-02-10 17:55:33.923514458 +0100 +++ bval_dir/Makefile 2010-02-23 10:38:31.247646372 +0100 @@ -1,9 +1,9 @@ #===================================================================== F77 = gfortran -BIN = profnet_prof +BIN = profnet_bval #===================================================================== ARCH = LINUX FFLAGS := $(FFLAGS) -O2 -Wuninitialized FFLAGS := $(FFLAGS) -Wall -Wno-unused #===================================================================== NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/prof.f bval_dir/prof.f --- src/prof.f 2010-02-11 12:59:41.891647105 +0100 +++ bval_dir/prof.f 2010-02-23 10:38:31.367649047 +0100 @@ -1850,45 +1850,45 @@ C---- interpret IF (HC(1:5) .EQ.'NUMIN') THEN NUMIN=VARIN - CALL RDPAR_ERR('NUMIN ',VARIN) + CALL RDPAR_ERR('NUMIN',VARIN) ELSEIF (HC(1:6) .EQ.'NUMHID') THEN NUMHID=VARIN - CALL RDPAR_ERR('NUMHID ',VARIN) + CALL RDPAR_ERR('NUMHID',VARIN) ELSEIF (HC(1:6) .EQ.'NUMOUT') THEN NUMOUT=VARIN - CALL RDPAR_ERR('NUMOUT ',VARIN) + CALL RDPAR_ERR('NUMOUT',VARIN) ELSEIF (HC(1:9) .EQ.'NUMLAYERS') THEN NUMLAYERS=VARIN ELSEIF (HC(1:6) .EQ.'NUMSAM') THEN NUMSAM=VARIN - CALL RDPAR_ERR('NUMSAM ',VARIN) + CALL RDPAR_ERR('NUMSAM',VARIN) C---- C---- number of files C---- ELSEIF (HC(1:12).EQ.'NUMFILEIN_IN') THEN NUMFILEIN_IN=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) ELSEIF (HC(1:13).EQ.'NUMFILEIN_OUT') THEN NUMFILEIN_OUT=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) ELSEIF (HC(1:14).EQ.'NUMFILEOUT_OUT') THEN NUMFILEOUT_OUT=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) ELSEIF (HC(1:14).EQ.'NUMFILEOUT_JCT') THEN NUMFILEOUT_JCT=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) C---- C---- training times C---- ELSEIF (HC(1:9) .EQ.'STPSWPMAX') THEN STPSWPMAX=VARIN - CALL RDPAR_ERR('STPSWPMAX ',VARIN) + CALL RDPAR_ERR('STPSWPMAX',VARIN) ELSEIF (HC(1:6) .EQ.'STPMAX') THEN STPMAX=VARIN - CALL RDPAR_ERR('STPMAX ',VARIN) + CALL RDPAR_ERR('STPMAX',VARIN) ELSEIF (HC(1:6) .EQ.'STPINF') THEN STPINF=VARIN - CALL RDPAR_ERR('STPINF ',VARIN) + CALL RDPAR_ERR('STPINF',VARIN) ELSEIF (HC(1:6) .EQ.'BITACC') THEN BITACC=VARIN ELSEIF (HC(1:10).EQ.'ERRBINSTOP') THEN @@ -2176,23 +2176,19 @@ C---- ------------------------------------------------------------------ C---- C---- ------------------------------------------------------------------ - IF (CHAR_RD(1:6) .EQ. 'NUMIN ' .AND. - + NUMIN .GT. NUMIN_MAX) THEN + IF (CHAR_RD .EQ. 'NUMIN' .AND. NUMIN .GT. NUMIN_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMIN read=',NUMIN,' NUMIN_MAX=',NUMIN_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' - ELSEIF (CHAR_RD(1:7) .EQ. 'NUMHID ' .AND. - + NUMHID .GT. NUMHID_MAX) THEN + ELSEIF (CHAR_RD .EQ. 'NUMHID' .AND. NUMHID .GT. NUMHID_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMHID read=',NUMHID,' NUMHID_MAX=',NUMHID_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' - ELSEIF (CHAR_RD(1:7) .EQ. 'NUMOUT ' .AND. - + NUMOUT .GT. NUMOUT_MAX) THEN + ELSEIF (CHAR_RD .EQ. 'NUMOUT' .AND. NUMOUT .GT. NUMOUT_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMOUT read=',NUMOUT,' NUMOUT_MAX=',NUMOUT_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' - ELSEIF (CHAR_RD(1:7) .EQ. 'NUMSAM ' .AND. - + NUMSAM .GT. NUMSAM_MAX) THEN + ELSEIF (CHAR_RD .EQ. 'NUMSAM' .AND. NUMSAM .GT. NUMSAM_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMSAM read=',NUMSAM,' NUMSAM_MAX=',NUMSAM_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f bval_dir/profPar.f --- src/profPar.f 2010-02-23 10:17:25.315661972 +0100 +++ bval_dir/profPar.f 2010-02-23 10:38:31.375656536 +0100 @@ -30,17 +30,17 @@ C lkajan: Tune these to the particular network in question - understand C lkajan: what it needs. -C lkajan: The below numbers are the values used by prof as in -C lkajan: prof{sec,acc}: - PARAMETER (NUMIN_MAX= 800) -C lkajan: The below number of 10000 is suitable for a method that -C lkajan: presents a sample for each amino acids of a protein because -C lkajan: we do not encounter a protein longer than 10000AA very often. - PARAMETER (NUMSAM_MAX= 10000) - PARAMETER (NUMHID_MAX= 100) - PARAMETER (NUMOUT_MAX= 10) - PARAMETER (NUMFILES_MAX= 2) - PARAMETER (STPSWPMAX_MAX= 5) + PARAMETER (NUMIN_MAX= 194) +C lkajan: We need the big number for NUMSAM_MAX to make up for the +C lkajan: under-defined NUMIN_MAX (194 instead of 209). +C lkajan: Same for NUMHID_MAX. +C lkajan: PARAMETER (NUMSAM_MAX= 822700) + PARAMETER (NUMSAM_MAX= 40000) + PARAMETER (NUMHID_MAX= 500) + PARAMETER (NUMOUT_MAX= 2) + PARAMETER (NUMFILES_MAX= 336) + PARAMETER (STPSWPMAX_MAX= 200) +C lkajan: PARAMETER (STPMAX_MAX= 99999999) C lkajan: STPMAX_MAX somehow controls the number of input vectors that can C lkajan: be evaluated in one go. There is a simple integer array that gets C lkajan: allocated to STPMAX_MAX size. profnet-1.0.22/chop.patch0000644015075101507510000000074112021362712014517 0ustar lkajanlkajandiff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile chop_dir/Makefile --- src/Makefile 2010-02-10 17:55:33.923514458 +0100 +++ chop_dir/Makefile 2010-05-12 20:05:09.819459484 +0200 @@ -1,6 +1,6 @@ #===================================================================== F77 = gfortran -BIN = profnet_prof +BIN = profnet_chop #===================================================================== ARCH = LINUX FFLAGS := -O3 -fbounds-check -Wuninitialized profnet-1.0.22/con.patch0000644015075101507510000000360012021362710014340 0ustar lkajanlkajandiff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile con_dir/Makefile --- src/Makefile 2010-02-10 17:55:33.923514458 +0100 +++ con_dir/Makefile 2010-02-23 10:48:22.263658539 +0100 @@ -1,6 +1,6 @@ #===================================================================== F77 = gfortran -BIN = profnet_prof +BIN = profnet_con #===================================================================== ARCH = LINUX FFLAGS := -O3 -fbounds-check -Wuninitialized diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f con_dir/profPar.f --- src/profPar.f 2010-02-23 10:17:25.315661972 +0100 +++ con_dir/profPar.f 2010-02-23 10:47:35.907691244 +0100 @@ -32,19 +32,20 @@ C lkajan: what it needs. C lkajan: The below numbers are the values used by prof as in C lkajan: prof{sec,acc}: - PARAMETER (NUMIN_MAX= 800) + PARAMETER (NUMIN_MAX= 767) C lkajan: The below number of 10000 is suitable for a method that C lkajan: presents a sample for each amino acids of a protein because C lkajan: we do not encounter a protein longer than 10000AA very often. - PARAMETER (NUMSAM_MAX= 10000) + PARAMETER (NUMSAM_MAX= 310000) PARAMETER (NUMHID_MAX= 100) PARAMETER (NUMOUT_MAX= 10) - PARAMETER (NUMFILES_MAX= 2) - PARAMETER (STPSWPMAX_MAX= 5) + PARAMETER (NUMFILES_MAX= 336) + PARAMETER (STPSWPMAX_MAX= 200) C lkajan: STPMAX_MAX somehow controls the number of input vectors that can C lkajan: be evaluated in one go. There is a simple integer array that gets C lkajan: allocated to STPMAX_MAX size. - PARAMETER (STPMAX_MAX= 5) +C PARAMETER (STPMAX_MAX= 99999999) seems unreasonably high + PARAMETER (STPMAX_MAX= 1000000) PARAMETER (NUMARG_MAX= 500) C G M T profnet-1.0.22/isis.patch0000644015075101507510000000363612021362710014541 0ustar lkajanlkajandiff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile isis_dir/Makefile --- src/Makefile 2010-02-10 17:55:33.923514458 +0100 +++ isis_dir/Makefile 2010-02-26 11:22:10.199787414 +0100 @@ -1,6 +1,6 @@ #===================================================================== F77 = gfortran -BIN = profnet_prof +BIN = profnet_isis #===================================================================== ARCH = LINUX FFLAGS := -O3 -fbounds-check -Wuninitialized diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f isis_dir/profPar.f --- src/profPar.f 2010-02-23 10:17:25.315661972 +0100 +++ isis_dir/profPar.f 2010-02-26 11:20:32.863648133 +0100 @@ -32,19 +32,23 @@ C lkajan: what it needs. C lkajan: The below numbers are the values used by prof as in C lkajan: prof{sec,acc}: +C PARAMETER (NUMIN_MAX= 270) PARAMETER (NUMIN_MAX= 800) C lkajan: The below number of 10000 is suitable for a method that C lkajan: presents a sample for each amino acids of a protein because C lkajan: we do not encounter a protein longer than 10000AA very often. - PARAMETER (NUMSAM_MAX= 10000) + PARAMETER (NUMSAM_MAX= 422700) +C PARAMETER (NUMHID_MAX= 50) PARAMETER (NUMHID_MAX= 100) PARAMETER (NUMOUT_MAX= 10) +C PARAMETER (NUMFILES_MAX= 336) PARAMETER (NUMFILES_MAX= 2) - PARAMETER (STPSWPMAX_MAX= 5) + PARAMETER (STPSWPMAX_MAX= 200) C lkajan: STPMAX_MAX somehow controls the number of input vectors that can C lkajan: be evaluated in one go. There is a simple integer array that gets C lkajan: allocated to STPMAX_MAX size. - PARAMETER (STPMAX_MAX= 5) +C PARAMETER (STPMAX_MAX= 99999999) + PARAMETER (STPMAX_MAX= 1000000) PARAMETER (NUMARG_MAX= 500) C G M T profnet-1.0.22/md.patch0000644015075101507510000001377312021363617014204 0ustar lkajanlkajandiff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile md_dir/Makefile --- src/Makefile 2010-02-10 17:55:33.923514458 +0100 +++ md_dir/Makefile 2010-02-23 10:38:31.247646372 +0100 @@ -1,9 +1,9 @@ #===================================================================== F77 = gfortran -BIN = profnet_prof +BIN = profnet_md #===================================================================== ARCH = LINUX FFLAGS := $(FFLAGS) -O2 -Wuninitialized FFLAGS := $(FFLAGS) -Wall -Wno-unused #===================================================================== NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/prof.f md_dir/prof.f --- src/prof.f 2010-02-11 12:59:41.891647105 +0100 +++ md_dir/prof.f 2010-02-23 10:38:31.367649047 +0100 @@ -1850,45 +1850,45 @@ C---- interpret IF (HC(1:5) .EQ.'NUMIN') THEN NUMIN=VARIN - CALL RDPAR_ERR('NUMIN ',VARIN) + CALL RDPAR_ERR('NUMIN',VARIN) ELSEIF (HC(1:6) .EQ.'NUMHID') THEN NUMHID=VARIN - CALL RDPAR_ERR('NUMHID ',VARIN) + CALL RDPAR_ERR('NUMHID',VARIN) ELSEIF (HC(1:6) .EQ.'NUMOUT') THEN NUMOUT=VARIN - CALL RDPAR_ERR('NUMOUT ',VARIN) + CALL RDPAR_ERR('NUMOUT',VARIN) ELSEIF (HC(1:9) .EQ.'NUMLAYERS') THEN NUMLAYERS=VARIN ELSEIF (HC(1:6) .EQ.'NUMSAM') THEN NUMSAM=VARIN - CALL RDPAR_ERR('NUMSAM ',VARIN) + CALL RDPAR_ERR('NUMSAM',VARIN) C---- C---- number of files C---- ELSEIF (HC(1:12).EQ.'NUMFILEIN_IN') THEN NUMFILEIN_IN=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) ELSEIF (HC(1:13).EQ.'NUMFILEIN_OUT') THEN NUMFILEIN_OUT=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) ELSEIF (HC(1:14).EQ.'NUMFILEOUT_OUT') THEN NUMFILEOUT_OUT=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) ELSEIF (HC(1:14).EQ.'NUMFILEOUT_JCT') THEN NUMFILEOUT_JCT=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) C---- C---- training times C---- ELSEIF (HC(1:9) .EQ.'STPSWPMAX') THEN STPSWPMAX=VARIN - CALL RDPAR_ERR('STPSWPMAX ',VARIN) + CALL RDPAR_ERR('STPSWPMAX',VARIN) ELSEIF (HC(1:6) .EQ.'STPMAX') THEN STPMAX=VARIN - CALL RDPAR_ERR('STPMAX ',VARIN) + CALL RDPAR_ERR('STPMAX',VARIN) ELSEIF (HC(1:6) .EQ.'STPINF') THEN STPINF=VARIN - CALL RDPAR_ERR('STPINF ',VARIN) + CALL RDPAR_ERR('STPINF',VARIN) ELSEIF (HC(1:6) .EQ.'BITACC') THEN BITACC=VARIN ELSEIF (HC(1:10).EQ.'ERRBINSTOP') THEN @@ -2176,23 +2176,19 @@ C---- ------------------------------------------------------------------ C---- C---- ------------------------------------------------------------------ - IF (CHAR_RD(1:6) .EQ. 'NUMIN ' .AND. - + NUMIN .GT. NUMIN_MAX) THEN + IF (CHAR_RD .EQ. 'NUMIN' .AND. NUMIN .GT. NUMIN_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMIN read=',NUMIN,' NUMIN_MAX=',NUMIN_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' - ELSEIF (CHAR_RD(1:7) .EQ. 'NUMHID ' .AND. - + NUMHID .GT. NUMHID_MAX) THEN + ELSEIF (CHAR_RD .EQ. 'NUMHID' .AND. NUMHID .GT. NUMHID_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMHID read=',NUMHID,' NUMHID_MAX=',NUMHID_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' - ELSEIF (CHAR_RD(1:7) .EQ. 'NUMOUT ' .AND. - + NUMOUT .GT. NUMOUT_MAX) THEN + ELSEIF (CHAR_RD .EQ. 'NUMOUT' .AND. NUMOUT .GT. NUMOUT_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMOUT read=',NUMOUT,' NUMOUT_MAX=',NUMOUT_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' - ELSEIF (CHAR_RD(1:7) .EQ. 'NUMSAM ' .AND. - + NUMSAM .GT. NUMSAM_MAX) THEN + ELSEIF (CHAR_RD .EQ. 'NUMSAM' .AND. NUMSAM .GT. NUMSAM_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMSAM read=',NUMSAM,' NUMSAM_MAX=',NUMSAM_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f md_dir/profPar.f --- src/profPar.f 2010-02-23 10:17:25.315661972 +0100 +++ md_dir/profPar.f 2010-02-23 10:38:31.375656536 +0100 @@ -30,21 +30,21 @@ C lkajan: Tune these to the particular network in question - understand C lkajan: what it needs. -C lkajan: The below numbers are the values used by prof as in -C lkajan: prof{sec,acc}: - PARAMETER (NUMIN_MAX= 800) -C lkajan: The below number of 10000 is suitable for a method that -C lkajan: presents a sample for each amino acids of a protein because -C lkajan: we do not encounter a protein longer than 10000AA very often. - PARAMETER (NUMSAM_MAX= 10000) - PARAMETER (NUMHID_MAX= 100) - PARAMETER (NUMOUT_MAX= 10) - PARAMETER (NUMFILES_MAX= 2) - PARAMETER (STPSWPMAX_MAX= 5) + PARAMETER (NUMIN_MAX= 194) +C lkajan: We need the big number for NUMSAM_MAX to make up for the +C lkajan: under-defined NUMIN_MAX (194 instead of 699). +C lkajan: Same for NUMHID_MAX. +C lkajan: PARAMETER (NUMSAM_MAX= 822700) + PARAMETER (NUMSAM_MAX= 160000) + PARAMETER (NUMHID_MAX= 500) + PARAMETER (NUMOUT_MAX= 2) + PARAMETER (NUMFILES_MAX= 336) + PARAMETER (STPSWPMAX_MAX= 200) +C lkajan: PARAMETER (STPMAX_MAX= 99999999) C lkajan: STPMAX_MAX somehow controls the number of input vectors that can C lkajan: be evaluated in one go. There is a simple integer array that gets C lkajan: allocated to STPMAX_MAX size. - PARAMETER (STPMAX_MAX= 5) + PARAMETER (STPMAX_MAX= 1000000) PARAMETER (NUMARG_MAX= 500) C G M T profnet-1.0.22/norsnet.patch0000644015075101507510000001355012021364514015262 0ustar lkajanlkajandiff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile norsnet_dir/Makefile --- src/Makefile 2010-02-10 17:55:33.923514458 +0100 +++ norsnet_dir/Makefile 2010-02-23 10:38:31.339646898 +0100 @@ -1,9 +1,9 @@ #===================================================================== F77 = gfortran -BIN = profnet_prof +BIN = profnet_norsnet #===================================================================== ARCH = LINUX FFLAGS := $(FFLAGS) -O2 -Wuninitialized FFLAGS := $(FFLAGS) -Wall -Wno-unused #===================================================================== NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/prof.f norsnet_dir/prof.f --- src/prof.f 2010-02-11 12:59:41.891647105 +0100 +++ norsnet_dir/prof.f 2010-02-23 10:38:31.371648007 +0100 @@ -1850,45 +1850,45 @@ C---- interpret IF (HC(1:5) .EQ.'NUMIN') THEN NUMIN=VARIN - CALL RDPAR_ERR('NUMIN ',VARIN) + CALL RDPAR_ERR('NUMIN',VARIN) ELSEIF (HC(1:6) .EQ.'NUMHID') THEN NUMHID=VARIN - CALL RDPAR_ERR('NUMHID ',VARIN) + CALL RDPAR_ERR('NUMHID',VARIN) ELSEIF (HC(1:6) .EQ.'NUMOUT') THEN NUMOUT=VARIN - CALL RDPAR_ERR('NUMOUT ',VARIN) + CALL RDPAR_ERR('NUMOUT',VARIN) ELSEIF (HC(1:9) .EQ.'NUMLAYERS') THEN NUMLAYERS=VARIN ELSEIF (HC(1:6) .EQ.'NUMSAM') THEN NUMSAM=VARIN - CALL RDPAR_ERR('NUMSAM ',VARIN) + CALL RDPAR_ERR('NUMSAM',VARIN) C---- C---- number of files C---- ELSEIF (HC(1:12).EQ.'NUMFILEIN_IN') THEN NUMFILEIN_IN=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) ELSEIF (HC(1:13).EQ.'NUMFILEIN_OUT') THEN NUMFILEIN_OUT=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) ELSEIF (HC(1:14).EQ.'NUMFILEOUT_OUT') THEN NUMFILEOUT_OUT=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) ELSEIF (HC(1:14).EQ.'NUMFILEOUT_JCT') THEN NUMFILEOUT_JCT=VARIN - CALL RDPAR_ERR(HC // ' ',VARIN) + CALL RDPAR_ERR(HC,VARIN) C---- C---- training times C---- ELSEIF (HC(1:9) .EQ.'STPSWPMAX') THEN STPSWPMAX=VARIN - CALL RDPAR_ERR('STPSWPMAX ',VARIN) + CALL RDPAR_ERR('STPSWPMAX',VARIN) ELSEIF (HC(1:6) .EQ.'STPMAX') THEN STPMAX=VARIN - CALL RDPAR_ERR('STPMAX ',VARIN) + CALL RDPAR_ERR('STPMAX',VARIN) ELSEIF (HC(1:6) .EQ.'STPINF') THEN STPINF=VARIN - CALL RDPAR_ERR('STPINF ',VARIN) + CALL RDPAR_ERR('STPINF',VARIN) ELSEIF (HC(1:6) .EQ.'BITACC') THEN BITACC=VARIN ELSEIF (HC(1:10).EQ.'ERRBINSTOP') THEN @@ -2176,23 +2176,19 @@ C---- ------------------------------------------------------------------ C---- C---- ------------------------------------------------------------------ - IF (CHAR_RD(1:6) .EQ. 'NUMIN ' .AND. - + NUMIN .GT. NUMIN_MAX) THEN + IF (CHAR_RD .EQ. 'NUMIN' .AND. NUMIN .GT. NUMIN_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMIN read=',NUMIN,' NUMIN_MAX=',NUMIN_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' - ELSEIF (CHAR_RD(1:7) .EQ. 'NUMHID ' .AND. - + NUMHID .GT. NUMHID_MAX) THEN + ELSEIF (CHAR_RD .EQ. 'NUMHID' .AND. NUMHID .GT. NUMHID_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMHID read=',NUMHID,' NUMHID_MAX=',NUMHID_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' - ELSEIF (CHAR_RD(1:7) .EQ. 'NUMOUT ' .AND. - + NUMOUT .GT. NUMOUT_MAX) THEN + ELSEIF (CHAR_RD .EQ. 'NUMOUT' .AND. NUMOUT .GT. NUMOUT_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMOUT read=',NUMOUT,' NUMOUT_MAX=',NUMOUT_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' - ELSEIF (CHAR_RD(1:7) .EQ. 'NUMSAM ' .AND. - + NUMSAM .GT. NUMSAM_MAX) THEN + ELSEIF (CHAR_RD .EQ. 'NUMSAM' .AND. NUMSAM .GT. NUMSAM_MAX) THEN WRITE(6,'(A,T10,A,I8,A,I8)')'***', + 'RDPAR_ERR: NUMSAM read=',NUMSAM,' NUMSAM_MAX=',NUMSAM_MAX STOP '*** RDPAR_ERR: left due to error in RDPAR_I' diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f norsnet_dir/profPar.f --- src/profPar.f 2010-02-23 10:17:25.315661972 +0100 +++ norsnet_dir/profPar.f 2010-02-23 10:38:31.379648791 +0100 @@ -30,17 +30,17 @@ C lkajan: Tune these to the particular network in question - understand C lkajan: what it needs. -C lkajan: The below numbers are the values used by prof as in -C lkajan: prof{sec,acc}: - PARAMETER (NUMIN_MAX= 800) -C lkajan: The below number of 10000 is suitable for a method that -C lkajan: presents a sample for each amino acids of a protein because -C lkajan: we do not encounter a protein longer than 10000AA very often. - PARAMETER (NUMSAM_MAX= 10000) - PARAMETER (NUMHID_MAX= 100) - PARAMETER (NUMOUT_MAX= 10) - PARAMETER (NUMFILES_MAX= 2) - PARAMETER (STPSWPMAX_MAX= 5) + PARAMETER (NUMIN_MAX= 194) +C lkajan: We need the big number for NUMSAM_MAX to make up for the +C lkajan: under-defined NUMIN_MAX (194 instead of 416). +C lkajan: Same for NUMHID_MAX. +C lkajan: PARAMETER (NUMSAM_MAX= 822700) + PARAMETER (NUMSAM_MAX= 40000) + PARAMETER (NUMHID_MAX= 500) + PARAMETER (NUMOUT_MAX= 2) + PARAMETER (NUMFILES_MAX= 336) + PARAMETER (STPSWPMAX_MAX= 200) +C lkajan: PARAMETER (STPMAX_MAX= 99999999) C lkajan: STPMAX_MAX somehow controls the number of input vectors that can C lkajan: be evaluated in one go. There is a simple integer array that gets C lkajan: allocated to STPMAX_MAX size. profnet-1.0.22/prof.patch0000644015075101507510000000000012021362710014516 0ustar lkajanlkajanprofnet-1.0.22/profnet.pod0000644015075101507510000000361312021362702014726 0ustar lkajanlkajan=head1 NAME profnet_* - neural network implementations in Fortran =head1 SYNOPSIS profnet_* [OPTION|filePar] =head1 DESCRIPTION profnet_* binaries are neural network implementations in Fortran. Due to the original design of the code, a specific binary is compiled for each particular network architecture, changing certain constants in the source code. Therefore, there is a binary for every network architecture used. Note: certain array structures are intentionally indexed out of bounds in some of the binaries. Note: This binary should only be used to run with pre-made training data, do not try to use it to train your network as it will produce undesired results. It was made to be used I as part of wrapping (dependent) packages and not as a standalone neural network program. =head1 OPTIONS This list is not exhaustive. =over =item filePar file with input parameters (also gives fileIn, fileOut) =item 1 "switch" =item 2 number of input units =item 3 number of hidden units =item 4 number of output units =item 5 number of samples =item 6 bitacc (typically 100) =item 7 file with input vectors =item 8 file with junctions =item 9 file with output of NN ("none" -> no file written) =item 10 optional=dbg =item [inter] will bring up dialog =back =head1 NOTES 1st MUST be "switch"! tested only with 2 layers! =head1 AUTHOR Burkhard Rost Bug fixes and enhancements by Laszlo Kajan and Guy Yachdav =head1 COPYRIGHT AND LICENSE Copyright 1998-2011 by Burkhard Rost EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE) Copyright 2009-2011 by Laszlo Kajan Technical University Munich (Munich, DE) Copyright 2009-2011 by Guy Yachdav CUBIC (Columbia University, NY, USA) and Technical University Munich (Munich, DE) profnet-1.0.22/profnet.spec0000644015075101507510000000751012021362710015075 0ustar lkajanlkajanSummary: neural network architectures for Rost Lab prediction methods Name: profnet Version: 1.0.20 Release: 1 License: GPL Group: Applications/Science Source: ftp://rostlab.org/%{name}/%{name}-%{version}.tar.gz URL: http://rostlab.org/ BuildRoot: %{_tmppath}/%{name}-%{version}-root BuildRequires: gcc-gfortran, rsync %define common_desc Profnet is a component of the prediction methods that make up the \ Predict Protein service by the lab of Burkhard Rost. It provides the neural \ network component to a variety of predictors that perform protein feature \ prediction directly from sequence. This neural network implementation has \ to be compiled for every different network architecture. %description %{common_desc} %package bval Summary: neural network architecture for profbval Group: Applications/Science %description bval %{common_desc} . This package contains the neural network architecture for profbval. %package chop Summary: neural network architecture for profchop Group: Applications/Science %description chop %{common_desc} . This package contains the neural network architecture for profchop. %package con Summary: neural network architecture for profcon Group: Applications/Science %description con %{common_desc} . This package contains the neural network architecture for profcon. %package isis Summary: neural network architecture for profisis Group: Applications/Science %description isis %{common_desc} . This package contains the neural network architecture for profisis. %package md Summary: neural network architecture for metadisorder Group: Applications/Science %description md %{common_desc} . This package contains the neural network architecture for metadisorder. %package norsnet Summary: neural network architecture for norsnet Group: Applications/Science %description norsnet %{common_desc} . This package contains the neural network architecture for norsnet. %package prof Summary: neural network architecture for profacc Group: Applications/Science %description prof %{common_desc} . This package contains the neural network architecture for profacc. %package snapfun Summary: neural network architecture for snapfun Group: Applications/Science %description snapfun %{common_desc} . This package contains the neural network architecture for snapfun. %package phdnet Summary: neural network architecture for profphd Group: Applications/Science %description phdnet %{common_desc} . This package contains the neural network architecture for profphd. %prep %setup -q %build make prefix=%{_prefix} %install rm -rf $RPM_BUILD_ROOT make DESTDIR=%{buildroot} prefix=%{_prefix} install %clean rm -rf $RPM_BUILD_ROOT %files %defattr(-,root,root) %doc AUTHORS %doc COPYING %files bval %defattr(-,root,root) %doc AUTHORS %doc COPYING %{_bindir}/profnet_bval %{_mandir}/*/profnet_bval* %files chop %defattr(-,root,root) %doc AUTHORS %doc COPYING %{_bindir}/profnet_chop %{_mandir}/*/profnet_chop* %files con %defattr(-,root,root) %doc AUTHORS %doc COPYING %{_bindir}/profnet_con %{_mandir}/*/profnet_con* %files isis %defattr(-,root,root) %doc AUTHORS %doc COPYING %{_bindir}/profnet_isis %{_mandir}/*/profnet_isis* %files md %defattr(-,root,root) %doc AUTHORS %doc COPYING %{_bindir}/profnet_md %{_mandir}/*/profnet_md* %files norsnet %defattr(-,root,root) %doc AUTHORS %doc COPYING %{_bindir}/profnet_norsnet %{_mandir}/*/profnet_norsnet* %files prof %defattr(-,root,root) %doc AUTHORS %doc COPYING %{_bindir}/profnet_prof %{_mandir}/*/profnet_prof* %files snapfun %defattr(-,root,root) %doc AUTHORS %doc COPYING %{_bindir}/profnet_snapfun %{_mandir}/*/profnet_snapfun* %files phdnet %defattr(-,root,root) %doc AUTHORS %doc COPYING %{_bindir}/profphd_net %{_bindir}/phd1994 %{_mandir}/*/profphd_net* %{_mandir}/*/phd1994* %changelog * Fri Jun 17 2011 Laszlo Kajan - 1.0.rg1-1 - First rpm package profnet-1.0.22/snapfun.patch0000644015075101507510000000611412021365171015242 0ustar lkajanlkajandiff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile snapfun_dir/Makefile --- src/Makefile 2010-02-10 17:55:33.923514458 +0100 +++ snapfun_dir/Makefile 2010-02-23 10:38:31.391656287 +0100 @@ -1,6 +1,6 @@ #===================================================================== F77 = gfortran -BIN = profnet_prof +BIN = profnet_snapfun #===================================================================== ARCH = LINUX FFLAGS := $(FFLAGS) -O2 -Wuninitialized diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile.orig snapfun_dir/Makefile.orig --- src/Makefile.orig 1970-01-01 01:00:00.000000000 +0100 +++ snapfun_dir/Makefile.orig 2010-02-23 10:38:31.395653152 +0100 @@ -0,0 +1,29 @@ +#===================================================================== +F77 = gfortran +BIN = profnet_prof +#===================================================================== +ARCH = LINUX +FFLAGS := -O3 -fbounds-check -Wuninitialized +FFLAGS := $(FFLAGS) -Wall -Wno-unused +#===================================================================== +all: $(BIN) + +#===================================================================== +# Make Neural Network +#===================================================================== + +NN_OBJS=prof.f lib-prof.f lib-sys-$(ARCH).f + +$(BIN): $(NN_OBJS) + @echo --- making $(BIN) + $(F77) -o $@ $(FFLAGS) $(NN_OBJS) + +clean: + rm -f *.o $(BIN) + +install: + mkdir -p $(DESTDIR)$(prefix)/bin && \ + cp $(BIN) $(DESTDIR)$(prefix)/bin/ + +.PHONY: all clean install + diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f snapfun_dir/profPar.f --- src/profPar.f 2010-02-23 10:17:25.315661972 +0100 +++ snapfun_dir/profPar.f 2010-02-23 10:38:31.399648899 +0100 @@ -32,20 +32,20 @@ C lkajan: what it needs. C lkajan: The below numbers are the values used by prof as in C lkajan: prof{sec,acc}: - PARAMETER (NUMIN_MAX= 800) + PARAMETER (NUMIN_MAX= 900) C lkajan: The below number of 10000 is suitable for a method that C lkajan: presents a sample for each amino acids of a protein because C lkajan: we do not encounter a protein longer than 10000AA very often. - PARAMETER (NUMSAM_MAX= 10000) - PARAMETER (NUMHID_MAX= 100) - PARAMETER (NUMOUT_MAX= 10) - PARAMETER (NUMFILES_MAX= 2) - PARAMETER (STPSWPMAX_MAX= 5) + PARAMETER (NUMSAM_MAX= 100000) + PARAMETER (NUMHID_MAX= 50) + PARAMETER (NUMOUT_MAX= 2) + PARAMETER (NUMFILES_MAX= 336) + PARAMETER (STPSWPMAX_MAX= 400) C lkajan: STPMAX_MAX somehow controls the number of input vectors that can C lkajan: be evaluated in one go. There is a simple integer array that gets C lkajan: allocated to STPMAX_MAX size. - PARAMETER (STPMAX_MAX= 5) - PARAMETER (NUMARG_MAX= 500) + PARAMETER (STPMAX_MAX= 100000) + PARAMETER (NUMARG_MAX= 400) C G M T *---- ------------------------------------------------- *