debian/0000755000000000000000000000000012214270400007156 5ustar debian/control0000644000000000000000000000321612214270245010572 0ustar Source: embassy-domainatrix Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), emboss-lib (>= 6.6.0-1~), emboss-lib (<< 6.6.1~), libx11-dev, libgd2-xpm-dev, libmysqlclient-dev, libpq-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/embassy-domainatrix/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/embassy-domainatrix/trunk/ Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX Package: embassy-domainatrix Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (>= 6.6.0-1~), emboss-lib (<< 6.6.1~) Recommends: emboss Suggests: embassy Description: Extra EMBOSS commands to handle domain classification file The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. . Applications in the current domainatrix release are cathparse (generates DCF file from raw CATH files), domainnr (removes redundant domains from a DCF file), domainreso (removes low resolution domains from a DCF file), domainseqs (adds sequence records to a DCF file), domainsse (adds secondary structure records to a DCF file), scopparse (generates DCF file from raw SCOP files) and ssematch (searches a DCF file for secondary structure matches). debian/rules0000755000000000000000000000043511770535610010255 0ustar #!/usr/bin/make -f CFLAGS += -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib LDFLAGS += -Wl,--as-needed %: dh $@ override_dh_auto_configure: dh_auto_configure -- --enable-systemlibs debian/manpages/0000755000000000000000000000000012214267474010772 5ustar debian/manpages/domainseqs.1e0000644000000000000000000001271111430506065013355 0ustar '\" t .\" Title: DOMAINSEQS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMAINATRIX 0.1.0+20100721 .\" Language: English .\" .TH "DOMAINSEQS" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domainseqs \- Adds sequence records to a DCF file\&. .SH "SYNOPSIS" .HP \w'\fBdomainseqs\fR\ 'u \fBdomainseqs\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dpdbdir\ \fR\fB\fIdirectory\fR\fR \fB\-getswiss\ \fR\fB\fItoggle\fR\fR \fB\-pdbtospfile\ \fR\fB\fIinfile\fR\fR \fB\-datafile\ \fR\fB\fImatrixf\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomainseqs\fR\ 'u \fBdomainseqs\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomainseqs\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dcfinfile\fR \fIinfile\fR .RS 4 This option specifies the name of DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. .RE .PP \fB\-dpdbdir\fR \fIdirectory\fR .RS 4 This option specifies the location of domain CCF file (clean coordinate files) (input)\&. A \*(Aqclean cordinate file\*(Aq contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \*(Aqcleaned\-up\*(Aq data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./ .RE .PP \fB\-getswiss\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-pdbtospfile\fR \fIinfile\fR .RS 4 This option specifies the name of the pdbcodes to swissprot indexing file\&. The swissprot:PDB equivalence file is generated by PDBTOSP .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This option specifies the residue substitution matrix, which is used for sequence comparison\&. Default value: EBLOSUM62 .RE .SS "Required section" .SS "Additional section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 This option specifies the gap insertion penalty\&. This is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10 .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 This option specifies the gap extension penalty\&. This is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5 .RE .SS "Output section" .PP \fB\-dcfoutfile\fR \fIoutfile\fR .RS 4 This option specifies the name of DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: domainseqs\&.out .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while domainseqs ran\&. Default value: domainseqs\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domainseqs is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/libscanout.1e0000644000000000000000000000625111430506065013357 0ustar '\" t .\" Title: LIBSCANOUT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMAINATRIX 0.1.0+20100721 .\" Language: English .\" .TH "LIBSCANOUT" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" libscanout \- Reads a DHF file and writes a file of top\-scoring Classes, Folds and Superfamilies\&. .SH "SYNOPSIS" .HP \w'\fBlibscanout\fR\ 'u \fBlibscanout\fR \fB\-dhfinfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBlibscanout\fR\ 'u \fBlibscanout\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBlibscanout\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dhfinfile\fR \fIinfile\fR .RS 4 This option specifies the location of the DHF file (domain hits file) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. .RE .SS "Required section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 This option specifies the location of the summary file (output)\&. The summary file contains lists of domain Classes, Superfamilies and Families rank\-ordered on the basis of score (highest\-scoring first)\&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP libscanout is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/scopparse.1e0000644000000000000000000001060511430506065013211 0ustar '\" t .\" Title: SCOPPARSE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMAINATRIX 0.1.0+20100721 .\" Language: English .\" .TH "SCOPPARSE" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" scopparse \- Generate DCF file from raw SCOP files\&. .SH "SYNOPSIS" .HP \w'\fBscopparse\fR\ 'u \fBscopparse\fR \fB\-classfile\ \fR\fB\fIinfile\fR\fR \fB\-desinfile\ \fR\fB\fIinfile\fR\fR \fB\-nosegments\ \fR\fB\fIboolean\fR\fR \fB\-nomultichain\ \fR\fB\fIboolean\fR\fR [\fB\-nominor\ \fR\fB\fIboolean\fR\fR] \fB\-dcffile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBscopparse\fR\ 'u \fBscopparse\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBscopparse\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-classfile\fR \fIinfile\fR .RS 4 This option specifies the name of raw SCOP classification file dir\&.cla\&.scop\&.txt_X\&.XX (input)\&. This is the raw SCOP classification file available at http://scop\&.mrc\-lmb\&.cam\&.ac\&.uk/scop/parse/dir\&.cla\&.scop\&.txt_1\&.57\&. .RE .PP \fB\-desinfile\fR \fIinfile\fR .RS 4 This option specifies the name of raw SCOP description file dir\&.des\&.scop\&.txt_X\&.XX (input)\&. This is the raw SCOP description file available at http://scop\&.mrc\-lmb\&.cam\&.ac\&.uk/scop/parse/dir\&.des\&.scop\&.txt_1\&.57\&. .RE .SS "Required section" .PP \fB\-nosegments\fR \fIboolean\fR .RS 4 This option specifies whether to omit domains comprising of more than one segment\&. This is necessary if a continuous residue sequence is required\&. Default value: N .RE .PP \fB\-nomultichain\fR \fIboolean\fR .RS 4 This option specifies whether to omit domains comprising segments from more than one chain\&. This is necessary if a continuous residue sequence is required\&. Default value: N .RE .SS "Additional section" .PP \fB\-nominor\fR \fIboolean\fR .RS 4 This option specifies whether to omit domains from minor classes (defined as anything not in class \*(AqAll alpha proteins\*(Aq, \*(AqAll beta proteins\*(Aq, \*(AqAlpha and beta proteins (a/b)\*(Aq or \*(AqAlpha and beta proteins (a+b)\*(Aq)\&. This is necessary or appropriate for many analyses\&. Default value: N .RE .SS "Output section" .PP \fB\-dcffile\fR \fIoutfile\fR .RS 4 This option specifies the name of SCOP DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from the SCOP or CATH databases\&. The file is generated by using DOMAINER and is in DCF format (EMBL\-like)\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP scopparse is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ssematch.1e0000644000000000000000000001376211430506065013030 0ustar '\" t .\" Title: SSEMATCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMAINATRIX 0.1.0+20100721 .\" Language: English .\" .TH "SSEMATCH" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ssematch \- Search a DCF file for secondary structure matches\&. .SH "SYNOPSIS" .HP \w'\fBssematch\fR\ 'u \fBssematch\fR \fB\-ssinfile\ \fR\fB\fIinfile\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-maxhits\ \fR\fB\fIinteger\fR\fR [\fB\-rgapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-rgapextend\ \fR\fB\fIfloat\fR\fR] [\fB\-egapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-egapextend\ \fR\fB\fIfloat\fR\fR] \fB\-outssfile\ \fR\fB\fIoutfile\fR\fR \fB\-outsefile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBssematch\fR\ 'u \fBssematch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBssematch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-ssinfile\fR \fIinfile\fR .RS 4 This option specifies the name of the file of secondary structure (input)\&. .RE .PP \fB\-dcfinfile\fR \fIinfile\fR .RS 4 This option specifies the name of the DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This option specifies the secondary structure substitution matrix\&. Default value: SSSUB .RE .SS "Required section" .PP \fB\-maxhits\fR \fIinteger\fR .RS 4 This option specifies the number of top\-scoring matches to report\&. Default value: 5 .RE .SS "Additional section" .PP \fB\-rgapopen\fR \fIfloat\fR .RS 4 This options specifies the gap insertion penalty for reside\-based alignment\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10 .RE .PP \fB\-rgapextend\fR \fIfloat\fR .RS 4 This options specifies the gap extension penalty for residue\-based alignment\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5 .RE .PP \fB\-egapopen\fR \fIfloat\fR .RS 4 This options specifies the gap insertion penalty for element\-based alignment\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10 .RE .PP \fB\-egapextend\fR \fIfloat\fR .RS 4 This options specifies the gap extension penalty for secondary structure element\-based alignment\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5 .RE .SS "Output section" .PP \fB\-outssfile\fR \fIoutfile\fR .RS 4 This option specifies the name of the file containing top\-scoring domains for residue\-based alignment (output)\&.A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. .RE .PP \fB\-outsefile\fR \fIoutfile\fR .RS 4 This option specifies the name of the file containing top\-scoring domains for secondary structure element\-based alignment (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of the ssematch log file (output)\&. Default value: ssematch\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ssematch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/libscan.1e0000644000000000000000000001735011430506065012631 0ustar '\" t .\" Title: LIBSCAN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMAINATRIX 0.1.0+20100721 .\" Language: English .\" .TH "LIBSCAN" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" libscan \- Diagnostic searches for protein families\&. .SH "SYNOPSIS" .HP \w'\fBlibscan\fR\ 'u \fBlibscan\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-grib\ \fR\fB\fIboolean\fR\fR \fB\-henik\ \fR\fB\fIboolean\fR\fR \fB\-hmm\ \fR\fB\fIboolean\fR\fR \fB\-sam\ \fR\fB\fIboolean\fR\fR \fB\-pssm\ \fR\fB\fIboolean\fR\fR \fB\-sig\ \fR\fB\fIboolean\fR\fR \fB\-hmmpath\ \fR\fB\fIstring\fR\fR \fB\-hmmextn\ \fR\fB\fIstring\fR\fR \fB\-hmmoutpath\ \fR\fB\fIstring\fR\fR \fB\-hmmoutextn\ \fR\fB\fIstring\fR\fR \fB\-sampath\ \fR\fB\fIstring\fR\fR \fB\-samextn\ \fR\fB\fIstring\fR\fR \fB\-samoutpath\ \fR\fB\fIstring\fR\fR \fB\-samoutextn\ \fR\fB\fIstring\fR\fR \fB\-pssmpath\ \fR\fB\fIstring\fR\fR \fB\-pssmextn\ \fR\fB\fIstring\fR\fR \fB\-niter\ \fR\fB\fIinteger\fR\fR \fB\-thresh\ \fR\fB\fIfloat\fR\fR \fB\-maxhit\ \fR\fB\fIinteger\fR\fR \fB\-pssmoutpath\ \fR\fB\fIstring\fR\fR \fB\-pssmoutextn\ \fR\fB\fIstring\fR\fR \fB\-gbvpath\ \fR\fB\fIstring\fR\fR \fB\-gbvextn\ \fR\fB\fIstring\fR\fR \fB\-gbvgapo\ \fR\fB\fIfloat\fR\fR \fB\-gbvgape\ \fR\fB\fIfloat\fR\fR \fB\-gbvoutpath\ \fR\fB\fIstring\fR\fR \fB\-gbvoutextn\ \fR\fB\fIstring\fR\fR \fB\-hnfpath\ \fR\fB\fIstring\fR\fR \fB\-hnfextn\ \fR\fB\fIstring\fR\fR \fB\-hnfgapo\ \fR\fB\fIfloat\fR\fR \fB\-hnfgape\ \fR\fB\fIfloat\fR\fR \fB\-hnfoutpath\ \fR\fB\fIstring\fR\fR \fB\-hnfoutextn\ \fR\fB\fIstring\fR\fR \fB\-sigpath\ \fR\fB\fIstring\fR\fR \fB\-sigextn\ \fR\fB\fIstring\fR\fR \fB\-nterm\ \fR\fB\fIlist\fR\fR \fB\-sub\ \fR\fB\fImatrixf\fR\fR \fB\-siggapo\ \fR\fB\fIfloat\fR\fR \fB\-siggape\ \fR\fB\fIfloat\fR\fR \fB\-sigoutpath\ \fR\fB\fIstring\fR\fR \fB\-sigoutextn\ \fR\fB\fIstring\fR\fR \fB\-db\ \fR\fB\fIseqset\fR\fR \fB\-scopf\ \fR\fB\fIinfile\fR\fR .HP \w'\fBlibscan\fR\ 'u \fBlibscan\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBlibscan\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .PP \fB\-mode\fR \fIlist\fR .RS 4 libscan runs in one of two modes either (i) database search mode or (ii) library screen mode\&. In database search mode libscan reads one or more directories each containing a single type of discriminating element, the permitted types are sparse sequence signature, Gribskov profile, Henikoff profile or hidden Markov model\&. In library screen mode, libscan reads a sequence set, screens each sequence against the library (directories of discriminating elements) and writes a library scan file (of top\-scoring families) for each one\&. Default value: 2 .RE .PP \fB\-grib\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-henik\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-hmm\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-sam\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-pssm\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-sig\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-hmmpath\fR \fIstring\fR .RS 4 Default value: \&./lib/ .RE .PP \fB\-hmmextn\fR \fIstring\fR .RS 4 Default value: \&.hmm .RE .PP \fB\-hmmoutpath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-hmmoutextn\fR \fIstring\fR .RS 4 Default value: \&.hmmout .RE .PP \fB\-sampath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-samextn\fR \fIstring\fR .RS 4 Default value: \&.mod .RE .PP \fB\-samoutpath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-samoutextn\fR \fIstring\fR .RS 4 Default value: \&.samout .RE .PP \fB\-pssmpath\fR \fIstring\fR .RS 4 Default value: /data/structure/lib/pssm/ .RE .PP \fB\-pssmextn\fR \fIstring\fR .RS 4 Default value: \&.chk .RE .PP \fB\-niter\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-thresh\fR \fIfloat\fR .RS 4 Default value: 100 .RE .PP \fB\-maxhit\fR \fIinteger\fR .RS 4 Default value: 1000 .RE .PP \fB\-pssmoutpath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-pssmoutextn\fR \fIstring\fR .RS 4 Default value: \&.pssmout .RE .PP \fB\-gbvpath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-gbvextn\fR \fIstring\fR .RS 4 Default value: \&.grib .RE .PP \fB\-gbvgapo\fR \fIfloat\fR .RS 4 Default value: 10\&.0 .RE .PP \fB\-gbvgape\fR \fIfloat\fR .RS 4 Default value: 0\&.5 .RE .PP \fB\-gbvoutpath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-gbvoutextn\fR \fIstring\fR .RS 4 Default value: \&.gribout .RE .PP \fB\-hnfpath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-hnfextn\fR \fIstring\fR .RS 4 Default value: \&.henik .RE .PP \fB\-hnfgapo\fR \fIfloat\fR .RS 4 Default value: 10\&.0 .RE .PP \fB\-hnfgape\fR \fIfloat\fR .RS 4 Default value: 0\&.5 .RE .PP \fB\-hnfoutpath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-hnfoutextn\fR \fIstring\fR .RS 4 Default value: \&.henikout .RE .PP \fB\-sigpath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-sigextn\fR \fIstring\fR .RS 4 Default value: \&.sig .RE .PP \fB\-nterm\fR \fIlist\fR .RS 4 Default value: 1 .RE .PP \fB\-sub\fR \fImatrixf\fR .RS 4 Default value: EBLOSUM62 .RE .PP \fB\-siggapo\fR \fIfloat\fR .RS 4 Default value: 10\&.0 .RE .PP \fB\-siggape\fR \fIfloat\fR .RS 4 Default value: 0\&.5 .RE .PP \fB\-sigoutpath\fR \fIstring\fR .RS 4 Default value: \&./ .RE .PP \fB\-sigoutextn\fR \fIstring\fR .RS 4 Default value: \&.sigout .RE .PP \fB\-db\fR \fIseqset\fR .RS 4 In database search mode libscan scans each discriminating element against a sequence set\&. In library screen mode, libscan reads a sequence set and screens each sequence against the library (directories of disciminating elements) Default value: 49142\&.vdhf .RE .PP \fB\-scopf\fR \fIinfile\fR .RS 4 In either mode, a \*(Aqscop classification file\*(Aq is required as a source of family classification data\&. A scop classification file contains classification and other data for domains from the scop database\&. The file is in embl\-like format and is generated by scopparse\&. Domain sequence information can be added to the file by using scopseqs\&. Default value: /data/structure/dcf/scop_raw\&.dcf .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP libscan is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/domainnr.1e0000644000000000000000000001661211430506065013025 0ustar '\" t .\" Title: DOMAINNR .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMAINATRIX 0.1.0+20100721 .\" Language: English .\" .TH "DOMAINNR" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domainnr \- Removes redundant domains from a DCF file\&. .SH "SYNOPSIS" .HP \w'\fBdomainnr\fR\ 'u \fBdomainnr\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-retain\ \fR\fB\fItoggle\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-threshlow\ \fR\fB\fIfloat\fR\fR \fB\-threshup\ \fR\fB\fIfloat\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-redoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomainnr\fR\ 'u \fBdomainnr\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomainnr\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dcfinfile\fR \fIinfile\fR .RS 4 This option specifies name of DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This option specifies the residue substitution matrix\&. This is used for sequence comparison\&. Default value: EBLOSUM62 .RE .PP \fB\-retain\fR \fItoggle\fR .RS 4 This option specifies whether to write redundant domains to a separate file\&. If this option is selected, redundant domains are written to a separate output file\&. Default value: N .RE .SS "Required section" .PP \fB\-node\fR \fIlist\fR .RS 4 This option specifies the node for redundancy removal\&. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies\&. For example by selecting \*(AqClass\*(Aq entries belonging to the same Class will be non\-redundant\&. Default value: 1 .RE .PP \fB\-mode\fR \fIlist\fR .RS 4 This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity\&. All permutations of pair\-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\&. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\&. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\&. Default value: 1 .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\&. Default value: 95\&.0 .RE .PP \fB\-threshlow\fR \fIfloat\fR .RS 4 This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 30\&.0 .RE .PP \fB\-threshup\fR \fIfloat\fR .RS 4 This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 90\&.0 .RE .SS "Additional section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 This option specifies the gap insertion penalty\&. This is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10 .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 This option specifies the gap extension penalty\&. This is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5 .RE .SS "Advanced section" .SS "Output section" .PP \fB\-dcfoutfile\fR \fIoutfile\fR .RS 4 This option specifies the name of non\-redundant DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop .RE .PP \fB\-redoutfile\fR \fIoutfile\fR .RS 4 This option specifies the name of DCF file (domain classification file) for redundant sequences (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while domainnr ran\&. Default value: domainnr\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domainnr is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/domainreso.1e0000644000000000000000000001020711430506065013350 0ustar '\" t .\" Title: DOMAINRESO .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMAINATRIX 0.1.0+20100721 .\" Language: English .\" .TH "DOMAINRESO" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domainreso \- Remove low resolution domains from a DCF file\&. .SH "SYNOPSIS" .HP \w'\fBdomainreso\fR\ 'u \fBdomainreso\fR \fB\-cpdbpath\ \fR\fB\fIdirlist\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomainreso\fR\ 'u \fBdomainreso\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomainreso\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "PROTEIN:3D STRUCTURE" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-cpdbpath\fR \fIdirlist\fR .RS 4 This option specifies the location of domain CCF file (clean coordinate files) (input)\&. A \*(Aqclean cordinate file\*(Aq contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (pdb files) or DOMAINER (domains), contain \*(Aqcleaned\-up\*(Aq data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./ .RE .PP \fB\-dcfinfile\fR \fIinfile\fR .RS 4 This option specifies the name of DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. .RE .SS "Required section" .PP \fB\-threshold\fR \fIfloat\fR .RS 4 This option specifies the threshold for inclusion (Angstroms)\&. Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file\&. Default value: 2\&.8 .RE .SS "Output section" .PP \fB\-dcfoutfile\fR \fIoutfile\fR .RS 4 This option specifies the name of DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domainreso is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/domainsse.1e0000644000000000000000000001025411430506065013174 0ustar '\" t .\" Title: DOMAINSSE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMAINATRIX 0.1.0+20100721 .\" Language: English .\" .TH "DOMAINSSE" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domainsse \- Add secondary structure records to a DCF file\&. .SH "SYNOPSIS" .HP \w'\fBdomainsse\fR\ 'u \fBdomainsse\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dccfdir\ \fR\fB\fIdirectory\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomainsse\fR\ 'u \fBdomainsse\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomainsse\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dcfinfile\fR \fIinfile\fR .RS 4 This option specifies the name of the DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. .RE .PP \fB\-dccfdir\fR \fIdirectory\fR .RS 4 This option specifies the location of the domain CCF file (clean coordinate files) (input)\&. A \*(Aqclean cordinate file\*(Aq contains protein coordinate and derived data for a single PDB file (\*(Aqprotein clean coordinate file\*(Aq) or a single domain from SCOP or CATH (\*(Aqdomain clean coordinate file\*(Aq), in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \*(Aqcleaned\-up\*(Aq data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./ .RE .SS "Required section" .SS "Advanced section" .SS "Output section" .PP \fB\-dcfoutfile\fR \fIoutfile\fR .RS 4 This option specifies the name of the DCF file (domain classification file) with secondary structure records (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of the DOMAINSSE log file\&. Default value: domainsse\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domainsse is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cathparse.1e0000644000000000000000000001001111430506065013153 0ustar '\" t .\" Title: CATHPARSE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMAINATRIX 0.1.0+20100721 .\" Language: English .\" .TH "CATHPARSE" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cathparse \- Generates DCF file from raw CATH files\&. .SH "SYNOPSIS" .HP \w'\fBcathparse\fR\ 'u \fBcathparse\fR \fB\-listfile\ \fR\fB\fIinfile\fR\fR \fB\-domfile\ \fR\fB\fIinfile\fR\fR \fB\-namesfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcathparse\fR\ 'u \fBcathparse\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcathparse\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-listfile\fR \fIinfile\fR .RS 4 This option specifies the name of raw CATH classification file (caths\&.list\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: caths\&.list\&.v2\&.4 .RE .PP \fB\-domfile\fR \fIinfile\fR .RS 4 This option specifies the name of raw CATH classification file (domlist\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: domlist\&.v2\&.4 .RE .PP \fB\-namesfile\fR \fIinfile\fR .RS 4 This option specifies the name of raw CATH classification file (CAT\&.names\&.all\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: CAT\&.names\&.all\&.v2\&.4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 This option specifies the name of CATH DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: Ecath\&.dat .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of the CATHPARSE log file\&. Default value: cathparse\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cathparse is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/watch0000644000000000000000000000015311235651126010220 0ustar version=3 opts=dversionmangle=s/\+\d+$// \ ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-(.*)\.tar\.gz debian/embassy-domainatrix.lintian-overrides0000644000000000000000000000027111562440326016531 0ustar # The embassy packages use privately some of the EMBOSS libraries. They have # the same upstream authors and are released together. embassy-domainatrix: binary-or-shlib-defines-rpath * debian/copyright0000644000000000000000000000246011770542306011130 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: DOMAINATRIX Source: ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.0.tar.gz Files: * Copyright: Alan Bleasby (ableasby@ebi.ac.uk) Matt Blades Mike Hurley Jon Ison (jison@ebi.ac.uk) Amanda O'Reilly Ranjeeva Ranasinghe License: GPL-2+ Files: debian/* Copyright: 2007-2011 Charles Plessy 2012 Andreas Tille License: GPL-2+ License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. debian/source/0000755000000000000000000000000012214267474010477 5ustar debian/source/format0000644000000000000000000000001411507156767011713 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000732512214270400011037 0ustar embassy-domainatrix (0.1.650-1) unstable; urgency=low * New upstream version * debian/control: - cme fix dpkg-control - Bumped versioned depends from emboss-lib - anonscm in VCS fields -- Andreas Tille Thu, 12 Sep 2013 09:38:23 +0200 embassy-domainatrix (0.1.0+20110714-1) unstable; urgency=low * New upstream version * debian/control: - Standards-Version: 3.9.3 (no changes needed) - debhelper version 9 - Adapted versioned (build-)depends to latest emboss version * added debian/compat: 9 * debian/source/format: 3.0 (quilt) * debian/rules: short dh * debian/copyright: DEP5 fixes -- Andreas Tille Thu, 21 Jun 2012 08:10:07 +0200 embassy-domainatrix (0.1.0+20100721-3) unstable; urgency=low * Set RPATH with “-Wl,--rpath” as GCC 4.6 does not accept “-R” anymore. (debian/rules) Closes: #625162, LP: #770920. * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). * Updated debian/embassy-domainatrix.lintian-overrides for lintian 2.5. * debian/copyright validated with config-edit. -- Charles Plessy Wed, 11 May 2011 14:37:28 +0900 embassy-domainatrix (0.1.0+20100721-2) unstable; urgency=low * Built on emboss-lib 6.3.1-6, pre-emptively depending on versions lower than 6.3.2, because backwards compatibility is sometimes broken (debian/control, debian/rules). * Set an RPATH to /usr/lib/emboss/lib for using EMBOSS private libraries (debian/rules, debian/embassy-domainatrix.lintian-overrides). * Refreshed debian/copyright to test the latest DEP-5 format. -- Charles Plessy Thu, 23 Sep 2010 10:54:35 +0900 embassy-domainatrix (0.1.0+20100721-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * Build-Depends on emboss 6.3.1 (debian/control, debian/rules, closes: #591130). * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed. * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules). * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). -- Charles Plessy Wed, 11 Aug 2010 19:53:32 +0900 embassy-domainatrix (0.1.0+20100115-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * debian/control: - Build against EMBOSS 6.2 (Closes: #587118) - Checked conformance with Policy 3.8.4 (no changes needed). * debian/*manpages* refreshed -- Charles Plessy Sat, 26 Jun 2010 17:18:45 +0900 embassy-domainatrix (0.1.0+20090715-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * debian/control: - Build against EMBOSS 6.1 - Checked conformance with Policy 3.8.2 (no changes needed). * debian/watch: mangle Debian version to ignore the timestamp. * Refreshed and experimented on debian/copyright. * debian/*manpages* refreshed and moved to section 1e. -- Charles Plessy Mon, 03 Aug 2009 19:38:00 +0900 embassy-domainatrix (0.1.0+20080715-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * debian/control: - Updated my email address. - Build against EMBOSS 6. - Using debhelper 7. - Checked conformance with Policy 3.8.0 (no changes needed). - Corrected DM-Upload-Allowed. * debian/copyright updated to latest format. -- Charles Plessy Thu, 26 Feb 2009 09:57:33 +0900 embassy-domainatrix (0.1.0-1) unstable; urgency=low * Initial release -- Charles Plessy Tue, 25 Sep 2007 13:52:47 +0900 debian/compat0000644000000000000000000000000211770332430010364 0ustar 9 debian/embassy-domainatrix.manpages0000644000000000000000000000040411426467754014701 0ustar debian/manpages/cathparse.1e debian/manpages/domainnr.1e debian/manpages/domainreso.1e debian/manpages/domainseqs.1e debian/manpages/domainsse.1e debian/manpages/libscan.1e debian/manpages/libscanout.1e debian/manpages/scopparse.1e debian/manpages/ssematch.1e