debian/0000755000000000000000000000000011764427732007203 5ustar debian/rules0000755000000000000000000000026611764427457010273 0ustar #!/usr/bin/make -f #export DH_VERBOSE=1 %: dh $@ --with python2 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) override_dh_auto_test: (cd tests; PYTHONPATH=.. ./test_all) endif debian/control0000644000000000000000000000163711764427726010620 0ustar Source: fmcs Section: science Priority: optional Maintainer: Debichem Team Uploaders: Michael Banck Build-Depends: debhelper (>= 8), python-all, python-argparse, python-rdkit Standards-Version: 3.9.3 Homepage: https://bitbucket.org/dalke/fmcs/overview Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/fmcs/ Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/fmcs/ DM-Upload-Allowed: yes Package: python-fmcs Section: python Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-argparse, python-rdkit Description: Find Maximum Common Substructure Fcms finds the maximum common substructure (MCS) of a group (or cluster) of chemical structures and report the result as a SMARTS string. . More specifically, the MCS found is a common edge subgraph, and not a common induced subgraph. Only connected MCSes are found. debian/source/0000755000000000000000000000000011764424634010501 5ustar debian/source/format0000644000000000000000000000001411764424634011707 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000022311764427145011050 0ustar fmcs (1.0-1) unstable; urgency=low * Initial release (Closes: #676667). -- Michael Banck Fri, 08 Jun 2012 18:34:35 +0200 debian/compat0000644000000000000000000000000211764427375010404 0ustar 8 debian/copyright0000644000000000000000000000342211764427323011133 0ustar This work was packaged for Debian by: Michael Banck on Fri, 08 Jun 2012 18:34:35 +0200 It was downloaded from: https://bitbucket.org/dalke/fmcs/downloads Upstream Author: Andrew Dalke Copyright: Copyright (c) 2012 Andrew Dalke Scientific AB License: Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. The Debian packaging is: Copyright (C) 2012 Michael Banck and is licensed under the same BSD license as the upstream project. debian/python-fmcs.manpages0000644000000000000000000000001611764427345013164 0ustar debian/fmcs.1 debian/docs0000644000000000000000000000001411764424634010047 0ustar README TODO debian/fmcs.10000644000000000000000000001217511764426205010215 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH FMCS "1" "June 2012" "fmcs 1.0" "User Commands" .SH NAME fmcs \- fmcs .SH DESCRIPTION usage: fmcs [\-h] [\-\-maximize {atoms,bonds}] [\-\-min\-num\-atoms INT] .IP [\-\-compare {topology,elements,types}] [\-\-atom\-compare {any,elements,isotopes}] [\-\-bond\-compare {any,bondtypes}] [\-\-atom\-class\-tag TAG] [\-\-ring\-matches\-ring\-only] [\-\-complete\-rings\-only] [\-\-select SELECT] [\-\-timeout SECONDS] [\-\-output FILENAME] [\-\-output\-format {smarts,fragment\-smiles,fragment\-sdf,complete\-sdf}] [\-\-output\-all] [\-\-save\-atom\-class\-tag TAG] [\-\-save\-counts\-tag TAG] [\-\-save\-atom\-indices\-tag TAG] [\-\-save\-smarts\-tag TAG] [\-\-save\-smiles\-tag TAG] [\-\-times] [\-v] [\-\-version] filename .PP Find the maximum common substructure of a set of structures .SS "positional arguments:" .TP filename SDF or SMILES file .SS "optional arguments:" .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit .TP \fB\-\-maximize\fR {atoms,bonds} Maximize the number of 'atoms' or 'bonds' in the MCS. (Default: bonds) .TP \fB\-\-min\-num\-atoms\fR INT Minimimum number of atoms in the MCS (Default: 2) .TP \fB\-\-compare\fR {topology,elements,types} Use 'topology' as a shorthand for '\-\-atom\-compare any \fB\-\-bond\-compare\fR any', 'elements' is '\-\-atom\-compare elements \fB\-\-bond\-compare\fR any', and 'types' is '\-\-atomcompare elements \fB\-\-bond\-compare\fR bondtypes' (Default: types) .TP \fB\-\-atom\-compare\fR {any,elements,isotopes} Specify the atom comparison method. With 'any', every atom matches every other atom. With 'elements', atoms match only if they contain the same element. With \&'isotopes', atoms match only if they have the same isotope number; element information is ignored so [5C] and [5P] are identical. This can be used to implement user\-defined atom typing. (Default: elements) .TP \fB\-\-bond\-compare\fR {any,bondtypes} Specify the bond comparison method. With 'any', every bond matches every other bond. With 'bondtypes', bonds are the same only if their bond types are the same. (Default: bondtypes) .TP \fB\-\-atom\-class\-tag\fR TAG Use atom class assignments from the field 'TAG'. The tag data must contain a space separated list of integers in the range 1\-10000, one for each atom. Atoms are identical if and only if their corresponding atom classes are the same. Note that '003' and '3' are treated as identical values. (Not used by default) .TP \fB\-\-ring\-matches\-ring\-only\fR Modify the bond comparison so that ring bonds only match ring bonds and chain bonds only match chain bonds. (Ring atoms can still match non\-ring atoms.) .TP \fB\-\-complete\-rings\-only\fR If a bond is a ring bond in the input structures and a bond is in the MCS then the bond must also be in a ring in the MCS. Selecting this option also enables \fB\-\-ring\-matches\-ring\-only\fR. .TP \fB\-\-select\fR SELECT Select a subset of the input records to process. Example: 1\-10,13,20,50\- (Default: '1\-', which selects all structures) .TP \fB\-\-timeout\fR SECONDS Report the best solution after running for at most \&'timeout' seconds. Use 'none' for no timeout. (Default: none) .TP \fB\-\-output\fR FILENAME, \fB\-o\fR FILENAME Write the results to FILENAME (Default: use stdout) .TP \fB\-\-output\-format\fR {smarts,fragment\-smiles,fragment\-sdf,complete\-sdf} \&'smarts' writes the SMARTS pattern including the atom and bond criteria. 'fragment\-smiles' writes a matching fragment as a SMILES string. 'fragment\-sdf' writes a matching fragment as a SD file; see \fB\-\-save\-atom\-class\fR for details on how atom class information is saved. \&'complete\-sdf' writes the entire SD file with the fragment information stored in the tag specified by \fB\-\-save\-fragment\-indices\-tag\fR. (Default: smarts) .TP \fB\-\-output\-all\fR By default the structure output formats only show an MCS for the first input structure. If this option is enabled then an MCS for all of the structures are shown. .TP \fB\-\-save\-atom\-class\-tag\fR TAG If atom classes are specified (via \fB\-\-class\-tag\fR) and the output format is 'fragment\-sdf' then save the substructure atom classes to the tag TAG, in fragment atom order. By default this is the value of \fB\-\-atomclass\-tag\fR. .TP \fB\-\-save\-counts\-tag\fR TAG Save the fragment count, atom count, and bond count to the specified SD tag as space separated integers, like \&'1 9 8'. (The fragment count will not be larger than 1 until fmcs supports disconnected MCSes.) .TP \fB\-\-save\-atom\-indices\-tag\fR TAG If atom classes are specified and the output format is \&'complete\-sdf' then save the MCS fragment atom indices to the tag TAG, in MCS order. (Default: mcs\-atomindices) .TP \fB\-\-save\-smarts\-tag\fR TAG Save the MCS SMARTS to the specified SD tag. Uses '\-' if there is no MCS .TP \fB\-\-save\-smiles\-tag\fR TAG Save the fragment SMILES to the specified SD tag. Uses \&'\-' if there is no MCS .TP \fB\-\-times\fR Print timing information to stderr .TP \fB\-v\fR, \fB\-\-verbose\fR Print progress statistics to stderr. Use twice for higher verbosity. .HP \fB\-\-version\fR .PP For more details on these options, see https://bitbucket.org/dalke/fmcs/