Mercurial > repos > deepakjadmin > mayatool3_test2
diff bin/MolFilesToSD.pl @ 0:4816e4a8ae95 draft default tip
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author | deepakjadmin |
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date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/MolFilesToSD.pl Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,318 @@ +#!/usr/bin/perl -w +# +# $RCSfile: MolFilesToSD.pl,v $ +# $Date: 2015/02/28 20:46:20 $ +# $Revision: 1.38 $ +# +# Author: Manish Sud <msud@san.rr.com> +# +# Copyright (C) 2015 Manish Sud. All rights reserved. +# +# This file is part of MayaChemTools. +# +# MayaChemTools is free software; you can redistribute it and/or modify it under +# the terms of the GNU Lesser General Public License as published by the Free +# Software Foundation; either version 3 of the License, or (at your option) any +# later version. +# +# MayaChemTools is distributed in the hope that it will be useful, but without +# any warranty; without even the implied warranty of merchantability of fitness +# for a particular purpose. See the GNU Lesser General Public License for more +# details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or +# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, +# Boston, MA, 02111-1307, USA. +# + +use strict; +use FindBin; use lib "$FindBin::Bin/../lib"; +use Getopt::Long; +use File::Basename; +use Text::ParseWords; +use Benchmark; +use SDFileUtil; +use FileUtil; +use TextUtil; + +my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); + +# Autoflush STDOUT +$| = 1; + +# Starting message... +$ScriptName = basename $0; +print "\n$ScriptName:Starting...\n\n"; +$StartTime = new Benchmark; + +# Get the options and setup script... +SetupScriptUsage(); +if ($Options{help} || @ARGV < 1) { + die GetUsageFromPod("$FindBin::Bin/$ScriptName"); +} + +my(@MOLFilesList); +@MOLFilesList = ExpandFileNames(\@ARGV, "mol"); + +# Process options... +print "Processing options...\n"; +my(%OptionsInfo); +ProcessOptions(); + +print "Generating SD file $OptionsInfo{SDFile}...\n"; +GenerateSDFile(); + +print "\n$ScriptName:Done...\n\n"; + +$EndTime = new Benchmark; +$TotalTime = timediff ($EndTime, $StartTime); +print "Total time: ", timestr($TotalTime), "\n"; + +############################################################################### + +# Generate a SD file using all valid MDL MOL files... +sub GenerateSDFile { + my($MOLFile, $Index, $FileCount, $FileOkayCount, $MolNameLine, $CmpdID, $FileDir, $FileName, $FileExt); + + open SDFILE, ">$OptionsInfo{SDFile}" or die "Error: Can't open $OptionsInfo{SDFile}: $! \n"; + $FileCount = 0; + $FileOkayCount = 0; + + FILELIST: for $Index (0 .. $#MOLFilesList) { + $MOLFile = $MOLFilesList[$Index]; + $FileCount++; + + print "Processing file $MOLFile...\n"; + + if (!(-e $MOLFile)) { + warn "Warning: Ignoring file $MOLFile: It doesn't exist\n"; + next FILELIST; + } + + if (!CheckFileType($MOLFile, "mol")) { + warn "Warning: Ignoring file $MOLFile: It's not a MDLMOL file\n"; + next FILELIST; + } + + if (!open MOLFILE, "$MOLFile") { + warn "Warning: Ignoring file $MOLFile: Couldn't open it: $! \n"; + next FILELIST; + } + + $FileOkayCount++; + + if ($OptionsInfo{ModifyData}) { + $MolNameLine = <MOLFILE>; + if ($OptionsInfo{UseFilePrefix}) { + ($FileDir, $FileName, $FileExt) = ParseFileName($MOLFile); + $CmpdID = $FileName; + } + else { + $CmpdID = $OptionsInfo{CompoundID} . "$FileCount"; + } + + if ($OptionsInfo{AddMolNameLine}) { + print SDFILE "$CmpdID\n"; + } + else { + $MolNameLine =~ s/(\r\n)|(\r)/\n/g; + print SDFILE $MolNameLine; + } + + while (<MOLFILE>) { + s/(\r\n)|(\r)/\n/g; + print SDFILE; + } + + if ($OptionsInfo{AddDataField}) { + print SDFILE "> <$OptionsInfo{DataFieldLabel}>\n${CmpdID}\n"; + } + } + else { + while (<MOLFILE>) { + s/(\r\n)|(\r)/\n/g; + print SDFILE; + } + } + print SDFILE "\n\$\$\$\$\n"; + close MOLFILE; + } + close SDFILE; + + print "\nNumber of files: $FileCount\n"; + print "Number of files processed successfully: $FileOkayCount\n"; + print "Number of files ignored: " . ($FileCount - $FileOkayCount) . "\n"; +} + +# Process option values... +sub ProcessOptions { + %OptionsInfo = (); + + $OptionsInfo{Mode} = $Options{mode}; + + $OptionsInfo{CompoundID} = $Options{compoundid}; + $OptionsInfo{DataFieldLabel} = $Options{datafieldlabel}; + + $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef; + $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef; + + $OptionsInfo{AddMolNameLine} = ($Options{mode} =~ /^(molnameline|both)$/i) ? 1 : 0; + $OptionsInfo{AddDataField} = ($Options{mode} =~ /^(datafield|both)$/i) ? 1 : 0; + + $OptionsInfo{AddMolNameLine} = ($Options{mode} =~ /^(molnameline|both)$/i) ? 1 : 0; + $OptionsInfo{AddDataField} = ($Options{mode} =~ /^(datafield|both)$/i) ? 1 : 0; + + $OptionsInfo{ModifyData} = ($OptionsInfo{AddMolNameLine} || $OptionsInfo{AddDataField}) ? 1 : 0; + + $OptionsInfo{UseFilePrefix} = ($Options{compoundid} =~ /^usefileprefix$/i) ? 1 : 0; + + # Setup SD file name... + my($FileDir, $FileName, $FileExt, $SDFile); + if ($Options{root}) { + $FileDir = ""; $FileName = ""; $FileExt = ""; + ($FileDir, $FileName, $FileExt) = ParseFileName($Options{root}); + if ($FileName && $FileExt) { + $SDFile = $FileName; + } + else { + $SDFile = $Options{root}; + } + $SDFile .= ".sdf"; + } + else { + $FileDir = ""; $FileName = ""; $FileExt = ""; + ($FileDir, $FileName, $FileExt) = ParseFileName($MOLFilesList[0]); + $SDFile = $FileName . "1To" . @MOLFilesList . ".sdf"; + } + + if (!$Options{overwrite}) { + if (-e $SDFile) { + die "Error: The file $SDFile already exists.\n"; + } + } + $OptionsInfo{SDFile} = $SDFile; + +} + +# Setup script usage and retrieve command line arguments specified using various options... +sub SetupScriptUsage { + + # Retrieve all the options... + %Options = (); + $Options{compoundid} = "Cmpd"; + $Options{datafieldlabel} = "Cmpd_ID"; + $Options{mode} = "none"; + + if (!GetOptions(\%Options, "compoundid|c=s", "datafieldlabel|d=s", "help|h", "mode|m=s", "overwrite|o", "root|r=s", "workingdir|w=s")) { + die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; + } + if ($Options{workingdir}) { + if (! -d $Options{workingdir}) { + die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; + } + chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; + } + if ($Options{mode} !~ /^(molnameline|datafield|both|none)$/i ) { + die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: molnameline, datafield, both, or none\n"; + } +} + +__END__ + +=head1 NAME + +MolFilesToSD.pl - Generate a SD file from MDLMOL File(s) + +=head1 SYNOPSIS + +MolFilesToSD.pl MDLMOLFile(s)... + +MolFilesToSD.pl [B<-c, --compoundid> usefileprefix | idlabel] [B<-d, --datafieldlabel> fieldlabel] +[B<-h, --help>] [B<-m, --mode> molnameline | datafield | both | none] [B<-o, --overwrite>] +[B<-r, --root> rootname] [B<-w, --workingdir> dirname] MDLMOLFile(s)... + +=head1 DESCRIPTION + +Generate a SD file from I<MDLMOL File(s)>. Multiple file names are separated by spaces. +The valid file extension is I<.mol>. All other file names are ignored. All the files in a current +directory can be specified by I<*.mol>, or the current directory name. + +=head1 OPTIONS + +=over 4 + +=item B<-c, --compoundid> I<usefileprefix | idlabel> + +Specify how to generate compound IDs: use MOL filename prefix or generate +a new compound ID by combining I<idlabel> with compound number. Possible +values: I<usefileprefix | idlabel>. By default, I<Cmd> is used as a I<idlabel> to generate +these types of compound IDs: Cmpd1, Cmpd2 and so on. + +Example: To generate compound IDs like Mol_ID1, Mol_ID2 and so on, specify +"MolID" value for this option. + +=item B<-d, --datafieldlabel> I<fieldlabel> + +Specify data field label for adding compound ID field into SD file during I<datafield | both> +values of B<-m, --mode> option. Default: <Cmpd_ID>. + +=item B<-h, --help> + +Print this help message. + +=item B<-m, --mode> I<molnameline | datafield | both | none> + +Specify how to add compopund ID into SD file: relplace the molname line, +add a new data field, replace the molname line and add data field, or do +nothing. Possible values: I<molnameline | datafield | both | none>. +Default: I<nothing>. + +Use B<-c, --compoundid> to specify compound ID generation process. + +=item B<-o, --overwrite> + +Overwrite existing files. + +=item B<-r, --root> I<rootname> + +New SD file name is generated using the root: <Root>.sdf. Default new file +name: <InitialMOLFileName>1To<Count>.sdf. + +=item B<-w, --workingdir> I<dirname> + +Location of working directory. Default: current directory. + +=back + +=head1 EXAMPLES + +To generate NewSample.sdf file from Sample*.mol files, type: + + % MolFilesToSD.pl -r NewSample -o Sample*.mol + +To generate NewSample.sdf with Cmpd1, Cmpd2 and so on as compound ID in +MolName line and Cmpd_ID datafield from Sample*.mol files, type: + + % MolFilesToSD.pl -r NewSample -m both -o Sample*.mol + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +InfoSDFiles.pl, SDToMolFiles.pl + +=head1 COPYRIGHT + +Copyright (C) 2015 Manish Sud. All rights reserved. + +This file is part of MayaChemTools. + +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version. + +=cut