diff bin/MolFilesToSD.pl @ 0:4816e4a8ae95 draft default tip

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author deepakjadmin
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