diff mayachemtools/bin/JoinSDFiles.pl @ 0:73ae111cf86f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtools/bin/JoinSDFiles.pl	Wed Jan 20 11:55:01 2016 -0500
@@ -0,0 +1,266 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: JoinSDFiles.pl,v $
+# $Date: 2015/02/28 20:46:20 $
+# $Revision: 1.35 $
+#
+# Author: Manish Sud <[e-mail]>
+#
+# 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 "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Benchmark;
+use SDFileUtil;
+use FileUtil;
+
+my($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(@SDFilesList);
+@SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
+if (@SDFilesList == 1) {
+  die "Error: Specify more than one SD file.\n";
+}
+
+# Process options...
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+# Setup information about input files...
+print "Checking input SD files...\n";
+my(%SDFilesInfo);
+RetrieveSDFilesInfo();
+
+# Join files...
+print "\nGenerating new SD file $OptionsInfo{NewSDFile}...\n";
+JoinSDFiles();
+
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Join all valid SD files...
+sub JoinSDFiles {
+  my($FileIndex, $SDFile, $NewSDFile);
+
+  $NewSDFile = $OptionsInfo{NewSDFile};
+
+  open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
+  FILELIST: for $FileIndex (0 .. $#SDFilesList) {
+    if (!$SDFilesInfo{FileOkay}[$FileIndex]) {
+      next FILELIST;
+    }
+    $SDFile = $SDFilesList[$FileIndex];
+    print "\nProcessing file $SDFile...\n";
+
+    open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
+    while (<SDFILE>) {
+      s/(\r\n)|(\r)/\n/g;
+      print NEWSDFILE;
+    }
+    close SDFILE;
+  }
+
+  close NEWSDFILE;
+}
+
+# Retrieve information about SD files...
+sub RetrieveSDFilesInfo {
+  my($Index, $SDFile);
+
+  %SDFilesInfo = ();
+  @{$SDFilesInfo{FileOkay}} = ();
+
+  FILELIST: for $Index (0 .. $#SDFilesList) {
+    $SDFilesInfo{FileOkay}[$Index] = 0;
+
+    $SDFile = $SDFilesList[$Index];
+    if (!(-e $SDFile)) {
+      warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
+      next FILELIST;
+    }
+    if (!CheckFileType($SDFile, "sdf sd")) {
+      warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
+      next FILELIST;
+    }
+    if (! open SDFILE, "$SDFile") {
+      warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
+      next FILELIST;
+    }
+    close SDFILE;
+
+    $SDFilesInfo{FileOkay}[$Index] = 1;
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+  my($FileDir, $FileName, $FileExt, $NewSDFile);
+
+  %OptionsInfo = ();
+
+  $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : undef;
+  $OptionsInfo{Overwrite} = $Options{overwrite} ? $Options{overwrite} : undef;
+
+  if ($Options{root}) {
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($Options{root});
+    if ($FileName && $FileExt) {
+      $NewSDFile = $FileName . "." . $FileExt;
+    }
+    else {
+      $NewSDFile =  $Options{root} . ".sdf";
+    }
+  }
+  else {
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($SDFilesList[0]);
+    $NewSDFile = $FileName . "1To" . @SDFilesList . "Joined.sdf";
+  }
+
+  if (!$Options{overwrite}) {
+    if (-e $NewSDFile) {
+      die "Error: The file $NewSDFile already exists.\n";
+    }
+  }
+  if ($Options{root}) {
+    my($FileIndex);
+    for $FileIndex (0 .. $#SDFilesList) {
+      if (lc($NewSDFile) eq lc($SDFilesList[$FileIndex])) {
+	die "Error: Output filename, $NewSDFile, is similar to a input file name.\nSpecify a different name using \"-r --root\" option or use default name.\n";
+      }
+    }
+  }
+  $OptionsInfo{NewSDFile} = $NewSDFile;
+
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  if (!GetOptions(\%Options, "help|h", "overwrite|o", "root|r=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+JoinSDFiles.pl - Join multiple SDFiles into a single SDFile
+
+=head1 SYNOPSIS
+
+JoinSDFiles.pl  SDFiles...
+
+JoinSDFiles.pl [B<-h, --help>] [B<-o, --overwrite>] [B<-r, --root> rootname]
+[B<-w, --workingdir> dirname] SDFiles...
+
+=head1 DESCRIPTION
+
+Multiple I<SDFiles> are joined to generate a single SDFile. The file names
+are separated by spaces. The valid file extensions are I<.sdf> and I<.sd>.
+All other file names are ignored. All the SD files in a current directory can be
+specified either by I<*.sdf> or the current directory name.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-h, --help>
+
+Print this help message.
+
+=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 file
+name:<FirstSDFileName>1To<Count>Joined.sdf.
+
+=item B<-w, --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To join SD files, type:
+
+    % JoinSDFiles.pl -o Sample1.sdf Sample2.sdf
+    % JoinSDFiles.pl -o *.sdf
+
+To join all Sample*.sdf files in a directory, SomeDir, and generate a new file NewSample.sdf, type:
+
+    % JoinSDFiles.pl -r NewSample -w SomeDir -o *.sdf
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+InfoSDFiles.pl, MolFilesToSD.pl, SDToMolFiles.pl, SplitSDFiles.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