       1 #!/usr/bin/perl -w
       2 #
       3 # $RCSfile: SDToMolFiles.pl,v $
       4 # $Date: 2015/02/28 20:46:20 $
       5 # $Revision: 1.35 $
       6 #
       7 # Author: Manish Sud <msud@san.rr.com>
       8 #
       9 # Copyright (C) 2015 Manish Sud. All rights reserved.
      10 #
      11 # This file is part of MayaChemTools.
      12 #
      13 # MayaChemTools is free software; you can redistribute it and/or modify it under
      14 # the terms of the GNU Lesser General Public License as published by the Free
      15 # Software Foundation; either version 3 of the License, or (at your option) any
      16 # later version.
      17 #
      18 # MayaChemTools is distributed in the hope that it will be useful, but without
      19 # any warranty; without even the implied warranty of merchantability of fitness
      20 # for a particular purpose.  See the GNU Lesser General Public License for more
      21 # details.
      22 #
      23 # You should have received a copy of the GNU Lesser General Public License
      24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
      25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
      26 # Boston, MA, 02111-1307, USA.
      27 #
      28
      29 use strict;
      30 use FindBin; use lib "$FindBin::Bin/../lib";
      31 use Getopt::Long;
      32 use File::Basename;
      33 use Text::ParseWords;
      34 use Benchmark;
      35 use SDFileUtil;
      36 use FileUtil;
      37
      38 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      39
      40 # Autoflush STDOUT
      41 $| = 1;
      42
      43 # Starting message...
      44 $ScriptName = basename $0;
      45 print "\n$ScriptName:Starting...\n\n";
      46 $StartTime = new Benchmark;
      47
      48 # Get the options and setup script...
      49 SetupScriptUsage();
      50 if ($Options{help} || @ARGV < 1) {
      51   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      52 }
      53
      54 my(@SDFilesList);
      55 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
      56
      57 # Process options...
      58 print "Processing options...\n";
      59 my(%OptionsInfo);
      60 ProcessOptions();
      61
      62 # Setup information about input files...
      63 print "Checking input SD file(s)...\n";
      64 my(%SDFilesInfo);
      65 RetrieveSDFilesInfo();
      66
      67 # Process input files..
      68 my($FileIndex);
      69 if (@SDFilesList > 1) {
      70   print "\nProcessing SD files...\n";
      71 }
      72 for $FileIndex (0 .. $#SDFilesList) {
      73   if ($SDFilesInfo{FileOkay}[$FileIndex]) {
      74     print "\nProcessing file $SDFilesList[$FileIndex]...\n";
      75     GenerateMolFiles($FileIndex);
      76   }
      77 }
      78 print "\n$ScriptName:Done...\n\n";
      79
      80 $EndTime = new Benchmark;
      81 $TotalTime = timediff ($EndTime, $StartTime);
      82 print "Total time: ", timestr($TotalTime), "\n";
      83
      84 ###############################################################################
      85
      86 # Generate MOL files for a SD file...
      87 #
      88 sub GenerateMolFiles {
      89   my($FileIndex) = @_;
      90   my($SDFile, $MOLFile, $MOLFileRoot, $OutFileRoot, $OverwriteFiles, $UseDataField, $DataFieldName, $UseMolName, $CmpdCount, $MolEndDelimiter, $CmpdString, @CmpdLines, %DataFieldValues);
      91
      92   $SDFile = $SDFilesList[$FileIndex];
      93
      94   if (!open SDFILE, "$SDFile") {
      95     warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
      96     return;
      97   }
      98
      99   $CmpdCount = 0;
     100   $MolEndDelimiter = "M  END";
     101
     102   $OutFileRoot = $SDFilesInfo{OutFileRoot}[$FileIndex];
     103   $OverwriteFiles = $OptionsInfo{OverwriteFiles};
     104
     105   $UseDataField = ($OptionsInfo{Mode} =~ /^DataField$/i) ? 1 : 0;
     106   $DataFieldName = $OptionsInfo{DataField};
     107
     108   $UseMolName = ($OptionsInfo{Mode} =~ /^MolName$/i) ? 1 : 0;
     109
     110   CMPDSTRING: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
     111     $CmpdCount++;
     112
     113     # Setup MOL file name...
     114     $MOLFileRoot = '';
     115     if ($UseDataField) {
     116       @CmpdLines = split "\n", $CmpdString;
     117       %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     118       if (exists $DataFieldValues{$DataFieldName}) {
     119         $MOLFileRoot = $DataFieldValues{$DataFieldName};
     120       }
     121     }
     122     elsif ($UseMolName) {
     123       @CmpdLines = split "\n", $CmpdString;
     124       $MOLFileRoot = $CmpdLines[0];
     125     }
     126
     127     # Check for any invalid file name characters in data field or molname values...
     128     if ($MOLFileRoot && $MOLFileRoot =~ /[^a-zA-Z0-9_]/) {
     129       $MOLFileRoot =~ s/[^a-zA-Z0-9_]//g;
     130     }
     131     # Fall back plan for MOL file name...
     132     if (!$MOLFileRoot) {
     133       $MOLFileRoot = "${OutFileRoot}Cmpd${CmpdCount}";
     134     }
     135
     136     $MOLFile = "${MOLFileRoot}.mol";
     137
     138     if (!$OverwriteFiles) {
     139       if (-e $MOLFile) {
     140         warn "Warning: Ignoring compound number, $CmpdCount, in $SDFile: New MOL file, $MOLFile, already exists\n";
     141         next CMPDSTRING;
     142       }
     143     }
     144
     145     if (!($CmpdString =~ /$MolEndDelimiter/)) {
     146       warn "Warning: Ignoring compound number, $CmpdCount, in $SDFile: Invalid compound data\n";
     147       next CMPDSTRING;
     148     }
     149
     150     # Write out MOL file...
     151
     152     print "Generating $MOLFile file...\n";
     153     open MOLFILE, ">$MOLFile" or die "Error: Can't open $MOLFile: $! \n";
     154     ($CmpdString) = split "$MolEndDelimiter", $CmpdString;
     155     print MOLFILE "$CmpdString";
     156     print MOLFILE "$MolEndDelimiter\n";
     157     close MOLFILE;
     158
     159   }
     160
     161   close SDFILE;
     162 }
     163
     164 # Retrieve information about SD files...
     165 #
     166 sub RetrieveSDFilesInfo {
     167   my($SDFile, $Index, $FileDir, $FileName, $FileExt, $OutFileRoot);
     168
     169   %SDFilesInfo = ();
     170   @{$SDFilesInfo{FileOkay}} = ();
     171   @{$SDFilesInfo{OutFileRoot}} = ();
     172
     173   FILELIST: for $Index (0 .. $#SDFilesList) {
     174     $SDFile = $SDFilesList[$Index];
     175
     176     $SDFilesInfo{FileOkay}[$Index] = 0;
     177     $SDFilesInfo{OutFileRoot}[$Index] = '';
     178
     179     $SDFile = $SDFilesList[$Index];
     180     if (!(-e $SDFile)) {
     181       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     182       next FILELIST;
     183     }
     184     if (!CheckFileType($SDFile, "sd sdf")) {
     185       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     186       next FILELIST;
     187     }
     188
     189     # Setup output file root...
     190     $FileDir = ""; $FileName = ""; $FileExt = "";
     191     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     192
     193     if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
     194       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
     195       if ($RootFileName && $RootFileExt) {
     196         $FileName = $RootFileName;
     197       }
     198       else {
     199         $FileName = $OptionsInfo{OutFileRoot};
     200       }
     201       $OutFileRoot = $FileName;
     202     }
     203     else {
     204       $OutFileRoot = "$FileName";
     205     }
     206
     207     $SDFilesInfo{FileOkay}[$Index] = 1;
     208     $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
     209   }
     210 }
     211
     212 # Process option values...
     213 sub ProcessOptions {
     214   %OptionsInfo = ();
     215
     216   $OptionsInfo{Mode} = $Options{mode};
     217
     218   $OptionsInfo{DataField} = '';
     219   if ($Options{mode} =~ /^DataField$/i) {
     220     if (!$Options{datafield}) {
     221       die "Error: You must specify a value for \"-d, --DataField\" option in \"DataField\" \"-m, --mode\". \n";
     222     }
     223     $OptionsInfo{DataField} = $Options{datafield};
     224   }
     225
     226   $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
     227
     228   $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
     229 }
     230
     231 # Setup script usage  and retrieve command line arguments specified using various options...
     232 sub SetupScriptUsage {
     233
     234   # Retrieve all the options...
     235   %Options = ();
     236
     237   $Options{mode} = 'RootPrefix';
     238
     239   if (!GetOptions(\%Options, "datafield|d=s", "help|h", "mode|m=s", "overwrite|o", "root|r=s", "workingdir|w=s")) {
     240     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     241   }
     242   if ($Options{workingdir}) {
     243     if (! -d $Options{workingdir}) {
     244       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     245     }
     246     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     247   }
     248
     249   if ($Options{mode} !~ /^(DataField|MolName|RootPrefix)$/i) {
     250     die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: DataField, MolName, RootPrefix\n";
     251   }
     252 }
     253