       1 #!/usr/bin/perl -w
       2 #
       3 # File: SDToMolFiles.pl
       4 # Author: Manish Sud <msud@san.rr.com>
       5 #
       6 # Copyright (C) 2018 Manish Sud. All rights reserved.
       7 #
       8 # This file is part of MayaChemTools.
       9 #
      10 # MayaChemTools is free software; you can redistribute it and/or modify it under
      11 # the terms of the GNU Lesser General Public License as published by the Free
      12 # Software Foundation; either version 3 of the License, or (at your option) any
      13 # later version.
      14 #
      15 # MayaChemTools is distributed in the hope that it will be useful, but without
      16 # any warranty; without even the implied warranty of merchantability of fitness
      17 # for a particular purpose.  See the GNU Lesser General Public License for more
      18 # details.
      19 #
      20 # You should have received a copy of the GNU Lesser General Public License
      21 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
      22 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
      23 # Boston, MA, 02111-1307, USA.
      24 #
      25
      26 use strict;
      27 use FindBin; use lib "$FindBin::Bin/../lib";
      28 use Getopt::Long;
      29 use File::Basename;
      30 use Text::ParseWords;
      31 use Benchmark;
      32 use SDFileUtil;
      33 use FileUtil;
      34
      35 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      36
      37 # Autoflush STDOUT
      38 $| = 1;
      39
      40 # Starting message...
      41 $ScriptName = basename $0;
      42 print "\n$ScriptName:Starting...\n\n";
      43 $StartTime = new Benchmark;
      44
      45 # Get the options and setup script...
      46 SetupScriptUsage();
      47 if ($Options{help} || @ARGV < 1) {
      48   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      49 }
      50
      51 my(@SDFilesList);
      52 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
      53
      54 # Process options...
      55 print "Processing options...\n";
      56 my(%OptionsInfo);
      57 ProcessOptions();
      58
      59 # Setup information about input files...
      60 print "Checking input SD file(s)...\n";
      61 my(%SDFilesInfo);
      62 RetrieveSDFilesInfo();
      63
      64 # Process input files..
      65 my($FileIndex);
      66 if (@SDFilesList > 1) {
      67   print "\nProcessing SD files...\n";
      68 }
      69 for $FileIndex (0 .. $#SDFilesList) {
      70   if ($SDFilesInfo{FileOkay}[$FileIndex]) {
      71     print "\nProcessing file $SDFilesList[$FileIndex]...\n";
      72     GenerateMolFiles($FileIndex);
      73   }
      74 }
      75 print "\n$ScriptName:Done...\n\n";
      76
      77 $EndTime = new Benchmark;
      78 $TotalTime = timediff ($EndTime, $StartTime);
      79 print "Total time: ", timestr($TotalTime), "\n";
      80
      81 ###############################################################################
      82
      83 # Generate MOL files for a SD file...
      84 #
      85 sub GenerateMolFiles {
      86   my($FileIndex) = @_;
      87   my($SDFile, $MOLFile, $MOLFileRoot, $OutFileRoot, $OverwriteFiles, $UseDataField, $DataFieldName, $UseMolName, $CmpdCount, $MolEndDelimiter, $CmpdString, @CmpdLines, %DataFieldValues);
      88
      89   $SDFile = $SDFilesList[$FileIndex];
      90
      91   if (!open SDFILE, "$SDFile") {
      92     warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
      93     return;
      94   }
      95
      96   $CmpdCount = 0;
      97   $MolEndDelimiter = "M  END";
      98
      99   $OutFileRoot = $SDFilesInfo{OutFileRoot}[$FileIndex];
     100   $OverwriteFiles = $OptionsInfo{OverwriteFiles};
     101
     102   $UseDataField = ($OptionsInfo{Mode} =~ /^DataField$/i) ? 1 : 0;
     103   $DataFieldName = $OptionsInfo{DataField};
     104
     105   $UseMolName = ($OptionsInfo{Mode} =~ /^MolName$/i) ? 1 : 0;
     106
     107   CMPDSTRING: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
     108     $CmpdCount++;
     109
     110     # Setup MOL file name...
     111     $MOLFileRoot = '';
     112     if ($UseDataField) {
     113       @CmpdLines = split "\n", $CmpdString;
     114       %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     115       if (exists $DataFieldValues{$DataFieldName}) {
     116         $MOLFileRoot = $DataFieldValues{$DataFieldName};
     117       }
     118     }
     119     elsif ($UseMolName) {
     120       @CmpdLines = split "\n", $CmpdString;
     121       $MOLFileRoot = $CmpdLines[0];
     122     }
     123
     124     # Check for any invalid file name characters in data field or molname values...
     125     if ($MOLFileRoot && $MOLFileRoot =~ /[^a-zA-Z0-9_]/) {
     126       $MOLFileRoot =~ s/[^a-zA-Z0-9_]//g;
     127     }
     128     # Fall back plan for MOL file name...
     129     if (!$MOLFileRoot) {
     130       $MOLFileRoot = "${OutFileRoot}Cmpd${CmpdCount}";
     131     }
     132
     133     $MOLFile = "${MOLFileRoot}.mol";
     134
     135     if (!$OverwriteFiles) {
     136       if (-e $MOLFile) {
     137         warn "Warning: Ignoring compound number, $CmpdCount, in $SDFile: New MOL file, $MOLFile, already exists\n";
     138         next CMPDSTRING;
     139       }
     140     }
     141
     142     if (!($CmpdString =~ /$MolEndDelimiter/)) {
     143       warn "Warning: Ignoring compound number, $CmpdCount, in $SDFile: Invalid compound data\n";
     144       next CMPDSTRING;
     145     }
     146
     147     # Write out MOL file...
     148
     149     print "Generating $MOLFile file...\n";
     150     open MOLFILE, ">$MOLFile" or die "Error: Can't open $MOLFile: $! \n";
     151     ($CmpdString) = split "$MolEndDelimiter", $CmpdString;
     152     print MOLFILE "$CmpdString";
     153     print MOLFILE "$MolEndDelimiter\n";
     154     close MOLFILE;
     155
     156   }
     157
     158   close SDFILE;
     159 }
     160
     161 # Retrieve information about SD files...
     162 #
     163 sub RetrieveSDFilesInfo {
     164   my($SDFile, $Index, $FileDir, $FileName, $FileExt, $OutFileRoot);
     165
     166   %SDFilesInfo = ();
     167   @{$SDFilesInfo{FileOkay}} = ();
     168   @{$SDFilesInfo{OutFileRoot}} = ();
     169
     170   FILELIST: for $Index (0 .. $#SDFilesList) {
     171     $SDFile = $SDFilesList[$Index];
     172
     173     $SDFilesInfo{FileOkay}[$Index] = 0;
     174     $SDFilesInfo{OutFileRoot}[$Index] = '';
     175
     176     $SDFile = $SDFilesList[$Index];
     177     if (!(-e $SDFile)) {
     178       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     179       next FILELIST;
     180     }
     181     if (!CheckFileType($SDFile, "sd sdf")) {
     182       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     183       next FILELIST;
     184     }
     185
     186     # Setup output file root...
     187     $FileDir = ""; $FileName = ""; $FileExt = "";
     188     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     189
     190     if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
     191       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
     192       if ($RootFileName && $RootFileExt) {
     193         $FileName = $RootFileName;
     194       }
     195       else {
     196         $FileName = $OptionsInfo{OutFileRoot};
     197       }
     198       $OutFileRoot = $FileName;
     199     }
     200     else {
     201       $OutFileRoot = "$FileName";
     202     }
     203
     204     $SDFilesInfo{FileOkay}[$Index] = 1;
     205     $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
     206   }
     207 }
     208
     209 # Process option values...
     210 sub ProcessOptions {
     211   %OptionsInfo = ();
     212
     213   $OptionsInfo{Mode} = $Options{mode};
     214
     215   $OptionsInfo{DataField} = '';
     216   if ($Options{mode} =~ /^DataField$/i) {
     217     if (!$Options{datafield}) {
     218       die "Error: You must specify a value for \"-d, --DataField\" option in \"DataField\" \"-m, --mode\". \n";
     219     }
     220     $OptionsInfo{DataField} = $Options{datafield};
     221   }
     222
     223   $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
     224
     225   $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
     226 }
     227
     228 # Setup script usage  and retrieve command line arguments specified using various options...
     229 sub SetupScriptUsage {
     230
     231   # Retrieve all the options...
     232   %Options = ();
     233
     234   $Options{mode} = 'RootPrefix';
     235
     236   if (!GetOptions(\%Options, "datafield|d=s", "help|h", "mode|m=s", "overwrite|o", "root|r=s", "workingdir|w=s")) {
     237     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     238   }
     239   if ($Options{workingdir}) {
     240     if (! -d $Options{workingdir}) {
     241       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     242     }
     243     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     244   }
     245
     246   if ($Options{mode} !~ /^(DataField|MolName|RootPrefix)$/i) {
     247     die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: DataField, MolName, RootPrefix\n";
     248   }
     249 }
     250