       1 #!/usr/bin/perl -w
       2 #
       3 # File: ModifySDFilesDataFields.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 "$FindBin::Bin/../lib";
      28 use Getopt::Long;
      29 use File::Basename;
      30 use Text::ParseWords;
      31 use Benchmark;
      32 use FileUtil;
      33 use SDFileUtil;
      34 use TextUtil;
      35
      36 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      37
      38 # Autoflush STDOUT
      39 $| = 1;
      40
      41 # Starting message...
      42 $ScriptName = basename($0);
      43 print "\n$ScriptName: Starting...\n\n";
      44 $StartTime = new Benchmark;
      45
      46 # Get the options and setup script...
      47 SetupScriptUsage();
      48 if ($Options{help} || @ARGV < 1) {
      49   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      50 }
      51
      52 my(@SDFilesList);
      53 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
      54
      55 # Process options...
      56 print "Processing options...\n";
      57 my(%OptionsInfo);
      58 ProcessOptions();
      59
      60 print "Checking input SD file(s)...\n";
      61 my(%SDFilesInfo);
      62 RetrieveSDFilesInfo();
      63
      64 # Generate output 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     ModifySDFile($FileIndex);
      73   }
      74 }
      75 print "\n$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 # Modify SD file data fields....
      84 sub ModifySDFile {
      85   my($Index) = @_;
      86   my($SDFile, $NewSDFile);
      87
      88   $SDFile = $SDFilesList[$Index];
      89   $NewSDFile = $SDFilesInfo{OutFile}[$Index];
      90
      91   print "Generating new SD file $NewSDFile...\n";
      92   open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
      93   open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
      94
      95   my($CmpdCount, $CmpdString, $CmpdData, $MolName, $OldSDField, $NewSDField, $CommonSDField, $Label, $Value, $FieldValues, $MolNameDataField, $URLCmpdIdFieldName, @CmpdLines, %DataFieldAndValues, @DataFieldLabels);
      96   $CmpdCount = 0;
      97
      98   COMPOUND: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
      99       $CmpdCount++;
     100       @CmpdLines = split "\n", $CmpdString;
     101       if ($OptionsInfo{UseDataFieldForMolName} || $OptionsInfo{ModifyDataFields}) {
     102         %DataFieldAndValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     103       }
     104       if ($OptionsInfo{ModifyMolName}) {
     105         if ($OptionsInfo{AlwaysReplaceMolName} || !IsNotEmpty($CmpdLines[0])) {
     106           $MolNameDataField = $OptionsInfo{MolNameDataField};
     107           if ($OptionsInfo{UseDataFieldForMolName} && exists($DataFieldAndValues{$MolNameDataField})) {
     108             $MolName = $DataFieldAndValues{$MolNameDataField};
     109             if (length($MolName) > 80) {
     110               $MolName = substr($MolName, 0, 80);
     111             }
     112           }
     113           else {
     114             $MolName = "$OptionsInfo{MolNamePrefix}${CmpdCount}";
     115           }
     116           $CmpdLines[0] = $MolName;
     117           $CmpdString = join "\n", @CmpdLines;
     118         }
     119       }
     120       if (!$OptionsInfo{ModifyDataFields}) {
     121         # Just write the data and get the next compound...
     122         print NEWSDFILE "$CmpdString\n";
     123         next COMPOUND;
     124       }
     125       # Write out the structure data now and handle the old data fields later...
     126       ($CmpdData) = split /\n>/, $CmpdString;
     127       print NEWSDFILE "$CmpdData\n";
     128
     129       # Modify specified data fields...
     130       for $NewSDField (sort keys %{$OptionsInfo{SpecifiedNewToOldSDFieldMap}}) {
     131         $FieldValues = "";
     132         for $OldSDField (@{$OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}}) {
     133           if (exists($DataFieldAndValues{$OldSDField}) && length($DataFieldAndValues{$OldSDField})) {
     134             $Value = $DataFieldAndValues{$OldSDField};
     135             $FieldValues .= ($FieldValues) ? "\n$Value" : $Value;
     136           }
     137         }
     138         print NEWSDFILE "> <$NewSDField>\n$FieldValues\n\n";
     139       }
     140       # Add specified common fields...
     141       for $CommonSDField (sort keys %{$OptionsInfo{SpecifiedCommonFieldMap}}) {
     142         $Value = $OptionsInfo{SpecifiedCommonFieldMap}{$CommonSDField};
     143         print NEWSDFILE "> <$CommonSDField>\n$Value\n\n";
     144       }
     145       if ($OptionsInfo{CreateDataFieldURL}) {
     146         $Value = "";
     147         $URLCmpdIdFieldName = $OptionsInfo{URLCmpdIdFieldName};
     148         if (exists($DataFieldAndValues{$URLCmpdIdFieldName}) && length($DataFieldAndValues{$URLCmpdIdFieldName})) {
     149           $Value = $DataFieldAndValues{$URLCmpdIdFieldName};
     150           $Value = "$OptionsInfo{URLCGIScriptName}?$OptionsInfo{URLParamName}=${Value}";
     151         }
     152         print NEWSDFILE "> <$OptionsInfo{URLDataFieldLabel}>\n$Value\n\n";
     153       }
     154
     155       # Handle old data fields and write 'em in the same order as they appear in the input
     156       # files...
     157       if ($OptionsInfo{KeepAllOldDataFields} || $OptionsInfo{KeepUnMappedOldDataFields}) {
     158         my($KeepLabel);
     159         @DataFieldLabels = GetCmpdDataHeaderLabels(\@CmpdLines);
     160         LABEL: for $Label (@DataFieldLabels) {
     161           $KeepLabel = $OptionsInfo{KeepAllOldDataFields} ? 1 : ( exists($OptionsInfo{SpecifiedOldToNewSDFieldMap}{$Label}) ? 0 : 1  );
     162           if (!$KeepLabel) {
     163             next LABEL;
     164           }
     165           $Value = $DataFieldAndValues{$Label};
     166           print NEWSDFILE "> <$Label>\n$Value\n\n";
     167         }
     168       }
     169
     170       print NEWSDFILE "\$\$\$\$\n";
     171   }
     172   close NEWSDFILE;
     173   close SDFILE;
     174 }
     175
     176 # Process option values...
     177 sub ProcessOptions {
     178   %OptionsInfo = ();
     179
     180   $OptionsInfo{Mode} = $Options{mode};
     181
     182   $OptionsInfo{ModifyMolName} = 1; $OptionsInfo{ModifyDataFields} = 0;
     183   if ($Options{mode} =~ /^both$/i) {
     184     $OptionsInfo{ModifyMolName} = 1; $OptionsInfo{ModifyDataFields} = 1;
     185   }
     186   elsif ($Options{mode} =~ /^datafields$/i) {
     187     $OptionsInfo{ModifyMolName} = 0; $OptionsInfo{ModifyDataFields} = 1;
     188   }
     189
     190   $OptionsInfo{KeepOldDataFields} = $Options{keepolddatafields};
     191   $OptionsInfo{KeepAllOldDataFields} = ($Options{keepolddatafields} =~ /^all$/i) ? 1 : 0;
     192   $OptionsInfo{KeepUnMappedOldDataFields} = ($Options{keepolddatafields} =~ /^unmappedonly$/i) ? 1 : 0;
     193
     194   $OptionsInfo{MolNameMode} = $Options{molnamemode};
     195   $OptionsInfo{UseDataFieldForMolName} = ($Options{molnamemode} =~ /^datafield$/i) ? 1 : 0;
     196
     197   $OptionsInfo{MolName} = $Options{molname};
     198   $OptionsInfo{MolNameDataField} = ""; $OptionsInfo{MolNamePrefix} = "Cmpd";
     199   if ($Options{molname}) {
     200     if ($OptionsInfo{UseDataFieldForMolName}) {
     201       $OptionsInfo{MolNameDataField} = $Options{molname};
     202     }
     203     else {
     204       $OptionsInfo{MolNamePrefix} = $Options{molname};
     205     }
     206   }
     207
     208   $OptionsInfo{MolNameReplace} = $Options{molnamereplace};
     209   $OptionsInfo{AlwaysReplaceMolName} = ($Options{molnamereplace} =~ /^always$/i) ? 1 : 0;
     210
     211   if ($Options{datafieldsmap} && $Options{datafieldsmapfile}) {
     212     die "Error: Both \"--datafieldsmap\" and  \"--datafieldsmapfile\" options specified: only one is allowed at a time\n";
     213   }
     214
     215   $OptionsInfo{DataFieldsMap} = $Options{datafieldsmap} ? $Options{datafieldsmap} : '';
     216   $OptionsInfo{DataFieldsMapFile} = $Options{datafieldsmapfile} ? $Options{datafieldsmapfile} : '';
     217
     218   my($SpecifiedDataFieldMap);
     219
     220   %{$OptionsInfo{SpecifiedNewToOldSDFieldMap}} = ();
     221   %{$OptionsInfo{SpecifiedOldToNewSDFieldMap}} = ();
     222
     223   $SpecifiedDataFieldMap = "";
     224   if ($Options{datafieldsmap}) {
     225     $SpecifiedDataFieldMap = $Options{datafieldsmap};
     226   }
     227   elsif ($Options{datafieldsmapfile}) {
     228     my($Line, @LineWords);
     229     open DATAFIELDSFILE, "$Options{datafieldsmapfile}" or die "Couldn't  open $Options{datafieldsmapfile}: $! \n";
     230     while ($Line = GetTextLine(\*DATAFIELDSFILE)) {
     231       @LineWords = quotewords(";", 0, $Line);
     232       $SpecifiedDataFieldMap .= JoinWords(\@LineWords, ";", 0);
     233     }
     234     close DATAFIELDSFILE;
     235   }
     236
     237   if ($SpecifiedDataFieldMap) {
     238     my($DataFieldMap, $DataField, $NewSDField, @OldSDFields, @DataFieldMapSplit, @DataFieldsSplit, $FirstField);
     239     @DataFieldMapSplit = split ";", $SpecifiedDataFieldMap;
     240     for $DataFieldMap (@DataFieldMapSplit) {
     241       @DataFieldsSplit = split ",", $DataFieldMap;
     242       if (@DataFieldsSplit == 1) {
     243         die "Error: Invalid number of comma delimited values, ", scalar(@DataFieldsSplit), ", specified,  @DataFieldsSplit, using \"--datafieldsmap or --datafieldsmapfile\" option: it must contain more than one value.\n";
     244       }
     245       $FirstField = 1;
     246       @OldSDFields = ();
     247       for $DataField (@DataFieldsSplit) {
     248         if (!(defined($DataField) && length($DataField))) {
     249           die "Error: One of the comma delimited values, \"", join(",", @DataFieldsSplit), "\", specified using \"--datafieldsmap or --datafieldsmapfile\" option is empty.\n";
     250         }
     251         if ($FirstField) {
     252           $FirstField = 0;
     253           $NewSDField = $DataField;
     254         }
     255         else {
     256           push @OldSDFields, $DataField;
     257         }
     258       }
     259       # Make sure a datafield is only specified once...
     260       if (exists $OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}) {
     261         die "Error: New data field, $NewSDField, specified more than once using \"--datafieldsmap or --datafieldsmapfile\" option.\n";
     262       }
     263       @{$OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}} = ();
     264       push @{$OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}}, @OldSDFields;
     265       for $DataField (@OldSDFields) {
     266         if (exists $OptionsInfo{SpecifiedOldToNewSDFieldMap}{$DataField} ) {
     267           die "Error: SD field, $DataField, specified more than once using \"--datafieldsmap or --datafieldsmapfile\" option.\n";
     268         }
     269         else {
     270           $OptionsInfo{SpecifiedOldToNewSDFieldMap}{$DataField} = $NewSDField;
     271         }
     272       }
     273
     274     }
     275   }
     276
     277   $OptionsInfo{DataFieldsCommon} = $Options{datafieldscommon} ? $Options{datafieldscommon} : '';
     278   %{$OptionsInfo{SpecifiedCommonFieldMap}} = ();
     279
     280   if ($Options{datafieldscommon}) {
     281     my($DataFieldName, $DataFieldValue, $Index, @CommonDataFieldsSplit);
     282     @CommonDataFieldsSplit = split ",", $Options{datafieldscommon};
     283     if (@CommonDataFieldsSplit % 2) {
     284         die "Error: Invalid number of comma delimited values, ", scalar(@CommonDataFieldsSplit), ", specified \"",  join(",", @CommonDataFieldsSplit), "\" using \"--datafieldscommon\" option: it must contain even number of values.\n";
     285     }
     286     for ($Index = 0; $Index < @CommonDataFieldsSplit; $Index += 2) {
     287       $DataFieldName = $CommonDataFieldsSplit[$Index];
     288       $DataFieldValue = $CommonDataFieldsSplit[$Index + 1];
     289       if (exists $OptionsInfo{SpecifiedCommonFieldMap}{$DataFieldName}) {
     290         die "Error: Common data field, $DataFieldName, specified more than once using \"--datafieldscommon\" option.\n";
     291       }
     292       if (exists($OptionsInfo{SpecifiedNewToOldSDFieldMap}{$DataFieldName}) || exists($OptionsInfo{SpecifiedOldToNewSDFieldMap}{$DataFieldName})) {
     293         die "Error: Common data field, $DataFieldName, specified using \"--datafieldscommon\" option cannot be specified in \"--datafieldsmap or --datafieldsmapfile\" option.\n";
     294       }
     295       $OptionsInfo{SpecifiedCommonFieldMap}{$DataFieldName} = $DataFieldValue;
     296     }
     297   }
     298
     299   $OptionsInfo{DataFieldURL} = $Options{datafieldurl} ? $Options{datafieldurl} : '';
     300   $OptionsInfo{CreateDataFieldURL} = (exists($Options{datafieldurl}) && length($Options{datafieldurl}) ) ? 1 : 0;
     301
     302   $OptionsInfo{URLDataFieldLabel} = ""; $OptionsInfo{URLCGIScriptName} = "";
     303   $OptionsInfo{URLParamName} = ""; $OptionsInfo{URLCmpdIdFieldName} = "";
     304
     305   if ($OptionsInfo{CreateDataFieldURL}) {
     306     my(@DataFieldURLSplit, $Value);
     307     @DataFieldURLSplit = split ",", $Options{datafieldurl};
     308     if (@DataFieldURLSplit != 4) {
     309       die "Error: Invalid number of values, ", scalar(@DataFieldURLSplit), ", specified using \"--datafieldURL\" option: it must contain 4 values.\n";
     310     }
     311     for $Value (@DataFieldURLSplit) {
     312       if (!IsNotEmpty($Value)) {
     313         die "Error: One of the values, $Options{datafieldurl}, specified using \"--datafieldURL\" option is empty.\n";
     314       }
     315     }
     316     $OptionsInfo{URLDataFieldLabel} = $DataFieldURLSplit[0];
     317     $OptionsInfo{URLCGIScriptName} = $DataFieldURLSplit[1];
     318     $OptionsInfo{URLParamName}  = $DataFieldURLSplit[2];
     319     $OptionsInfo{URLCmpdIdFieldName} = $DataFieldURLSplit[3];
     320   }
     321
     322 }
     323
     324 # Retrieve information about input SD files...
     325 sub RetrieveSDFilesInfo {
     326   my($Index, $SDFile, $FileDir, $FileName, $FileExt, $OutFileRoot,  $OutFile, $DataFieldName);
     327
     328   %SDFilesInfo = ();
     329   @{$SDFilesInfo{FileOkay}} = ();
     330   @{$SDFilesInfo{OutFile}} = ();
     331
     332    FILELIST: for $Index (0 .. $#SDFilesList) {
     333     $SDFile = $SDFilesList[$Index];
     334
     335     $SDFilesInfo{FileOkay}[$Index] = 0;
     336     $SDFilesInfo{OutFile}[$Index] = '';
     337
     338     if (!(-e $SDFile)) {
     339       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     340       next FILELIST;
     341     }
     342     if (!CheckFileType($SDFile, "sd sdf")) {
     343       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     344       next FILELIST;
     345     }
     346     $FileDir = ""; $FileName = ""; $FileExt = "";
     347     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     348     if ($Options{root} && (@SDFilesList == 1)) {
     349       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
     350       if ($RootFileName && $RootFileExt) {
     351         $FileName = $RootFileName;
     352       }
     353       else {
     354         $FileName = $Options{root};
     355       }
     356       $OutFileRoot = $FileName;
     357     }
     358     else {
     359       $OutFileRoot = $FileName . "ModifiedDataFields";
     360     }
     361
     362     $OutFile = $OutFileRoot . ".$FileExt";
     363     if (lc($OutFile) eq lc($SDFile)) {
     364       warn "Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n";
     365       next FILELIST;
     366     }
     367     if (!$Options{overwrite}) {
     368       if (-e $OutFile) {
     369         warn "Warning: Ignoring file $SDFile: The file $OutFile already exists\n";
     370         next FILELIST;
     371       }
     372     }
     373
     374     $SDFilesInfo{FileOkay}[$Index] = 1;
     375     $SDFilesInfo{OutFile}[$Index] = $OutFile;
     376   }
     377 }
     378
     379 # Setup script usage  and retrieve command line arguments specified using various options...
     380 sub SetupScriptUsage {
     381
     382   # Retrieve all the options...
     383   %Options = ();
     384   $Options{detail} = 1;
     385   $Options{keepolddatafields} = "none";
     386   $Options{mode} = "molname";
     387   $Options{molnamemode} = "labelprefix";
     388   $Options{molnamereplace} = "empty";
     389
     390   if (!GetOptions(\%Options, "detail|d=i", "datafieldscommon=s", "datafieldsmap=s", "datafieldsmapfile=s", "datafieldurl=s", "help|h", "keepolddatafields|k=s", "mode|m=s", "molname=s", "molnamemode=s", "molnamereplace=s", "overwrite|o", "root|r=s", "workingdir|w=s")) {
     391     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     392   }
     393   if ($Options{workingdir}) {
     394     if (! -d $Options{workingdir}) {
     395       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     396     }
     397     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     398   }
     399   if ($Options{keepolddatafields} !~ /^(all|unmappedonly|none)$/i) {
     400     die "Error: The value specified, $Options{keepolddatafields}, for option \"-k --keepolddatafields\" is not valid. Allowed values: all, unmappedonly, or none\n";
     401   }
     402   if ($Options{mode} !~ /^(molname|datafields|both)$/i) {
     403     die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: molname, datafields, or both\n";
     404   }
     405   if ($Options{molnamemode} !~ /^(datafield|labelprefix)$/i) {
     406     die "Error: The value specified, $Options{molnamemode}, for option \"--molnamemode\" is not valid. Allowed values: datafield or labelprefix\n";
     407   }
     408   if ($Options{molnamereplace} !~ /^(always|empty)$/i) {
     409     die "Error: The value specified, $Options{molnamereplace}, for option \"--molnamereplace\" is not valid. Allowed values: always or empty\n";
     410   }
     411   if (!IsPositiveInteger($Options{detail})) {
     412     die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
     413   }
     414 }
     415