       1 #!/usr/bin/perl -w
       2 #
       3 # File: ElementalAnalysisSDFiles.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 "$FindBin::Bin/../lib";
      28 use Getopt::Long;
      29 use File::Basename;
      30 use Text::ParseWords;
      31 use Benchmark;
      32 use FileUtil;
      33 use SDFileUtil;
      34 use TextUtil;
      35 use MolecularFormula;
      36 use FileIO::SDFileIO;
      37 use Molecule;
      38
      39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      40
      41 # Autoflush STDOUT
      42 $| = 1;
      43
      44 # Starting message...
      45 $ScriptName = basename($0);
      46 print "\n$ScriptName: Starting...\n\n";
      47 $StartTime = new Benchmark;
      48
      49 # Get the options and setup script...
      50 SetupScriptUsage();
      51 if ($Options{help} || @ARGV < 1) {
      52   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      53 }
      54
      55 my(@SDFilesList);
      56 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
      57
      58 print "Processing options...\n";
      59 my(%OptionsInfo);
      60 ProcessOptions();
      61
      62 print "Checking input SD file(s)...\n";
      63 my(%SDFilesInfo);
      64 RetrieveSDFilesInfo();
      65
      66 # Generate output files...
      67 my($FileIndex);
      68 if (@SDFilesList > 1) {
      69   print "\nProcessing SD files...\n";
      70 }
      71 for $FileIndex (0 .. $#SDFilesList) {
      72   if ($SDFilesInfo{FileOkay}[$FileIndex]) {
      73     print "\nProcessing file $SDFilesList[$FileIndex]...\n";
      74     PerformElementalAnalysis($FileIndex);
      75   }
      76 }
      77 print "\n$ScriptName:Done...\n\n";
      78
      79 $EndTime = new Benchmark;
      80 $TotalTime = timediff ($EndTime, $StartTime);
      81 print "Total time: ", timestr($TotalTime), "\n";
      82
      83 ###############################################################################
      84
      85 # Perform analysis...
      86 sub PerformElementalAnalysis {
      87   my($Index) = @_;
      88   my($SDFile, $NewSDFile, $KeyDataFieldName, $CmpdCount, $CurrentFormula, $FormulaFieldName, $CmpdString, $Value, $CalculationType, $CalculatedValue, $ErrorMsg, $Status, $ElementsRef, $ElementCompositionRef, $Molecule, @CalculatedValues, @CmpdLines, %DataFieldValuesMap);
      89
      90   $SDFile = $SDFilesList[$Index];
      91   $NewSDFile = $SDFilesInfo{OutFile}[$Index];
      92
      93   print "Generating new SD file $NewSDFile...\n";
      94   open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
      95   open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
      96
      97
      98   $CmpdCount = 0;
      99   $FormulaFieldName = $SDFilesInfo{FormulaFieldName}[$Index];
     100
     101   COMPOUND: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
     102     $CmpdCount++;
     103     @CmpdLines = split "\n", $CmpdString;
     104     %DataFieldValuesMap = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     105
     106     @CalculatedValues = ();
     107     for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
     108       push @CalculatedValues, '';
     109     }
     110
     111     $CurrentFormula = undef;
     112
     113     if ($OptionsInfo{UseStructureData}) {
     114       $Molecule = FileIO::SDFileIO::ParseMoleculeString($CmpdString);
     115       $CurrentFormula = $Molecule->GetMolecularFormula();
     116     }
     117     else {
     118       if (!exists $DataFieldValuesMap{$FormulaFieldName}) {
     119         $ErrorMsg = "Ignoring compound record $CmpdCount: Formula field $FormulaFieldName not found";
     120         PrintErrorMsg($CmpdString, $ErrorMsg);
     121         WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues);
     122         next COMPOUND;
     123       }
     124
     125       # Make sure it's a valid molecular formula...
     126       $CurrentFormula = $DataFieldValuesMap{$FormulaFieldName};
     127       if ($OptionsInfo{CheckFormula}) {
     128         ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($CurrentFormula);
     129         if (!$Status) {
     130           $ErrorMsg = "Ignoring compound record $CmpdCount: Formula field value $CurrentFormula is not valid: $ErrorMsg";
     131           PrintErrorMsg($CmpdString, $ErrorMsg);
     132           WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues);
     133           next COMPOUND;
     134         }
     135       }
     136     }
     137
     138     # Calculate appropriate values and write 'em out...
     139     @CalculatedValues = ();
     140     for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
     141       if ($CalculationType =~ /^ElementalAnalysis$/i) {
     142         ($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($CurrentFormula);
     143         $CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : '';
     144       }
     145       elsif ($CalculationType =~ /^MolecularWeight$/i) {
     146         $CalculatedValue = MolecularFormula::CalculateMolecularWeight($CurrentFormula);
     147         $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
     148       }
     149       elsif ($CalculationType =~ /^ExactMass$/i) {
     150         $CalculatedValue = MolecularFormula::CalculateExactMass($CurrentFormula);
     151         $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
     152       }
     153       else {
     154         $CalculatedValue = '';
     155       }
     156       push @CalculatedValues, $CalculatedValue;
     157     }
     158     WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues, $CurrentFormula);
     159   }
     160   close NEWSDFILE;
     161   close SDFILE;
     162 }
     163
     164 # Write out compound record with calculated values...
     165 sub WriteNewCompoundRecord {
     166   my($Index, $SDFileRef, $CmpdLinesRef, $CalculatedValuesRef, $MolecularFormula) = @_;
     167
     168   # Write out compound lines except the last line which contains $$$$...
     169   my($LineIndex);
     170   for $LineIndex (0 .. ($#{$CmpdLinesRef} - 1)) {
     171     print $SDFileRef "$CmpdLinesRef->[$LineIndex]\n";
     172   }
     173
     174   # Write out calculated values...
     175   my($CalcIndex, $FieldName, $FieldValue);
     176   for $CalcIndex (0 .. $#{$OptionsInfo{SpecifiedCalculations}}) {
     177     $FieldName = $SDFilesInfo{ValueFieldNamesMap}[$Index]{$OptionsInfo{SpecifiedCalculations}[$CalcIndex]};
     178     $FieldValue = $CalculatedValuesRef->[$CalcIndex];
     179     print  $SDFileRef ">  <$FieldName>\n$FieldValue\n\n";
     180   }
     181
     182   if ($OptionsInfo{UseStructureData} && $OptionsInfo{WriteOutFormula} && defined($MolecularFormula)) {
     183     $FieldName = $SDFilesInfo{ValueFieldNamesMap}[$Index]{MolecularFormula};
     184     $FieldValue = $MolecularFormula;
     185     print  $SDFileRef ">  <$FieldName>\n$FieldValue\n\n";
     186   }
     187
     188   print $SDFileRef  "\$\$\$\$\n";
     189 }
     190
     191 # Print out error message...
     192 sub PrintErrorMsg {
     193   my($CmpdString, $ErrorMsg) = @_;
     194
     195   if ($OptionsInfo{DetailLevel} >= 2 ) {
     196     print "$ErrorMsg:\n$CmpdString\n";
     197   }
     198   elsif ($OptionsInfo{DetailLevel} >= 1) {
     199     print "$ErrorMsg\n";
     200   }
     201 }
     202
     203 # Retrieve information about input SD files...
     204 sub RetrieveSDFilesInfo {
     205   my($Index, $SDFile, $FileDir, $FileName, $FileExt, $OutFileRoot,  $OutFile, $FormulaFieldName, $Value, $FieldName, $NewFieldName, $Count);
     206
     207   my(%NewValueFieldNames) = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass', MolecularFormula => 'MolecularFormula');
     208   if (@{$OptionsInfo{SpecifiedValueFieldNames}}) {
     209     for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueFieldNames}}; $Index +=2) {
     210       $Value = $OptionsInfo{SpecifiedValueFieldNames}[$Index];
     211       $FieldName = $OptionsInfo{SpecifiedValueFieldNames}[$Index + 1];
     212       if (exists $NewValueFieldNames{$Value}) {
     213         $NewValueFieldNames{$Value} = $FieldName;
     214       }
     215     }
     216   }
     217
     218   %SDFilesInfo = ();
     219
     220   @{$SDFilesInfo{FileOkay}} = ();
     221   @{$SDFilesInfo{OutFile}} = ();
     222   @{$SDFilesInfo{FormulaFieldName}} = ();
     223   @{$SDFilesInfo{ValueFieldNamesMap}} = ();
     224
     225   FILELIST: for $Index (0 .. $#SDFilesList) {
     226     $SDFile = $SDFilesList[$Index];
     227
     228     $SDFilesInfo{FileOkay}[$Index] = 0;
     229     $SDFilesInfo{OutFile}[$Index] = '';
     230     $SDFilesInfo{FormulaFieldName}[$Index] = '';
     231
     232     %{$SDFilesInfo{ValueFieldNamesMap}[$Index]} = ();
     233
     234     if (!(-e $SDFile)) {
     235       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     236       next FILELIST;
     237     }
     238     if (!CheckFileType($SDFile, "sd sdf")) {
     239       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     240       next FILELIST;
     241     }
     242     $FileDir = ""; $FileName = ""; $FileExt = "";
     243     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     244     if ($Options{root} && (@SDFilesList == 1)) {
     245       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
     246       if ($RootFileName && $RootFileExt) {
     247         $FileName = $RootFileName;
     248       }
     249       else {
     250         $FileName = $Options{root};
     251       }
     252       $OutFileRoot = $FileName;
     253     }
     254     else {
     255       $OutFileRoot = $FileName . "ElementalAnalysis";
     256     }
     257
     258     $OutFile = $OutFileRoot . ".$FileExt";
     259     if (lc($OutFile) eq lc($SDFile)) {
     260       warn "Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n";
     261       next FILELIST;
     262     }
     263     if (!$Options{overwrite}) {
     264       if (-e $OutFile) {
     265         warn "Warning: Ignoring file $SDFile: The file $OutFile already exists\n";
     266         next FILELIST;
     267       }
     268     }
     269     # Get data field names and values...
     270     my($CmpdString, $FieldName, @CmpdLines, @DataFieldNames, %DataFieldNamesMap);
     271     @DataFieldNames = ();
     272     if (!open(SDFILE, "$SDFile")) {
     273       warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
     274       next FILELIST;
     275     }
     276     $CmpdString = ReadCmpdString(\*SDFILE);
     277     close SDFILE;
     278
     279     @CmpdLines = split "\n", $CmpdString;
     280     @DataFieldNames = GetCmpdDataHeaderLabels(\@CmpdLines);
     281     %DataFieldNamesMap = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     282
     283     # Setup formula field name...
     284     $FormulaFieldName = '';
     285     if ($OptionsInfo{UseDataField}) {
     286       if ($OptionsInfo{SpecifiedFormulaFieldName}) {
     287         $FormulaFieldName = $OptionsInfo{SpecifiedFormulaFieldName};
     288       }
     289       else {
     290       FIELDNAME: for $FieldName (@DataFieldNames) {
     291           if ($FieldName =~ /Formula/i) {
     292             $FormulaFieldName = $FieldName;
     293             last FIELDNAME;
     294           }
     295         }
     296         if (!$FormulaFieldName) {
     297           warn "Warning: Ignoring file $SDFile: Data field label containing the word Formula doesn't exist\n";
     298           next FILELIST;
     299         }
     300       }
     301     }
     302     $SDFilesInfo{FileOkay}[$Index] = 1;
     303     $SDFilesInfo{OutFile}[$Index] = $OutFile;
     304     $SDFilesInfo{FormulaFieldName}[$Index] = $FormulaFieldName;
     305
     306     # Setup value data field names for calculated values...
     307     for $Value (keys %NewValueFieldNames) {
     308       $FieldName = $NewValueFieldNames{$Value};
     309
     310       # Make sure it doesn't already exists...
     311       $Count = 1;
     312       $NewFieldName = $FieldName;
     313       while (exists $DataFieldNamesMap{$NewFieldName}) {
     314         $Count++;
     315         $NewFieldName = $FieldName . $Count;
     316       }
     317       $SDFilesInfo{ValueFieldNamesMap}[$Index]{$Value} = $NewFieldName;
     318     }
     319   }
     320 }
     321
     322 # Process option values...
     323 sub ProcessOptions {
     324   %OptionsInfo = ();
     325
     326   $OptionsInfo{Mode} = $Options{mode};
     327   $OptionsInfo{FormulaMode} = $Options{formulamode};
     328
     329   $OptionsInfo{WriteOutFormula} = ($Options{formulaout} =~ /^Yes$/i) ? 1 : 0;
     330
     331   $OptionsInfo{UseStructureData} = ($Options{formulamode} =~ /^StructureData$/i) ? 1 : 0;
     332   $OptionsInfo{UseDataField} = ($Options{formulamode} =~ /^DataField$/i) ? 1 : 0;
     333
     334   $OptionsInfo{Fast} = defined $Options{fast} ? $Options{fast} : undef;
     335
     336   $OptionsInfo{DetailLevel} = $Options{detail};
     337   $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1;
     338   $OptionsInfo{Precision} = $Options{precision};
     339
     340   $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
     341
     342   $OptionsInfo{FormulaField} = defined $Options{formulafield} ? $Options{formulafield} : undef;
     343   $OptionsInfo{SpecifiedFormulaFieldName} = "";
     344
     345   if (defined $Options{formulafield}) {
     346     $OptionsInfo{SpecifiedFormulaFieldName} = $Options{formulafield};
     347   }
     348   # Setup what to calculate...
     349   @{$OptionsInfo{SpecifiedCalculations}} = ();
     350   if ($Options{mode} =~ /^All$/i) {
     351     @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass);
     352   }
     353   else {
     354     my($Mode, $ModeValue, @SpecifiedModeValues);
     355     $Mode = $Options{mode};
     356     $Mode =~ s/ //g;
     357     @SpecifiedModeValues = split /\,/, $Mode;
     358     for $ModeValue (@SpecifiedModeValues) {
     359       if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
     360         if ($ModeValue =~ /^All$/i) {
     361           die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n";
     362         }
     363         else {
     364           die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
     365         }
     366       }
     367       push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue;
     368     }
     369   }
     370
     371   $OptionsInfo{ValueFieldNames} = defined $Options{valuefieldnames} ? $Options{valuefieldnames} : undef;
     372   @{$OptionsInfo{SpecifiedValueFieldNames}} = ();
     373
     374   if ($Options{valuefieldnames}) {
     375     my($Value, $Label, @ValueLabels);
     376     @ValueLabels = split /\,/, $Options{valuefieldnames};
     377     if (@ValueLabels % 2) {
     378       die "Error: The value specified, $Options{valuefieldnames}, for option \"-v --valuefieldnames\" is not valid: It must contain even number of comma delimited values\n";
     379     }
     380     my($Index);
     381     for ($Index = 0; $Index < @ValueLabels; $Index +=2) {
     382       $Value = $ValueLabels[$Index];
     383       $Value =~ s/ //g;
     384       $Label = $ValueLabels[$Index + 1];
     385       if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass|MolecularFormula)$/i) {
     386         die "Error: The value specified, $Value, using option \"-v --valuefieldnames\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, ExactMass, or MolecularFormula\n";
     387       }
     388       push @{$OptionsInfo{SpecifiedValueFieldNames}}, ($Value, $Label);
     389     }
     390   }
     391 }
     392
     393 # Setup script usage  and retrieve command line arguments specified using various options...
     394 sub SetupScriptUsage {
     395
     396   # Retrieve all the options...
     397   %Options = ();
     398   $Options{detail} = 1;
     399   $Options{formulamode} = "DataField";
     400   $Options{formulaout} = "No";
     401   $Options{mode} = "All";
     402   $Options{precision} = 2;
     403
     404   if (!GetOptions(\%Options, "detail|d=i", "fast", "formulafield=s", "formulamode|f=s", "formulaout=s", "mode|m=s", "help|h", "overwrite|o", "precision|p=i", "root|r=s", "valuefieldnames|v=s", "workingdir|w=s")) {
     405     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     406   }
     407   if ($Options{workingdir}) {
     408     if (! -d $Options{workingdir}) {
     409       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     410     }
     411     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     412   }
     413   if (!IsPositiveInteger($Options{detail})) {
     414     die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
     415   }
     416   if ($Options{formulamode} !~ /^(StructureData|DataField)$/i) {
     417     die "Error: The value specified, $Options{formulamode}, for option \"-f, --formulamode\" is not valid. Allowed values: StructureData or DataField \n";
     418   }
     419   if ($Options{formulaout} !~ /^(Yes|No)$/i) {
     420     die "Error: The value specified, $Options{formulaout}, for option \"--formulaout\" is not valid. Allowed values: Yes or No \n";
     421   }
     422   if (!IsPositiveInteger($Options{precision})) {
     423     die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
     424   }
     425 }
     426