MayaChemTools

   1 #!/usr/bin/perl -w
   2 #
   3 # $RCSfile: ElementalAnalysisSDFiles.pl,v $
   4 # $Date: 2015/02/28 20:46:19 $
   5 # $Revision: 1.24 $
   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 "$FindBin::Bin/../lib";
  31 use Getopt::Long;
  32 use File::Basename;
  33 use Text::ParseWords;
  34 use Benchmark;
  35 use FileUtil;
  36 use SDFileUtil;
  37 use TextUtil;
  38 use MolecularFormula;
  39 use FileIO::SDFileIO;
  40 use Molecule;
  41 
  42 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
  43 
  44 # Autoflush STDOUT
  45 $| = 1;
  46 
  47 # Starting message...
  48 $ScriptName = basename($0);
  49 print "\n$ScriptName: Starting...\n\n";
  50 $StartTime = new Benchmark;
  51 
  52 # Get the options and setup script...
  53 SetupScriptUsage();
  54 if ($Options{help} || @ARGV < 1) {
  55   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
  56 }
  57 
  58 my(@SDFilesList);
  59 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
  60 
  61 print "Processing options...\n";
  62 my(%OptionsInfo);
  63 ProcessOptions();
  64 
  65 print "Checking input SD file(s)...\n";
  66 my(%SDFilesInfo);
  67 RetrieveSDFilesInfo();
  68 
  69 # Generate output files...
  70 my($FileIndex);
  71 if (@SDFilesList > 1) {
  72   print "\nProcessing SD files...\n";
  73 }
  74 for $FileIndex (0 .. $#SDFilesList) {
  75   if ($SDFilesInfo{FileOkay}[$FileIndex]) {
  76     print "\nProcessing file $SDFilesList[$FileIndex]...\n";
  77     PerformElementalAnalysis($FileIndex);
  78   }
  79 }
  80 print "\n$ScriptName:Done...\n\n";
  81 
  82 $EndTime = new Benchmark;
  83 $TotalTime = timediff ($EndTime, $StartTime);
  84 print "Total time: ", timestr($TotalTime), "\n";
  85 
  86 ###############################################################################
  87 
  88 # Perform analysis...
  89 sub PerformElementalAnalysis {
  90   my($Index) = @_;
  91   my($SDFile, $NewSDFile, $KeyDataFieldName, $CmpdCount, $CurrentFormula, $FormulaFieldName, $CmpdString, $Value, $CalculationType, $CalculatedValue, $ErrorMsg, $Status, $ElementsRef, $ElementCompositionRef, $Molecule, @CalculatedValues, @CmpdLines, %DataFieldValuesMap);
  92 
  93   $SDFile = $SDFilesList[$Index];
  94   $NewSDFile = $SDFilesInfo{OutFile}[$Index];
  95 
  96   print "Generating new SD file $NewSDFile...\n";
  97   open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
  98   open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
  99 
 100 
 101   $CmpdCount = 0;
 102   $FormulaFieldName = $SDFilesInfo{FormulaFieldName}[$Index];
 103 
 104   COMPOUND: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
 105     $CmpdCount++;
 106     @CmpdLines = split "\n", $CmpdString;
 107     %DataFieldValuesMap = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
 108 
 109     @CalculatedValues = ();
 110     for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
 111       push @CalculatedValues, '';
 112     }
 113 
 114     $CurrentFormula = undef;
 115 
 116     if ($OptionsInfo{UseStructureData}) {
 117       $Molecule = FileIO::SDFileIO::ParseMoleculeString($CmpdString);
 118       $CurrentFormula = $Molecule->GetMolecularFormula();
 119     }
 120     else {
 121       if (!exists $DataFieldValuesMap{$FormulaFieldName}) {
 122         $ErrorMsg = "Ignoring compound record $CmpdCount: Formula field $FormulaFieldName not found";
 123         PrintErrorMsg($CmpdString, $ErrorMsg);
 124         WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues);
 125         next COMPOUND;
 126       }
 127 
 128       # Make sure it's a valid molecular formula...
 129       $CurrentFormula = $DataFieldValuesMap{$FormulaFieldName};
 130       if ($OptionsInfo{CheckFormula}) {
 131         ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($CurrentFormula);
 132         if (!$Status) {
 133           $ErrorMsg = "Ignoring compound record $CmpdCount: Formula field value $CurrentFormula is not valid: $ErrorMsg";
 134           PrintErrorMsg($CmpdString, $ErrorMsg);
 135           WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues);
 136           next COMPOUND;
 137         }
 138       }
 139     }
 140 
 141     # Calculate appropriate values and write 'em out...
 142     @CalculatedValues = ();
 143     for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
 144       if ($CalculationType =~ /^ElementalAnalysis$/i) {
 145         ($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($CurrentFormula);
 146         $CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : '';
 147       }
 148       elsif ($CalculationType =~ /^MolecularWeight$/i) {
 149         $CalculatedValue = MolecularFormula::CalculateMolecularWeight($CurrentFormula);
 150         $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
 151       }
 152       elsif ($CalculationType =~ /^ExactMass$/i) {
 153         $CalculatedValue = MolecularFormula::CalculateExactMass($CurrentFormula);
 154         $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
 155       }
 156       else {
 157         $CalculatedValue = '';
 158       }
 159       push @CalculatedValues, $CalculatedValue;
 160     }
 161     WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues, $CurrentFormula);
 162   }
 163   close NEWSDFILE;
 164   close SDFILE;
 165 }
 166 
 167 # Write out compound record with calculated values...
 168 sub WriteNewCompoundRecord {
 169   my($Index, $SDFileRef, $CmpdLinesRef, $CalculatedValuesRef, $MolecularFormula) = @_;
 170 
 171   # Write out compound lines except the last line which contains $$$$...
 172   my($LineIndex);
 173   for $LineIndex (0 .. ($#{$CmpdLinesRef} - 1)) {
 174     print $SDFileRef "$CmpdLinesRef->[$LineIndex]\n";
 175   }
 176 
 177   # Write out calculated values...
 178   my($CalcIndex, $FieldName, $FieldValue);
 179   for $CalcIndex (0 .. $#{$OptionsInfo{SpecifiedCalculations}}) {
 180     $FieldName = $SDFilesInfo{ValueFieldNamesMap}[$Index]{$OptionsInfo{SpecifiedCalculations}[$CalcIndex]};
 181     $FieldValue = $CalculatedValuesRef->[$CalcIndex];
 182     print  $SDFileRef ">  <$FieldName>\n$FieldValue\n\n";
 183   }
 184 
 185   if ($OptionsInfo{UseStructureData} && $OptionsInfo{WriteOutFormula} && defined($MolecularFormula)) {
 186     $FieldName = $SDFilesInfo{ValueFieldNamesMap}[$Index]{MolecularFormula};
 187     $FieldValue = $MolecularFormula;
 188     print  $SDFileRef ">  <$FieldName>\n$FieldValue\n\n";
 189   }
 190 
 191   print $SDFileRef  "\$\$\$\$\n";
 192 }
 193 
 194 # Print out error message...
 195 sub PrintErrorMsg {
 196   my($CmpdString, $ErrorMsg) = @_;
 197 
 198   if ($OptionsInfo{DetailLevel} >= 2 ) {
 199     print "$ErrorMsg:\n$CmpdString\n";
 200   }
 201   elsif ($OptionsInfo{DetailLevel} >= 1) {
 202     print "$ErrorMsg\n";
 203   }
 204 }
 205 
 206 # Retrieve information about input SD files...
 207 sub RetrieveSDFilesInfo {
 208   my($Index, $SDFile, $FileDir, $FileName, $FileExt, $OutFileRoot,  $OutFile, $FormulaFieldName, $Value, $FieldName, $NewFieldName, $Count);
 209 
 210   my(%NewValueFieldNames) = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass', MolecularFormula => 'MolecularFormula');
 211   if (@{$OptionsInfo{SpecifiedValueFieldNames}}) {
 212     for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueFieldNames}}; $Index +=2) {
 213       $Value = $OptionsInfo{SpecifiedValueFieldNames}[$Index];
 214       $FieldName = $OptionsInfo{SpecifiedValueFieldNames}[$Index + 1];
 215       if (exists $NewValueFieldNames{$Value}) {
 216         $NewValueFieldNames{$Value} = $FieldName;
 217       }
 218     }
 219   }
 220 
 221   %SDFilesInfo = ();
 222 
 223   @{$SDFilesInfo{FileOkay}} = ();
 224   @{$SDFilesInfo{OutFile}} = ();
 225   @{$SDFilesInfo{FormulaFieldName}} = ();
 226   @{$SDFilesInfo{ValueFieldNamesMap}} = ();
 227 
 228   FILELIST: for $Index (0 .. $#SDFilesList) {
 229     $SDFile = $SDFilesList[$Index];
 230 
 231     $SDFilesInfo{FileOkay}[$Index] = 0;
 232     $SDFilesInfo{OutFile}[$Index] = '';
 233     $SDFilesInfo{FormulaFieldName}[$Index] = '';
 234 
 235     %{$SDFilesInfo{ValueFieldNamesMap}[$Index]} = ();
 236 
 237     if (!(-e $SDFile)) {
 238       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
 239       next FILELIST;
 240     }
 241     if (!CheckFileType($SDFile, "sd sdf")) {
 242       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
 243       next FILELIST;
 244     }
 245     $FileDir = ""; $FileName = ""; $FileExt = "";
 246     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
 247     if ($Options{root} && (@SDFilesList == 1)) {
 248       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
 249       if ($RootFileName && $RootFileExt) {
 250         $FileName = $RootFileName;
 251       }
 252       else {
 253         $FileName = $Options{root};
 254       }
 255       $OutFileRoot = $FileName;
 256     }
 257     else {
 258       $OutFileRoot = $FileName . "ElementalAnalysis";
 259     }
 260 
 261     $OutFile = $OutFileRoot . ".$FileExt";
 262     if (lc($OutFile) eq lc($SDFile)) {
 263       warn "Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n";
 264       next FILELIST;
 265     }
 266     if (!$Options{overwrite}) {
 267       if (-e $OutFile) {
 268         warn "Warning: Ignoring file $SDFile: The file $OutFile already exists\n";
 269         next FILELIST;
 270       }
 271     }
 272     # Get data field names and values...
 273     my($CmpdString, $FieldName, @CmpdLines, @DataFieldNames, %DataFieldNamesMap);
 274     @DataFieldNames = ();
 275     if (!open(SDFILE, "$SDFile")) {
 276       warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
 277       next FILELIST;
 278     }
 279     $CmpdString = ReadCmpdString(\*SDFILE);
 280     close SDFILE;
 281 
 282     @CmpdLines = split "\n", $CmpdString;
 283     @DataFieldNames = GetCmpdDataHeaderLabels(\@CmpdLines);
 284     %DataFieldNamesMap = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
 285 
 286     # Setup formula field name...
 287     $FormulaFieldName = '';
 288     if ($OptionsInfo{UseDataField}) {
 289       if ($OptionsInfo{SpecifiedFormulaFieldName}) {
 290         $FormulaFieldName = $OptionsInfo{SpecifiedFormulaFieldName};
 291       }
 292       else {
 293       FIELDNAME: for $FieldName (@DataFieldNames) {
 294           if ($FieldName =~ /Formula/i) {
 295             $FormulaFieldName = $FieldName;
 296             last FIELDNAME;
 297           }
 298         }
 299         if (!$FormulaFieldName) {
 300           warn "Warning: Ignoring file $SDFile: Data field label containing the word Formula doesn't exist\n";
 301           next FILELIST;
 302         }
 303       }
 304     }
 305     $SDFilesInfo{FileOkay}[$Index] = 1;
 306     $SDFilesInfo{OutFile}[$Index] = $OutFile;
 307     $SDFilesInfo{FormulaFieldName}[$Index] = $FormulaFieldName;
 308 
 309     # Setup value data field names for calculated values...
 310     for $Value (keys %NewValueFieldNames) {
 311       $FieldName = $NewValueFieldNames{$Value};
 312 
 313       # Make sure it doesn't already exists...
 314       $Count = 1;
 315       $NewFieldName = $FieldName;
 316       while (exists $DataFieldNamesMap{$NewFieldName}) {
 317         $Count++;
 318         $NewFieldName = $FieldName . $Count;
 319       }
 320       $SDFilesInfo{ValueFieldNamesMap}[$Index]{$Value} = $NewFieldName;
 321     }
 322   }
 323 }
 324 
 325 # Process option values...
 326 sub ProcessOptions {
 327   %OptionsInfo = ();
 328 
 329   $OptionsInfo{Mode} = $Options{mode};
 330   $OptionsInfo{FormulaMode} = $Options{formulamode};
 331 
 332   $OptionsInfo{WriteOutFormula} = ($Options{formulaout} =~ /^Yes$/i) ? 1 : 0;
 333 
 334   $OptionsInfo{UseStructureData} = ($Options{formulamode} =~ /^StructureData$/i) ? 1 : 0;
 335   $OptionsInfo{UseDataField} = ($Options{formulamode} =~ /^DataField$/i) ? 1 : 0;
 336 
 337   $OptionsInfo{Fast} = defined $Options{fast} ? $Options{fast} : undef;
 338 
 339   $OptionsInfo{DetailLevel} = $Options{detail};
 340   $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1;
 341   $OptionsInfo{Precision} = $Options{precision};
 342 
 343   $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
 344 
 345   $OptionsInfo{FormulaField} = defined $Options{formulafield} ? $Options{formulafield} : undef;
 346   $OptionsInfo{SpecifiedFormulaFieldName} = "";
 347 
 348   if (defined $Options{formulafield}) {
 349     $OptionsInfo{SpecifiedFormulaFieldName} = $Options{formulafield};
 350   }
 351   # Setup what to calculate...
 352   @{$OptionsInfo{SpecifiedCalculations}} = ();
 353   if ($Options{mode} =~ /^All$/i) {
 354     @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass);
 355   }
 356   else {
 357     my($Mode, $ModeValue, @SpecifiedModeValues);
 358     $Mode = $Options{mode};
 359     $Mode =~ s/ //g;
 360     @SpecifiedModeValues = split /\,/, $Mode;
 361     for $ModeValue (@SpecifiedModeValues) {
 362       if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
 363         if ($ModeValue =~ /^All$/i) {
 364           die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n";
 365         }
 366         else {
 367           die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
 368         }
 369       }
 370       push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue;
 371     }
 372   }
 373 
 374   $OptionsInfo{ValueFieldNames} = defined $Options{valuefieldnames} ? $Options{valuefieldnames} : undef;
 375   @{$OptionsInfo{SpecifiedValueFieldNames}} = ();
 376 
 377   if ($Options{valuefieldnames}) {
 378     my($Value, $Label, @ValueLabels);
 379     @ValueLabels = split /\,/, $Options{valuefieldnames};
 380     if (@ValueLabels % 2) {
 381       die "Error: The value specified, $Options{valuefieldnames}, for option \"-v --valuefieldnames\" is not valid: It must contain even number of comma delimited values\n";
 382     }
 383     my($Index);
 384     for ($Index = 0; $Index < @ValueLabels; $Index +=2) {
 385       $Value = $ValueLabels[$Index];
 386       $Value =~ s/ //g;
 387       $Label = $ValueLabels[$Index + 1];
 388       if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass|MolecularFormula)$/i) {
 389         die "Error: The value specified, $Value, using option \"-v --valuefieldnames\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, ExactMass, or MolecularFormula\n";
 390       }
 391       push @{$OptionsInfo{SpecifiedValueFieldNames}}, ($Value, $Label);
 392     }
 393   }
 394 }
 395 
 396 # Setup script usage  and retrieve command line arguments specified using various options...
 397 sub SetupScriptUsage {
 398 
 399   # Retrieve all the options...
 400   %Options = ();
 401   $Options{detail} = 1;
 402   $Options{formulamode} = "DataField";
 403   $Options{formulaout} = "No";
 404   $Options{mode} = "All";
 405   $Options{precision} = 2;
 406 
 407   if (!GetOptions(\%Options, "detail|d=i", "fast", "formulafield=s", "formulamode|f=s", "formulaout=s", "mode|m=s", "help|h", "overwrite|o", "precision|p=i", "root|r=s", "valuefieldnames|v=s", "workingdir|w=s")) {
 408     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
 409   }
 410   if ($Options{workingdir}) {
 411     if (! -d $Options{workingdir}) {
 412       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
 413     }
 414     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
 415   }
 416   if (!IsPositiveInteger($Options{detail})) {
 417     die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
 418   }
 419   if ($Options{formulamode} !~ /^(StructureData|DataField)$/i) {
 420     die "Error: The value specified, $Options{formulamode}, for option \"-f, --formulamode\" is not valid. Allowed values: StructureData or DataField \n";
 421   }
 422   if ($Options{formulaout} !~ /^(Yes|No)$/i) {
 423     die "Error: The value specified, $Options{formulaout}, for option \"--formulaout\" is not valid. Allowed values: Yes or No \n";
 424   }
 425   if (!IsPositiveInteger($Options{precision})) {
 426     die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
 427   }
 428 }
 429