diff bin/ElementalAnalysisSDFiles.pl @ 0:4816e4a8ae95 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/ElementalAnalysisSDFiles.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,580 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: ElementalAnalysisSDFiles.pl,v $
+# $Date: 2015/02/28 20:46:19 $
+# $Revision: 1.24 $
+#
+# Author: Manish Sud <[e-mail]>
+#
+# Copyright (C) 2015 Manish Sud. All rights reserved.
+#
+# This file is part of MayaChemTools.
+#
+# MayaChemTools is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# MayaChemTools is distributed in the hope that it will be useful, but without
+# any warranty; without even the implied warranty of merchantability of fitness
+# for a particular purpose.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
+# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
+# Boston, MA, 02111-1307, USA.
+#
+
+use strict;
+use FindBin; use lib "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use SDFileUtil;
+use TextUtil;
+use MolecularFormula;
+use FileIO::SDFileIO;
+use Molecule;
+
+my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
+
+# Autoflush STDOUT
+$| = 1;
+
+# Starting message...
+$ScriptName = basename($0);
+print "\n$ScriptName: Starting...\n\n";
+$StartTime = new Benchmark;
+
+# Get the options and setup script...
+SetupScriptUsage();
+if ($Options{help} || @ARGV < 1) {
+  die GetUsageFromPod("$FindBin::Bin/$ScriptName");
+}
+
+my(@SDFilesList);
+@SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
+
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+print "Checking input SD file(s)...\n";
+my(%SDFilesInfo);
+RetrieveSDFilesInfo();
+
+# Generate output files...
+my($FileIndex);
+if (@SDFilesList > 1) {
+  print "\nProcessing SD files...\n";
+}
+for $FileIndex (0 .. $#SDFilesList) {
+  if ($SDFilesInfo{FileOkay}[$FileIndex]) {
+    print "\nProcessing file $SDFilesList[$FileIndex]...\n";
+    PerformElementalAnalysis($FileIndex);
+  }
+}
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Perform analysis...
+sub PerformElementalAnalysis {
+  my($Index) = @_;
+  my($SDFile, $NewSDFile, $KeyDataFieldName, $CmpdCount, $CurrentFormula, $FormulaFieldName, $CmpdString, $Value, $CalculationType, $CalculatedValue, $ErrorMsg, $Status, $ElementsRef, $ElementCompositionRef, $Molecule, @CalculatedValues, @CmpdLines, %DataFieldValuesMap);
+
+  $SDFile = $SDFilesList[$Index];
+  $NewSDFile = $SDFilesInfo{OutFile}[$Index];
+
+  print "Generating new SD file $NewSDFile...\n";
+  open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
+  open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
+
+
+  $CmpdCount = 0;
+  $FormulaFieldName = $SDFilesInfo{FormulaFieldName}[$Index];
+
+  COMPOUND: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
+    $CmpdCount++;
+    @CmpdLines = split "\n", $CmpdString;
+    %DataFieldValuesMap = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
+
+    @CalculatedValues = ();
+    for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
+      push @CalculatedValues, '';
+    }
+
+    $CurrentFormula = undef;
+
+    if ($OptionsInfo{UseStructureData}) {
+      $Molecule = FileIO::SDFileIO::ParseMoleculeString($CmpdString);
+      $CurrentFormula = $Molecule->GetMolecularFormula();
+    }
+    else {
+      if (!exists $DataFieldValuesMap{$FormulaFieldName}) {
+	$ErrorMsg = "Ignoring compound record $CmpdCount: Formula field $FormulaFieldName not found";
+	PrintErrorMsg($CmpdString, $ErrorMsg);
+	WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues);
+	next COMPOUND;
+      }
+
+      # Make sure it's a valid molecular formula...
+      $CurrentFormula = $DataFieldValuesMap{$FormulaFieldName};
+      if ($OptionsInfo{CheckFormula}) {
+	($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($CurrentFormula);
+	if (!$Status) {
+	  $ErrorMsg = "Ignoring compound record $CmpdCount: Formula field value $CurrentFormula is not valid: $ErrorMsg";
+	  PrintErrorMsg($CmpdString, $ErrorMsg);
+	  WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues);
+	  next COMPOUND;
+	}
+      }
+    }
+
+    # Calculate appropriate values and write 'em out...
+    @CalculatedValues = ();
+    for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
+      if ($CalculationType =~ /^ElementalAnalysis$/i) {
+	($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($CurrentFormula);
+	$CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : '';
+      }
+      elsif ($CalculationType =~ /^MolecularWeight$/i) {
+	$CalculatedValue = MolecularFormula::CalculateMolecularWeight($CurrentFormula);
+	$CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
+      }
+      elsif ($CalculationType =~ /^ExactMass$/i) {
+	$CalculatedValue = MolecularFormula::CalculateExactMass($CurrentFormula);
+	$CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
+      }
+      else {
+	$CalculatedValue = '';
+      }
+      push @CalculatedValues, $CalculatedValue;
+    }
+    WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues, $CurrentFormula);
+  }
+  close NEWSDFILE;
+  close SDFILE;
+}
+
+# Write out compound record with calculated values...
+sub WriteNewCompoundRecord {
+  my($Index, $SDFileRef, $CmpdLinesRef, $CalculatedValuesRef, $MolecularFormula) = @_;
+
+  # Write out compound lines except the last line which contains $$$$...
+  my($LineIndex);
+  for $LineIndex (0 .. ($#{$CmpdLinesRef} - 1)) {
+    print $SDFileRef "$CmpdLinesRef->[$LineIndex]\n";
+  }
+
+  # Write out calculated values...
+  my($CalcIndex, $FieldName, $FieldValue);
+  for $CalcIndex (0 .. $#{$OptionsInfo{SpecifiedCalculations}}) {
+    $FieldName = $SDFilesInfo{ValueFieldNamesMap}[$Index]{$OptionsInfo{SpecifiedCalculations}[$CalcIndex]};
+    $FieldValue = $CalculatedValuesRef->[$CalcIndex];
+    print  $SDFileRef ">  <$FieldName>\n$FieldValue\n\n";
+  }
+
+  if ($OptionsInfo{UseStructureData} && $OptionsInfo{WriteOutFormula} && defined($MolecularFormula)) {
+    $FieldName = $SDFilesInfo{ValueFieldNamesMap}[$Index]{MolecularFormula};
+    $FieldValue = $MolecularFormula;
+    print  $SDFileRef ">  <$FieldName>\n$FieldValue\n\n";
+  }
+
+  print $SDFileRef  "\$\$\$\$\n";
+}
+
+# Print out error message...
+sub PrintErrorMsg {
+  my($CmpdString, $ErrorMsg) = @_;
+
+  if ($OptionsInfo{DetailLevel} >= 2 ) {
+    print "$ErrorMsg:\n$CmpdString\n";
+  }
+  elsif ($OptionsInfo{DetailLevel} >= 1) {
+    print "$ErrorMsg\n";
+  }
+}
+
+# Retrieve information about input SD files...
+sub RetrieveSDFilesInfo {
+  my($Index, $SDFile, $FileDir, $FileName, $FileExt, $OutFileRoot,  $OutFile, $FormulaFieldName, $Value, $FieldName, $NewFieldName, $Count);
+
+  my(%NewValueFieldNames) = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass', MolecularFormula => 'MolecularFormula');
+  if (@{$OptionsInfo{SpecifiedValueFieldNames}}) {
+    for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueFieldNames}}; $Index +=2) {
+      $Value = $OptionsInfo{SpecifiedValueFieldNames}[$Index];
+      $FieldName = $OptionsInfo{SpecifiedValueFieldNames}[$Index + 1];
+      if (exists $NewValueFieldNames{$Value}) {
+	$NewValueFieldNames{$Value} = $FieldName;
+      }
+    }
+  }
+
+  %SDFilesInfo = ();
+
+  @{$SDFilesInfo{FileOkay}} = ();
+  @{$SDFilesInfo{OutFile}} = ();
+  @{$SDFilesInfo{FormulaFieldName}} = ();
+  @{$SDFilesInfo{ValueFieldNamesMap}} = ();
+
+  FILELIST: for $Index (0 .. $#SDFilesList) {
+    $SDFile = $SDFilesList[$Index];
+
+    $SDFilesInfo{FileOkay}[$Index] = 0;
+    $SDFilesInfo{OutFile}[$Index] = '';
+    $SDFilesInfo{FormulaFieldName}[$Index] = '';
+
+    %{$SDFilesInfo{ValueFieldNamesMap}[$Index]} = ();
+
+    if (!(-e $SDFile)) {
+      warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
+      next FILELIST;
+    }
+    if (!CheckFileType($SDFile, "sd sdf")) {
+      warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
+      next FILELIST;
+    }
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
+    if ($Options{root} && (@SDFilesList == 1)) {
+      my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
+      if ($RootFileName && $RootFileExt) {
+	$FileName = $RootFileName;
+      }
+      else {
+	$FileName = $Options{root};
+      }
+      $OutFileRoot = $FileName;
+    }
+    else {
+      $OutFileRoot = $FileName . "ElementalAnalysis";
+    }
+
+    $OutFile = $OutFileRoot . ".$FileExt";
+    if (lc($OutFile) eq lc($SDFile)) {
+      warn "Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n";
+      next FILELIST;
+    }
+    if (!$Options{overwrite}) {
+      if (-e $OutFile) {
+	warn "Warning: Ignoring file $SDFile: The file $OutFile already exists\n";
+	next FILELIST;
+      }
+    }
+    # Get data field names and values...
+    my($CmpdString, $FieldName, @CmpdLines, @DataFieldNames, %DataFieldNamesMap);
+    @DataFieldNames = ();
+    if (!open(SDFILE, "$SDFile")) {
+      warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
+      next FILELIST;
+    }
+    $CmpdString = ReadCmpdString(\*SDFILE);
+    close SDFILE;
+
+    @CmpdLines = split "\n", $CmpdString;
+    @DataFieldNames = GetCmpdDataHeaderLabels(\@CmpdLines);
+    %DataFieldNamesMap = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
+
+    # Setup formula field name...
+    $FormulaFieldName = '';
+    if ($OptionsInfo{UseDataField}) {
+      if ($OptionsInfo{SpecifiedFormulaFieldName}) {
+	$FormulaFieldName = $OptionsInfo{SpecifiedFormulaFieldName};
+      }
+      else {
+      FIELDNAME: for $FieldName (@DataFieldNames) {
+	  if ($FieldName =~ /Formula/i) {
+	    $FormulaFieldName = $FieldName;
+	    last FIELDNAME;
+	  }
+	}
+	if (!$FormulaFieldName) {
+	  warn "Warning: Ignoring file $SDFile: Data field label containing the word Formula doesn't exist\n";
+	  next FILELIST;
+	}
+      }
+    }
+    $SDFilesInfo{FileOkay}[$Index] = 1;
+    $SDFilesInfo{OutFile}[$Index] = $OutFile;
+    $SDFilesInfo{FormulaFieldName}[$Index] = $FormulaFieldName;
+
+    # Setup value data field names for calculated values...
+    for $Value (keys %NewValueFieldNames) {
+      $FieldName = $NewValueFieldNames{$Value};
+
+      # Make sure it doesn't already exists...
+      $Count = 1;
+      $NewFieldName = $FieldName;
+      while (exists $DataFieldNamesMap{$NewFieldName}) {
+	$Count++;
+	$NewFieldName = $FieldName . $Count;
+      }
+      $SDFilesInfo{ValueFieldNamesMap}[$Index]{$Value} = $NewFieldName;
+    }
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+  %OptionsInfo = ();
+
+  $OptionsInfo{Mode} = $Options{mode};
+  $OptionsInfo{FormulaMode} = $Options{formulamode};
+
+  $OptionsInfo{WriteOutFormula} = ($Options{formulaout} =~ /^Yes$/i) ? 1 : 0;
+
+  $OptionsInfo{UseStructureData} = ($Options{formulamode} =~ /^StructureData$/i) ? 1 : 0;
+  $OptionsInfo{UseDataField} = ($Options{formulamode} =~ /^DataField$/i) ? 1 : 0;
+
+  $OptionsInfo{Fast} = defined $Options{fast} ? $Options{fast} : undef;
+
+  $OptionsInfo{DetailLevel} = $Options{detail};
+  $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1;
+  $OptionsInfo{Precision} = $Options{precision};
+
+  $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
+
+  $OptionsInfo{FormulaField} = defined $Options{formulafield} ? $Options{formulafield} : undef;
+  $OptionsInfo{SpecifiedFormulaFieldName} = "";
+
+  if (defined $Options{formulafield}) {
+    $OptionsInfo{SpecifiedFormulaFieldName} = $Options{formulafield};
+  }
+  # Setup what to calculate...
+  @{$OptionsInfo{SpecifiedCalculations}} = ();
+  if ($Options{mode} =~ /^All$/i) {
+    @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass);
+  }
+  else {
+    my($Mode, $ModeValue, @SpecifiedModeValues);
+    $Mode = $Options{mode};
+    $Mode =~ s/ //g;
+    @SpecifiedModeValues = split /\,/, $Mode;
+    for $ModeValue (@SpecifiedModeValues) {
+      if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
+	if ($ModeValue =~ /^All$/i) {
+	  die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n";
+	}
+	else {
+	  die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
+	}
+      }
+      push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue;
+    }
+  }
+
+  $OptionsInfo{ValueFieldNames} = defined $Options{valuefieldnames} ? $Options{valuefieldnames} : undef;
+  @{$OptionsInfo{SpecifiedValueFieldNames}} = ();
+
+  if ($Options{valuefieldnames}) {
+    my($Value, $Label, @ValueLabels);
+    @ValueLabels = split /\,/, $Options{valuefieldnames};
+    if (@ValueLabels % 2) {
+      die "Error: The value specified, $Options{valuefieldnames}, for option \"-v --valuefieldnames\" is not valid: It must contain even number of comma delimited values\n";
+    }
+    my($Index);
+    for ($Index = 0; $Index < @ValueLabels; $Index +=2) {
+      $Value = $ValueLabels[$Index];
+      $Value =~ s/ //g;
+      $Label = $ValueLabels[$Index + 1];
+      if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass|MolecularFormula)$/i) {
+	die "Error: The value specified, $Value, using option \"-v --valuefieldnames\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, ExactMass, or MolecularFormula\n";
+      }
+      push @{$OptionsInfo{SpecifiedValueFieldNames}}, ($Value, $Label);
+    }
+  }
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{detail} = 1;
+  $Options{formulamode} = "DataField";
+  $Options{formulaout} = "No";
+  $Options{mode} = "All";
+  $Options{precision} = 2;
+
+  if (!GetOptions(\%Options, "detail|d=i", "fast", "formulafield=s", "formulamode|f=s", "formulaout=s", "mode|m=s", "help|h", "overwrite|o", "precision|p=i", "root|r=s", "valuefieldnames|v=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
+  }
+  if ($Options{workingdir}) {
+    if (! -d $Options{workingdir}) {
+      die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
+    }
+    chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
+  }
+  if (!IsPositiveInteger($Options{detail})) {
+    die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
+  }
+  if ($Options{formulamode} !~ /^(StructureData|DataField)$/i) {
+    die "Error: The value specified, $Options{formulamode}, for option \"-f, --formulamode\" is not valid. Allowed values: StructureData or DataField \n";
+  }
+  if ($Options{formulaout} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{formulaout}, for option \"--formulaout\" is not valid. Allowed values: Yes or No \n";
+  }
+  if (!IsPositiveInteger($Options{precision})) {
+    die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+ElementalAnalysisSDFiles.pl - Perform elemental analysis using formula data field in SDFile(s)
+
+=head1 SYNOPSIS
+
+ElementalAnalysisSDFiles.pl SDFile(s)...
+
+ElementalAnalysisSDFiles.pl [B<-d, --detail> infolevel] [B<--fast>]
+[B<--formulafield> SD data field name] [B<-f, --formulamode> I<DataField | StructureData>]
+[B<--formulaout> yes or no] [B<-m, --mode> All | "ElementalAnalysis, [MolecularWeight, ExactMass]"]
+[B<-h, --help>] [B<-o, --overwrite>] [B<-r, --root> rootname]
+[B<-v --valuefieldnames> Name, Label, [Name, Label,...]] [B<-w, --workingdir> dirname] SDFile(s)...
+
+=head1 DESCRIPTION
+
+Perform elemental analysis using molecular formula specified by a data field name or generated
+from structure data in I<SDFile(s)>.
+
+In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
+other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
+8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
+D and T, are not supported.
+
+The file names are separated by space.The valid file extensions are I<.sdf> and I<.sd>.
+All other file names are ignored. All the SD files in a current directory can be specified
+either by I<*.sdf> or the current directory name.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-d, --detail> I<infolevel>
+
+Level of information to print about compound records being ignored. Default: I<1>. Possible
+values: I<1, 2 or 3>.
+
+=item B<--fast>
+
+In this mode, the formula data field specified using B<-f, --formulafield> option is assumed
+to contain valid molecular formula data and initial formula validation check is skipped.
+
+=item B<--formulafield> I<SD data field name>
+
+I<SDFile(s)> data field name containing molecular formulas used for performing
+elemental analysis during I<DataField> value of B<-f, --formulamode> option.
+Default value: I<SD data field containing the word formula in its name>.
+
+This option is ignore during I<StructureData> value of B<-f, --formulamode> option.
+
+=item B<-f, --formulamode> I<DataField | StructureData>
+
+Specify source of molecular formula used for performing elemental analysis: retrieve
+formula using I<SDFile(s)> data field name or generate formula from structure. Possible
+values: I<DataField or StructureData>. Default value: I<DataField>.
+
+=item B<--formulaout> I<yes or no>
+
+Specify whether to write out formula to SD file during I<StructureData> value of
+B<-f, --formulamode> option. Possible values: I<Yes or No>. Default: I<No>.
+
+=item B<-m, --mode> I<All | "ElementalAnalysis,[MolecularWeight,ExactMass]">
+
+Specify what values to calculate using molecular formula data field or structure data from
+I<SDFile(s)>: calculate all supported values or specify a comma delimited list of values.
+Possible values: I<All | "ElementalAnalysis, [MolecularWeight, ExactMass]">. Default: I<All>
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<-p, --precision> I<number>
+
+Precision of calculated values in the output file. Default: up to I<2> decimal places.
+Valid values: positive integers.
+
+=item B<-r, --root> I<rootname>
+
+New SD file name is generated using the root: <Root>.<Ext>. Default new file
+name: <InitialSDFileName>ElementalAnalysis.<Ext>. This option is ignored for multiple
+input files.
+
+=item B<-v --valuefieldnames> I<Name,Label,[Name,Label,...]>
+
+Specify SD data field names to use for calculated values. In general, it's a comma delimited
+list of value name and SD field name  pairs. Supported value names: I<ElementalAnalysis,
+MolecularWeight, ExactMass, and MolecularFormula>. Default labels: I<ElementalAnalysis,
+MolecularWeight, ExactMass, and MolecularFormula>.
+
+I<MolecularFormula> label is only used during I<StructureData> value of
+B<-f, --formulamode> option.
+
+=item B<-w, --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To perform elemental analysis, calculate molecular weight and exact mass using SD
+field name value with the word Formula in its name and generate a new SD file
+NewSample1.sdf, type:
+
+    % ElementalAnalysisSDFiles.pl -o -r NewSample1 Sample1.sdf
+
+To perform elemental analysis, calculate molecular weight and exact mass using
+structure data in SD file and generate a new SD file NewSample1.sdf, type:
+
+    % ElementalAnalysisSDFiles.pl --formulamode StructureData -o
+      -r NewSample1 Sample1.sdf
+
+To perform elemental analysis using formulas in SD field name Formula, use field name
+Analysis for calculated data, and generate a new SD file NewSample1.sdf, type:
+
+    % ElementalAnalysisSDFiles.pl --m ElementalAnalysis --formulafield
+      Formula --valuefieldnames "ElementalAnalysis,Analysis" -o
+      -r NewSample1 Sample1.sdf
+
+To calculate molecular weight, using formulas in SD field name Formula, with four decimal
+precision and generate a new SD file NewSample1.sdf, type
+
+    % ElementalAnalysisSDFiles.pl --m MolecularWeight --formulafield
+      Formula --precision 4 -o -r NewSample1 Sample1.sdf
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+AnalyzeSDFilesData.pl, InfoSDFiles.pl, ExtractFromSDFiles.pl
+
+=head1 COPYRIGHT
+
+Copyright (C) 2015 Manish Sud. All rights reserved.
+
+This file is part of MayaChemTools.
+
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.
+
+=cut