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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/ElementalAnalysis.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,537 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: ElementalAnalysis.pl,v $
+# $Date: 2015/02/28 20:46:19 $
+# $Revision: 1.19 $
+#
+# 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 "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+use MolecularFormula;
+
+my($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}) {
+  die GetUsageFromPod("$FindBin::Bin/$ScriptName");
+}
+
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+PerformElementalAnalysis();
+
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Elemental analysis...
+sub PerformElementalAnalysis {
+  my($Formula, $FormulaDataRef, $ValueLabel, $CalculationType, $CalculatedValue, $ElementsRef, $ElementCompositionRef, $Status, $ErrorMsg, @ValueLabels, @CalculatedValues);
+
+  print "Performing elemental analysis...\n";
+
+  if ($OptionsInfo{FileOutput}) {
+    print "Generating file $OptionsInfo{OutFileName}...\n";
+    open OUTFILE, ">$OptionsInfo{OutFileName}" or die "Couldn't open $OptionsInfo{OutFileName}: $!\n";
+  }
+
+  # Setup value labels...
+  @ValueLabels = ();
+  if ($OptionsInfo{RowsOutput}) {
+    push @ValueLabels, "Formula";
+  }
+  for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
+    push @ValueLabels, $OptionsInfo{ValueLabelsMap}{$CalculationType};
+  }
+
+  if ($OptionsInfo{RowsOutput}) {
+    ListHeaderRowData(\@ValueLabels);
+  }
+
+  # Go over specified properties...
+  FORMULA: for $Formula (@{$OptionsInfo{SpecifiedFormulas}}) {
+    if (!$OptionsInfo{RowsOutput}) {
+      if ($OptionsInfo{FileOutput}) {
+	print OUTFILE "\nPerforming elemental analysis using formula $Formula...\n\n";
+      }
+      else {
+	print "\nPerforming elemental analysis using formula  $Formula...\n\n";
+      }
+    }
+    # Calculate appropriate values and write 'em out...
+    if ($OptionsInfo{CheckFormula}) {
+      ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($Formula);
+      if (!$Status) {
+	warn("Warning: Ignoring formula $Formula: It's not a valid value: $ErrorMsg\n");
+	next FORMULA;
+      }
+    }
+    @CalculatedValues = ();
+    if ($OptionsInfo{RowsOutput}) {
+      push @CalculatedValues, $Formula;
+    }
+    for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
+      if ($CalculationType =~ /^ElementalAnalysis$/i) {
+	($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($Formula);
+	$CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : '';
+      }
+      elsif ($CalculationType =~ /^MolecularWeight$/i) {
+	$CalculatedValue = MolecularFormula::CalculateMolecularWeight($Formula);
+	$CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
+      }
+      elsif ($CalculationType =~ /^ExactMass$/i) {
+	$CalculatedValue = MolecularFormula::CalculateExactMass($Formula);
+	$CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
+      }
+      else {
+	$CalculatedValue = '';
+      }
+      push @CalculatedValues, $CalculatedValue;
+    }
+    # List data...
+    ListFormulaData(\@ValueLabels, \@CalculatedValues);
+  }
+  if ($OptionsInfo{FileOutput}) {
+    close OUTFILE;
+  }
+  print "\n";
+}
+
+# List calculated data values...
+sub ListFormulaData {
+  my($DataLabelRef, $DataValueRef) = @_;
+  my($Index, $Line, $Value);
+
+  if ($OptionsInfo{RowsOutput}) {
+    $Line = '';
+    # Format data...
+    if ($OptionsInfo{OutQuote} || $Options{outdelim} !~ /^comma$/i) {
+      $Line = JoinWords($DataValueRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
+    }
+    else {
+      # Always quote values containing commas...
+      $Line = ($DataValueRef->[0] =~ /\,/) ? qq("$DataValueRef->[0]") : $DataValueRef->[0];
+      for $Index (1 .. $#{$DataValueRef} ) {
+	$Value = $DataValueRef->[$Index];
+	if ($Value =~ /\,/) {
+	  $Value = qq("$Value");
+	}
+	$Line .= $OptionsInfo{OutDelim} . $Value;
+      }
+    }
+    if ($OptionsInfo{FileOutput}) {
+      print OUTFILE "$Line\n";
+    }
+    else {
+      print "$Line\n";
+    }
+  }
+  else {
+    # Format and list data...
+    $Line = '';
+    for $Index (0 .. $#{$DataLabelRef} ) {
+      $Line = $DataLabelRef->[$Index] . ': ' . $DataValueRef->[$Index];
+      if ($OptionsInfo{FileOutput}) {
+	print OUTFILE "$Line\n";
+      }
+      else {
+	print "$Line\n";
+      }
+    }
+  }
+}
+
+# List calculated data for a formula...
+sub ListHeaderRowData {
+  my($DataLabelRef) = @_;
+  my($Line);
+
+  # Format data...
+  $Line = JoinWords($DataLabelRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
+  $Line =~ s/\://g;
+  # List data...
+  if ($OptionsInfo{FileOutput}) {
+    print OUTFILE "$Line\n";
+  }
+  else {
+    print "$Line\n";
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+  %OptionsInfo = ();
+
+  $OptionsInfo{Mode} = $Options{mode};
+
+  $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
+  $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
+
+  $OptionsInfo{Output} = $Options{output};
+  $OptionsInfo{OutputStyle} = $Options{outputstyle};
+
+  $OptionsInfo{RowsOutput} = ($Options{outputstyle} =~ /^FormulaRows$/i) ? 1 : 0;
+  $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0;
+  $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1;
+
+  $OptionsInfo{Precision} = $Options{precision};
+
+  $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
+  $OptionsInfo{ValueLabels} = defined $Options{valuelabels} ? $Options{valuelabels} : undef;
+
+  # Setup formulas...
+  @{$OptionsInfo{SpecifiedFormulas}} = ();
+  if (@ARGV >= 1) {
+    push @{$OptionsInfo{SpecifiedFormulas}}, @ARGV;
+  }
+  else {
+    # Setup mode specified default values...
+    push @{$OptionsInfo{SpecifiedFormulas}}, 'H2O';
+  }
+
+  # 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}}, $ModeValue;
+    }
+  }
+  my($Index, $Value, $Label);
+  # Set up labels for calculated values...
+  @{$OptionsInfo{SpecifiedValueLabels}} = ();
+  if ($Options{valuelabels}) {
+    my($Value, $Label, @ValueLabels);
+    @ValueLabels = split /\,/, $Options{valuelabels};
+    if (@ValueLabels % 2) {
+      die "Error: The value specified, $Options{valuelabels}, for option \"-v --valuelabels\" is not valid: It must contain even number of comma delimited values\n";
+    }
+    for ($Index = 0; $Index < @ValueLabels; $Index +=2) {
+      $Value = $ValueLabels[$Index];
+      $Value =~ s/ //g;
+      $Label = $ValueLabels[$Index + 1];
+      if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
+	die "Error: The value specified, $Value, using option \"-v --valuelabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
+      }
+      push @{$OptionsInfo{SpecifiedValueLabels}}, ($Value, $Label);
+    }
+  }
+
+  # Set up calculation type to label map...
+  %{$OptionsInfo{ValueLabelsMap}} = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass');
+  if (@{$OptionsInfo{SpecifiedValueLabels}}) {
+    for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueLabels}}; $Index +=2) {
+      $Value = $OptionsInfo{SpecifiedValueLabels}[$Index];
+      $Label = $OptionsInfo{SpecifiedValueLabels}[$Index + 1];
+      if (exists $OptionsInfo{ValueLabelsMap}{$Value}) {
+	$OptionsInfo{ValueLabelsMap}{$Value} = $Label;
+      }
+    }
+  }
+
+  # Setup output file name...
+  $OptionsInfo{OutFileName} = '';
+  if ($OptionsInfo{FileOutput}) {
+    my($OutFileRoot, $OutFileExt);
+
+    $OutFileRoot = '';
+    $OutFileExt = "csv";
+    if ($Options{outdelim} =~ /^tab$/i) {
+      $OutFileExt = "tsv";
+    }
+    if ($Options{root}) {
+      my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
+      if ($RootFileName && $RootFileExt) {
+	$OutFileRoot = $RootFileName;
+      }
+      else {
+	$OutFileRoot = $Options{root};
+      }
+    }
+    else {
+      $OutFileRoot = 'FormulasElementalAnalysis';
+    }
+    $OptionsInfo{OutFileName} = $OutFileRoot . '.' . $OutFileExt;
+    if (!$Options{overwrite}) {
+      if (-e $OptionsInfo{OutFileName}) {
+	die "Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n";
+      }
+    }
+  }
+}
+
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{mode} = "All";
+  $Options{outdelim} = "comma";
+  $Options{output} = "STDOUT";
+  $Options{outputstyle} = "FormulaBlock";
+  $Options{precision} = 2;
+  $Options{quote} = "yes";
+
+  if (!GetOptions(\%Options, "help|h", "fast", "mode|m=s", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "quote|q=s", "root|r=s", "valuelabels|v=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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}: $! \n";
+  }
+  if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
+    die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
+  }
+  if ($Options{output} !~ /^(STDOUT|File)$/i) {
+    die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n";
+  }
+  if ($Options{outputstyle} !~ /^(FormulaBlock|FormulaRows)$/i) {
+    die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: FormulaBlock or FormulaRows\n";
+  }
+  if (!IsPositiveInteger($Options{precision})) {
+    die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
+  }
+  if ($Options{quote} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+ElementalAnalysis.pl - Perform elemental analysis using specified formulas
+
+=head1 SYNOPSIS
+
+ElementalAnalysis.pl Formula(s)...
+
+ElementalAnalysis.pl [B<-h, --help>]
+[B<-m, --mode> All | "ElementalAnalysis, [MolecularWeight, ExactMass]"]
+[B<--outdelim> comma | tab | semicolon]
+[B<--output> STDOUT | File] [B<--outputstyle> FormulaBlock | FormulaRows]
+[B<-o, --overwrite>] [B<--precision> number] [B<-q, --quote> yes | no] [B<-r, --root> rootname]
+[B<-v --valuelabels> [Name, Label, [Name, Label,...]]
+[B<-w, --workingdir> dirname] Formula(s)...
+
+=head1 DESCRIPTION
+
+Perform elemental analysis using molecular formula(s) specified on the command line.
+
+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.
+
+=head1 PARAMETERS
+
+=over 4
+
+=item B<Formulas> I<Formula1 [Formula2...]>
+
+I<Formulas> is a space delimited list of molecular formulas to use for elemental analysis.
+
+Input value format is: I<Formula1 [Formula2 Formula3...]>. Default: I<H2O>.
+Examples:
+
+    HCl
+    HCl, C3H7O2N
+    H2O2 Ca3(PO4)2 [PCl4]+
+
+=back
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<--fast>
+
+In this mode, the specified formulas are considered valid and initial formula
+validation check is skipped.
+
+=item B<-m, --mode> I<All | "ElementalAnalysis,[MolecularWeight,ExactMass]">
+
+Specify what values to calculate using molecular formulas specified on command
+line: calculate all supported values or specify a comma delimited list of values. Possible
+values: I<All | "ElementalAnalysis, [MolecularWeight, ExactMass]">. Default: I<All>.
+
+=item B<--outdelim> I<comma | tab | semicolon>
+
+Output text file delimiter. Possible values: I<comma, tab, or semicolon>
+Default value: I<comma>.
+
+=item B<--output> I<STDOUT | File>
+
+List information at STDOUT or write it to a file. Possible values: I<STDOUT or File>. Default:
+I<STDOUT>. B<-r, --root> option is used to generate output file name.
+
+=item B<--outputstyle> I<FormulaBlock | FormulaRows>
+
+Specify how to list calculated values: add a new line for each property and present it as a block
+for each formula; or include all properties in one line and show it as a single line.
+
+Possible values: I<FormulaBlock | FormulaRows>. Default: I<FormulaBlock>
+
+An example for I<FormulaBlock> output style:
+
+    Formula: H2O
+    ElementalAnalysis: H: H: 11.1898%; O: 88.8102%
+    MolecularWeight: 18.0153
+    ExactMass: 18.0106
+    ... ...
+    ... ...
+    ... ...
+
+    Formula: H2O2
+    ElementalAnalysis: H: 5.9265%; O: 94.0735%
+    MolecularWeight: 34.0147
+    ExactMass: 34.0055
+    ... ...
+    ... ...
+    ... ...
+
+An example for I<FormulaRows> output style:
+
+    Formula,ElementalAnalysis,MolecularWeight,ExactMass
+    H2O,H: 11.1898%; O: 88.8102%,18.0153,18.0106
+    H2O2,H: 5.9265%; O: 94.0735%,34.0147,34.0055
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<--precision> I<number>
+
+Precision for listing numerical values. Default: up to I<4> decimal places.
+Valid values: positive integers.
+
+=item B<-r, --root> I<rootname>
+
+New text file name is generated using the root: <Root>.<Ext>. File name is only
+used during I<File> value of B<-o, --output> option.
+
+Default file name: FormulsElementalAnalysis.<Ext>. The csv, and tsv
+<Ext> values are used for comma/semicolon, and tab delimited text files respectively.
+
+=item B<-v --valuelabels> I<Name,Label,[Name,Label,...]>
+
+Specify labels to use for calculated values. In general, it's a comma delimited
+list of value name and column label pairs. Supported value names: I<ElementalAnalysis,
+MolecularWeight,  and ExactMass>. Default labels: I<ElementalAnalysis, MolecularWeight,
+and ExactMass>.
+
+=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 for H2O,
+type:
+
+    % ElementalAnalysis.pl
+
+To perform elemental analysis, calculate molecular weight and exact mass for
+Ca3(PO4)2 and [PCl4]+, type:
+
+    % ElementalAnalysis.pl "Ca3(PO4)2" "[PCl4]+"
+
+To perform elemental analysis, use label analysis for calculated data, and generate a
+new CSV file ElementalAnalysis.csv for H2O and H2O2, type:
+
+    % ElementalAnalysis.pl --m ElementalAnalysis --output File
+      --valuelabels "ElementalAnalysis,Analysis" -o -r ElementalAnalysis.csv
+      H2O H2O2
+
+To calculate molecular weight and exact mass with four decimal precision and
+generate a new CSV file WeightAndMass.csv with data rows for H2O and H2O2, type:
+
+    % ElementalAnalysis.pl --m "MolecularWeight,ExactMass" --output File
+      --outputstyle FormulaRows -o -r WeightAndMass.csv
+      H2O H2O2
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+ElementalAnalysisSDFiles.pl, ElementalAnalysisTextFiles.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