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

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author deepakjadmin
date Wed, 20 Jan 2016 09:23:18 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/InfoPeriodicTableElements.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,829 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: InfoPeriodicTableElements.pl,v $
+# $Date: 2015/02/28 20:46:20 $
+# $Revision: 1.28 $
+#
+# Author: Manish Sud <msud@san.rr.com>
+#
+# 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 "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+use PeriodicTable;
+
+my($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();
+
+ListElementProperties();
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# List atomic properties for elements...
+sub ListElementProperties {
+  my($ElementID, $ElementDataRef, $PropertyName, $PropertyValue, $PropertyUnits, $PropertyUnitsRef, @PropertyLabels, @PropertyValues);
+
+  print "Listing information for periodic table element(s)...\n";
+
+  if ($OptionsInfo{FileOutput}) {
+    print "Generating file $OptionsInfo{OutFileName}...\n";
+    open OUTFILE, ">$OptionsInfo{OutFileName}" or die "Couldn't open $OptionsInfo{OutFileName}: $!\n";
+  }
+
+  # Setup property labels...
+  @PropertyLabels = ();
+  $PropertyUnitsRef = PeriodicTable::GetElementPropertiesNamesAndUnits();
+  for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) {
+    $PropertyUnits = (exists $PropertyUnitsRef->{$PropertyName}) ? $PropertyUnitsRef->{$PropertyName} : '';
+    if ($PropertyName =~ /^NaturalIsotopeData$/i) {
+      push @PropertyLabels, qw(MassNumber: RelativeAtomicMass: NaturalAbundance:);
+    }
+    else {
+      push @PropertyLabels, ($PropertyUnits ? "$PropertyName ($PropertyUnits):" : "$PropertyName:");
+    }
+  }
+
+  if ($OptionsInfo{ElementRowsOutput}) {
+    ListHeaderRowData(\@PropertyLabels);
+  }
+
+  # Go over specified properties...
+  for $ElementID (@{$OptionsInfo{SpecifiedElementIDs}}) {
+    $ElementDataRef = PeriodicTable::GetElementPropertiesData($ElementID);
+
+    if (!$OptionsInfo{ElementRowsOutput}) {
+      if ($OptionsInfo{FileOutput}) {
+	print OUTFILE "\nListing atomic properties for element $ElementID...\n\n";
+      }
+      else {
+	print "\nListing atomic properties for element $ElementID...\n\n";
+      }
+    }
+
+    # Collect data..
+    @PropertyValues = ();
+    for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) {
+      if ($PropertyName =~ /^NaturalIsotopeData$/i) {
+	push @PropertyValues, SetupIsotopeData($ElementID);
+      }
+      else {
+	$PropertyValue = $ElementDataRef->{$PropertyName};
+	if (IsFloat($PropertyValue)) {
+	  $PropertyValue = sprintf("%.$OptionsInfo{Precision}f", $PropertyValue) + 0;
+	}
+	push @PropertyValues, $PropertyValue;
+      }
+    }
+    # List data...
+    ListElementData(\@PropertyLabels, \@PropertyValues);
+  }
+  if ($OptionsInfo{FileOutput}) {
+    close OUTFILE;
+  }
+  print "\n";
+}
+
+# List data for an element...
+sub ListElementData {
+  my($DataLabelRef, $DataValueRef) = @_;
+  my($Index, $Line, $Value);
+
+  if ($OptionsInfo{ElementRowsOutput}) {
+    $Line = '';
+    # Format data...
+    if ($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 "$Line\n";
+      }
+    }
+  }
+}
+
+# List data for an element...
+sub ListHeaderRowData {
+  my($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";
+  }
+}
+
+# Setup isotope data strings...
+sub SetupIsotopeData {
+  my($ElementID) = @_;
+  my($MassNumber, $RelativeAtomicMass, $NaturalAbundance, $NaturalIsotopeDataRef, @MassNumbers, @RelativeAtomicMasses, @NaturalAbundances);
+
+  # Get natural isotope data: MassNumber, RelativeAtomicMass and NaturalAbundance
+  @MassNumbers = (); @RelativeAtomicMasses = (); @NaturalAbundances = ();
+  $NaturalIsotopeDataRef = PeriodicTable::GetElementNaturalIsotopesData($ElementID);
+  for $MassNumber (sort {$a <=> $b} keys %{$NaturalIsotopeDataRef}) {
+    $RelativeAtomicMass = $NaturalIsotopeDataRef->{$MassNumber}{RelativeAtomicMass};
+    $NaturalAbundance = $NaturalIsotopeDataRef->{$MassNumber}{NaturalAbundance};
+    push @MassNumbers, $MassNumber;
+    $RelativeAtomicMass = ($RelativeAtomicMass > 0) ? (sprintf("%.$OptionsInfo{Precision}f", $RelativeAtomicMass) + 0) : '';
+    push @RelativeAtomicMasses, $RelativeAtomicMass;
+    $NaturalAbundance = ($NaturalAbundance > 0) ? (sprintf("%.$OptionsInfo{Precision}f", $NaturalAbundance) + 0) : '';
+    push @NaturalAbundances, $NaturalAbundance;
+  }
+  $MassNumber = JoinWords(\@MassNumbers, ",", 0);
+  $RelativeAtomicMass = JoinWords(\@RelativeAtomicMasses, ",", 0);
+  $NaturalAbundance = JoinWords(\@NaturalAbundances, ",", 0);
+  return ($MassNumber, $RelativeAtomicMass, $NaturalAbundance);
+}
+
+# Get propery names from categories...
+sub GetPropertyNamesFromCategories {
+  my($CategoryName) = @_;
+  my(@PropertyNames);
+
+  @PropertyNames = ();
+  if ($CategoryName =~ /^Basic$/i) {
+    @PropertyNames = ('AtomicNumber', 'ElementSymbol', 'ElementName', 'AtomicWeight', 'GroundStateConfiguration', 'GroupNumber', 'PeriodNumber', 'FirstIonizationEnergy');
+  } elsif ($CategoryName =~ /^BasicAndNaturalIsotope$/i) {
+    # Natural isotope data includes: 'MassNumber', 'RelativeAtomicMass', 'NaturalAbundance'
+    @PropertyNames = ('AtomicNumber', 'ElementSymbol', 'ElementName', 'AtomicWeight', 'GroundStateConfiguration', 'GroupNumber', 'PeriodNumber', 'FirstIonizationEnergy', 'NaturalIsotopeData');
+  } elsif ($CategoryName =~ /^NaturalIsotope$/i) {
+    @PropertyNames = ('AtomicNumber', 'ElementSymbol', 'ElementName', 'NaturalIsotopeData');
+  }
+
+  return @PropertyNames;
+}
+
+# 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{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
+  $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
+
+  $OptionsInfo{Output} = $Options{output};
+  $OptionsInfo{OutputStyle} = $Options{outputstyle};
+
+  $OptionsInfo{ElementRowsOutput} = ($Options{outputstyle} =~ /^ElementRows$/i) ? 1 : 0;
+  $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0;
+
+  $OptionsInfo{Precision} = $Options{precision};
+
+  my($ElementID, @ElementIDs, @GroupElements, @PeriodElements, %GroupNamesMap);
+
+  @{$OptionsInfo{SpecifiedElementIDs}} = ();
+  if (@ARGV >=1 && ($Options{mode} =~ /^All$/i) ) {
+    warn "Warning: Ignoring comman line element IDs: Not valid for All value of \"-m --mode\" option...\n";
+  }
+
+  # Set up element IDs except for All mode...
+  @ElementIDs = ();
+  %GroupNamesMap = ();
+
+  if (@ARGV >=1 ) {
+    if ($Options{mode} !~ /^All$/i) {
+      push @ElementIDs, @ARGV;
+    }
+  }
+  else {
+    # Setup mode specified default values...
+    my($Nothing);
+    MODE: {
+	if ($Options{mode} =~ /^ElementID$/i) { push @ElementIDs, 'H'; last MODE; };
+	if ($Options{mode} =~ /^AmericanGroupLabel$/i) { push @ElementIDs, 'IA'; last MODE; };
+	if ($Options{mode} =~ /^EuropeanGroupLabel$/i) { push @ElementIDs, 'IA'; last MODE; };
+	if ($Options{mode} =~ /^GroupNumber$/i) { push @ElementIDs, '1'; last MODE; };
+	if ($Options{mode} =~ /^GroupName$/i) { push @ElementIDs, 'AlkaliMetals'; last MODE; };
+	if ($Options{mode} =~ /^PeriodNumber$/i) { push @ElementIDs, '1'; last MODE; };
+	$Nothing = 1;
+      }
+  }
+  if ($Options{mode} =~ /^GroupName$/i) {
+    # Map group names to what's stored in Perioidic table data file...
+    %GroupNamesMap = ('alkalimetals', 'Alkali metal', 'alkalineearthmetals', 'Alkaline earth metal', 'chalcogens', 'Chalcogen', 'coinagemetals', 'Coinage metal', 'halogens', 'Halogen', 'noblegases', 'Noble gas', 'pnictogens', 'Pnictogen', 'lanthanides', 'Lanthanoid', 'lanthanoids', 'Lanthanoid', 'actinides', 'Actinoid', 'actinoids', 'Actinoid' );
+  }
+
+  # Generate list of elements...
+  if ($Options{mode} =~ /^All$/i) {
+    push @{$OptionsInfo{SpecifiedElementIDs}}, PeriodicTable::GetElements();
+  }
+  else {
+    ELEMENTID: for $ElementID (@ElementIDs) {
+      if ($Options{mode} =~ /^ElementID$/i) {
+	if (PeriodicTable::IsElement($ElementID)) {
+	  push @{$OptionsInfo{SpecifiedElementIDs}}, $ElementID;
+	}
+	else {
+	  warn "Ignoring element ID, $ElementID, specified using command line parameter: Unknown element ID...\n";
+	  next ELEMENTID;
+	}
+      }
+      elsif ($Options{mode} =~ /^AmericanGroupLabel$/i) {
+	if (@GroupElements = PeriodicTable::GetElementsByAmericanStyleGroupLabel($ElementID)) {
+	  push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
+	}
+	else {
+	  warn "Ignoring American style group label, $ElementID, specified using command line parameter: Unknown group label...\n";
+	  next ELEMENTID;
+	}
+      }
+      elsif ($Options{mode} =~ /^EuropeanGroupLabel$/i) {
+	if (@GroupElements = PeriodicTable::GetElementsByEuropeanStyleGroupLabel($ElementID)) {
+	  push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
+	}
+	else {
+	  warn "Ignoring American style group label, $ElementID, specified using command line parameter: Unknown group label...\n";
+	  next ELEMENTID;
+	}
+      }
+      elsif ($Options{mode} =~ /^GroupNumber$/i) {
+	if (@GroupElements = PeriodicTable::GetElementsByGroupNumber($ElementID)) {
+	  push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
+	}
+	else {
+	  warn "Ignoring group number, $ElementID, specified using command line parameter: Unknown group number...\n";
+	  next ELEMENTID;
+	}
+      }
+      elsif ($Options{mode} =~ /^GroupName$/i) {
+	if (exists $GroupNamesMap{lc($ElementID)}) {
+	  @GroupElements = PeriodicTable::GetElementsByGroupName($GroupNamesMap{lc($ElementID)});
+	  push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
+	}
+	else {
+	  warn "Ignoring group name, $ElementID, specified using command line parameter: Unknown group name...\n";
+	  next ELEMENTID;
+	}
+      }
+      elsif ($Options{mode} =~ /^PeriodNumber$/i) {
+	if (@GroupElements = PeriodicTable::GetElementsByPeriodNumber($ElementID)) {
+	  push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
+	}
+	else {
+	  warn "Ignoring period number, $ElementID, specified using command line parameter: Unknown period number...\n";
+	  next ELEMENTID;
+	}
+      }
+    }
+  }
+  SetupSpecifiedProperties();
+
+  # 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 = 'PeriodicTableElementsInfo' . $Options{mode};
+    }
+    $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 properties to list...
+sub SetupSpecifiedProperties {
+  $OptionsInfo{Properties} = defined $Options{properties} ? $Options{properties} : undef;
+
+  $OptionsInfo{PropertiesMode} = $Options{propertiesmode};
+  $OptionsInfo{PropertiesListing} = $Options{propertieslisting};
+
+  # Make sure atomic appropriate properties/category names are specified...
+  @{$OptionsInfo{SpecifiedProperies}} = ();
+  if ($Options{properties} && ($Options{propertiesmode} =~ /^All$/i) ) {
+    warn "Warning: Ignoring values specifed by \"-p --properties\" option: Not valid for All value of \"--propertiesmode\" option...\n";
+  }
+  if ($Options{propertiesmode} =~ /^All$/i) {
+    if ($Options{propertieslisting} =~ /^Alphabetical$/i) {
+      push @{$OptionsInfo{SpecifiedProperies}}, PeriodicTable::GetElementPropertiesNames('Alphabetical');
+    }
+    else {
+      push @{$OptionsInfo{SpecifiedProperies}}, PeriodicTable::GetElementPropertiesNames();
+    }
+    push @{$OptionsInfo{SpecifiedProperies}}, 'NaturalIsotopeData';
+  }
+  else {
+    if ($Options{properties}) {
+      if ($Options{propertiesmode} =~ /^Categories$/i) {
+	# Check category name...
+	if ($Options{properties} !~ /^(Basic|BasicAndNaturalIsotope|NaturalIsotope)$/i) {
+	  die "Error: The value specified, $Options{properties}, for option \"-p --properties\" in conjunction with \"Categories\" value for option \"--propertiesmode\" is not valid. Allowed values: Basic, BasicAndNaturalIsotope, NaturalIsotope\n";
+	}
+	# Set propertynames...
+	push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories($Options{properties});
+      }
+      else {
+	# Check property names..
+	my($Name, $PropertyName, @Names);
+	@Names = split /\,/, $Options{properties};
+	NAME: for $Name (@Names) {
+	  $PropertyName = RemoveLeadingAndTrailingWhiteSpaces($Name);
+	  if ($PropertyName =~ /^NaturalIsotopeData$/i) {
+	    push @{$OptionsInfo{SpecifiedProperies}}, $PropertyName;
+	    next NAME;
+	  }
+	  if (PeriodicTable::IsElementProperty($PropertyName)) {
+	    push @{$OptionsInfo{SpecifiedProperies}}, $PropertyName;
+	  }
+	  else {
+	    warn "Warning: Ignoring value, $Name, specifed by \"-p --properties\" option: Unknown property name...\n";
+	  }
+	}
+	if ($Options{propertieslisting} =~ /^Alphabetical$/i) {
+	  # AtomicNumber, ElementSymbol and ElementName are always listed first and
+	  # NaturalIsotopeData in the end...
+	  my($AtomicNumberPresent, $ElementSymbolPresent, $ElementNamePresent, $NaturalIsotopeDataPresent, @AlphabeticalProperties, %PropertiesMap);
+	  %PropertiesMap = ();
+	  @AlphabeticalProperties = ();
+	  $AtomicNumberPresent = 0; $ElementSymbolPresent = 0; $ElementNamePresent = 0; $NaturalIsotopeDataPresent = 0;
+	  NAME: for $Name (@{$OptionsInfo{SpecifiedProperies}}) {
+	    if ($Name =~ /^AtomicNumber$/i) {
+	      $AtomicNumberPresent = 1;
+	      next NAME;
+	    }
+	    if ($Name =~ /^ElementSymbol$/i) {
+	      $ElementSymbolPresent = 1;
+	      next NAME;
+	    }
+	    if ($Name =~ /^ElementName$/i) {
+	      $ElementNamePresent = 1;
+	      next NAME;
+	    }
+	    if ($Name =~ /^NaturalIsotopeData$/i) {
+	      $NaturalIsotopeDataPresent = 1;
+	      next NAME;
+	    }
+	    $PropertiesMap{$Name} = $Name;
+	  }
+	  # Setup the alphabetical list...
+	  if ($AtomicNumberPresent) {
+	    push @AlphabeticalProperties, 'AtomicNumber';
+	  }
+	  if ($ElementSymbolPresent) {
+	    push @AlphabeticalProperties, 'ElementSymbol';
+	  }
+	  if ($ElementNamePresent) {
+	    push @AlphabeticalProperties, 'ElementName';
+	  }
+	  for $Name (sort keys %PropertiesMap) {
+	    push @AlphabeticalProperties, $Name;
+	  }
+	  if ($NaturalIsotopeDataPresent) {
+	    push @AlphabeticalProperties, 'NaturalIsotopeData';
+	  }
+	  @{$OptionsInfo{SpecifiedProperies}} = ();
+	  push @{$OptionsInfo{SpecifiedProperies}}, @AlphabeticalProperties;
+	}
+      }
+    }
+    else {
+      # Set default value...
+      push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories('Basic');
+    }
+  }
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{mode} = "ElementID";
+  $Options{outdelim} = "comma";
+  $Options{output} = "STDOUT";
+  $Options{outputstyle} = "ElementBlock";
+  $Options{precision} = 4;
+  $Options{propertiesmode} = "Categories";
+  $Options{propertieslisting} = "ByGroup";
+  $Options{quote} = "yes";
+
+  if (!GetOptions(\%Options, "help|h", "mode|m=s", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "properties|p=s", "propertieslisting=s", "propertiesmode=s", "quote|q=s", "root|r=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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{mode} !~ /^(ElementID|AmericanGroupLabel|EuropeanGroupLabel|GroupNumber|GroupName|PeriodNumber|All)$/i) {
+    die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: ElementID, AmericanGroupLabel, EuropeanGroupLabel, GroupNumber, GroupName, PeriodNumber, or All\n";
+  }
+  if ($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} !~ /^(ElementBlock|ElementRows)$/i) {
+    die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: ElementBlock or ElementRows\n";
+  }
+  if (!IsPositiveInteger($Options{precision})) {
+    die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
+  }
+  if ($Options{propertiesmode} !~ /^(Categories|Names|All)$/i) {
+    die "Error: The value specified, $Options{propertiesmode}, for option \"--propertiesmode\" is not valid. Allowed values: Categories, Names, or All\n";
+  }
+  if ($Options{propertieslisting} !~ /^(ByGroup|Alphabetical)$/i) {
+    die "Error: The value specified, $Options{propertieslisting}, for option \"--propertieslisting\" is not valid. Allowed values: ByGroup, or Alphabetical\n";
+  }
+  if ($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
+
+InfoPeriodicTableElements.pl - List atomic properties of elements
+
+=head1 SYNOPSIS
+
+InfoPeriodicTableElements.pl ElementID(s)...
+
+InfoPeriodicTableElements.pl [B<-h, --help>]
+[B<-m, --mode> ElementID | AmericanGroupLabel | EuropeanGroupLabel | GroupNumber | GroupName | PeriodNumber | All]
+[B<--outdelim> comma | tab | semicolon] [B<--output> STDOUT | File] [B<--outputstyle> ElementBlock | ElementRows]
+[B<-o, --overwrite>] [B<--precision> number] [B<--propertiesmode> Categories | Names | All]
+[B<-p, --properties> CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]]
+[B<--propertieslinting> ByGroup | Alphabetical] [B<-q, --quote> yes | no] [B<-r, --root> rootname]
+[B<-w, --workingdir> dirname] ElementID(s)...
+
+=head1 DESCRIPTION
+
+List atomic properties of elements in the periodic table. A variety of methods are available to
+specify elements of interest: atomic numbers, element symbols, American or European style group
+labels, IUPAC group numbers, period numbers, and group names.
+
+Atomic properties data, in addition to basic information about the periodic table elements, is
+also available for these categories: atomic radii, bulk properties, common valences, electronegativities,
+electron affinities, historical data, ionization energies, natural isotopes, oxidation states,
+and thermal properties.
+
+Natural isotopes data include mass number, relative atomic mass and percent natural
+abundance for each isotope of an element.
+
+=head1 PARAMETERS
+
+=over 4
+
+=item B<ElementIDs> I<ElementSymbol [AtomicNumber...] | GroupLabel [GroupLabel...] | GroupNumbel [GroupNumber...] | PeriodNumber [PeriodNumbe...]>
+
+Command line specification of elements is mode specific. In general, it's a space delimited list of values to identify
+elements. All element IDs must correspond to a specific mode; mixed specifications is not supported.
+
+For I<ElementID> mode, input value format is: I<AtomicNumber [ElementSymbol ...]>. Default: I<H>.
+Examples:
+
+    C
+    6
+    C N O P S Cl
+    6 7 8 15 16 17
+    C 7 8 15 S 17
+
+For I<AmericanGroupLabel> mode, input value format is: I<GroupLabel [GroupLabel ...]>. Default: I<IA>. Possible
+group label values are: I<IA IIA IIIB IVB VB VIB VIIB VIII or VIIIB IB IIB IIIA IVA VA,
+VIA, VIIA, VIIA>. Examples:
+
+    IA
+    IA IVA IIB
+
+For I<EuropeanGroupLabel> mode, input value format is: I<GroupLabel [GroupLabel ...]>. Default: I<IA>. Possible
+group label values are: I<IA IIA IIIA IVA VA VIA VIIA VIII or VIIIA IB IIB IIIB IVB VB,
+VIB VIIB VIIB>. Examples:
+
+    IA
+    IA IVB IIB
+
+For IUPAC I<GroupNumber> mode, input value format is: I<GroupNumber [GroupNumber...]>. Default: I<1>. Possible
+group label values are: I<1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18>. Examples:
+
+    1
+    1 14 12
+
+For  I<GroupName> mode, input value format is: I<GroupName [GroupName...]>. Default: I<AlkaliMetals>. Possible
+group name values are: I<AlkaliMetals AlkalineEarthMetals Chalcogens CoinageMetals Halogens
+NobleGases Pnictogens Lanthanides or Lanthanoids, Actinides or Actinoids>. Examples:
+
+    AlkaliMetals
+    AlkaliMetals Halogens NobleGases
+
+For I<PeriodNumber> mode, input value format is: I<PeriodNumber [PeriodNumber,...]>. Default: I<1>. Possible
+group label values are: I<1 2 3 4 5 6 7>. Examples:
+
+    1
+    1 2 3
+
+For I<All> mode, no input value is needed and atomic properties information is listed for all the
+elements.
+
+=back
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<-m, --mode> I<ElementID | AmericanGroupLabel | EuropeanGroupLabel | GroupNumber | GroupName | PeriodNumber | All>
+
+Specify elements for listing atomic properties using one of these methods: atomic numbers
+and/or element symbols list, American style group labels, European style group labels, IUPAC
+group number, group names, period numbers, or all elements.
+
+Possible values: I<ElementID, AmericanGroupLabel, EuropeanGroupLabel, GroupNumber,
+GroupName, PeriodNumber, All>. Default: I<ElementID>.
+
+=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<ElementBlock | ElementRows>
+
+Specify how to list element information: add a new line for each property and present it as a block
+for each element; or include all properties in one line and show it as a single line.
+
+Possible values: I<ElementBlock | ElementRows>. Default: I<ElementBlock>
+
+An example for I<ElementBlock> output style:
+
+    Atomic number: 1
+    Element symbol: H
+    Element name: Hydrogen
+    Atomic weight: 1.00794
+    ... ...
+    ... ...
+
+    Atomic number: 6
+    Element symbol: C
+    Element name: Carbon
+    Atomic weight: 12.0107
+    ... ...
+    ... ...
+
+An example for I<ElementRows> output style:
+
+    Atomic number, Element symbol, Elemenet name, Atomic weight, ...
+    1,H,Hydrogen,1.00794,..
+    6,C,Carbon,12.0107,..
+
+=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<--propertiesmode> I<Categories | Names | All>
+
+Specify how property names are specified: use category names; explicit list of property names; or
+use all available properties. Possible values: I<Categories, Names, or All>. Default: I<Categories>.
+
+This option is used in conjunction with B<-p, --properties> option to specify properties of
+interest.
+
+=item B<-p, --properties> I<CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]>
+
+This option is B<--propertiesmode> specific. In general, it's a list of comma separated category or
+property names.
+
+Specify which atomic properties information to list for the elements specified using command line
+parameters: list basic and/or isotope information; list all available information; or specify a comma
+separated list of atomic property names.
+
+Possible values: I<Basic| BasicAndNaturalIsotope | NaturalIsotope | PropertyName,[PropertyName,...]>.
+Default: I<Basic>.
+
+I<Basic> includes: I<AtomicNumber, ElementSymbol, ElementName, AtomicWeight, GroundStateConfiguration,
+GroupNumber, PeriodNumber, FirstIonizationEnergy>.
+
+I<NaturalIsotope> includes: I<AtomicNumber, ElementSymbol, ElementName, MassNumber,
+RelativeAtomicMass, NaturalAbundance>.
+
+Here is a complete list of available properties: AllenElectronegativity, AllredRochowElectronegativity, AtomicNumber,
+AtomicRadiusCalculated, AtomicRadiusEmpirical, AtomicWeight, Block, BoilingPoint, BondLength,
+BrinellHardness, BulkModulus, Classification, CoefficientOfLinearExpansion, Color,
+CommonValences, LowestCommonValence, HighestCommonValence,
+CommonOxidationNumbers, LowestCommonOxidationNumber, HighestCommonOxidationNumber,
+CovalentRadiusEmpirical, CriticalTemperature, DensityOfSolid, DiscoveredAt, DiscoveredBy,
+DiscoveredWhen, ElectricalResistivity, ElectronAffinity, ElementName, ElementSymbol, EnthalpyOfAtmization,
+EnthalpyOfFusion, EnthalpyOfVaporization, FirstIonizationEnergy, GroundStateConfiguration, GroundStateLevel,
+GroupName, GroupNumber, NaturalIsotopeData, MeltingPoint, MineralHardness, MolarVolume,
+MullikenJaffeElectronegativity, OriginOfName, PaulingElectronegativity, PeriodNumber, PoissonsRatio,
+Reflectivity, RefractiveIndex, RigidityModulus, SandersonElectronegativity, StandardState,
+SuperconductionTemperature, ThermalConductivity, VanderWaalsRadius, VelocityOfSound, VickersHardness,
+YoungsModulus.
+
+=item B<--propertieslisting> I<ByGroup | Alphabetical>
+
+Specify how to list properties for elements: group by category or an alphabetical by
+property names. Possible values: I<ByGroup or Alphabetical>. Default: I<ByGroup>.
+During I<Alphabetical> listing, element identification data - I<AtomicNumber, ElementSymbol,
+ElementName> - is show first,  and natural isotope data - I<MassNumber, RelativeAtomicMass,
+NaturalAbundance> - is listed in the end.
+
+=item B<-q, --quote> I<yes | no>
+
+Put quotes around column values in output text file. Possible values: I<yes or
+no>. Default value: I<yes>.
+
+=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: PeriodicTableElementsInfo<mode>.<Ext>. The csv, and tsv
+<Ext> values are used for comma/semicolon, and tab delimited text files respectively.
+
+=item B<-w, --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To list basic atomic properties information for element H, type:
+
+    % InfoPeriodicTableElements.pl
+
+To list basic atomic properties information for elements C,N,O and F, type:
+
+    % InfoPeriodicTableElements.pl C N O F
+
+To list all available atomic properties information for elements C,N,O and F, type:
+
+    % InfoPeriodicTableElements.pl --propertiesmode all 6 N O 9
+
+To list basic and natural isotope information for elements C,N,O and F, type:
+
+    % InfoPeriodicTableElements.pl --propertiesmode Categories
+      --properties BasicAndNaturalIsotope  C N O F
+
+To list AtomicNumber, ElementName, AtomicWeight and CommonValences information
+for elements C,N,O and F, type:
+
+    % InfoPeriodicTableElements.pl --propertiesmode Names
+      --properties AtomicNumber,ElementName,AtomicWeight,CommonValences
+      C N O F
+
+To alphabetically list basic and natural isotope information for elements C,N,O and F in rows instead of
+element blocks with quotes around the values, type:
+
+    % InfoPeriodicTableElements.pl --propertiesmode Categories
+      --properties BasicAndNaturalIsotope --propertieslisting alphabetical
+      --outdelim comma --outputstyle ElementRows --quote yes C N O F
+
+To alphabetically list all available atomic information for elements C,N,O and F in rows instead of
+element blocks with quotes around the values and write them into a file ElementProperties.csv, type:
+
+    % InfoPeriodicTableElements.pl --propertiesmode Categories
+      --properties BasicAndNaturalIsotope --propertieslisting alphabetical
+      --outdelim comma --outputstyle ElementRows --quote yes
+      --output File -r ElementsProperties -o -m All
+
+To list basic atomic properties information for elements in groups IA and VIA using American
+style group labels, type:
+
+    % InfoPeriodicTableElements.pl -m AmericanGroupLabel IA VIA
+
+To list basic atomic properties information for elements in groups IA and VB using European
+style group labels, type:
+
+    % InfoPeriodicTableElements.pl -m AmericanGroupLabel IA VB
+
+To list basic atomic properties information for elements in groups Halogens and NobleGases, type:
+
+    % InfoPeriodicTableElements.pl -m GroupName Halogens NobleGases
+
+=head1 AUTHOR
+
+Manish Sud <msud@san.rr.com>
+
+=head1 SEE ALSO
+
+InfoAminoAcids.pl InfoNucleicAcids.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