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1 package MolecularFormula;
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2 #
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3 # $RCSfile: MolecularFormula.pm,v $
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4 # $Date: 2015/02/28 20:47:18 $
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5 # $Revision: 1.25 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use Carp;
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31 use Text::ParseWords;
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32 use TextUtil;
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33 use PeriodicTable;
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34
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35 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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36
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37 @ISA = qw(Exporter);
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38 @EXPORT = qw();
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39 @EXPORT_OK = qw(CalculateMolecularWeight CalculateExactMass CalculateElementalComposition FormatCompositionInfomation GetElementsAndCount IsMolecularFormula);
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40
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41 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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42
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43 #
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44 # Calculate molecular weight assuming its a valid molecular formula...
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45 #
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46 sub CalculateMolecularWeight {
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47 my($MolecularFormula) = @_;
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48 my($Index, $MolecularWeight, $ElementSymbol, $ElementCount, $AtomicWeight, $FormulaElementsRef, $FormulaElementCountRef);
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49
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50 ($FormulaElementsRef, $FormulaElementCountRef) = _ProcessMolecularFormula($MolecularFormula);
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51 if (!(defined($FormulaElementsRef) && defined($FormulaElementCountRef))) {
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52 return undef;
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53 }
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54
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55 $MolecularWeight = 0;
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56
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57 for $Index (0 .. $#{$FormulaElementsRef}) {
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58 $ElementSymbol = $FormulaElementsRef->[$Index];
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59 $ElementCount = $FormulaElementCountRef->[$Index];
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60 $AtomicWeight = PeriodicTable::GetElementAtomicWeight($ElementSymbol);
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61 $MolecularWeight += $AtomicWeight * $ElementCount;
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62 }
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63 return $MolecularWeight;
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64 }
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65
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66 #
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67 # Calculate exact mass assuming it's a valid formula...
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68 #
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69 sub CalculateExactMass {
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70 my($MolecularFormula) = @_;
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71 my($Index, $ElementSymbol, $ElementCount, $ExactMass, $RelativeAtomicMass, $FormulaElementsRef, $FormulaElementCountRef);
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72
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73 ($FormulaElementsRef, $FormulaElementCountRef) = _ProcessMolecularFormula($MolecularFormula);
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74 if (!(defined($FormulaElementsRef) && defined($FormulaElementCountRef))) {
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75 return undef;
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76 }
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77 $ExactMass = 0;
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78
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79 for $Index (0 .. $#{$FormulaElementsRef}) {
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80 $ElementSymbol = $FormulaElementsRef->[$Index];
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81 $ElementCount = $FormulaElementCountRef->[$Index];
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82 $RelativeAtomicMass = PeriodicTable::GetElementMostAbundantNaturalIsotopeMass($ElementSymbol);
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83 if (!defined($RelativeAtomicMass)) {
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84 next ELEMENT;
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85 }
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86 $ExactMass += $RelativeAtomicMass * $ElementCount;
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87 }
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88 return $ExactMass;
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89 }
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90
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91
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92 #
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93 # Calculate elemental composition and return reference to arrays
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94 # containing elements and their percent composition...
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95 #
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96 sub CalculateElementalComposition {
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97 my($MolecularFormula) = @_;
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98 my($Index, $MolecularWeight, $ElementSymbol, $ElementCount, $AtomicWeight, $Composition, $CompositionMultiplier, $FormulaElementsRef, $FormulaElementCountRef, @FormulaElements, @FormulaElementComposition);
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99
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100 $MolecularWeight = CalculateMolecularWeight($MolecularFormula);
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101 if (! defined $MolecularWeight) {
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102 return (undef, undef);
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103 }
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104 ($FormulaElementsRef, $FormulaElementCountRef) = _ProcessMolecularFormula($MolecularFormula);
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105
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106 @FormulaElements = ();
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107 @FormulaElementComposition = ();
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108
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109 if (!$MolecularWeight) {
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110 return ( \@FormulaElements, \@FormulaElementComposition);
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111 }
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112
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113 $CompositionMultiplier = 100 / $MolecularWeight;
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114
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115 for $Index (0 .. $#{$FormulaElementsRef}) {
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116 $ElementSymbol = $FormulaElementsRef->[$Index];
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117 $ElementCount = $FormulaElementCountRef->[$Index];
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118 $AtomicWeight = PeriodicTable::GetElementAtomicWeight($ElementSymbol);
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119 $Composition = ($AtomicWeight * $ElementCount) * $CompositionMultiplier;
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120
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121 push @FormulaElements, $ElementSymbol;
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122 push @FormulaElementComposition, $Composition;
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123 }
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124
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125 return ( \@FormulaElements, \@FormulaElementComposition);
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126 }
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127
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128 # Using refernece to element and its composition arrays, format composition information
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129 # as: Element: Composition;...
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130 #
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131 sub FormatCompositionInfomation {
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132 my($Index, $ElementSymbol, $ElementComposition, $ElementsRef, $ElementCompositionRef, $Precision, $Composition);
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133
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134 $Precision = 2;
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135 if (@_ == 3) {
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136 ($ElementsRef, $ElementCompositionRef, $Precision) = @_;
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137 }
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138 else {
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139 ($ElementsRef, $ElementCompositionRef) = @_;
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140 }
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141
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142 $Composition = '';
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143 for $Index (0 .. $#{$ElementsRef}) {
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144 $ElementSymbol = $ElementsRef->[$Index];
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145 $ElementComposition = $ElementCompositionRef->[$Index];
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146 $ElementComposition = sprintf("%.${Precision}f", $ElementComposition);
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147
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148 $Composition .= ($Composition) ? '; ' : '';
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149 $Composition .= "${ElementSymbol}: ${ElementComposition}%";
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150 }
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151
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152 return $Composition;
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153 }
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154
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155 #
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156 # Get elements and their count...
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157 #
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158 sub GetElementsAndCount {
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159 my($MolecularFormula) = @_;
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160 my($FormulaElementsRef, $FormulaElementCountRef, $ErrorMsg);
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161
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162 ($FormulaElementsRef, $FormulaElementCountRef, $ErrorMsg) = _ProcessMolecularFormula($MolecularFormula);
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163
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164 return ($FormulaElementsRef, $FormulaElementCountRef);
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165 }
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166
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167 #
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168 # Is it a valid molecular formula?
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169 #
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170 sub IsMolecularFormula {
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171 my($MolecularFormula, $PrintErrorMsg, $Status, $FormulaElementsRef, $FormulaElementCountRef, $ErrorMsg);
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172
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173 ($MolecularFormula) = @_;
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174
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175 ($FormulaElementsRef, $FormulaElementCountRef, $ErrorMsg) = _ProcessMolecularFormula($MolecularFormula);
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176 $Status = (defined($FormulaElementsRef) && defined($FormulaElementCountRef)) ? 1 : 0;
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177
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178 return (wantarray ? ($Status, $ErrorMsg) : $Status);
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179 }
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180
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181 #
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182 # Process molecular formula. For a valid formula, return references to arrays conatining elements
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183 # and element count; otherwsie, return undef.
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184 #
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185 sub _ProcessMolecularFormula {
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186 my($MolecularFormula) = @_;
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187 my($ErrorMsg) = '';
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188
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189 $MolecularFormula = _CleanUpFormula($MolecularFormula);
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190
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191 # Make sure it only contains numbers and letters...
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192 if ($MolecularFormula =~ /[^a-zA-Z0-9\(\)\[\]]/) {
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193 $ErrorMsg = 'Molecular formula contains characters other than a-zA-Z0-9';
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194 return (undef, undef, $ErrorMsg);
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195 }
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196
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197 # Parse the formula...
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198 my($ElementSpec, $FormulaElementSpec, $Spec, $ElementSymbol, $ElementCount, @FormulaElements, @ElementCount, %FormulaElementsToCountMap, @SubFormulaElements, %SubFormulaElementsToCountMap);
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199
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200 @FormulaElements = (); @ElementCount = ();
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201 %FormulaElementsToCountMap = ();
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202
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203 # Setup element symbol and count regular expression...
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204 # IUPAC: http://www.iupac.org/reports/provisional/abstract04/RB-prs310804/Chap4-3.04.pdf
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205 #
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206
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207 $FormulaElementSpec = qr/
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208 \G( # $1
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209 (?:
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210 ([A-Z][a-z]?) # Two or one letter element symbol; $2
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211 ([0-9]*) # Optionally followed by element count; $3
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212 )
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213 | \( | \[
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214 | \)[0-9]* | \][0-9]*
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215 | .
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216 )
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217 /x;
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218
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219 my($ProcessingParenthesis);
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220 $ProcessingParenthesis = 0;
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221 # Go over the formula...
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222 FORMULA: while ($MolecularFormula =~ /$FormulaElementSpec/gx) {
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223 ($Spec, $ElementSymbol, $ElementCount) = ($1, $2, $3);
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224
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225 # Handle parenthesis in formula to indicate repeating units...
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226 if ($Spec =~ /^(\(|\[)/) {
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227 if ($ProcessingParenthesis) {
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228 $ErrorMsg = "Molecular formula contains multiple level of () or []";
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229 return (undef, undef, $ErrorMsg);
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230 }
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231 $ProcessingParenthesis = 1;
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232 @SubFormulaElements = ();
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233 %SubFormulaElementsToCountMap = ();
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234 next FORMULA;
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235 }
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236 elsif ($Spec =~ /^(\)|\])/) {
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237 $ProcessingParenthesis = 0;
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238
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239 # Retrieve repeat count and move data to @FormulaElements and %FormulaElementsToCountMap;
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240 my($RepeatCount, $Symbol, $Count);
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241 $RepeatCount = $Spec;
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242 $RepeatCount =~ s/(\)|\])//g;
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243 if (!$RepeatCount) {
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244 $RepeatCount = 1;
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245 }
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246 # Copy data...
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247 for $Symbol (@SubFormulaElements) {
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248 $Count = $SubFormulaElementsToCountMap{$Symbol} * $RepeatCount;
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249 _SetupFormulaElementData(\@FormulaElements, \%FormulaElementsToCountMap, $Symbol, $Count);
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250 }
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251
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252 # Get ready again...
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253 @SubFormulaElements = ();
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254 %SubFormulaElementsToCountMap = ();
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255
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256 next FORMULA;
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257 }
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258
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259 # Retrieve element symbol and count...
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260 $ElementSymbol = ($Spec && !$ElementSymbol) ? $Spec : ($ElementSymbol ? $ElementSymbol : '');
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261 $ElementCount = $ElementCount ? $ElementCount : 1;
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262 if (!PeriodicTable::IsElement($ElementSymbol)) {
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263 $ErrorMsg = "Molecular formula contains unknown elemental symbol $ElementSymbol";
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264 return (undef, undef, $ErrorMsg);
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265 }
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266
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267 if ($ProcessingParenthesis) {
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268 _SetupFormulaElementData(\@SubFormulaElements, \%SubFormulaElementsToCountMap, $ElementSymbol, $ElementCount);
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269 }
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270 else {
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271 _SetupFormulaElementData(\@FormulaElements, \%FormulaElementsToCountMap, $ElementSymbol, $ElementCount);
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272 }
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273 }
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274
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275 # Setup element count array...
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276 for $ElementSymbol (@FormulaElements) {
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277 $ElementCount = $FormulaElementsToCountMap{$ElementSymbol};
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278 push @ElementCount, $ElementCount;
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279 }
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280
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281 # Make sure it all adds up to 100%; otherwise, adjust the last value..
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282
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283 return (\@FormulaElements, \@ElementCount, $ErrorMsg);
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284 }
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285
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286 # Clean it up...
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287 sub _CleanUpFormula {
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288 my($MolecularFormula) = @_;
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289 #Take out any spaces...
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290 $MolecularFormula =~ s/ //g;
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291
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292 # Eliminate any charge specifications: +, - or [1-9]+[+-]
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293 # e.g NO+ [Al(H2O)6]3+ [H2NO3]+
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294 if ($MolecularFormula =~ /[\+\-]/) {
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295 if ($MolecularFormula =~ /\][0-9]+[\+\-]/) {
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296 # Bracket followed optionally by number and then, +/- ...
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297 # [Al(H2O)6]3+ ...
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298 $MolecularFormula =~ s/\][0-9]+[\+\-]/\]/g;
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299 }
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300 elsif ($MolecularFormula =~ /[\+\-][0-9]*/) {
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301 # +/- followed optionally by a number...
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302 # C37H42N2O6+2, Cu+
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303 $MolecularFormula =~ s/[\+\-][0-9]*//g;
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304 }
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305 }
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306
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307 # Eliminate any brackets - ] or ) - not followed by numbers:
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308 # e.g. Li[H2PO4]
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309 if ($MolecularFormula !~ /\][0-9]+/) {
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310 $MolecularFormula =~ s/[\[\]]//g;
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311 }
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312 if ($MolecularFormula !~ /\)[0-9]+/) {
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313 $MolecularFormula =~ s/[\(\)]//g;
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314 }
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315 # Change adducts to parenthesis format...
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316 # Na2CO3.10H2O -> Na2CO3(H2O)10
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317 # 3CdSO4.8H2O -> (CdSO4)3(H2O)8
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318 if ($MolecularFormula =~ /\./) {
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319 my($SubFormula, $Count, $Spec);
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320 my(@MolecularFormulaSplits) = split /\./, $MolecularFormula;
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321 $MolecularFormula = '';
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322 for $SubFormula (@MolecularFormulaSplits) {
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323 ($Count, $Spec) = $SubFormula =~ /^([0-9]*)(.*?)$/;
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324 if ($Count) {
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325 $MolecularFormula .= "(${Spec})${Count}";
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326 }
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327 else {
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328 $MolecularFormula .= $Spec;
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329 }
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330 }
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331 }
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332
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333 return $MolecularFormula;
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334 }
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335
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336 # Store the element and count...
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337 sub _SetupFormulaElementData {
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338 my($ElementsRef, $ElementsToCountMapRef, $Element, $Count) = @_;
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339
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340 if (exists $ElementsToCountMapRef->{$Element}) {
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341 $ElementsToCountMapRef->{$Element} += $Count;
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342 }
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343 else {
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344 push @{$ElementsRef}, $Element;
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345 $ElementsToCountMapRef->{$Element} = $Count;
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346 }
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347 }
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348
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349 1;
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350
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351 __END__
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352
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353 =head1 NAME
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354
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355 MolecularFormula
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356
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357 =head1 SYNOPSIS
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358
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359 use MolecularFormula;
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360
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361 use MolecularFormula qw(:all);
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362
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363 =head1 DESCRIPTION
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364
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365 B<MolecularFormula> module provides the following functions:
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366
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367 CalculateElementalComposition, CalculateExactMass, CalculateMolecularWeight,
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368 FormatCompositionInfomation, GetElementsAndCount, IsMolecularFormula
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369
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370 =head1 FUNCTIONS
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371
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372 =over 4
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373
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374 =item B<CalculateMolecularWeight>
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375
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376 $MolecularWeight = CalculateMolecularWeight($MolecularFormula);
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377
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378 Calculates and returns the molecular weight for a specified I<MolecularFormula>.
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379
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380 =item B<CalculateElementalComposition>
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381
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382 ($ElementsRef, $ElementCompositionRef) =
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383 CalculateElementalComposition($MolecularFormula);
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384
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385 Calculates the percent composition in a specified I<MolecularFormula> and returns references
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386 to arrays containing elements and their percent composition.
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387
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388 =item B<CalculateExactMass>
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389
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390 $ExactMass = CalculateMolecularWeight($MolecularFormula);
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391
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392 Calculates and returns the exact mass for a specified I<MolecularFormula>.
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393
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394 =item B<FormatCompositionInfomation>
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395
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396 $FormattedString = FormatCompositionInfomation($ElementsRef,
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397 $ElementCompositionRef, [$Precision]);
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398
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399 Returns a formatted elemental composition string using references to elements and elemental
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400 composition arrays. Precision is an optional parameter; its default value is I<2>.
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401
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402 =item B<GetElementsAndCount>
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403
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404 ($ElementsRef, $ElementCountRef) = GetElementsAndCount(
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405 $MolecularFormula);
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406
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407 Retrieves elements and their count composition in a specified I<MolecularFormula> and
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408 returns references to arrays containing elements and their count.
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409
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410 =item B<IsMolecularFormula>
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411
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412 $Status = IsMolecularFormula($MolecularFormula);
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413 ($Status, $ErrorMsg) = IsMolecularFormula($MolecularFormula);
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414
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415 Returns 1 or 0 a based on whether it's a valid I<MolecularFormula>.
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416
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417 =back
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418
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419 =head1 AUTHOR
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420
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421 Manish Sud <msud@san.rr.com>
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422
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423 =head1 SEE ALSO
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424
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425 Molecule.pm
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426
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427 =head1 COPYRIGHT
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428
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429 Copyright (C) 2015 Manish Sud. All rights reserved.
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430
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431 This file is part of MayaChemTools.
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432
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433 MayaChemTools is free software; you can redistribute it and/or modify it under
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434 the terms of the GNU Lesser General Public License as published by the Free
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435 Software Foundation; either version 3 of the License, or (at your option)
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436 any later version.
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437
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438 =cut
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