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13 <pre>
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14 <a name="package-MolecularFormula-"></a> 1 <span class="k">package </span><span class="i">MolecularFormula</span><span class="sc">;</span>
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: MolecularFormula.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span>
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18 5 <span class="c"># $Revision: 1.25 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">PeriodicTable</span><span class="sc">;</span>
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47 34
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48 35 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span>
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49 36
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50 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span>
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51 38 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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52 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw(CalculateMolecularWeight CalculateExactMass CalculateElementalComposition FormatCompositionInfomation GetElementsAndCount IsMolecularFormula)</span><span class="sc">;</span>
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53 40
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54 41 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
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55 42
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56 43 <span class="c">#</span>
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57 44 <span class="c"># Calculate molecular weight assuming its a valid molecular formula...</span>
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58 45 <span class="c">#</span>
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59 <a name="CalculateMolecularWeight-"></a> 46 <span class="k">sub </span><span class="m">CalculateMolecularWeight</span> <span class="s">{</span>
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60 47 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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61 48 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$AtomicWeight</span><span class="cm">,</span> <span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="s">)</span><span class="sc">;</span>
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62 49
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63 50 <span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="s">)</span> = <span class="i">_ProcessMolecularFormula</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span>
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64 51 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementCountRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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65 52 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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66 53 <span class="s">}</span>
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67 54
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68 55 <span class="i">$MolecularWeight</span> = <span class="n">0</span><span class="sc">;</span>
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69 56
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70 57 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FormulaElementsRef</span>}<span class="s">)</span> <span class="s">{</span>
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71 58 <span class="i">$ElementSymbol</span> = <span class="i">$FormulaElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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72 59 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementCountRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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73 60 <span class="i">$AtomicWeight</span> = <span class="i">PeriodicTable::GetElementAtomicWeight</span><span class="s">(</span><span class="i">$ElementSymbol</span><span class="s">)</span><span class="sc">;</span>
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74 61 <span class="i">$MolecularWeight</span> += <span class="i">$AtomicWeight</span> * <span class="i">$ElementCount</span><span class="sc">;</span>
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75 62 <span class="s">}</span>
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76 63 <span class="k">return</span> <span class="i">$MolecularWeight</span><span class="sc">;</span>
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77 64 <span class="s">}</span>
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78 65
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79 66 <span class="c">#</span>
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80 67 <span class="c"># Calculate exact mass assuming it's a valid formula...</span>
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81 68 <span class="c">#</span>
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82 <a name="CalculateExactMass-"></a> 69 <span class="k">sub </span><span class="m">CalculateExactMass</span> <span class="s">{</span>
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83 70 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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84 71 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$ExactMass</span><span class="cm">,</span> <span class="i">$RelativeAtomicMass</span><span class="cm">,</span> <span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="s">)</span><span class="sc">;</span>
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85 72
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86 73 <span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="s">)</span> = <span class="i">_ProcessMolecularFormula</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span>
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87 74 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementCountRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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88 75 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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89 76 <span class="s">}</span>
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90 77 <span class="i">$ExactMass</span> = <span class="n">0</span><span class="sc">;</span>
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91 78
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92 79 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FormulaElementsRef</span>}<span class="s">)</span> <span class="s">{</span>
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93 80 <span class="i">$ElementSymbol</span> = <span class="i">$FormulaElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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94 81 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementCountRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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95 82 <span class="i">$RelativeAtomicMass</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMass</span><span class="s">(</span><span class="i">$ElementSymbol</span><span class="s">)</span><span class="sc">;</span>
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96 83 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$RelativeAtomicMass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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97 84 <span class="k">next</span> <span class="j">ELEMENT</span><span class="sc">;</span>
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98 85 <span class="s">}</span>
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99 86 <span class="i">$ExactMass</span> += <span class="i">$RelativeAtomicMass</span> * <span class="i">$ElementCount</span><span class="sc">;</span>
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100 87 <span class="s">}</span>
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101 88 <span class="k">return</span> <span class="i">$ExactMass</span><span class="sc">;</span>
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102 89 <span class="s">}</span>
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103 90
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104 91
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105 92 <span class="c">#</span>
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106 93 <span class="c"># Calculate elemental composition and return reference to arrays</span>
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107 94 <span class="c"># containing elements and their percent composition...</span>
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108 95 <span class="c">#</span>
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109 <a name="CalculateElementalComposition-"></a> 96 <span class="k">sub </span><span class="m">CalculateElementalComposition</span> <span class="s">{</span>
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110 97 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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111 98 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$AtomicWeight</span><span class="cm">,</span> <span class="i">$Composition</span><span class="cm">,</span> <span class="i">$CompositionMultiplier</span><span class="cm">,</span> <span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="cm">,</span> <span class="i">@FormulaElements</span><span class="cm">,</span> <span class="i">@FormulaElementComposition</span><span class="s">)</span><span class="sc">;</span>
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112 99
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113 100 <span class="i">$MolecularWeight</span> = <span class="i">CalculateMolecularWeight</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span>
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114 101 <span class="k">if</span> <span class="s">(</span>! <span class="k">defined</span> <span class="i">$MolecularWeight</span><span class="s">)</span> <span class="s">{</span>
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115 102 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
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116 103 <span class="s">}</span>
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117 104 <span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="s">)</span> = <span class="i">_ProcessMolecularFormula</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span>
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118 105
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119 106 <span class="i">@FormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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120 107 <span class="i">@FormulaElementComposition</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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121 108
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122 109 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MolecularWeight</span><span class="s">)</span> <span class="s">{</span>
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123 110 <span class="k">return</span> <span class="s">(</span> \<span class="i">@FormulaElements</span><span class="cm">,</span> \<span class="i">@FormulaElementComposition</span><span class="s">)</span><span class="sc">;</span>
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124 111 <span class="s">}</span>
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125 112
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126 113 <span class="i">$CompositionMultiplier</span> = <span class="n">100</span> / <span class="i">$MolecularWeight</span><span class="sc">;</span>
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127 114
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128 115 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FormulaElementsRef</span>}<span class="s">)</span> <span class="s">{</span>
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129 116 <span class="i">$ElementSymbol</span> = <span class="i">$FormulaElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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130 117 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementCountRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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131 118 <span class="i">$AtomicWeight</span> = <span class="i">PeriodicTable::GetElementAtomicWeight</span><span class="s">(</span><span class="i">$ElementSymbol</span><span class="s">)</span><span class="sc">;</span>
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132 119 <span class="i">$Composition</span> = <span class="s">(</span><span class="i">$AtomicWeight</span> * <span class="i">$ElementCount</span><span class="s">)</span> * <span class="i">$CompositionMultiplier</span><span class="sc">;</span>
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133 120
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134 121 <span class="k">push</span> <span class="i">@FormulaElements</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="sc">;</span>
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135 122 <span class="k">push</span> <span class="i">@FormulaElementComposition</span><span class="cm">,</span> <span class="i">$Composition</span><span class="sc">;</span>
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136 123 <span class="s">}</span>
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137 124
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138 125 <span class="k">return</span> <span class="s">(</span> \<span class="i">@FormulaElements</span><span class="cm">,</span> \<span class="i">@FormulaElementComposition</span><span class="s">)</span><span class="sc">;</span>
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139 126 <span class="s">}</span>
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140 127
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141 128 <span class="c"># Using refernece to element and its composition arrays, format composition information</span>
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142 129 <span class="c"># as: Element: Composition;...</span>
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143 130 <span class="c">#</span>
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144 <a name="FormatCompositionInfomation-"></a> 131 <span class="k">sub </span><span class="m">FormatCompositionInfomation</span> <span class="s">{</span>
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145 132 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementComposition</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="cm">,</span> <span class="i">$Composition</span><span class="s">)</span><span class="sc">;</span>
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146 133
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147 134 <span class="i">$Precision</span> = <span class="n">2</span><span class="sc">;</span>
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148 135 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
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149 136 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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150 137 <span class="s">}</span>
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151 138 <span class="k">else</span> <span class="s">{</span>
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152 139 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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153 140 <span class="s">}</span>
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154 141
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155 142 <span class="i">$Composition</span> = <span class="q">''</span><span class="sc">;</span>
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156 143 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ElementsRef</span>}<span class="s">)</span> <span class="s">{</span>
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157 144 <span class="i">$ElementSymbol</span> = <span class="i">$ElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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158 145 <span class="i">$ElementComposition</span> = <span class="i">$ElementCompositionRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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159 146 <span class="i">$ElementComposition</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.${Precision}f"</span><span class="cm">,</span> <span class="i">$ElementComposition</span><span class="s">)</span><span class="sc">;</span>
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160 147
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161 148 <span class="i">$Composition</span> .= <span class="s">(</span><span class="i">$Composition</span><span class="s">)</span> ? <span class="q">'; '</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
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162 149 <span class="i">$Composition</span> .= <span class="q">"${ElementSymbol}: ${ElementComposition}%"</span><span class="sc">;</span>
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163 150 <span class="s">}</span>
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164 151
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165 152 <span class="k">return</span> <span class="i">$Composition</span><span class="sc">;</span>
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166 153 <span class="s">}</span>
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167 154
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168 155 <span class="c">#</span>
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169 156 <span class="c"># Get elements and their count...</span>
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170 157 <span class="c">#</span>
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171 <a name="GetElementsAndCount-"></a> 158 <span class="k">sub </span><span class="m">GetElementsAndCount</span> <span class="s">{</span>
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172 159 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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173 160 <span class="k">my</span><span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
|
|
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174 161
|
|
|
175 162 <span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span> = <span class="i">_ProcessMolecularFormula</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span>
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176 163
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|
177 164 <span class="k">return</span> <span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="s">)</span><span class="sc">;</span>
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178 165 <span class="s">}</span>
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179 166
|
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180 167 <span class="c">#</span>
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|
181 168 <span class="c"># Is it a valid molecular formula?</span>
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|
182 169 <span class="c">#</span>
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183 <a name="IsMolecularFormula-"></a> 170 <span class="k">sub </span><span class="m">IsMolecularFormula</span> <span class="s">{</span>
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184 171 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="cm">,</span> <span class="i">$PrintErrorMsg</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
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185 172
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186 173 <span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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187 174
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188 175 <span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="cm">,</span> <span class="i">$FormulaElementCountRef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span> = <span class="i">_ProcessMolecularFormula</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span>
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189 176 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementCountRef</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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190 177
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|
191 178 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span> <span class="co">:</span> <span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
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192 179 <span class="s">}</span>
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193 180
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194 181 <span class="c">#</span>
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195 182 <span class="c"># Process molecular formula. For a valid formula, return references to arrays conatining elements</span>
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196 183 <span class="c"># and element count; otherwsie, return undef.</span>
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197 184 <span class="c">#</span>
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198 <a name="_ProcessMolecularFormula-"></a> 185 <span class="k">sub </span><span class="m">_ProcessMolecularFormula</span> <span class="s">{</span>
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199 186 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
200 187 <span class="k">my</span><span class="s">(</span><span class="i">$ErrorMsg</span><span class="s">)</span> = <span class="q">''</span><span class="sc">;</span>
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201 188
|
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|
202 189 <span class="i">$MolecularFormula</span> = <span class="i">_CleanUpFormula</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span>
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203 190
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|
204 191 <span class="c"># Make sure it only contains numbers and letters...</span>
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205 192 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/[^a-zA-Z0-9\(\)\[\]]/</span><span class="s">)</span> <span class="s">{</span>
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|
|
206 193 <span class="i">$ErrorMsg</span> = <span class="q">'Molecular formula contains characters other than a-zA-Z0-9'</span><span class="sc">;</span>
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|
|
207 194 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
|
|
|
208 195 <span class="s">}</span>
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209 196
|
|
|
210 197 <span class="c"># Parse the formula...</span>
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|
211 198 <span class="k">my</span><span class="s">(</span><span class="i">$ElementSpec</span><span class="cm">,</span> <span class="i">$FormulaElementSpec</span><span class="cm">,</span> <span class="i">$Spec</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">@FormulaElements</span><span class="cm">,</span> <span class="i">@ElementCount</span><span class="cm">,</span> <span class="i">%FormulaElementsToCountMap</span><span class="cm">,</span> <span class="i">@SubFormulaElements</span><span class="cm">,</span> <span class="i">%SubFormulaElementsToCountMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
212 199
|
|
|
213 200 <span class="i">@FormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@ElementCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
214 201 <span class="i">%FormulaElementsToCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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215 202
|
|
|
216 203 <span class="c"># Setup element symbol and count regular expression...</span>
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|
217 204 <span class="c"># IUPAC: http://www.iupac.org/reports/provisional/abstract04/RB-prs310804/Chap4-3.04.pdf</span>
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|
|
218 205 <span class="c">#</span>
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|
|
219 206
|
|
|
220 207 <span class="i">$FormulaElementSpec</span> = <span class="q">qr/</span>
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|
221 208 <span class="q"> \G( # $1</span>
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|
222 209 <span class="q"> (?:</span>
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|
223 210 <span class="q"> ([A-Z][a-z]?) # Two or one letter element symbol; $2</span>
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|
224 211 <span class="q"> ([0-9]*) # Optionally followed by element count; $3</span>
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|
225 212 <span class="q"> )</span>
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|
226 213 <span class="q"> | \( | \[</span>
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|
227 214 <span class="q"> | \)[0-9]* | \][0-9]*</span>
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|
228 215 <span class="q"> | .</span>
|
|
|
229 216 <span class="q"> )</span>
|
|
|
230 217 <span class="q"> /x</span><span class="sc">;</span>
|
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|
231 218
|
|
|
232 219 <span class="k">my</span><span class="s">(</span><span class="i">$ProcessingParenthesis</span><span class="s">)</span><span class="sc">;</span>
|
|
|
233 220 <span class="i">$ProcessingParenthesis</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
234 221 <span class="c"># Go over the formula...</span>
|
|
|
235 222 <span class="j">FORMULA:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/$FormulaElementSpec/gx</span><span class="s">)</span> <span class="s">{</span>
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|
236 223 <span class="s">(</span><span class="i">$Spec</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="s">)</span> = <span class="s">(</span><span class="i">$1</span><span class="cm">,</span> <span class="i">$2</span><span class="cm">,</span> <span class="i">$3</span><span class="s">)</span><span class="sc">;</span>
|
|
|
237 224
|
|
|
238 225 <span class="c"># Handle parenthesis in formula to indicate repeating units...</span>
|
|
|
239 226 <span class="k">if</span> <span class="s">(</span><span class="i">$Spec</span> =~ <span class="q">/^(\(|\[)/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$ProcessingParenthesis</span><span class="s">)</span> <span class="s">{</span>
|
|
|
241 228 <span class="i">$ErrorMsg</span> = <span class="q">"Molecular formula contains multiple level of () or []"</span><span class="sc">;</span>
|
|
|
242 229 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
|
|
|
243 230 <span class="s">}</span>
|
|
|
244 231 <span class="i">$ProcessingParenthesis</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
245 232 <span class="i">@SubFormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
246 233 <span class="i">%SubFormulaElementsToCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
247 234 <span class="k">next</span> <span class="j">FORMULA</span><span class="sc">;</span>
|
|
|
248 235 <span class="s">}</span>
|
|
|
249 236 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Spec</span> =~ <span class="q">/^(\)|\])/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
250 237 <span class="i">$ProcessingParenthesis</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
251 238
|
|
|
252 239 <span class="c"># Retrieve repeat count and move data to @FormulaElements and %FormulaElementsToCountMap;</span>
|
|
|
253 240 <span class="k">my</span><span class="s">(</span><span class="i">$RepeatCount</span><span class="cm">,</span> <span class="i">$Symbol</span><span class="cm">,</span> <span class="i">$Count</span><span class="s">)</span><span class="sc">;</span>
|
|
|
254 241 <span class="i">$RepeatCount</span> = <span class="i">$Spec</span><span class="sc">;</span>
|
|
|
255 242 <span class="i">$RepeatCount</span> =~ <span class="q">s/(\)|\])//g</span><span class="sc">;</span>
|
|
|
256 243 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RepeatCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
257 244 <span class="i">$RepeatCount</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
258 245 <span class="s">}</span>
|
|
|
259 246 <span class="c"># Copy data...</span>
|
|
|
260 247 <span class="k">for</span> <span class="i">$Symbol</span> <span class="s">(</span><span class="i">@SubFormulaElements</span><span class="s">)</span> <span class="s">{</span>
|
|
|
261 248 <span class="i">$Count</span> = <span class="i">$SubFormulaElementsToCountMap</span>{<span class="i">$Symbol</span>} * <span class="i">$RepeatCount</span><span class="sc">;</span>
|
|
|
262 249 <span class="i">_SetupFormulaElementData</span><span class="s">(</span>\<span class="i">@FormulaElements</span><span class="cm">,</span> \<span class="i">%FormulaElementsToCountMap</span><span class="cm">,</span> <span class="i">$Symbol</span><span class="cm">,</span> <span class="i">$Count</span><span class="s">)</span><span class="sc">;</span>
|
|
|
263 250 <span class="s">}</span>
|
|
|
264 251
|
|
|
265 252 <span class="c"># Get ready again...</span>
|
|
|
266 253 <span class="i">@SubFormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
267 254 <span class="i">%SubFormulaElementsToCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
268 255
|
|
|
269 256 <span class="k">next</span> <span class="j">FORMULA</span><span class="sc">;</span>
|
|
|
270 257 <span class="s">}</span>
|
|
|
271 258
|
|
|
272 259 <span class="c"># Retrieve element symbol and count...</span>
|
|
|
273 260 <span class="i">$ElementSymbol</span> = <span class="s">(</span><span class="i">$Spec</span> && !<span class="i">$ElementSymbol</span><span class="s">)</span> ? <span class="i">$Spec</span> <span class="co">:</span> <span class="s">(</span><span class="i">$ElementSymbol</span> ? <span class="i">$ElementSymbol</span> <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span>
|
|
|
274 261 <span class="i">$ElementCount</span> = <span class="i">$ElementCount</span> ? <span class="i">$ElementCount</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
275 262 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElement</span><span class="s">(</span><span class="i">$ElementSymbol</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
276 263 <span class="i">$ErrorMsg</span> = <span class="q">"Molecular formula contains unknown elemental symbol $ElementSymbol"</span><span class="sc">;</span>
|
|
|
277 264 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
|
|
|
278 265 <span class="s">}</span>
|
|
|
279 266
|
|
|
280 267 <span class="k">if</span> <span class="s">(</span><span class="i">$ProcessingParenthesis</span><span class="s">)</span> <span class="s">{</span>
|
|
|
281 268 <span class="i">_SetupFormulaElementData</span><span class="s">(</span>\<span class="i">@SubFormulaElements</span><span class="cm">,</span> \<span class="i">%SubFormulaElementsToCountMap</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
282 269 <span class="s">}</span>
|
|
|
283 270 <span class="k">else</span> <span class="s">{</span>
|
|
|
284 271 <span class="i">_SetupFormulaElementData</span><span class="s">(</span>\<span class="i">@FormulaElements</span><span class="cm">,</span> \<span class="i">%FormulaElementsToCountMap</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
285 272 <span class="s">}</span>
|
|
|
286 273 <span class="s">}</span>
|
|
|
287 274
|
|
|
288 275 <span class="c"># Setup element count array...</span>
|
|
|
289 276 <span class="k">for</span> <span class="i">$ElementSymbol</span> <span class="s">(</span><span class="i">@FormulaElements</span><span class="s">)</span> <span class="s">{</span>
|
|
|
290 277 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementsToCountMap</span>{<span class="i">$ElementSymbol</span>}<span class="sc">;</span>
|
|
|
291 278 <span class="k">push</span> <span class="i">@ElementCount</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="sc">;</span>
|
|
|
292 279 <span class="s">}</span>
|
|
|
293 280
|
|
|
294 281 <span class="c"># Make sure it all adds up to 100%; otherwise, adjust the last value..</span>
|
|
|
295 282
|
|
|
296 283 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FormulaElements</span><span class="cm">,</span> \<span class="i">@ElementCount</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
|
|
|
297 284 <span class="s">}</span>
|
|
|
298 285
|
|
|
299 286 <span class="c"># Clean it up...</span>
|
|
|
300 <a name="_CleanUpFormula-"></a> 287 <span class="k">sub </span><span class="m">_CleanUpFormula</span> <span class="s">{</span>
|
|
|
301 288 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
302 289 <span class="c">#Take out any spaces...</span>
|
|
|
303 290 <span class="i">$MolecularFormula</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
304 291
|
|
|
305 292 <span class="c"># Eliminate any charge specifications: +, - or [1-9]+[+-]</span>
|
|
|
306 293 <span class="c"># e.g NO+ [Al(H2O)6]3+ [H2NO3]+</span>
|
|
|
307 294 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/[\+\-]/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
308 295 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/\][0-9]+[\+\-]/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
309 296 <span class="c"># Bracket followed optionally by number and then, +/- ...</span>
|
|
|
310 297 <span class="c"># [Al(H2O)6]3+ ...</span>
|
|
|
311 298 <span class="i">$MolecularFormula</span> =~ <span class="q">s/\][0-9]+[\+\-]/\]/g</span><span class="sc">;</span>
|
|
|
312 299 <span class="s">}</span>
|
|
|
313 300 <span class="k">elsif</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/[\+\-][0-9]*/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
314 301 <span class="c"># +/- followed optionally by a number...</span>
|
|
|
315 302 <span class="c"># C37H42N2O6+2, Cu+</span>
|
|
|
316 303 <span class="i">$MolecularFormula</span> =~ <span class="q">s/[\+\-][0-9]*//g</span><span class="sc">;</span>
|
|
|
317 304 <span class="s">}</span>
|
|
|
318 305 <span class="s">}</span>
|
|
|
319 306
|
|
|
320 307 <span class="c"># Eliminate any brackets - ] or ) - not followed by numbers:</span>
|
|
|
321 308 <span class="c"># e.g. Li[H2PO4]</span>
|
|
|
322 309 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> !~ <span class="q">/\][0-9]+/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
323 310 <span class="i">$MolecularFormula</span> =~ <span class="q">s/[\[\]]//g</span><span class="sc">;</span>
|
|
|
324 311 <span class="s">}</span>
|
|
|
325 312 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> !~ <span class="q">/\)[0-9]+/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
326 313 <span class="i">$MolecularFormula</span> =~ <span class="q">s/[\(\)]//g</span><span class="sc">;</span>
|
|
|
327 314 <span class="s">}</span>
|
|
|
328 315 <span class="c"># Change adducts to parenthesis format...</span>
|
|
|
329 316 <span class="c"># Na2CO3.10H2O -> Na2CO3(H2O)10</span>
|
|
|
330 317 <span class="c"># 3CdSO4.8H2O -> (CdSO4)3(H2O)8</span>
|
|
|
331 318 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/\./</span><span class="s">)</span> <span class="s">{</span>
|
|
|
332 319 <span class="k">my</span><span class="s">(</span><span class="i">$SubFormula</span><span class="cm">,</span> <span class="i">$Count</span><span class="cm">,</span> <span class="i">$Spec</span><span class="s">)</span><span class="sc">;</span>
|
|
|
333 320 <span class="k">my</span><span class="s">(</span><span class="i">@MolecularFormulaSplits</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$MolecularFormula</span><span class="sc">;</span>
|
|
|
334 321 <span class="i">$MolecularFormula</span> = <span class="q">''</span><span class="sc">;</span>
|
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335 322 <span class="k">for</span> <span class="i">$SubFormula</span> <span class="s">(</span><span class="i">@MolecularFormulaSplits</span><span class="s">)</span> <span class="s">{</span>
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336 323 <span class="s">(</span><span class="i">$Count</span><span class="cm">,</span> <span class="i">$Spec</span><span class="s">)</span> = <span class="i">$SubFormula</span> =~ <span class="q">/^([0-9]*)(.*?)$/</span><span class="sc">;</span>
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337 324 <span class="k">if</span> <span class="s">(</span><span class="i">$Count</span><span class="s">)</span> <span class="s">{</span>
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338 325 <span class="i">$MolecularFormula</span> .= <span class="q">"(${Spec})${Count}"</span><span class="sc">;</span>
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339 326 <span class="s">}</span>
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340 327 <span class="k">else</span> <span class="s">{</span>
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341 328 <span class="i">$MolecularFormula</span> .= <span class="i">$Spec</span><span class="sc">;</span>
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342 329 <span class="s">}</span>
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343 330 <span class="s">}</span>
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344 331 <span class="s">}</span>
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345 332
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346 333 <span class="k">return</span> <span class="i">$MolecularFormula</span><span class="sc">;</span>
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347 334 <span class="s">}</span>
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348 335
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349 336 <span class="c"># Store the element and count...</span>
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350 <a name="_SetupFormulaElementData-"></a> 337 <span class="k">sub </span><span class="m">_SetupFormulaElementData</span> <span class="s">{</span>
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351 338 <span class="k">my</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsToCountMapRef</span><span class="cm">,</span> <span class="i">$Element</span><span class="cm">,</span> <span class="i">$Count</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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352 339
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353 340 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsToCountMapRef</span>->{<span class="i">$Element</span>}<span class="s">)</span> <span class="s">{</span>
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354 341 <span class="i">$ElementsToCountMapRef</span>->{<span class="i">$Element</span>} += <span class="i">$Count</span><span class="sc">;</span>
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355 342 <span class="s">}</span>
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356 343 <span class="k">else</span> <span class="s">{</span>
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357 344 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ElementsRef</span>}<span class="cm">,</span> <span class="i">$Element</span><span class="sc">;</span>
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358 345 <span class="i">$ElementsToCountMapRef</span>->{<span class="i">$Element</span>} = <span class="i">$Count</span><span class="sc">;</span>
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359 346 <span class="s">}</span>
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360 347 <span class="s">}</span>
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361 348
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362 <a name="EOF-"></a></pre>
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363 <p> </p>
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364 <br />
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365 <center>
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366 <img src="../../../images/h2o2.png">
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367 </center>
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368 </body>
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369 </html>
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