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comparison mayachemtools/docs/modules/html/code/MolecularFormula.html @ 0:73ae111cf86f draft
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:MolecularFormula.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-MolecularFormula-"></a> 1 <span class="k">package </span><span class="i">MolecularFormula</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: MolecularFormula.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span> | |
| 18 5 <span class="c"># $Revision: 1.25 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">PeriodicTable</span><span class="sc">;</span> | |
| 47 34 | |
| 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> | |
| 49 36 | |
| 50 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> | |
| 51 38 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 52 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw(CalculateMolecularWeight CalculateExactMass CalculateElementalComposition FormatCompositionInfomation GetElementsAndCount IsMolecularFormula)</span><span class="sc">;</span> | |
| 53 40 | |
| 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> | |
| 55 42 | |
| 56 43 <span class="c">#</span> | |
| 57 44 <span class="c"># Calculate molecular weight assuming its a valid molecular formula...</span> | |
| 58 45 <span class="c">#</span> | |
| 59 <a name="CalculateMolecularWeight-"></a> 46 <span class="k">sub </span><span class="m">CalculateMolecularWeight</span> <span class="s">{</span> | |
| 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> | |
| 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">$FormulaElementCountRef</span><span class="s">)</span><span class="sc">;</span> | |
| 62 49 | |
| 63 50 <span class="s">(</span><span class="i">$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> | |
| 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> | |
| 65 52 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 66 53 <span class="s">}</span> | |
| 67 54 | |
| 68 55 <span class="i">$MolecularWeight</span> = <span class="n">0</span><span class="sc">;</span> | |
| 69 56 | |
| 70 57 <span class="k">for</span> <span class="i">$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> | |
| 71 58 <span class="i">$ElementSymbol</span> = <span class="i">$FormulaElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 72 59 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementCountRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 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> | |
| 74 61 <span class="i">$MolecularWeight</span> += <span class="i">$AtomicWeight</span> * <span class="i">$ElementCount</span><span class="sc">;</span> | |
| 75 62 <span class="s">}</span> | |
| 76 63 <span class="k">return</span> <span class="i">$MolecularWeight</span><span class="sc">;</span> | |
| 77 64 <span class="s">}</span> | |
| 78 65 | |
| 79 66 <span class="c">#</span> | |
| 80 67 <span class="c"># Calculate exact mass assuming it's a valid formula...</span> | |
| 81 68 <span class="c">#</span> | |
| 82 <a name="CalculateExactMass-"></a> 69 <span class="k">sub </span><span class="m">CalculateExactMass</span> <span class="s">{</span> | |
| 83 70 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 84 71 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 85 72 | |
| 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">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span> | |
| 87 74 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementCountRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 88 75 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 89 76 <span class="s">}</span> | |
| 90 77 <span class="i">$ExactMass</span> = <span class="n">0</span><span class="sc">;</span> | |
| 91 78 | |
| 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">$FormulaElementsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 93 80 <span class="i">$ElementSymbol</span> = <span class="i">$FormulaElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 94 81 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementCountRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 95 82 <span class="i">$RelativeAtomicMass</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMass</span><span class="s">(</span><span class="i">$ElementSymbol</span><span class="s">)</span><span class="sc">;</span> | |
| 96 83 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$RelativeAtomicMass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 97 84 <span class="k">next</span> <span class="j">ELEMENT</span><span class="sc">;</span> | |
| 98 85 <span class="s">}</span> | |
| 99 86 <span class="i">$ExactMass</span> += <span class="i">$RelativeAtomicMass</span> * <span class="i">$ElementCount</span><span class="sc">;</span> | |
| 100 87 <span class="s">}</span> | |
| 101 88 <span class="k">return</span> <span class="i">$ExactMass</span><span class="sc">;</span> | |
| 102 89 <span class="s">}</span> | |
| 103 90 | |
| 104 91 | |
| 105 92 <span class="c">#</span> | |
| 106 93 <span class="c"># Calculate elemental composition and return reference to arrays</span> | |
| 107 94 <span class="c"># containing elements and their percent composition...</span> | |
| 108 95 <span class="c">#</span> | |
| 109 <a name="CalculateElementalComposition-"></a> 96 <span class="k">sub </span><span class="m">CalculateElementalComposition</span> <span class="s">{</span> | |
| 110 97 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 111 98 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 112 99 | |
| 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> | |
| 114 101 <span class="k">if</span> <span class="s">(</span>! <span class="k">defined</span> <span class="i">$MolecularWeight</span><span class="s">)</span> <span class="s">{</span> | |
| 115 102 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 116 103 <span class="s">}</span> | |
| 117 104 <span class="s">(</span><span class="i">$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> | |
| 118 105 | |
| 119 106 <span class="i">@FormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 120 107 <span class="i">@FormulaElementComposition</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 121 108 | |
| 122 109 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MolecularWeight</span><span class="s">)</span> <span class="s">{</span> | |
| 123 110 <span class="k">return</span> <span class="s">(</span> \<span class="i">@FormulaElements</span><span class="cm">,</span> \<span class="i">@FormulaElementComposition</span><span class="s">)</span><span class="sc">;</span> | |
| 124 111 <span class="s">}</span> | |
| 125 112 | |
| 126 113 <span class="i">$CompositionMultiplier</span> = <span class="n">100</span> / <span class="i">$MolecularWeight</span><span class="sc">;</span> | |
| 127 114 | |
| 128 115 <span class="k">for</span> <span class="i">$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> | |
| 129 116 <span class="i">$ElementSymbol</span> = <span class="i">$FormulaElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 130 117 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementCountRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 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> | |
| 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> | |
| 133 120 | |
| 134 121 <span class="k">push</span> <span class="i">@FormulaElements</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="sc">;</span> | |
| 135 122 <span class="k">push</span> <span class="i">@FormulaElementComposition</span><span class="cm">,</span> <span class="i">$Composition</span><span class="sc">;</span> | |
| 136 123 <span class="s">}</span> | |
| 137 124 | |
| 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> | |
| 139 126 <span class="s">}</span> | |
| 140 127 | |
| 141 128 <span class="c"># Using refernece to element and its composition arrays, format composition information</span> | |
| 142 129 <span class="c"># as: Element: Composition;...</span> | |
| 143 130 <span class="c">#</span> | |
| 144 <a name="FormatCompositionInfomation-"></a> 131 <span class="k">sub </span><span class="m">FormatCompositionInfomation</span> <span class="s">{</span> | |
| 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">$Composition</span><span class="s">)</span><span class="sc">;</span> | |
| 146 133 | |
| 147 134 <span class="i">$Precision</span> = <span class="n">2</span><span class="sc">;</span> | |
| 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> | |
| 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">$Precision</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 150 137 <span class="s">}</span> | |
| 151 138 <span class="k">else</span> <span class="s">{</span> | |
| 152 139 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 153 140 <span class="s">}</span> | |
| 154 141 | |
| 155 142 <span class="i">$Composition</span> = <span class="q">''</span><span class="sc">;</span> | |
| 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">$ElementsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 157 144 <span class="i">$ElementSymbol</span> = <span class="i">$ElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 158 145 <span class="i">$ElementComposition</span> = <span class="i">$ElementCompositionRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 159 146 <span class="i">$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> | |
| 160 147 | |
| 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> | |
| 162 149 <span class="i">$Composition</span> .= <span class="q">"${ElementSymbol}: ${ElementComposition}%"</span><span class="sc">;</span> | |
| 163 150 <span class="s">}</span> | |
| 164 151 | |
| 165 152 <span class="k">return</span> <span class="i">$Composition</span><span class="sc">;</span> | |
| 166 153 <span class="s">}</span> | |
| 167 154 | |
| 168 155 <span class="c">#</span> | |
| 169 156 <span class="c"># Get elements and their count...</span> | |
| 170 157 <span class="c">#</span> | |
| 171 <a name="GetElementsAndCount-"></a> 158 <span class="k">sub </span><span class="m">GetElementsAndCount</span> <span class="s">{</span> | |
| 172 159 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 173 160 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 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> | |
| 176 163 | |
| 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> | |
| 178 165 <span class="s">}</span> | |
| 179 166 | |
| 180 167 <span class="c">#</span> | |
| 181 168 <span class="c"># Is it a valid molecular formula?</span> | |
| 182 169 <span class="c">#</span> | |
| 183 <a name="IsMolecularFormula-"></a> 170 <span class="k">sub </span><span class="m">IsMolecularFormula</span> <span class="s">{</span> | |
| 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> | |
| 185 172 | |
| 186 173 <span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 187 174 | |
| 188 175 <span class="s">(</span><span class="i">$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">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span> | |
| 189 176 <span class="i">$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> | |
| 190 177 | |
| 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">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 192 179 <span class="s">}</span> | |
| 193 180 | |
| 194 181 <span class="c">#</span> | |
| 195 182 <span class="c"># Process molecular formula. For a valid formula, return references to arrays conatining elements</span> | |
| 196 183 <span class="c"># and element count; otherwsie, return undef.</span> | |
| 197 184 <span class="c">#</span> | |
| 198 <a name="_ProcessMolecularFormula-"></a> 185 <span class="k">sub </span><span class="m">_ProcessMolecularFormula</span> <span class="s">{</span> | |
| 199 186 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 200 187 <span class="k">my</span><span class="s">(</span><span class="i">$ErrorMsg</span><span class="s">)</span> = <span class="q">''</span><span class="sc">;</span> | |
| 201 188 | |
| 202 189 <span class="i">$MolecularFormula</span> = <span class="i">_CleanUpFormula</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span> | |
| 203 190 | |
| 204 191 <span class="c"># Make sure it only contains numbers and letters...</span> | |
| 205 192 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/[^a-zA-Z0-9\(\)\[\]]/</span><span class="s">)</span> <span class="s">{</span> | |
| 206 193 <span class="i">$ErrorMsg</span> = <span class="q">'Molecular formula contains characters other than a-zA-Z0-9'</span><span class="sc">;</span> | |
| 207 194 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span> | |
| 208 195 <span class="s">}</span> | |
| 209 196 | |
| 210 197 <span class="c"># Parse the formula...</span> | |
| 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">$ElementCount</span><span class="cm">,</span> <span class="i">@FormulaElements</span><span class="cm">,</span> <span class="i">@ElementCount</span><span class="cm">,</span> <span class="i">%FormulaElementsToCountMap</span><span class="cm">,</span> <span class="i">@SubFormulaElements</span><span class="cm">,</span> <span class="i">%SubFormulaElementsToCountMap</span><span class="s">)</span><span class="sc">;</span> | |
| 212 199 | |
| 213 200 <span class="i">@FormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@ElementCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 214 201 <span class="i">%FormulaElementsToCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 215 202 | |
| 216 203 <span class="c"># Setup element symbol and count regular expression...</span> | |
| 217 204 <span class="c"># IUPAC: http://www.iupac.org/reports/provisional/abstract04/RB-prs310804/Chap4-3.04.pdf</span> | |
| 218 205 <span class="c">#</span> | |
| 219 206 | |
| 220 207 <span class="i">$FormulaElementSpec</span> = <span class="q">qr/</span> | |
| 221 208 <span class="q"> \G( # $1</span> | |
| 222 209 <span class="q"> (?:</span> | |
| 223 210 <span class="q"> ([A-Z][a-z]?) # Two or one letter element symbol; $2</span> | |
| 224 211 <span class="q"> ([0-9]*) # Optionally followed by element count; $3</span> | |
| 225 212 <span class="q"> )</span> | |
| 226 213 <span class="q"> | \( | \[</span> | |
| 227 214 <span class="q"> | \)[0-9]* | \][0-9]*</span> | |
| 228 215 <span class="q"> | .</span> | |
| 229 216 <span class="q"> )</span> | |
| 230 217 <span class="q"> /x</span><span class="sc">;</span> | |
| 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> | |
| 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> | |
| 335 322 <span class="k">for</span> <span class="i">$SubFormula</span> <span class="s">(</span><span class="i">@MolecularFormulaSplits</span><span class="s">)</span> <span class="s">{</span> | |
| 336 323 <span class="s">(</span><span class="i">$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]*)(.*?)$/</span><span class="sc">;</span> | |
| 337 324 <span class="k">if</span> <span class="s">(</span><span class="i">$Count</span><span class="s">)</span> <span class="s">{</span> | |
| 338 325 <span class="i">$MolecularFormula</span> .= <span class="q">"(${Spec})${Count}"</span><span class="sc">;</span> | |
| 339 326 <span class="s">}</span> | |
| 340 327 <span class="k">else</span> <span class="s">{</span> | |
| 341 328 <span class="i">$MolecularFormula</span> .= <span class="i">$Spec</span><span class="sc">;</span> | |
| 342 329 <span class="s">}</span> | |
| 343 330 <span class="s">}</span> | |
| 344 331 <span class="s">}</span> | |
| 345 332 | |
| 346 333 <span class="k">return</span> <span class="i">$MolecularFormula</span><span class="sc">;</span> | |
| 347 334 <span class="s">}</span> | |
| 348 335 | |
| 349 336 <span class="c"># Store the element and count...</span> | |
| 350 <a name="_SetupFormulaElementData-"></a> 337 <span class="k">sub </span><span class="m">_SetupFormulaElementData</span> <span class="s">{</span> | |
| 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> | |
| 352 339 | |
| 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> | |
| 354 341 <span class="i">$ElementsToCountMapRef</span>->{<span class="i">$Element</span>} += <span class="i">$Count</span><span class="sc">;</span> | |
| 355 342 <span class="s">}</span> | |
| 356 343 <span class="k">else</span> <span class="s">{</span> | |
| 357 344 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ElementsRef</span>}<span class="cm">,</span> <span class="i">$Element</span><span class="sc">;</span> | |
| 358 345 <span class="i">$ElementsToCountMapRef</span>->{<span class="i">$Element</span>} = <span class="i">$Count</span><span class="sc">;</span> | |
| 359 346 <span class="s">}</span> | |
| 360 347 <span class="s">}</span> | |
| 361 348 | |
| 362 <a name="EOF-"></a></pre> | |
| 363 <p> </p> | |
| 364 <br /> | |
| 365 <center> | |
| 366 <img src="../../../images/h2o2.png"> | |
| 367 </center> | |
| 368 </body> | |
| 369 </html> |