Mercurial > repos > deepakjadmin > mayatool3_test3
view mayachemtools/docs/modules/html/code/MolecularFormula.html @ 9:ab29fa5c8c1f draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Thu, 15 Dec 2016 14:18:03 -0500 |
| parents | 73ae111cf86f |
| children |
line wrap: on
line source
<html> <head> <title>MayaChemTools:Code:MolecularFormula.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-MolecularFormula-"></a> 1 <span class="k">package </span><span class="i">MolecularFormula</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: MolecularFormula.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span> 5 <span class="c"># $Revision: 1.25 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">PeriodicTable</span><span class="sc">;</span> 34 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> 36 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> 38 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw(CalculateMolecularWeight CalculateExactMass CalculateElementalComposition FormatCompositionInfomation GetElementsAndCount IsMolecularFormula)</span><span class="sc">;</span> 40 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> 42 43 <span class="c">#</span> 44 <span class="c"># Calculate molecular weight assuming its a valid molecular formula...</span> 45 <span class="c">#</span> <a name="CalculateMolecularWeight-"></a> 46 <span class="k">sub </span><span class="m">CalculateMolecularWeight</span> <span class="s">{</span> 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> 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">$FormulaElementCountRef</span><span class="s">)</span><span class="sc">;</span> 49 50 <span class="s">(</span><span class="i">$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> 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> 52 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 53 <span class="s">}</span> 54 55 <span class="i">$MolecularWeight</span> = <span class="n">0</span><span class="sc">;</span> 56 57 <span class="k">for</span> <span class="i">$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> 58 <span class="i">$ElementSymbol</span> = <span class="i">$FormulaElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 59 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementCountRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 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> 61 <span class="i">$MolecularWeight</span> += <span class="i">$AtomicWeight</span> * <span class="i">$ElementCount</span><span class="sc">;</span> 62 <span class="s">}</span> 63 <span class="k">return</span> <span class="i">$MolecularWeight</span><span class="sc">;</span> 64 <span class="s">}</span> 65 66 <span class="c">#</span> 67 <span class="c"># Calculate exact mass assuming it's a valid formula...</span> 68 <span class="c">#</span> <a name="CalculateExactMass-"></a> 69 <span class="k">sub </span><span class="m">CalculateExactMass</span> <span class="s">{</span> 70 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 71 <span class="k">my</span><span class="s">(</span><span class="i">$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> 72 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">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span> 74 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$FormulaElementCountRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 75 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 76 <span class="s">}</span> 77 <span class="i">$ExactMass</span> = <span class="n">0</span><span class="sc">;</span> 78 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">$FormulaElementsRef</span>}<span class="s">)</span> <span class="s">{</span> 80 <span class="i">$ElementSymbol</span> = <span class="i">$FormulaElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 81 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementCountRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 82 <span class="i">$RelativeAtomicMass</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMass</span><span class="s">(</span><span class="i">$ElementSymbol</span><span class="s">)</span><span class="sc">;</span> 83 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$RelativeAtomicMass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 84 <span class="k">next</span> <span class="j">ELEMENT</span><span class="sc">;</span> 85 <span class="s">}</span> 86 <span class="i">$ExactMass</span> += <span class="i">$RelativeAtomicMass</span> * <span class="i">$ElementCount</span><span class="sc">;</span> 87 <span class="s">}</span> 88 <span class="k">return</span> <span class="i">$ExactMass</span><span class="sc">;</span> 89 <span class="s">}</span> 90 91 92 <span class="c">#</span> 93 <span class="c"># Calculate elemental composition and return reference to arrays</span> 94 <span class="c"># containing elements and their percent composition...</span> 95 <span class="c">#</span> <a name="CalculateElementalComposition-"></a> 96 <span class="k">sub </span><span class="m">CalculateElementalComposition</span> <span class="s">{</span> 97 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 98 <span class="k">my</span><span class="s">(</span><span class="i">$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> 99 100 <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> 101 <span class="k">if</span> <span class="s">(</span>! <span class="k">defined</span> <span class="i">$MolecularWeight</span><span class="s">)</span> <span class="s">{</span> 102 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> 103 <span class="s">}</span> 104 <span class="s">(</span><span class="i">$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> 105 106 <span class="i">@FormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 107 <span class="i">@FormulaElementComposition</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 108 109 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MolecularWeight</span><span class="s">)</span> <span class="s">{</span> 110 <span class="k">return</span> <span class="s">(</span> \<span class="i">@FormulaElements</span><span class="cm">,</span> \<span class="i">@FormulaElementComposition</span><span class="s">)</span><span class="sc">;</span> 111 <span class="s">}</span> 112 113 <span class="i">$CompositionMultiplier</span> = <span class="n">100</span> / <span class="i">$MolecularWeight</span><span class="sc">;</span> 114 115 <span class="k">for</span> <span class="i">$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> 116 <span class="i">$ElementSymbol</span> = <span class="i">$FormulaElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 117 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementCountRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 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> 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> 120 121 <span class="k">push</span> <span class="i">@FormulaElements</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="sc">;</span> 122 <span class="k">push</span> <span class="i">@FormulaElementComposition</span><span class="cm">,</span> <span class="i">$Composition</span><span class="sc">;</span> 123 <span class="s">}</span> 124 125 <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> 126 <span class="s">}</span> 127 128 <span class="c"># Using refernece to element and its composition arrays, format composition information</span> 129 <span class="c"># as: Element: Composition;...</span> 130 <span class="c">#</span> <a name="FormatCompositionInfomation-"></a> 131 <span class="k">sub </span><span class="m">FormatCompositionInfomation</span> <span class="s">{</span> 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">$Composition</span><span class="s">)</span><span class="sc">;</span> 133 134 <span class="i">$Precision</span> = <span class="n">2</span><span class="sc">;</span> 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> 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">$Precision</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 137 <span class="s">}</span> 138 <span class="k">else</span> <span class="s">{</span> 139 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 140 <span class="s">}</span> 141 142 <span class="i">$Composition</span> = <span class="q">''</span><span class="sc">;</span> 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">$ElementsRef</span>}<span class="s">)</span> <span class="s">{</span> 144 <span class="i">$ElementSymbol</span> = <span class="i">$ElementsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 145 <span class="i">$ElementComposition</span> = <span class="i">$ElementCompositionRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 146 <span class="i">$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> 147 148 <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> 149 <span class="i">$Composition</span> .= <span class="q">"${ElementSymbol}: ${ElementComposition}%"</span><span class="sc">;</span> 150 <span class="s">}</span> 151 152 <span class="k">return</span> <span class="i">$Composition</span><span class="sc">;</span> 153 <span class="s">}</span> 154 155 <span class="c">#</span> 156 <span class="c"># Get elements and their count...</span> 157 <span class="c">#</span> <a name="GetElementsAndCount-"></a> 158 <span class="k">sub </span><span class="m">GetElementsAndCount</span> <span class="s">{</span> 159 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 160 <span class="k">my</span><span class="s">(</span><span class="i">$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> 161 162 <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> 163 164 <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> 165 <span class="s">}</span> 166 167 <span class="c">#</span> 168 <span class="c"># Is it a valid molecular formula?</span> 169 <span class="c">#</span> <a name="IsMolecularFormula-"></a> 170 <span class="k">sub </span><span class="m">IsMolecularFormula</span> <span class="s">{</span> 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> 172 173 <span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 174 175 <span class="s">(</span><span class="i">$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">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span> 176 <span class="i">$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> 177 178 <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">$Status</span><span class="s">)</span><span class="sc">;</span> 179 <span class="s">}</span> 180 181 <span class="c">#</span> 182 <span class="c"># Process molecular formula. For a valid formula, return references to arrays conatining elements</span> 183 <span class="c"># and element count; otherwsie, return undef.</span> 184 <span class="c">#</span> <a name="_ProcessMolecularFormula-"></a> 185 <span class="k">sub </span><span class="m">_ProcessMolecularFormula</span> <span class="s">{</span> 186 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 187 <span class="k">my</span><span class="s">(</span><span class="i">$ErrorMsg</span><span class="s">)</span> = <span class="q">''</span><span class="sc">;</span> 188 189 <span class="i">$MolecularFormula</span> = <span class="i">_CleanUpFormula</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span> 190 191 <span class="c"># Make sure it only contains numbers and letters...</span> 192 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/[^a-zA-Z0-9\(\)\[\]]/</span><span class="s">)</span> <span class="s">{</span> 193 <span class="i">$ErrorMsg</span> = <span class="q">'Molecular formula contains characters other than a-zA-Z0-9'</span><span class="sc">;</span> 194 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span> 195 <span class="s">}</span> 196 197 <span class="c"># Parse the formula...</span> 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">$ElementCount</span><span class="cm">,</span> <span class="i">@FormulaElements</span><span class="cm">,</span> <span class="i">@ElementCount</span><span class="cm">,</span> <span class="i">%FormulaElementsToCountMap</span><span class="cm">,</span> <span class="i">@SubFormulaElements</span><span class="cm">,</span> <span class="i">%SubFormulaElementsToCountMap</span><span class="s">)</span><span class="sc">;</span> 199 200 <span class="i">@FormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@ElementCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 201 <span class="i">%FormulaElementsToCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 202 203 <span class="c"># Setup element symbol and count regular expression...</span> 204 <span class="c"># IUPAC: http://www.iupac.org/reports/provisional/abstract04/RB-prs310804/Chap4-3.04.pdf</span> 205 <span class="c">#</span> 206 207 <span class="i">$FormulaElementSpec</span> = <span class="q">qr/</span> 208 <span class="q"> \G( # $1</span> 209 <span class="q"> (?:</span> 210 <span class="q"> ([A-Z][a-z]?) # Two or one letter element symbol; $2</span> 211 <span class="q"> ([0-9]*) # Optionally followed by element count; $3</span> 212 <span class="q"> )</span> 213 <span class="q"> | \( | \[</span> 214 <span class="q"> | \)[0-9]* | \][0-9]*</span> 215 <span class="q"> | .</span> 216 <span class="q"> )</span> 217 <span class="q"> /x</span><span class="sc">;</span> 218 219 <span class="k">my</span><span class="s">(</span><span class="i">$ProcessingParenthesis</span><span class="s">)</span><span class="sc">;</span> 220 <span class="i">$ProcessingParenthesis</span> = <span class="n">0</span><span class="sc">;</span> 221 <span class="c"># Go over the formula...</span> 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> 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">$3</span><span class="s">)</span><span class="sc">;</span> 224 225 <span class="c"># Handle parenthesis in formula to indicate repeating units...</span> 226 <span class="k">if</span> <span class="s">(</span><span class="i">$Spec</span> =~ <span class="q">/^(\(|\[)/</span><span class="s">)</span> <span class="s">{</span> 227 <span class="k">if</span> <span class="s">(</span><span class="i">$ProcessingParenthesis</span><span class="s">)</span> <span class="s">{</span> 228 <span class="i">$ErrorMsg</span> = <span class="q">"Molecular formula contains multiple level of () or []"</span><span class="sc">;</span> 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">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span> 230 <span class="s">}</span> 231 <span class="i">$ProcessingParenthesis</span> = <span class="n">1</span><span class="sc">;</span> 232 <span class="i">@SubFormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 233 <span class="i">%SubFormulaElementsToCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 234 <span class="k">next</span> <span class="j">FORMULA</span><span class="sc">;</span> 235 <span class="s">}</span> 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> 237 <span class="i">$ProcessingParenthesis</span> = <span class="n">0</span><span class="sc">;</span> 238 239 <span class="c"># Retrieve repeat count and move data to @FormulaElements and %FormulaElementsToCountMap;</span> 240 <span class="k">my</span><span class="s">(</span><span class="i">$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> 241 <span class="i">$RepeatCount</span> = <span class="i">$Spec</span><span class="sc">;</span> 242 <span class="i">$RepeatCount</span> =~ <span class="q">s/(\)|\])//g</span><span class="sc">;</span> 243 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RepeatCount</span><span class="s">)</span> <span class="s">{</span> 244 <span class="i">$RepeatCount</span> = <span class="n">1</span><span class="sc">;</span> 245 <span class="s">}</span> 246 <span class="c"># Copy data...</span> 247 <span class="k">for</span> <span class="i">$Symbol</span> <span class="s">(</span><span class="i">@SubFormulaElements</span><span class="s">)</span> <span class="s">{</span> 248 <span class="i">$Count</span> = <span class="i">$SubFormulaElementsToCountMap</span>{<span class="i">$Symbol</span>} * <span class="i">$RepeatCount</span><span class="sc">;</span> 249 <span class="i">_SetupFormulaElementData</span><span class="s">(</span>\<span class="i">@FormulaElements</span><span class="cm">,</span> \<span class="i">%FormulaElementsToCountMap</span><span class="cm">,</span> <span class="i">$Symbol</span><span class="cm">,</span> <span class="i">$Count</span><span class="s">)</span><span class="sc">;</span> 250 <span class="s">}</span> 251 252 <span class="c"># Get ready again...</span> 253 <span class="i">@SubFormulaElements</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 254 <span class="i">%SubFormulaElementsToCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 255 256 <span class="k">next</span> <span class="j">FORMULA</span><span class="sc">;</span> 257 <span class="s">}</span> 258 259 <span class="c"># Retrieve element symbol and count...</span> 260 <span class="i">$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">$ElementSymbol</span> <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> 261 <span class="i">$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> 262 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElement</span><span class="s">(</span><span class="i">$ElementSymbol</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 263 <span class="i">$ErrorMsg</span> = <span class="q">"Molecular formula contains unknown elemental symbol $ElementSymbol"</span><span class="sc">;</span> 264 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span> 265 <span class="s">}</span> 266 267 <span class="k">if</span> <span class="s">(</span><span class="i">$ProcessingParenthesis</span><span class="s">)</span> <span class="s">{</span> 268 <span class="i">_SetupFormulaElementData</span><span class="s">(</span>\<span class="i">@SubFormulaElements</span><span class="cm">,</span> \<span class="i">%SubFormulaElementsToCountMap</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="s">)</span><span class="sc">;</span> 269 <span class="s">}</span> 270 <span class="k">else</span> <span class="s">{</span> 271 <span class="i">_SetupFormulaElementData</span><span class="s">(</span>\<span class="i">@FormulaElements</span><span class="cm">,</span> \<span class="i">%FormulaElementsToCountMap</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="s">)</span><span class="sc">;</span> 272 <span class="s">}</span> 273 <span class="s">}</span> 274 275 <span class="c"># Setup element count array...</span> 276 <span class="k">for</span> <span class="i">$ElementSymbol</span> <span class="s">(</span><span class="i">@FormulaElements</span><span class="s">)</span> <span class="s">{</span> 277 <span class="i">$ElementCount</span> = <span class="i">$FormulaElementsToCountMap</span>{<span class="i">$ElementSymbol</span>}<span class="sc">;</span> 278 <span class="k">push</span> <span class="i">@ElementCount</span><span class="cm">,</span> <span class="i">$ElementCount</span><span class="sc">;</span> 279 <span class="s">}</span> 280 281 <span class="c"># Make sure it all adds up to 100%; otherwise, adjust the last value..</span> 282 283 <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">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span> 284 <span class="s">}</span> 285 286 <span class="c"># Clean it up...</span> <a name="_CleanUpFormula-"></a> 287 <span class="k">sub </span><span class="m">_CleanUpFormula</span> <span class="s">{</span> 288 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 289 <span class="c">#Take out any spaces...</span> 290 <span class="i">$MolecularFormula</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 291 292 <span class="c"># Eliminate any charge specifications: +, - or [1-9]+[+-]</span> 293 <span class="c"># e.g NO+ [Al(H2O)6]3+ [H2NO3]+</span> 294 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/[\+\-]/</span><span class="s">)</span> <span class="s">{</span> 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> 296 <span class="c"># Bracket followed optionally by number and then, +/- ...</span> 297 <span class="c"># [Al(H2O)6]3+ ...</span> 298 <span class="i">$MolecularFormula</span> =~ <span class="q">s/\][0-9]+[\+\-]/\]/g</span><span class="sc">;</span> 299 <span class="s">}</span> 300 <span class="k">elsif</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/[\+\-][0-9]*/</span><span class="s">)</span> <span class="s">{</span> 301 <span class="c"># +/- followed optionally by a number...</span> 302 <span class="c"># C37H42N2O6+2, Cu+</span> 303 <span class="i">$MolecularFormula</span> =~ <span class="q">s/[\+\-][0-9]*//g</span><span class="sc">;</span> 304 <span class="s">}</span> 305 <span class="s">}</span> 306 307 <span class="c"># Eliminate any brackets - ] or ) - not followed by numbers:</span> 308 <span class="c"># e.g. Li[H2PO4]</span> 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> 310 <span class="i">$MolecularFormula</span> =~ <span class="q">s/[\[\]]//g</span><span class="sc">;</span> 311 <span class="s">}</span> 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> 313 <span class="i">$MolecularFormula</span> =~ <span class="q">s/[\(\)]//g</span><span class="sc">;</span> 314 <span class="s">}</span> 315 <span class="c"># Change adducts to parenthesis format...</span> 316 <span class="c"># Na2CO3.10H2O -> Na2CO3(H2O)10</span> 317 <span class="c"># 3CdSO4.8H2O -> (CdSO4)3(H2O)8</span> 318 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularFormula</span> =~ <span class="q">/\./</span><span class="s">)</span> <span class="s">{</span> 319 <span class="k">my</span><span class="s">(</span><span class="i">$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> 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">$MolecularFormula</span><span class="sc">;</span> 321 <span class="i">$MolecularFormula</span> = <span class="q">''</span><span class="sc">;</span> 322 <span class="k">for</span> <span class="i">$SubFormula</span> <span class="s">(</span><span class="i">@MolecularFormulaSplits</span><span class="s">)</span> <span class="s">{</span> 323 <span class="s">(</span><span class="i">$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]*)(.*?)$/</span><span class="sc">;</span> 324 <span class="k">if</span> <span class="s">(</span><span class="i">$Count</span><span class="s">)</span> <span class="s">{</span> 325 <span class="i">$MolecularFormula</span> .= <span class="q">"(${Spec})${Count}"</span><span class="sc">;</span> 326 <span class="s">}</span> 327 <span class="k">else</span> <span class="s">{</span> 328 <span class="i">$MolecularFormula</span> .= <span class="i">$Spec</span><span class="sc">;</span> 329 <span class="s">}</span> 330 <span class="s">}</span> 331 <span class="s">}</span> 332 333 <span class="k">return</span> <span class="i">$MolecularFormula</span><span class="sc">;</span> 334 <span class="s">}</span> 335 336 <span class="c"># Store the element and count...</span> <a name="_SetupFormulaElementData-"></a> 337 <span class="k">sub </span><span class="m">_SetupFormulaElementData</span> <span class="s">{</span> 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> 339 340 <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> 341 <span class="i">$ElementsToCountMapRef</span>->{<span class="i">$Element</span>} += <span class="i">$Count</span><span class="sc">;</span> 342 <span class="s">}</span> 343 <span class="k">else</span> <span class="s">{</span> 344 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ElementsRef</span>}<span class="cm">,</span> <span class="i">$Element</span><span class="sc">;</span> 345 <span class="i">$ElementsToCountMapRef</span>->{<span class="i">$Element</span>} = <span class="i">$Count</span><span class="sc">;</span> 346 <span class="s">}</span> 347 <span class="s">}</span> 348 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>