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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/modules/html/code/MolecularFormula.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,369 @@ +<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>