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comparison mayachemtools/docs/modules/html/code/Atom.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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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:Atom.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-Atom-"></a> 1 <span class="k">package </span><span class="i">Atom</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: Atom.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span> | |
| 18 5 <span class="c"># $Revision: 1.62 $</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">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">Storable</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">PeriodicTable</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">Vector</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">MathUtil</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> | |
| 52 39 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> | |
| 53 40 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> | |
| 54 41 | |
| 55 42 <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> | |
| 56 43 | |
| 57 44 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> | |
| 58 45 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 59 46 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 60 47 | |
| 61 48 <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> | |
| 62 49 | |
| 63 50 <span class="c"># Setup class variables...</span> | |
| 64 51 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="cm">,</span> <span class="i">%MDLValenceModelDataMap</span><span class="cm">,</span> <span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 65 52 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 66 53 | |
| 67 54 <span class="c"># Overload Perl functions...</span> | |
| 68 55 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyAtom'</span><span class="sc">;</span> | |
| 69 56 | |
| 70 57 <span class="c"># Class constructor...</span> | |
| 71 <a name="new-"></a> 58 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 72 59 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 73 60 | |
| 74 61 <span class="c"># Initialize object...</span> | |
| 75 62 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> | |
| 76 63 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> | |
| 77 64 <span class="i">$This</span><span class="i">->_InitializeAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 78 65 | |
| 79 66 <span class="i">$This</span><span class="i">->_InitializeAtomProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 80 67 | |
| 81 68 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 82 69 <span class="s">}</span> | |
| 83 70 | |
| 84 71 <span class="c"># Initialize object data...</span> | |
| 85 <a name="_InitializeAtom-"></a> 72 <span class="k">sub </span><span class="m">_InitializeAtom</span> <span class="s">{</span> | |
| 86 73 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 87 74 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 88 75 | |
| 89 76 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> | |
| 90 77 <span class="c"># are implemented on-demand using ObjectProperty class.</span> | |
| 91 78 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span> | |
| 92 79 <span class="i">$This</span>->{<span class="w">Name</span>} = <span class="q">"Atom ${ObjectID}"</span><span class="sc">;</span> | |
| 93 80 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 94 81 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 95 82 <span class="i">$This</span>->{<span class="w">XYZ</span>} = <span class="w">Vector::ZeroVector</span><span class="sc">;</span> | |
| 96 83 <span class="s">}</span> | |
| 97 84 | |
| 98 85 <span class="c"># Initialize atom properties...</span> | |
| 99 <a name="_InitializeAtomProperties-"></a> 86 <span class="k">sub </span><span class="m">_InitializeAtomProperties</span> <span class="s">{</span> | |
| 100 87 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 101 88 | |
| 102 89 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 103 90 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 104 91 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 105 92 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 106 93 <span class="s">}</span> | |
| 107 94 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'AtomSymbol'</span>}<span class="s">)</span> <span class="s">{</span> | |
| 108 95 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Atom object instantiated without setting atom symbol..."</span><span class="sc">;</span> | |
| 109 96 <span class="s">}</span> | |
| 110 97 | |
| 111 98 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 112 99 <span class="s">}</span> | |
| 113 100 | |
| 114 101 <span class="c"># Initialize class ...</span> | |
| 115 <a name="_InitializeClass-"></a> 102 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 116 103 <span class="c">#Class name...</span> | |
| 117 104 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 118 105 | |
| 119 106 <span class="c"># ID to keep track of objects...</span> | |
| 120 107 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span> | |
| 121 108 | |
| 122 109 <span class="c"># Load atom class data...</span> | |
| 123 110 <span class="i">_LoadAtomClassData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 124 111 <span class="s">}</span> | |
| 125 112 | |
| 126 113 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span> | |
| 127 <a name="SetID-"></a> 114 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span> | |
| 128 115 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 129 116 | |
| 130 117 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> | |
| 131 118 | |
| 132 119 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 133 120 <span class="s">}</span> | |
| 134 121 | |
| 135 122 <span class="c"># Setup an explicit SetMolecule method to block setting of ID by AUTOLOAD function...</span> | |
| 136 <a name="SetMolecule-"></a> 123 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> | |
| 137 124 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 138 125 | |
| 139 126 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMolecule: Molecule property can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> | |
| 140 127 | |
| 141 128 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 142 129 <span class="s">}</span> | |
| 143 130 | |
| 144 131 <span class="c"># Assign atom to molecule...</span> | |
| 145 <a name="_SetMolecule-"></a> 132 <span class="k">sub </span><span class="m">_SetMolecule</span> <span class="s">{</span> | |
| 146 133 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 147 134 | |
| 148 135 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> | |
| 149 136 | |
| 150 137 <span class="c"># Weaken the reference to disable increment of reference count; otherwise,</span> | |
| 151 138 <span class="c"># it it becomes a circular reference and destruction of Molecule object doesn't</span> | |
| 152 139 <span class="c"># get initiated which in turn disables destruction of atom object.</span> | |
| 153 140 <span class="c">#</span> | |
| 154 141 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
| 155 142 | |
| 156 143 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 157 144 <span class="s">}</span> | |
| 158 145 | |
| 159 146 <span class="c"># Setup atom symbol and atomic number for the element...</span> | |
| 160 147 <span class="c">#</span> | |
| 161 148 <span class="c"># Possible atom symbol values:</span> | |
| 162 149 <span class="c"># . An element symbol or some other type of atom: L - Atom list; LP - Lone pair; R# - R group;</span> | |
| 163 150 <span class="c"># A, Q, * - unknown atom; or something else?</span> | |
| 164 151 <span class="c">#</span> | |
| 165 152 <span class="c"># Default mass number corresponds to the most abundant natural isotope unless it's explicity</span> | |
| 166 153 <span class="c"># set using "MassNumber" property.</span> | |
| 167 154 <span class="c">#</span> | |
| 168 <a name="SetAtomSymbol-"></a> 155 <span class="k">sub </span><span class="m">SetAtomSymbol</span> <span class="s">{</span> | |
| 169 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 170 157 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 171 158 | |
| 172 159 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="i">$AtomSymbol</span><span class="sc">;</span> | |
| 173 160 | |
| 174 161 <span class="i">$AtomicNumber</span> = <span class="i">PeriodicTable::GetElementAtomicNumber</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span> | |
| 175 162 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicNumber</span><span class="s">)</span> ? <span class="i">$AtomicNumber</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 176 163 | |
| 177 164 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 178 165 <span class="s">}</span> | |
| 179 166 | |
| 180 167 <span class="c"># Setup atom symbol and atomic number for the element...</span> | |
| 181 <a name="SetAtomicNumber-"></a> 168 <span class="k">sub </span><span class="m">SetAtomicNumber</span> <span class="s">{</span> | |
| 182 169 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 183 170 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span> | |
| 184 171 | |
| 185 172 <span class="i">$AtomSymbol</span> = <span class="i">PeriodicTable::GetElementAtomSymbol</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 186 173 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$AtomSymbol</span><span class="s">)</span> <span class="s">{</span> | |
| 187 174 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicNumber: Didn't set atomic number: Invalid atomic number, $AtomicNumber, specified..."</span><span class="sc">;</span> | |
| 188 175 <span class="k">return</span><span class="sc">;</span> | |
| 189 176 <span class="s">}</span> | |
| 190 177 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="i">$AtomicNumber</span><span class="sc">;</span> | |
| 191 178 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="i">$AtomSymbol</span><span class="sc">;</span> | |
| 192 179 | |
| 193 180 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 194 181 <span class="s">}</span> | |
| 195 182 | |
| 196 183 <span class="c"># Set atom as stereo center...</span> | |
| 197 184 <span class="c">#</span> | |
| 198 <a name="SetStereoCenter-"></a> 185 <span class="k">sub </span><span class="m">SetStereoCenter</span> <span class="s">{</span> | |
| 199 186 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StereoCenter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 200 187 | |
| 201 188 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="cm">,</span> <span class="i">$StereoCenter</span><span class="s">)</span><span class="sc">;</span> | |
| 202 189 | |
| 203 190 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 204 191 <span class="s">}</span> | |
| 205 192 | |
| 206 193 <span class="c"># Is it a stereo center?</span> | |
| 207 194 <span class="c">#</span> | |
| 208 <a name="IsStereoCenter-"></a> 195 <span class="k">sub </span><span class="m">IsStereoCenter</span> <span class="s">{</span> | |
| 209 196 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 210 197 <span class="k">my</span><span class="s">(</span><span class="i">$StereoCenter</span><span class="s">)</span><span class="sc">;</span> | |
| 211 198 | |
| 212 199 <span class="i">$StereoCenter</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="s">)</span><span class="sc">;</span> | |
| 213 200 | |
| 214 201 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StereoCenter</span><span class="s">)</span> && <span class="i">$StereoCenter</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 215 202 <span class="s">}</span> | |
| 216 203 | |
| 217 204 <span class="c"># Set atom stereochemistry.</span> | |
| 218 205 <span class="c">#</span> | |
| 219 206 <span class="c"># Supported values are: R, S.</span> | |
| 220 207 <span class="c">#</span> | |
| 221 208 <span class="c"># Notes:</span> | |
| 222 209 <span class="c">#</span> | |
| 223 210 <span class="c"># . After the ligands around a central stereocenter has been ranked using CIP priority scheme and</span> | |
| 224 211 <span class="c"># the lowest ranked ligand lies behind the center atom, then R and S values correspond to:</span> | |
| 225 212 <span class="c">#</span> | |
| 226 213 <span class="c"># R: Clockwise arrangement of remaining ligands around the central atom going from highest to lowest ranked ligand</span> | |
| 227 214 <span class="c"># S: CounterClockwise arrangement of remaining ligands around the central atom going from highest to lowest ranked ligand</span> | |
| 228 215 <span class="c">#</span> | |
| 229 216 <span class="c"># . Assignment of any other arbitray values besides R and S is also allowed; however, a warning is printed.</span> | |
| 230 217 <span class="c">#</span> | |
| 231 <a name="SetStereochemistry-"></a> 218 <span class="k">sub </span><span class="m">SetStereochemistry</span> <span class="s">{</span> | |
| 232 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 233 220 | |
| 234 221 <span class="k">if</span> <span class="s">(</span><span class="i">$Stereochemistry</span> !~ <span class="q">/^(R|S)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 235 222 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetStereochemistry: Assigning non-supported Stereochemistry value of $Stereochemistry. Supported values: R, S..."</span><span class="sc">;</span> | |
| 236 223 <span class="s">}</span> | |
| 237 224 | |
| 238 225 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 239 226 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'Stereochemistry'</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="s">)</span><span class="sc">;</span> | |
| 240 227 | |
| 241 228 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 242 229 <span class="s">}</span> | |
| 243 230 | |
| 244 231 <span class="c"># Setup mass number for atom...</span> | |
| 245 <a name="SetMassNumber-"></a> 232 <span class="k">sub </span><span class="m">SetMassNumber</span> <span class="s">{</span> | |
| 246 233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 247 234 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span> | |
| 248 235 | |
| 249 236 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 250 237 <span class="i">$AtomSymbol</span> = <span class="i">$This</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span> | |
| 251 238 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 252 239 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMassNumber: Didn't set mass number: Non standard atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol..."</span><span class="sc">;</span> | |
| 253 240 <span class="k">return</span><span class="sc">;</span> | |
| 254 241 <span class="s">}</span> | |
| 255 242 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 256 243 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMassNumber: Unknown mass number, $MassNumber, specified for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope..."</span><span class="sc">;</span> | |
| 257 244 <span class="s">}</span> | |
| 258 245 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 259 246 | |
| 260 247 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 261 248 <span class="s">}</span> | |
| 262 249 | |
| 263 250 <span class="c"># Get mass number...</span> | |
| 264 251 <span class="c">#</span> | |
| 265 <a name="GetMassNumber-"></a> 252 <span class="k">sub </span><span class="m">GetMassNumber</span> <span class="s">{</span> | |
| 266 253 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 267 254 | |
| 268 255 <span class="c"># Is mass number explicity set?</span> | |
| 269 256 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 270 257 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span> | |
| 271 258 <span class="s">}</span> | |
| 272 259 | |
| 273 260 <span class="c"># Is it an element symbol?</span> | |
| 274 261 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 275 262 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 276 263 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 277 264 <span class="s">}</span> | |
| 278 265 | |
| 279 266 <span class="c"># Return most abundant mass number...</span> | |
| 280 267 <span class="k">return</span> <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 281 268 <span class="s">}</span> | |
| 282 269 | |
| 283 270 <span class="c"># Get atomic weight:</span> | |
| 284 271 <span class="c"># . Explicitly set by the caller</span> | |
| 285 272 <span class="c"># . Using atomic number</span> | |
| 286 273 <span class="c">#</span> | |
| 287 <a name="GetAtomicWeight-"></a> 274 <span class="k">sub </span><span class="m">GetAtomicWeight</span> <span class="s">{</span> | |
| 288 275 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 289 276 | |
| 290 277 <span class="c"># Is atomic weight explicity set?</span> | |
| 291 278 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AtomicWeight'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 292 279 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'AtomicWeight'</span><span class="s">)</span><span class="sc">;</span> | |
| 293 280 <span class="s">}</span> | |
| 294 281 | |
| 295 282 <span class="c"># Is it an element symbol?</span> | |
| 296 283 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 297 284 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 298 285 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 299 286 <span class="s">}</span> | |
| 300 287 | |
| 301 288 <span class="c"># Return its atomic weight...</span> | |
| 302 289 <span class="k">return</span> <span class="i">PeriodicTable::GetElementAtomicWeight</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 303 290 <span class="s">}</span> | |
| 304 291 | |
| 305 292 <span class="c"># Get exact mass weight:</span> | |
| 306 293 <span class="c"># . Explicitly set by the caller</span> | |
| 307 294 <span class="c"># . Using atomic number and mass number explicity set by the caller</span> | |
| 308 295 <span class="c"># . Using atomic number and most abundant isotope</span> | |
| 309 296 <span class="c">#</span> | |
| 310 <a name="GetExactMass-"></a> 297 <span class="k">sub </span><span class="m">GetExactMass</span> <span class="s">{</span> | |
| 311 298 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 312 299 | |
| 313 300 <span class="c"># Is exact mass explicity set?</span> | |
| 314 301 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ExactMass'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 315 302 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ExactMass'</span><span class="s">)</span><span class="sc">;</span> | |
| 316 303 <span class="s">}</span> | |
| 317 304 | |
| 318 305 <span class="c"># Is it an element symbol?</span> | |
| 319 306 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 320 307 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 321 308 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 322 309 <span class="s">}</span> | |
| 323 310 | |
| 324 311 <span class="c"># Is mass number explicitly set?</span> | |
| 325 312 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 326 313 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span> | |
| 327 314 <span class="k">if</span> <span class="s">(</span><span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 328 315 <span class="k">return</span> <span class="i">PeriodicTable::GetElementNaturalIsotopeMass</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 329 316 <span class="s">}</span> | |
| 330 317 <span class="s">}</span> | |
| 331 318 | |
| 332 319 <span class="c"># Return most abundant isotope mass...</span> | |
| 333 320 <span class="k">return</span> <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMass</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 334 321 <span class="s">}</span> | |
| 335 322 | |
| 336 323 <span class="c"># Get formal charge:</span> | |
| 337 324 <span class="c"># . Explicitly set by the caller</span> | |
| 338 325 <span class="c"># . Or return zero insetad of undef</span> | |
| 339 326 <span class="c">#</span> | |
| 340 <a name="GetFormalCharge-"></a> 327 <span class="k">sub </span><span class="m">GetFormalCharge</span> <span class="s">{</span> | |
| 341 328 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 342 329 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> | |
| 343 330 | |
| 344 331 <span class="i">$FormalCharge</span> = <span class="n">0</span><span class="sc">;</span> | |
| 345 332 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 346 333 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="sc">;</span> | |
| 347 334 <span class="s">}</span> | |
| 348 335 | |
| 349 336 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> ? <span class="i">$FormalCharge</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 350 337 <span class="s">}</span> | |
| 351 338 | |
| 352 339 <span class="c"># Get spin multiplicity:</span> | |
| 353 340 <span class="c"># . Explicitly set by the caller</span> | |
| 354 341 <span class="c"># . From FreeRadicalElectrons value explicitly set by the caller</span> | |
| 355 342 <span class="c"># . Or return zero insetad of undef</span> | |
| 356 343 <span class="c">#</span> | |
| 357 <a name="GetSpinMultiplicity-"></a> 344 <span class="k">sub </span><span class="m">GetSpinMultiplicity</span> <span class="s">{</span> | |
| 358 345 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 359 346 <span class="k">my</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span> | |
| 360 347 | |
| 361 348 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> | |
| 362 349 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 363 350 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span> | |
| 364 351 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span> ? <span class="i">$SpinMultiplicity</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 365 352 <span class="s">}</span> | |
| 366 353 | |
| 367 354 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 368 355 <span class="k">my</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span><span class="sc">;</span> | |
| 369 356 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="sc">;</span> | |
| 370 357 | |
| 371 358 <span class="j">SPINMULTIPLICITY:</span> <span class="s">{</span> | |
| 372 359 <span class="k">if</span> <span class="s">(</span><span class="i">$FreeRadicalElectrons</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span> | |
| 373 360 <span class="k">if</span> <span class="s">(</span><span class="i">$FreeRadicalElectrons</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span> | |
| 374 361 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetSpinMultiplicity: It's not possible to determine spin multiplicity from the specified free radical electrons value, $FreeRadicalElectrons. It has been set to 0..."</span><span class="sc">;</span> | |
| 375 362 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> | |
| 376 363 <span class="s">}</span> | |
| 377 364 <span class="s">}</span> | |
| 378 365 | |
| 379 366 <span class="k">return</span> <span class="i">$SpinMultiplicity</span><span class="sc">;</span> | |
| 380 367 <span class="s">}</span> | |
| 381 368 | |
| 382 369 <span class="c"># Get number of free radical electrons:</span> | |
| 383 370 <span class="c"># . Explicitly set by the caller</span> | |
| 384 371 <span class="c"># . From SpinMultiplicity value explicitly set by the caller</span> | |
| 385 372 <span class="c"># . Or return zero insetad of undef</span> | |
| 386 373 <span class="c">#</span> | |
| 387 374 <span class="c"># Notes:</span> | |
| 388 375 <span class="c"># . For atoms with explicit assignment of SpinMultiplicity property values corresponding to</span> | |
| 389 376 <span class="c"># Singlet (two unpaired electrons corresponding to one spin state), Doublet (free radical; an unpaired</span> | |
| 390 377 <span class="c"># electron corresponding to two spin states), and Triplet (two unparied electrons corresponding to</span> | |
| 391 378 <span class="c"># three spin states; divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</span> | |
| 392 379 <span class="c">#</span> | |
| 393 380 <span class="c"># SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1</span> | |
| 394 381 <span class="c"># SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2</span> | |
| 395 382 <span class="c">#</span> | |
| 396 <a name="GetFreeRadicalElectrons-"></a> 383 <span class="k">sub </span><span class="m">GetFreeRadicalElectrons</span> <span class="s">{</span> | |
| 397 384 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 398 385 <span class="k">my</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span><span class="sc">;</span> | |
| 399 386 | |
| 400 387 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span> | |
| 401 388 | |
| 402 389 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 403 390 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="sc">;</span> | |
| 404 391 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span> ? <span class="i">$FreeRadicalElectrons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 405 392 <span class="s">}</span> | |
| 406 393 | |
| 407 394 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 408 395 <span class="k">my</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span> | |
| 409 396 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span> | |
| 410 397 | |
| 411 398 <span class="j">SPINMULTIPLICITY:</span> <span class="s">{</span> | |
| 412 399 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span> | |
| 413 400 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span> | |
| 414 401 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span> | |
| 415 402 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetFreeRadicalElectrons: It's not possible to determine free radical electrons from the specified spin multiplicity value, $FreeRadicalElectrons. It has been set to 0..."</span><span class="sc">;</span> | |
| 416 403 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span> | |
| 417 404 <span class="s">}</span> | |
| 418 405 <span class="s">}</span> | |
| 419 406 | |
| 420 407 <span class="k">return</span> <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span> | |
| 421 408 <span class="s">}</span> | |
| 422 409 | |
| 423 410 <span class="c"># Set atom coordinates using:</span> | |
| 424 411 <span class="c"># . An array reference with three values</span> | |
| 425 412 <span class="c"># . An array containg three values</span> | |
| 426 413 <span class="c"># . A 3D vector</span> | |
| 427 414 <span class="c">#</span> | |
| 428 <a name="SetXYZ-"></a> 415 <span class="k">sub </span><span class="m">SetXYZ</span> <span class="s">{</span> | |
| 429 416 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 430 417 | |
| 431 418 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 432 419 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetXYZ: No values specified..."</span><span class="sc">;</span> | |
| 433 420 <span class="k">return</span><span class="sc">;</span> | |
| 434 421 <span class="s">}</span> | |
| 435 422 | |
| 436 423 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetXYZ</span><span class="s">(</span><span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> | |
| 437 424 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 438 425 <span class="s">}</span> | |
| 439 426 | |
| 440 427 <span class="c"># Set X value...</span> | |
| 441 <a name="SetX-"></a> 428 <span class="k">sub </span><span class="m">SetX</span> <span class="s">{</span> | |
| 442 429 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 443 430 | |
| 444 431 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span> | |
| 445 432 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetX: Undefined X value..."</span><span class="sc">;</span> | |
| 446 433 <span class="k">return</span><span class="sc">;</span> | |
| 447 434 <span class="s">}</span> | |
| 448 435 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetX</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 449 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 450 437 <span class="s">}</span> | |
| 451 438 | |
| 452 439 <span class="c"># Set Y value...</span> | |
| 453 <a name="SetY-"></a> 440 <span class="k">sub </span><span class="m">SetY</span> <span class="s">{</span> | |
| 454 441 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 455 442 | |
| 456 443 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span> | |
| 457 444 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetY: Undefined Y value..."</span><span class="sc">;</span> | |
| 458 445 <span class="k">return</span><span class="sc">;</span> | |
| 459 446 <span class="s">}</span> | |
| 460 447 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetY</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 461 448 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 462 449 <span class="s">}</span> | |
| 463 450 | |
| 464 451 <span class="c"># Set Z value...</span> | |
| 465 <a name="SetZ-"></a> 452 <span class="k">sub </span><span class="m">SetZ</span> <span class="s">{</span> | |
| 466 453 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 467 454 | |
| 468 455 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span> | |
| 469 456 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetZ: Undefined Z value..."</span><span class="sc">;</span> | |
| 470 457 <span class="k">return</span><span class="sc">;</span> | |
| 471 458 <span class="s">}</span> | |
| 472 459 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetZ</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 473 460 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 474 461 <span class="s">}</span> | |
| 475 462 | |
| 476 463 <span class="c"># Return XYZ as:</span> | |
| 477 464 <span class="c"># . Reference to an array</span> | |
| 478 465 <span class="c"># . An array</span> | |
| 479 466 <span class="c">#</span> | |
| 480 <a name="GetXYZ-"></a> 467 <span class="k">sub </span><span class="m">GetXYZ</span> <span class="s">{</span> | |
| 481 468 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 482 469 | |
| 483 470 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetXYZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 484 471 <span class="s">}</span> | |
| 485 472 | |
| 486 473 <span class="c"># Return XYZ as a vector object...</span> | |
| 487 474 <span class="c">#</span> | |
| 488 <a name="GetXYZVector-"></a> 475 <span class="k">sub </span><span class="m">GetXYZVector</span> <span class="s">{</span> | |
| 489 476 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 490 477 | |
| 491 478 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="sc">;</span> | |
| 492 479 <span class="s">}</span> | |
| 493 480 | |
| 494 481 <span class="c"># Get X value...</span> | |
| 495 <a name="GetX-"></a> 482 <span class="k">sub </span><span class="m">GetX</span> <span class="s">{</span> | |
| 496 483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 497 484 | |
| 498 485 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetX</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 499 486 <span class="s">}</span> | |
| 500 487 | |
| 501 488 <span class="c"># Get Y value...</span> | |
| 502 <a name="GetY-"></a> 489 <span class="k">sub </span><span class="m">GetY</span> <span class="s">{</span> | |
| 503 490 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 504 491 | |
| 505 492 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetY</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 506 493 <span class="s">}</span> | |
| 507 494 | |
| 508 495 <span class="c"># Get Z value...</span> | |
| 509 <a name="GetZ-"></a> 496 <span class="k">sub </span><span class="m">GetZ</span> <span class="s">{</span> | |
| 510 497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 511 498 | |
| 512 499 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 513 500 <span class="s">}</span> | |
| 514 501 | |
| 515 502 <span class="c"># Delete atom...</span> | |
| 516 <a name="DeleteAtom-"></a> 503 <span class="k">sub </span><span class="m">DeleteAtom</span> <span class="s">{</span> | |
| 517 504 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 518 505 | |
| 519 506 <span class="c"># Is this atom in a molecule?</span> | |
| 520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 521 508 <span class="c"># Nothing to do...</span> | |
| 522 509 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 523 510 <span class="s">}</span> | |
| 524 511 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 525 512 | |
| 526 513 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 527 514 <span class="s">}</span> | |
| 528 515 | |
| 529 516 <span class="c"># Get atom neighbor objects as array. In scalar conetxt, return number of neighbors...</span> | |
| 530 <a name="GetNeighbors-"></a> 517 <span class="k">sub </span><span class="m">GetNeighbors</span> <span class="s">{</span> | |
| 531 518 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 532 519 | |
| 533 520 <span class="c"># Is this atom in a molecule?</span> | |
| 534 521 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 535 522 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 536 523 <span class="s">}</span> | |
| 537 524 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 538 525 | |
| 539 526 <span class="k">if</span> <span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span> | |
| 540 527 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 541 528 <span class="s">}</span> | |
| 542 529 <span class="k">else</span> <span class="s">{</span> | |
| 543 530 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 544 531 <span class="s">}</span> | |
| 545 532 <span class="s">}</span> | |
| 546 533 | |
| 547 534 <span class="c"># Get atom neighbor objects as array. In scalar conetxt, return number of neighbors...</span> | |
| 548 <a name="_GetAtomNeighbors-"></a> 535 <span class="k">sub </span><span class="m">_GetAtomNeighbors</span> <span class="s">{</span> | |
| 549 536 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 550 537 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 551 538 | |
| 552 539 <span class="k">if</span> <span class="s">(</span>!<span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span> | |
| 553 540 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 554 541 <span class="s">}</span> | |
| 555 542 | |
| 556 543 <span class="c"># Setup a map for neigbhors to exclude...</span> | |
| 557 544 <span class="k">my</span><span class="s">(</span><span class="i">$ExcludeNeighbor</span><span class="cm">,</span> <span class="i">$ExcludeNeighborID</span><span class="cm">,</span> <span class="i">%ExcludeNeighborsIDsMap</span><span class="s">)</span><span class="sc">;</span> | |
| 558 545 | |
| 559 546 <span class="i">%ExcludeNeighborsIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 560 547 <span class="k">for</span> <span class="i">$ExcludeNeighbor</span> <span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span> | |
| 561 548 <span class="i">$ExcludeNeighborID</span> = <span class="i">$ExcludeNeighbor</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 562 549 <span class="i">$ExcludeNeighborsIDsMap</span>{<span class="i">$ExcludeNeighborID</span>} = <span class="i">$ExcludeNeighborID</span><span class="sc">;</span> | |
| 563 550 <span class="s">}</span> | |
| 564 551 | |
| 565 552 <span class="c"># Generate a filtered neighbors list...</span> | |
| 566 553 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">$NeighborID</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 567 554 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 568 555 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 569 556 <span class="i">$NeighborID</span> = <span class="i">$Neighbor</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 570 557 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ExcludeNeighborsIDsMap</span>{<span class="i">$NeighborID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 571 558 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> | |
| 572 559 <span class="s">}</span> | |
| 573 560 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="sc">;</span> | |
| 574 561 <span class="s">}</span> | |
| 575 562 | |
| 576 563 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span> | |
| 577 564 <span class="s">}</span> | |
| 578 565 | |
| 579 566 <span class="c"># Get specific atom neighbor objects as array. In scalar conetxt, return number of neighbors.</span> | |
| 580 567 <span class="c">#</span> | |
| 581 568 <span class="c"># Notes:</span> | |
| 582 569 <span class="c"># . AtomSpecification correspond to any valid AtomicInvariant based atomic specifications</span> | |
| 583 570 <span class="c"># as implemented in DoesAtomNeighborhoodMatch method.</span> | |
| 584 571 <span class="c"># . Multiple atom specifications can be used in a string delimited by comma.</span> | |
| 585 572 <span class="c">#</span> | |
| 586 <a name="GetNeighborsUsingAtomSpecification-"></a> 573 <span class="k">sub </span><span class="m">GetNeighborsUsingAtomSpecification</span> <span class="s">{</span> | |
| 587 574 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomSpecification</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 588 575 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 589 576 | |
| 590 577 <span class="i">@AtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 591 578 <span class="i">@AtomNeighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 592 579 | |
| 593 580 <span class="c"># Does atom has any neighbors and do they need to be filtered?</span> | |
| 594 581 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@AtomNeighbors</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="s">)</span> && <span class="i">$AtomSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 595 582 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@AtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@AtomNeighbors</span><span class="sc">;</span> | |
| 596 583 <span class="s">}</span> | |
| 597 584 | |
| 598 585 <span class="c"># Filter neighbors using atom specification...</span> | |
| 599 586 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 600 587 | |
| 601 588 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 602 589 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span> <span class="s">{</span> | |
| 603 590 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNeighbor</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 604 591 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> | |
| 605 592 <span class="s">}</span> | |
| 606 593 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$AtomNeighbor</span><span class="sc">;</span> | |
| 607 594 <span class="s">}</span> | |
| 608 595 | |
| 609 596 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span> | |
| 610 597 <span class="s">}</span> | |
| 611 598 | |
| 612 599 | |
| 613 600 <span class="c"># Get non-hydrogen atom neighbor objects as array. In scalar context, return number of neighbors...</span> | |
| 614 <a name="GetHeavyAtomNeighbors-"></a> 601 <span class="k">sub </span><span class="m">GetHeavyAtomNeighbors</span> <span class="s">{</span> | |
| 615 602 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 616 603 | |
| 617 604 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 618 605 <span class="s">}</span> | |
| 619 606 | |
| 620 607 <span class="c"># Get non-hydrogen atom neighbor objects as array. In scalar context, return number of neighbors...</span> | |
| 621 <a name="GetNonHydrogenAtomNeighbors-"></a> 608 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighbors</span> <span class="s">{</span> | |
| 622 609 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 623 610 | |
| 624 611 <span class="c"># Is this atom in a molecule?</span> | |
| 625 612 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 626 613 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 627 614 <span class="s">}</span> | |
| 628 615 <span class="k">my</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> | |
| 629 616 | |
| 630 617 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFilteredAtomNeighbors</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> | |
| 631 618 <span class="s">}</span> | |
| 632 619 | |
| 633 620 <span class="c"># Get hydrogen atom neighbor objects as array. In scalar context, return numbe of neighbors...</span> | |
| 634 <a name="GetHydrogenAtomNeighbors-"></a> 621 <span class="k">sub </span><span class="m">GetHydrogenAtomNeighbors</span> <span class="s">{</span> | |
| 635 622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 636 623 | |
| 637 624 <span class="c"># Is this atom in a molecule?</span> | |
| 638 625 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 639 626 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 640 627 <span class="s">}</span> | |
| 641 628 <span class="k">my</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 642 629 | |
| 643 630 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFilteredAtomNeighbors</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> | |
| 644 631 <span class="s">}</span> | |
| 645 632 | |
| 646 633 <span class="c"># Get non-hydrogen neighbor of hydrogen atom...</span> | |
| 647 634 <span class="c">#</span> | |
| 648 <a name="GetNonHydrogenNeighborOfHydrogenAtom-"></a> 635 <span class="k">sub </span><span class="m">GetNonHydrogenNeighborOfHydrogenAtom</span> <span class="s">{</span> | |
| 649 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 650 637 | |
| 651 638 <span class="c"># Is it Hydrogen?</span> | |
| 652 639 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 653 640 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 654 641 <span class="s">}</span> | |
| 655 642 <span class="k">my</span><span class="s">(</span><span class="i">@Neighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 656 643 | |
| 657 644 <span class="i">@Neighbors</span> = <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 658 645 | |
| 659 646 <span class="k">return</span> <span class="s">(</span><span class="i">@Neighbors</span> == <span class="n">1</span><span class="s">)</span> ? <span class="i">$Neighbors</span>[<span class="n">0</span>] <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 660 647 <span class="s">}</span> | |
| 661 648 | |
| 662 649 <span class="c"># Get filtered atom atom neighbors</span> | |
| 663 <a name="_GetFilteredAtomNeighbors-"></a> 650 <span class="k">sub </span><span class="m">_GetFilteredAtomNeighbors</span> <span class="s">{</span> | |
| 664 651 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 665 652 | |
| 666 653 <span class="c"># Check flags...</span> | |
| 667 654 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 668 655 <span class="i">$NonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 669 656 <span class="s">}</span> | |
| 670 657 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 671 658 <span class="i">$HydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 672 659 <span class="s">}</span> | |
| 673 660 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 674 661 | |
| 675 662 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 676 663 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 677 664 <span class="k">if</span> <span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span> && <span class="i">$Neighbor</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 678 665 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> | |
| 679 666 <span class="s">}</span> | |
| 680 667 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenAtomsOnly</span> && <span class="s">(</span>!<span class="i">$Neighbor</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 681 668 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> | |
| 682 669 <span class="s">}</span> | |
| 683 670 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="sc">;</span> | |
| 684 671 <span class="s">}</span> | |
| 685 672 | |
| 686 673 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span> | |
| 687 674 <span class="s">}</span> | |
| 688 675 | |
| 689 676 <span class="c"># Get number of neighbors...</span> | |
| 690 677 <span class="c">#</span> | |
| 691 <a name="GetNumOfNeighbors-"></a> 678 <span class="k">sub </span><span class="m">GetNumOfNeighbors</span> <span class="s">{</span> | |
| 692 679 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 693 680 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 694 681 | |
| 695 682 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 696 683 | |
| 697 684 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 698 685 <span class="s">}</span> | |
| 699 686 | |
| 700 687 <span class="c"># Get number of neighbors which are non-hydrogen atoms...</span> | |
| 701 <a name="GetNumOfHeavyAtomNeighbors-"></a> 688 <span class="k">sub </span><span class="m">GetNumOfHeavyAtomNeighbors</span> <span class="s">{</span> | |
| 702 689 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 703 690 | |
| 704 691 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 705 692 <span class="s">}</span> | |
| 706 693 | |
| 707 694 <span class="c"># Get number of neighbors which are non-hydrogen atoms...</span> | |
| 708 <a name="GetNumOfNonHydrogenAtomNeighbors-"></a> 695 <span class="k">sub </span><span class="m">GetNumOfNonHydrogenAtomNeighbors</span> <span class="s">{</span> | |
| 709 696 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 710 697 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 711 698 | |
| 712 699 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 713 700 | |
| 714 701 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 715 702 <span class="s">}</span> | |
| 716 703 | |
| 717 704 <span class="c"># Get number of neighbors which are hydrogen atoms...</span> | |
| 718 <a name="GetNumOfHydrogenAtomNeighbors-"></a> 705 <span class="k">sub </span><span class="m">GetNumOfHydrogenAtomNeighbors</span> <span class="s">{</span> | |
| 719 706 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 720 707 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 721 708 | |
| 722 709 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 723 710 | |
| 724 711 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 725 712 <span class="s">}</span> | |
| 726 713 | |
| 727 714 <span class="c"># Get bond objects as array. In scalar context, return number of bonds...</span> | |
| 728 <a name="GetBonds-"></a> 715 <span class="k">sub </span><span class="m">GetBonds</span> <span class="s">{</span> | |
| 729 716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 730 717 | |
| 731 718 <span class="c"># Is this atom in a molecule?</span> | |
| 732 719 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 733 720 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 734 721 <span class="s">}</span> | |
| 735 722 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 736 723 | |
| 737 724 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomBonds</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 738 725 <span class="s">}</span> | |
| 739 726 | |
| 740 727 <span class="c"># Get bond to specified atom...</span> | |
| 741 <a name="GetBondToAtom-"></a> 728 <span class="k">sub </span><span class="m">GetBondToAtom</span> <span class="s">{</span> | |
| 742 729 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 743 730 | |
| 744 731 <span class="c"># Is this atom in a molecule?</span> | |
| 745 732 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 746 733 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 747 734 <span class="s">}</span> | |
| 748 735 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 749 736 | |
| 750 737 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondToAtom</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span><span class="sc">;</span> | |
| 751 738 <span class="s">}</span> | |
| 752 739 | |
| 753 740 <span class="c"># It it bonded to a specified atom?</span> | |
| 754 <a name="IsBondedToAtom-"></a> 741 <span class="k">sub </span><span class="m">IsBondedToAtom</span> <span class="s">{</span> | |
| 755 742 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 756 743 | |
| 757 744 <span class="c"># Is this atom in a molecule?</span> | |
| 758 745 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 759 746 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 760 747 <span class="s">}</span> | |
| 761 748 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 762 749 | |
| 763 750 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondedToAtom</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span><span class="sc">;</span> | |
| 764 751 <span class="s">}</span> | |
| 765 752 | |
| 766 753 <span class="c"># Get bond objects to non-hydrogen atoms as array. In scalar context, return number of bonds...</span> | |
| 767 <a name="GetBondsToHeavyAtoms-"></a> 754 <span class="k">sub </span><span class="m">GetBondsToHeavyAtoms</span> <span class="s">{</span> | |
| 768 755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 769 756 | |
| 770 757 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 771 758 <span class="s">}</span> | |
| 772 759 | |
| 773 760 <span class="c"># Get bond objects to non-hydrogen atoms as array. In scalar context, return number of bonds...</span> | |
| 774 <a name="GetBondsToNonHydrogenAtoms-"></a> 761 <span class="k">sub </span><span class="m">GetBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 775 762 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 776 763 | |
| 777 764 <span class="c"># Is this atom in a molecule?</span> | |
| 778 765 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 779 766 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 780 767 <span class="s">}</span> | |
| 781 768 <span class="k">my</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> | |
| 782 769 | |
| 783 770 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFilteredBonds</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> | |
| 784 771 <span class="s">}</span> | |
| 785 772 | |
| 786 773 <span class="c"># Get bond objects to hydrogen atoms as array. In scalar context, return number of bonds...</span> | |
| 787 <a name="GetBondsToHydrogenAtoms-"></a> 774 <span class="k">sub </span><span class="m">GetBondsToHydrogenAtoms</span> <span class="s">{</span> | |
| 788 775 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 789 776 | |
| 790 777 <span class="c"># Is this atom in a molecule?</span> | |
| 791 778 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 792 779 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 793 780 <span class="s">}</span> | |
| 794 781 <span class="k">my</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 795 782 | |
| 796 783 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFilteredBonds</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> | |
| 797 784 <span class="s">}</span> | |
| 798 785 | |
| 799 786 <span class="c"># Get filtered bonds...</span> | |
| 800 <a name="_GetFilteredBonds-"></a> 787 <span class="k">sub </span><span class="m">_GetFilteredBonds</span> <span class="s">{</span> | |
| 801 788 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 802 789 | |
| 803 790 <span class="c"># Check flags...</span> | |
| 804 791 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 805 792 <span class="i">$BondsToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 806 793 <span class="s">}</span> | |
| 807 794 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 808 795 <span class="i">$BondsToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 809 796 <span class="s">}</span> | |
| 810 797 | |
| 811 798 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">@FilteredBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 812 799 | |
| 813 800 <span class="i">@FilteredBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 814 801 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 815 802 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 816 803 <span class="k">if</span> <span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span> && <span class="i">$BondedAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 817 804 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 818 805 <span class="s">}</span> | |
| 819 806 <span class="k">if</span> <span class="s">(</span><span class="i">$BondsToHydrogenAtomsOnly</span> && <span class="s">(</span>!<span class="i">$BondedAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 820 807 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 821 808 <span class="s">}</span> | |
| 822 809 <span class="k">push</span> <span class="i">@FilteredBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="sc">;</span> | |
| 823 810 <span class="s">}</span> | |
| 824 811 | |
| 825 812 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredBonds</span> <span class="co">:</span> <span class="s">(</span><span class="k">scalar</span> <span class="i">@FilteredBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 826 813 <span class="s">}</span> | |
| 827 814 | |
| 828 815 <span class="c"># Get number of bonds...</span> | |
| 829 816 <span class="c">#</span> | |
| 830 <a name="GetNumOfBonds-"></a> 817 <span class="k">sub </span><span class="m">GetNumOfBonds</span> <span class="s">{</span> | |
| 831 818 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 832 819 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 833 820 | |
| 834 821 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 835 822 | |
| 836 823 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 837 824 <span class="s">}</span> | |
| 838 825 | |
| 839 826 <span class="c"># Get number of bonds to non-hydrogen atoms...</span> | |
| 840 <a name="GetNumOfBondsToHeavyAtoms-"></a> 827 <span class="k">sub </span><span class="m">GetNumOfBondsToHeavyAtoms</span> <span class="s">{</span> | |
| 841 828 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 842 829 | |
| 843 830 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 844 831 <span class="s">}</span> | |
| 845 832 | |
| 846 833 <span class="c"># Get number of bonds to non-hydrogen atoms...</span> | |
| 847 <a name="GetNumOfBondsToNonHydrogenAtoms-"></a> 834 <span class="k">sub </span><span class="m">GetNumOfBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 848 835 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 849 836 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 850 837 | |
| 851 838 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 852 839 | |
| 853 840 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 854 841 <span class="s">}</span> | |
| 855 842 | |
| 856 843 <span class="c"># Get number of single bonds to heavy atoms...</span> | |
| 857 <a name="GetNumOfSingleBondsToHeavyAtoms-"></a> 844 <span class="k">sub </span><span class="m">GetNumOfSingleBondsToHeavyAtoms</span> <span class="s">{</span> | |
| 858 845 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 859 846 | |
| 860 847 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 861 848 <span class="s">}</span> | |
| 862 849 | |
| 863 850 <span class="c"># Get number of single bonds to non-hydrogen atoms...</span> | |
| 864 <a name="GetNumOfSingleBondsToNonHydrogenAtoms-"></a> 851 <span class="k">sub </span><span class="m">GetNumOfSingleBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 865 852 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 866 853 | |
| 867 854 <span class="c"># Is this atom in a molecule?</span> | |
| 868 855 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 869 856 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 870 857 <span class="s">}</span> | |
| 871 858 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 872 859 <span class="s">}</span> | |
| 873 860 | |
| 874 861 <span class="c"># Get number of double bonds to heavy atoms...</span> | |
| 875 <a name="GetNumOfDoubleBondsToHeavyAtoms-"></a> 862 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToHeavyAtoms</span> <span class="s">{</span> | |
| 876 863 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 877 864 | |
| 878 865 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 879 866 <span class="s">}</span> | |
| 880 867 | |
| 881 868 <span class="c"># Get number of double bonds to non-hydrogen atoms...</span> | |
| 882 <a name="GetNumOfDoubleBondsToNonHydrogenAtoms-"></a> 869 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 883 870 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 884 871 | |
| 885 872 <span class="c"># Is this atom in a molecule?</span> | |
| 886 873 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 887 874 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 888 875 <span class="s">}</span> | |
| 889 876 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">2</span><span class="s">)</span><span class="sc">;</span> | |
| 890 877 <span class="s">}</span> | |
| 891 878 | |
| 892 879 <span class="c"># Get number of triple bonds to heavy atoms...</span> | |
| 893 <a name="GetNumOfTripleBondsToHeavyAtoms-"></a> 880 <span class="k">sub </span><span class="m">GetNumOfTripleBondsToHeavyAtoms</span> <span class="s">{</span> | |
| 894 881 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 895 882 | |
| 896 883 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 897 884 <span class="s">}</span> | |
| 898 885 | |
| 899 886 <span class="c"># Get number of triple bonds to non-hydrogen atoms...</span> | |
| 900 <a name="GetNumOfTripleBondsToNonHydrogenAtoms-"></a> 887 <span class="k">sub </span><span class="m">GetNumOfTripleBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 901 888 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 902 889 | |
| 903 890 <span class="c"># Is this atom in a molecule?</span> | |
| 904 891 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 905 892 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 906 893 <span class="s">}</span> | |
| 907 894 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">3</span><span class="s">)</span><span class="sc">;</span> | |
| 908 895 <span class="s">}</span> | |
| 909 896 | |
| 910 897 <span class="c"># Get number of bonds of specified bond order to non-hydrogen atoms...</span> | |
| 911 <a name="_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms-"></a> 898 <span class="k">sub </span><span class="m">_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 912 899 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$SpecifiedBondOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 913 900 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 914 901 | |
| 915 902 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span> | |
| 916 903 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 917 904 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 918 905 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 919 906 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedBondOrder</span> == <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 920 907 <span class="i">$NumOfBonds</span>++<span class="sc">;</span> | |
| 921 908 <span class="s">}</span> | |
| 922 909 <span class="s">}</span> | |
| 923 910 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span> | |
| 924 911 <span class="s">}</span> | |
| 925 912 | |
| 926 913 <span class="c"># Get number of aromatic bonds to heavy atoms...</span> | |
| 927 <a name="GetNumOfAromaticBondsToHeavyAtoms-"></a> 914 <span class="k">sub </span><span class="m">GetNumOfAromaticBondsToHeavyAtoms</span> <span class="s">{</span> | |
| 928 915 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 929 916 | |
| 930 917 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 931 918 <span class="s">}</span> | |
| 932 919 | |
| 933 920 <span class="c"># Get number of aromatic bonds to non-hydrogen atoms...</span> | |
| 934 <a name="GetNumOfAromaticBondsToNonHydrogenAtoms-"></a> 921 <span class="k">sub </span><span class="m">GetNumOfAromaticBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 935 922 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 936 923 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 937 924 | |
| 938 925 <span class="c"># Is this atom in a molecule?</span> | |
| 939 926 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 940 927 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 941 928 <span class="s">}</span> | |
| 942 929 | |
| 943 930 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span> | |
| 944 931 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 945 932 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 946 933 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfBonds</span>++<span class="sc">;</span> <span class="s">}</span> | |
| 947 934 <span class="s">}</span> | |
| 948 935 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span> | |
| 949 936 <span class="s">}</span> | |
| 950 937 | |
| 951 938 <span class="c"># Get number of different bond types to non-hydrogen atoms...</span> | |
| 952 939 <span class="c">#</span> | |
| 953 <a name="GetNumOfBondTypesToHeavyAtoms-"></a> 940 <span class="k">sub </span><span class="m">GetNumOfBondTypesToHeavyAtoms</span> <span class="s">{</span> | |
| 954 941 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CountAromaticBonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 955 942 | |
| 956 943 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 957 944 <span class="s">}</span> | |
| 958 945 | |
| 959 946 <span class="c"># Get number of single, double, triple, and aromatic bonds from an atom to all other</span> | |
| 960 947 <span class="c"># non-hydrogen atoms. Value of CountAtomaticBonds parameter controls whether</span> | |
| 961 948 <span class="c"># number of aromatic bonds is returned; default is not to count aromatic bonds. During</span> | |
| 962 949 <span class="c"># counting of aromatic bonds, the bond marked aromatic is not included in the count</span> | |
| 963 950 <span class="c"># of other bond types.</span> | |
| 964 951 <span class="c">#</span> | |
| 965 <a name="GetNumOfBondTypesToNonHydrogenAtoms-"></a> 952 <span class="k">sub </span><span class="m">GetNumOfBondTypesToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 966 953 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CountAromaticBonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 967 954 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="cm">,</span> <span class="i">$None</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 968 955 | |
| 969 956 <span class="i">$CountAromaticBonds</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span> ? <span class="i">$CountAromaticBonds</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 970 957 | |
| 971 958 <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> | |
| 972 959 <span class="i">$NumOfAromaticBonds</span> = <span class="i">$CountAromaticBonds</span> ? <span class="n">0</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 973 960 | |
| 974 961 <span class="c"># Is this atom in a molecule?</span> | |
| 975 962 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 976 963 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 977 964 <span class="s">}</span> | |
| 978 965 | |
| 979 966 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 980 967 | |
| 981 968 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 982 969 <span class="j">BONDTYPE:</span> <span class="s">{</span> | |
| 983 970 <span class="k">if</span> <span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span> <span class="s">{</span> | |
| 984 971 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfAromaticBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span> | |
| 985 972 <span class="s">}</span> | |
| 986 973 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsSingle</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfSingleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span> | |
| 987 974 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsDouble</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfDoubleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span> | |
| 988 975 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsTriple</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfTripleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span> | |
| 989 976 <span class="i">$None</span> = <span class="n">1</span><span class="sc">;</span> | |
| 990 977 <span class="s">}</span> | |
| 991 978 <span class="s">}</span> | |
| 992 979 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 993 980 <span class="s">}</span> | |
| 994 981 | |
| 995 982 <span class="c"># Get number of sigma and pi bonds to heavy atoms...</span> | |
| 996 983 <span class="c">#</span> | |
| 997 <a name="GetNumOfSigmaAndPiBondsToHeavyAtoms-"></a> 984 <span class="k">sub </span><span class="m">GetNumOfSigmaAndPiBondsToHeavyAtoms</span> <span class="s">{</span> | |
| 998 985 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 999 986 | |
| 1000 987 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1001 988 <span class="s">}</span> | |
| 1002 989 | |
| 1003 990 <span class="c"># Get number of sigma and pi bonds from an atom to all other non-hydrogen atoms.</span> | |
| 1004 991 <span class="c"># Sigma and pi bonds are counted using the following methodology: a single bond</span> | |
| 1005 992 <span class="c"># correspond to one sigma bond; a double bond contributes one to sigma bond count</span> | |
| 1006 993 <span class="c"># and one to pi bond count; a triple bond contributes one to sigma bond count and</span> | |
| 1007 994 <span class="c"># two to pi bond count.</span> | |
| 1008 995 <span class="c">#</span> | |
| 1009 <a name="GetNumOfSigmaAndPiBondsToNonHydrogenAtoms-"></a> 996 <span class="k">sub </span><span class="m">GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 1010 997 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1011 998 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfSigmaBonds</span><span class="cm">,</span> <span class="i">$NumOfPiBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 1012 999 | |
| 1013 1000 <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1014 1001 | |
| 1015 1002 <span class="i">$NumOfSigmaBonds</span> = <span class="i">$NumOfSingleBonds</span> + <span class="i">$NumOfDoubleBonds</span> + <span class="i">$NumOfTripleBonds</span><span class="sc">;</span> | |
| 1016 1003 <span class="i">$NumOfPiBonds</span> = <span class="i">$NumOfDoubleBonds</span> + <span class="n">2</span>*<span class="i">$NumOfTripleBonds</span><span class="sc">;</span> | |
| 1017 1004 | |
| 1018 1005 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSigmaBonds</span><span class="cm">,</span> <span class="i">$NumOfPiBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 1019 1006 <span class="s">}</span> | |
| 1020 1007 | |
| 1021 1008 <span class="c"># Get information related to atoms for all heavy atoms attached to an atom..</span> | |
| 1022 1009 <span class="c">#</span> | |
| 1023 <a name="GetHeavyAtomNeighborsAtomInformation-"></a>1010 <span class="k">sub </span><span class="m">GetHeavyAtomNeighborsAtomInformation</span> <span class="s">{</span> | |
| 1024 1011 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1025 1012 | |
| 1026 1013 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighborsAtomInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1027 1014 <span class="s">}</span> | |
| 1028 1015 | |
| 1029 1016 <span class="c"># Get information related to atoms for all non-hydrogen atoms attached to an atom..</span> | |
| 1030 1017 <span class="c">#</span> | |
| 1031 1018 <span class="c"># The following values are returned:</span> | |
| 1032 1019 <span class="c"># . Number of non-hydrogen atom neighbors</span> | |
| 1033 1020 <span class="c"># . A reference to an array containing atom objects correpsonding to non-hydrogen</span> | |
| 1034 1021 <span class="c"># atom neighbors</span> | |
| 1035 1022 <span class="c"># . Number of different types of non-hydrogen atom neighbors</span> | |
| 1036 1023 <span class="c"># . A reference to a hash containing atom symbol as key with value corresponding</span> | |
| 1037 1024 <span class="c"># to its count for non-hydrogen atom neighbors</span> | |
| 1038 1025 <span class="c">#</span> | |
| 1039 <a name="GetNonHydrogenAtomNeighborsAtomInformation-"></a>1026 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsAtomInformation</span> <span class="s">{</span> | |
| 1040 1027 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1041 1028 | |
| 1042 1029 <span class="c"># Is this atom in a molecule?</span> | |
| 1043 1030 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1044 1031 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 1045 1032 <span class="s">}</span> | |
| 1046 1033 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomNeighbor</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighbors</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighborsType</span><span class="cm">,</span> <span class="i">@AtomNeighbors</span><span class="cm">,</span> <span class="i">%AtomNeighborsTypeMap</span><span class="s">)</span><span class="sc">;</span> | |
| 1047 1034 | |
| 1048 1035 <span class="i">$NumOfAtomNeighbors</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">@AtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1049 1036 <span class="i">$NumOfAtomNeighborsType</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">%AtomNeighborsTypeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1050 1037 | |
| 1051 1038 <span class="i">@AtomNeighbors</span> = <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1052 1039 <span class="i">$NumOfAtomNeighbors</span> = <span class="k">scalar</span> <span class="i">@AtomNeighbors</span><span class="sc">;</span> | |
| 1053 1040 | |
| 1054 1041 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span> <span class="s">{</span> | |
| 1055 1042 <span class="i">$AtomSymbol</span> = <span class="i">$AtomNeighbor</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span> | |
| 1056 1043 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1057 1044 <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 1058 1045 <span class="s">}</span> | |
| 1059 1046 <span class="k">else</span> <span class="s">{</span> | |
| 1060 1047 <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 1061 1048 <span class="i">$NumOfAtomNeighborsType</span>++<span class="sc">;</span> | |
| 1062 1049 <span class="s">}</span> | |
| 1063 1050 <span class="s">}</span> | |
| 1064 1051 | |
| 1065 1052 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfAtomNeighbors</span><span class="cm">,</span> \<span class="i">@AtomNeighbors</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighborsType</span><span class="cm">,</span> \<span class="i">%AtomNeighborsTypeMap</span><span class="s">)</span><span class="sc">;</span> | |
| 1066 1053 <span class="s">}</span> | |
| 1067 1054 | |
| 1068 1055 <span class="c"># Get information related to bonds for all heavy atoms attached to an atom..</span> | |
| 1069 1056 <span class="c">#</span> | |
| 1070 <a name="GetHeavyAtomNeighborsBondformation-"></a>1057 <span class="k">sub </span><span class="m">GetHeavyAtomNeighborsBondformation</span> <span class="s">{</span> | |
| 1071 1058 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1072 1059 | |
| 1073 1060 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighborsBondInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1074 1061 <span class="s">}</span> | |
| 1075 1062 | |
| 1076 1063 <span class="c"># Get information related to bonds for all non-hydrogen atoms attached to an atom..</span> | |
| 1077 1064 <span class="c">#</span> | |
| 1078 1065 <span class="c"># The following values are returned:</span> | |
| 1079 1066 <span class="c"># . Number of bonds to non-hydrogen atom neighbors</span> | |
| 1080 1067 <span class="c"># . A reference to an array containing bond objects correpsonding to non-hydrogen</span> | |
| 1081 1068 <span class="c"># atom neighbors</span> | |
| 1082 1069 <span class="c"># . A reference to a hash containing bond type as key with value corresponding</span> | |
| 1083 1070 <span class="c"># to its count for non-hydrogen atom neighbors. Bond types are: Single, Double or Triple</span> | |
| 1084 1071 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span> | |
| 1085 1072 <span class="c"># key with values correponding to count of bond types for atom symbol for non-hydrogen</span> | |
| 1086 1073 <span class="c"># atom neighbors</span> | |
| 1087 1074 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span> | |
| 1088 1075 <span class="c"># key with values correponding to atom objects array involved in corresponding bond type for</span> | |
| 1089 1076 <span class="c"># atom symbol for non-hydrogen atom neighbors</span> | |
| 1090 1077 <span class="c">#</span> | |
| 1091 <a name="GetNonHydrogenAtomNeighborsBondInformation-"></a>1078 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsBondInformation</span> <span class="s">{</span> | |
| 1092 1079 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1093 1080 | |
| 1094 1081 <span class="c"># Is this atom in a molecule?</span> | |
| 1095 1082 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1096 1083 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 1097 1084 <span class="s">}</span> | |
| 1098 1085 <span class="k">my</span><span class="s">(</span><span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondedAtomSymbol</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$None</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="cm">,</span> <span class="i">%BondTypeCountMap</span><span class="cm">,</span> <span class="i">%AtomsBondTypesCountMap</span><span class="cm">,</span> <span class="i">%AtomsBondTypeAtomsMap</span><span class="s">)</span><span class="sc">;</span> | |
| 1099 1086 | |
| 1100 1087 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1101 1088 <span class="i">%BondTypeCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1102 1089 <span class="i">%AtomsBondTypesCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">%AtomsBondTypeAtomsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1103 1090 | |
| 1104 1091 <span class="i">$BondTypeCountMap</span>{<span class="w">Single</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 1105 1092 <span class="i">$BondTypeCountMap</span>{<span class="w">Double</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 1106 1093 <span class="i">$BondTypeCountMap</span>{<span class="w">Triple</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 1107 1094 | |
| 1108 1095 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1109 1096 <span class="i">$NumOfBonds</span> = <span class="k">scalar</span> <span class="i">@Bonds</span><span class="sc">;</span> | |
| 1110 1097 | |
| 1111 1098 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 1112 1099 <span class="i">$BondType</span> = <span class="i">$Bond</span><span class="i">->IsSingle</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"Single"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsDouble</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"Double"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsTriple</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"Triple"</span> <span class="co">:</span> <span class="q">""</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 1113 1100 <span class="k">if</span> <span class="s">(</span>!<span class="i">$BondType</span><span class="s">)</span> <span class="s">{</span> | |
| 1114 1101 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 1115 1102 <span class="s">}</span> | |
| 1116 1103 | |
| 1117 1104 <span class="c"># Track bond types...</span> | |
| 1118 1105 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1119 1106 <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 1120 1107 <span class="s">}</span> | |
| 1121 1108 <span class="k">else</span> <span class="s">{</span> | |
| 1122 1109 <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 1123 1110 <span class="s">}</span> | |
| 1124 1111 | |
| 1125 1112 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 1126 1113 <span class="i">$BondedAtomSymbol</span> = <span class="i">$BondedAtom</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span> | |
| 1127 1114 | |
| 1128 1115 <span class="c"># Track bond types count for atom types involved in specific bond types...</span> | |
| 1129 1116 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1130 1117 <span class="i">%</span>{<span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1131 1118 <span class="s">}</span> | |
| 1132 1119 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1133 1120 <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 1134 1121 <span class="s">}</span> | |
| 1135 1122 <span class="k">else</span> <span class="s">{</span> | |
| 1136 1123 <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 1137 1124 <span class="s">}</span> | |
| 1138 1125 | |
| 1139 1126 <span class="c"># Track atoms involved in specific bond types for specific atom types...</span> | |
| 1140 1127 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1141 1128 <span class="i">%</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1142 1129 <span class="s">}</span> | |
| 1143 1130 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1144 1131 <span class="i">@</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1145 1132 <span class="s">}</span> | |
| 1146 1133 <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}}<span class="cm">,</span> <span class="i">$BondedAtom</span><span class="sc">;</span> | |
| 1147 1134 <span class="s">}</span> | |
| 1148 1135 | |
| 1149 1136 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfBonds</span><span class="cm">,</span> \<span class="i">@Bonds</span><span class="cm">,</span> \<span class="i">%BondTypeCountMap</span><span class="cm">,</span> \<span class="i">%AtomsBondTypesCountMap</span><span class="cm">,</span> \<span class="i">%AtomsBondTypeAtomsMap</span><span class="s">)</span><span class="sc">;</span> | |
| 1150 1137 <span class="s">}</span> | |
| 1151 1138 | |
| 1152 1139 <span class="c"># Get number of bonds to hydrogen atoms...</span> | |
| 1153 <a name="GetNumOfBondsToHydrogenAtoms-"></a>1140 <span class="k">sub </span><span class="m">GetNumOfBondsToHydrogenAtoms</span> <span class="s">{</span> | |
| 1154 1141 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1155 1142 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 1156 1143 | |
| 1157 1144 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1158 1145 | |
| 1159 1146 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1160 1147 <span class="s">}</span> | |
| 1161 1148 | |
| 1162 1149 <span class="c"># Get sum of bond orders to all bonded atoms...</span> | |
| 1163 1150 <span class="c">#</span> | |
| 1164 <a name="GetSumOfBondOrders-"></a>1151 <span class="k">sub </span><span class="m">GetSumOfBondOrders</span> <span class="s">{</span> | |
| 1165 1152 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1166 1153 | |
| 1167 1154 <span class="c"># Is this atom in a molecule?</span> | |
| 1168 1155 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1169 1156 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1170 1157 <span class="s">}</span> | |
| 1171 1158 | |
| 1172 1159 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1173 1160 <span class="s">}</span> | |
| 1174 1161 | |
| 1175 1162 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span> | |
| 1176 1163 <span class="c">#</span> | |
| 1177 <a name="GetSumOfBondOrdersToHeavyAtoms-"></a>1164 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToHeavyAtoms</span> <span class="s">{</span> | |
| 1178 1165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1179 1166 | |
| 1180 1167 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1181 1168 <span class="s">}</span> | |
| 1182 1169 | |
| 1183 1170 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span> | |
| 1184 1171 <span class="c">#</span> | |
| 1185 <a name="GetSumOfBondOrdersToNonHydrogenAtoms-"></a>1172 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 1186 1173 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1187 1174 | |
| 1188 1175 <span class="c"># Is this atom in a molecule?</span> | |
| 1189 1176 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1190 1177 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1191 1178 <span class="s">}</span> | |
| 1192 1179 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> | |
| 1193 1180 | |
| 1194 1181 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetSumOfBondOrders</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> | |
| 1195 1182 <span class="s">}</span> | |
| 1196 1183 | |
| 1197 1184 <span class="c"># Get sum of bond orders to hydrogen atoms only...</span> | |
| 1198 1185 <span class="c">#</span> | |
| 1199 <a name="GetSumOfBondOrdersToHydrogenAtoms-"></a>1186 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToHydrogenAtoms</span> <span class="s">{</span> | |
| 1200 1187 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1201 1188 | |
| 1202 1189 <span class="c"># Is this atom in a molecule?</span> | |
| 1203 1190 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1204 1191 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1205 1192 <span class="s">}</span> | |
| 1206 1193 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 1207 1194 | |
| 1208 1195 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetSumOfBondOrders</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> | |
| 1209 1196 <span class="s">}</span> | |
| 1210 1197 | |
| 1211 1198 <span class="c"># Get sum of bond orders to all bonded atoms, non-hydrogen or hydrogen bonded atoms...</span> | |
| 1212 1199 <span class="c">#</span> | |
| 1213 <a name="_GetSumOfBondOrders-"></a>1200 <span class="k">sub </span><span class="m">_GetSumOfBondOrders</span> <span class="s">{</span> | |
| 1214 1201 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1215 1202 | |
| 1216 1203 <span class="c"># Check flags...</span> | |
| 1217 1204 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 1218 1205 <span class="i">$ToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1219 1206 <span class="s">}</span> | |
| 1220 1207 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 1221 1208 <span class="i">$ToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1222 1209 <span class="s">}</span> | |
| 1223 1210 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 1224 1211 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1225 1212 | |
| 1226 1213 <span class="k">if</span> <span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 1227 1214 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1228 1215 <span class="s">}</span> | |
| 1229 1216 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 1230 1217 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1231 1218 <span class="s">}</span> | |
| 1232 1219 <span class="k">else</span> <span class="s">{</span> | |
| 1233 1220 <span class="c"># All bonds...</span> | |
| 1234 1221 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1235 1222 <span class="s">}</span> | |
| 1236 1223 | |
| 1237 1224 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1238 1225 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 1239 1226 <span class="i">$SumOfBondOrders</span> += <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1240 1227 <span class="s">}</span> | |
| 1241 1228 | |
| 1242 1229 <span class="k">if</span> <span class="s">(</span><span class="i">$SumOfBondOrders</span> =~ <span class="q">/\./</span><span class="s">)</span> <span class="s">{</span> | |
| 1243 1230 <span class="c">#</span> | |
| 1244 1231 <span class="c"># Change any fractional bond order to next largest integer...</span> | |
| 1245 1232 <span class="c">#</span> | |
| 1246 1233 <span class="c"># As long as aromatic bond orders in a ring are correctly using using 4n + 2 Huckel rule</span> | |
| 1247 1234 <span class="c"># (BondOrder: 1.5) or explicity set as Kekule bonds (alternate single/double),</span> | |
| 1248 1235 <span class="c"># SumOfBondOrders should add up to an integer.</span> | |
| 1249 1236 <span class="c">#</span> | |
| 1250 1237 <span class="i">$SumOfBondOrders</span> = <span class="i">ceil</span><span class="s">(</span><span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span> | |
| 1251 1238 <span class="s">}</span> | |
| 1252 1239 | |
| 1253 1240 <span class="k">return</span> <span class="i">$SumOfBondOrders</span><span class="sc">;</span> | |
| 1254 1241 <span class="s">}</span> | |
| 1255 1242 | |
| 1256 1243 <span class="c"># Get largest bond order to any bonded atoms...</span> | |
| 1257 1244 <span class="c">#</span> | |
| 1258 <a name="GetLargestBondOrder-"></a>1245 <span class="k">sub </span><span class="m">GetLargestBondOrder</span> <span class="s">{</span> | |
| 1259 1246 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1260 1247 | |
| 1261 1248 <span class="c"># Is this atom in a molecule?</span> | |
| 1262 1249 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1263 1250 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1264 1251 <span class="s">}</span> | |
| 1265 1252 | |
| 1266 1253 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetLargestBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1267 1254 <span class="s">}</span> | |
| 1268 1255 | |
| 1269 1256 <span class="c"># Get largest bond order to bonded non-hydrogen atoms...</span> | |
| 1270 1257 <span class="c">#</span> | |
| 1271 <a name="GetLargestBondOrderToHeavyAtoms-"></a>1258 <span class="k">sub </span><span class="m">GetLargestBondOrderToHeavyAtoms</span> <span class="s">{</span> | |
| 1272 1259 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1273 1260 | |
| 1274 1261 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1275 1262 <span class="s">}</span> | |
| 1276 1263 | |
| 1277 1264 <span class="c"># Get largest bond order to bonded non-hydrogen atoms...</span> | |
| 1278 1265 <span class="c">#</span> | |
| 1279 <a name="GetLargestBondOrderToNonHydrogenAtoms-"></a>1266 <span class="k">sub </span><span class="m">GetLargestBondOrderToNonHydrogenAtoms</span> <span class="s">{</span> | |
| 1280 1267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1281 1268 | |
| 1282 1269 <span class="c"># Is this atom in a molecule?</span> | |
| 1283 1270 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1284 1271 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1285 1272 <span class="s">}</span> | |
| 1286 1273 | |
| 1287 1274 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 1288 1275 | |
| 1289 1276 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetLargestBondOrder</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> | |
| 1290 1277 <span class="s">}</span> | |
| 1291 1278 | |
| 1292 1279 <span class="c"># Get largest bond order to all bonded atoms, non-hydrogen or hydrogen bonded atoms...</span> | |
| 1293 1280 <span class="c">#</span> | |
| 1294 <a name="_GetLargestBondOrder-"></a>1281 <span class="k">sub </span><span class="m">_GetLargestBondOrder</span> <span class="s">{</span> | |
| 1295 1282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1296 1283 | |
| 1297 1284 <span class="c"># Check flags...</span> | |
| 1298 1285 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 1299 1286 <span class="i">$ToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1300 1287 <span class="s">}</span> | |
| 1301 1288 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 1302 1289 <span class="i">$ToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1303 1290 <span class="s">}</span> | |
| 1304 1291 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$LargestBondOrder</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 1305 1292 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1306 1293 | |
| 1307 1294 <span class="k">if</span> <span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 1308 1295 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1309 1296 <span class="s">}</span> | |
| 1310 1297 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 1311 1298 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1312 1299 <span class="s">}</span> | |
| 1313 1300 <span class="k">else</span> <span class="s">{</span> | |
| 1314 1301 <span class="c"># All bonds...</span> | |
| 1315 1302 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1316 1303 <span class="s">}</span> | |
| 1317 1304 | |
| 1318 1305 <span class="i">$LargestBondOrder</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1319 1306 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 1320 1307 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1321 1308 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> > <span class="i">$LargestBondOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 1322 1309 <span class="i">$LargestBondOrder</span> = <span class="i">$BondOrder</span><span class="sc">;</span> | |
| 1323 1310 <span class="s">}</span> | |
| 1324 1311 <span class="s">}</span> | |
| 1325 1312 | |
| 1326 1313 <span class="k">return</span> <span class="i">$LargestBondOrder</span><span class="sc">;</span> | |
| 1327 1314 <span class="s">}</span> | |
| 1328 1315 | |
| 1329 1316 <span class="c"># Get number of implicit hydrogen for atom...</span> | |
| 1330 1317 <span class="c">#</span> | |
| 1331 <a name="GetImplicitHydrogens-"></a>1318 <span class="k">sub </span><span class="m">GetImplicitHydrogens</span> <span class="s">{</span> | |
| 1332 1319 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1333 1320 | |
| 1334 1321 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1335 1322 <span class="s">}</span> | |
| 1336 1323 | |
| 1337 1324 <span class="c"># Get number of implicit hydrogen for atom...</span> | |
| 1338 1325 <span class="c">#</span> | |
| 1339 <a name="GetNumOfImplicitHydrogens-"></a>1326 <span class="k">sub </span><span class="m">GetNumOfImplicitHydrogens</span> <span class="s">{</span> | |
| 1340 1327 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1341 1328 | |
| 1342 1329 <span class="c"># Is this atom in a molecule?</span> | |
| 1343 1330 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1344 1331 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1345 1332 <span class="s">}</span> | |
| 1346 1333 | |
| 1347 1334 <span class="c"># Is ImplicitHydrogens property explicitly set?</span> | |
| 1348 1335 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1349 1336 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="sc">;</span> | |
| 1350 1337 <span class="s">}</span> | |
| 1351 1338 | |
| 1352 1339 <span class="c"># Is it an element symbol?</span> | |
| 1353 1340 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1354 1341 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1355 1342 <span class="s">}</span> | |
| 1356 1343 | |
| 1357 1344 <span class="k">my</span><span class="s">(</span><span class="i">$ImplicitHydrogens</span><span class="cm">,</span> <span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span> | |
| 1358 1345 | |
| 1359 1346 <span class="i">$ImplicitHydrogens</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1360 1347 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1361 1348 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->GetPotentialTotalCommonValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1362 1349 | |
| 1363 1350 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1364 1351 <span class="c"># Subtract sum of bond orders to non-hydrogen and hydrogen atom neighbors...</span> | |
| 1365 1352 <span class="i">$ImplicitHydrogens</span> = <span class="i">$PotentialTotalValence</span> - <span class="i">$SumOfBondOrders</span><span class="sc">;</span> | |
| 1366 1353 <span class="s">}</span> | |
| 1367 1354 | |
| 1368 1355 <span class="k">return</span> <span class="i">$ImplicitHydrogens</span> > <span class="n">0</span> ? <span class="i">$ImplicitHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 1369 1356 <span class="s">}</span> | |
| 1370 1357 | |
| 1371 1358 <span class="c"># Get number of bonds available to form additional bonds with heavy atoms, excluding</span> | |
| 1372 1359 <span class="c"># any implicit bonds to hydrogens set using ImplicitHydrogens property.</span> | |
| 1373 1360 <span class="c">#</span> | |
| 1374 1361 <span class="c"># It's different from number of implicit or missing hydrogens, both of which are equivalent.</span> | |
| 1375 1362 <span class="c">#</span> | |
| 1376 1363 <span class="c"># For example, in a SMILES string, [nH] ring atom corresponds to an aromatic nitrogen.</span> | |
| 1377 1364 <span class="c"># Although the hydrogen specified for n is treated internally as implicit hydrogen and shows</span> | |
| 1378 1365 <span class="c"># up in missing hydrogen count, it's not available to participate in double bonds to additional</span> | |
| 1379 1366 <span class="c"># heavy atoms.</span> | |
| 1380 1367 <span class="c">#</span> | |
| 1381 <a name="GetNumOfBondsAvailableForHeavyAtoms-"></a>1368 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForHeavyAtoms</span> <span class="s">{</span> | |
| 1382 1369 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1383 1370 | |
| 1384 1371 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfBondsAvailableForNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1385 1372 <span class="s">}</span> | |
| 1386 1373 | |
| 1387 1374 <span class="c"># It's another name for GetNumOfBondsAvailableForHeavyAtoms</span> | |
| 1388 1375 <span class="c">#</span> | |
| 1389 <a name="GetNumOfBondsAvailableForNonHydrogenAtoms-"></a>1376 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForNonHydrogenAtoms</span> <span class="s">{</span> | |
| 1390 1377 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1391 1378 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfAvailableBonds</span><span class="cm">,</span> <span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span> | |
| 1392 1379 | |
| 1393 1380 <span class="i">$NumOfAvailableBonds</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1394 1381 | |
| 1395 1382 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1396 1383 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->GetPotentialTotalCommonValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1397 1384 | |
| 1398 1385 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1399 1386 <span class="c"># Subtract sum of bond orders to non-hydrogen and hydrogen atom neighbors...</span> | |
| 1400 1387 <span class="i">$NumOfAvailableBonds</span> = <span class="i">$PotentialTotalValence</span> - <span class="i">$SumOfBondOrders</span><span class="sc">;</span> | |
| 1401 1388 <span class="s">}</span> | |
| 1402 1389 | |
| 1403 1390 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1404 1391 <span class="i">$NumOfAvailableBonds</span> -= <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="sc">;</span> | |
| 1405 1392 <span class="s">}</span> | |
| 1406 1393 | |
| 1407 1394 <span class="k">return</span> <span class="i">$NumOfAvailableBonds</span> > <span class="n">0</span> ? <span class="i">$NumOfAvailableBonds</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 1408 1395 <span class="s">}</span> | |
| 1409 1396 | |
| 1410 1397 <span class="c"># Disable setting of explicit hydrogens property...</span> | |
| 1411 <a name="SetExplicitHydrogens-"></a>1398 <span class="k">sub </span><span class="m">SetExplicitHydrogens</span> <span class="s">{</span> | |
| 1412 1399 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1413 1400 | |
| 1414 1401 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetExplicitHydrogens: Setting of explicit hydrogens is not supported..."</span><span class="sc">;</span> | |
| 1415 1402 | |
| 1416 1403 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1417 1404 <span class="s">}</span> | |
| 1418 1405 | |
| 1419 1406 <span class="c"># Get number of explicit hydrogens for atom...</span> | |
| 1420 1407 <span class="c">#</span> | |
| 1421 <a name="GetExplicitHydrogens-"></a>1408 <span class="k">sub </span><span class="m">GetExplicitHydrogens</span> <span class="s">{</span> | |
| 1422 1409 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1423 1410 | |
| 1424 1411 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1425 1412 <span class="s">}</span> | |
| 1426 1413 | |
| 1427 1414 <span class="c"># Get number of explicit hydrogens for atom...</span> | |
| 1428 1415 <span class="c">#</span> | |
| 1429 <a name="GetNumOfExplicitHydrogens-"></a>1416 <span class="k">sub </span><span class="m">GetNumOfExplicitHydrogens</span> <span class="s">{</span> | |
| 1430 1417 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1431 1418 <span class="k">my</span><span class="s">(</span><span class="i">$HydrogenAtomNbrs</span><span class="s">)</span><span class="sc">;</span> | |
| 1432 1419 | |
| 1433 1420 <span class="c"># Is this atom in a molecule?</span> | |
| 1434 1421 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1435 1422 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1436 1423 <span class="s">}</span> | |
| 1437 1424 | |
| 1438 1425 <span class="i">$HydrogenAtomNbrs</span> = <span class="i">$This</span><span class="i">->GetNumOfHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1439 1426 | |
| 1440 1427 <span class="k">return</span> <span class="k">defined</span> <span class="i">$HydrogenAtomNbrs</span> ? <span class="i">$HydrogenAtomNbrs</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 1441 1428 <span class="s">}</span> | |
| 1442 1429 | |
| 1443 1430 <span class="c"># Get num of missing hydrogens...</span> | |
| 1444 1431 <span class="c">#</span> | |
| 1445 <a name="GetMissingHydrogens-"></a>1432 <span class="k">sub </span><span class="m">GetMissingHydrogens</span> <span class="s">{</span> | |
| 1446 1433 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1447 1434 | |
| 1448 1435 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1449 1436 <span class="s">}</span> | |
| 1450 1437 | |
| 1451 1438 <span class="c"># Get num of missing hydrogens...</span> | |
| 1452 1439 <span class="c">#</span> | |
| 1453 <a name="GetNumOfMissingHydrogens-"></a>1440 <span class="k">sub </span><span class="m">GetNumOfMissingHydrogens</span> <span class="s">{</span> | |
| 1454 1441 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1455 1442 | |
| 1456 1443 <span class="c"># Is this atom in a molecule?</span> | |
| 1457 1444 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1458 1445 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1459 1446 <span class="s">}</span> | |
| 1460 1447 | |
| 1461 1448 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1462 1449 <span class="s">}</span> | |
| 1463 1450 | |
| 1464 1451 <span class="c"># Get total number of hydrogens...</span> | |
| 1465 1452 <span class="c">#</span> | |
| 1466 <a name="GetHydrogens-"></a>1453 <span class="k">sub </span><span class="m">GetHydrogens</span> <span class="s">{</span> | |
| 1467 1454 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1468 1455 | |
| 1469 1456 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1470 1457 <span class="s">}</span> | |
| 1471 1458 | |
| 1472 1459 <span class="c"># Get total number of hydrogens...</span> | |
| 1473 1460 <span class="c">#</span> | |
| 1474 <a name="GetNumOfHydrogens-"></a>1461 <span class="k">sub </span><span class="m">GetNumOfHydrogens</span> <span class="s">{</span> | |
| 1475 1462 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1476 1463 | |
| 1477 1464 <span class="c"># Is this atom in a molecule?</span> | |
| 1478 1465 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1479 1466 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1480 1467 <span class="s">}</span> | |
| 1481 1468 | |
| 1482 1469 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1483 1470 <span class="s">}</span> | |
| 1484 1471 | |
| 1485 1472 <span class="c"># Valence corresponds to the number of electrons used by an atom in bonding:</span> | |
| 1486 1473 <span class="c">#</span> | |
| 1487 1474 <span class="c"># Valence = ValenceElectrons - ValenceFreeElectrons = BondingElectrons</span> | |
| 1488 1475 <span class="c">#</span> | |
| 1489 1476 <span class="c"># Single, double, triple bonds with bond orders of 1, 2 and 3 correspond to contribution of</span> | |
| 1490 1477 <span class="c"># 1, 2, and 3 bonding electrons. So Valence can be computed using:</span> | |
| 1491 1478 <span class="c">#</span> | |
| 1492 1479 <span class="c"># Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</span> | |
| 1493 1480 <span class="c">#</span> | |
| 1494 1481 <span class="c"># where positive and negative values of FormalCharge increase and decrease the number</span> | |
| 1495 1482 <span class="c"># of bonding electrons respectively.</span> | |
| 1496 1483 <span class="c">#</span> | |
| 1497 1484 <span class="c"># The current release of MayaChemTools supports the following three valence models, which</span> | |
| 1498 1485 <span class="c"># are used during calculation of implicit hydrogens: MDLValenceModel, DaylightValenceModel,</span> | |
| 1499 1486 <span class="c"># InternalValenceModel or MayaChemToolsValenceModel.</span> | |
| 1500 1487 <span class="c">#</span> | |
| 1501 1488 <span class="c"># Notes:</span> | |
| 1502 1489 <span class="c"># . This doesn't always corresponds to explicit valence.</span> | |
| 1503 1490 <span class="c"># . Missing hydrogens are included in the valence.</span> | |
| 1504 1491 <span class="c"># . For neutral molecules, valence and sum of bond order are equal.</span> | |
| 1505 1492 <span class="c"># . For molecules containing only single bonds, SumOfBondOrders and NumOfBonds are equal.</span> | |
| 1506 1493 <span class="c"># . Free radical electrons lead to the decrease in valence. For atoms with explicit assignment</span> | |
| 1507 1494 <span class="c"># of SpinMultiplicity property values corresponding to Singlet (two unparied electrons</span> | |
| 1508 1495 <span class="c"># corresponding to one spin state), Doublet (free radical; an unpaired electron corresponding</span> | |
| 1509 1496 <span class="c"># to two spin states), and Triplet (two unparied electrons corresponding to three spin states;</span> | |
| 1510 1497 <span class="c"># divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</span> | |
| 1511 1498 <span class="c">#</span> | |
| 1512 1499 <span class="c"># SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1 (one valence electron not available for bonding)</span> | |
| 1513 1500 <span class="c"># SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2 (two valence electrons not available for bonding)</span> | |
| 1514 1501 <span class="c">#</span> | |
| 1515 <a name="GetValence-"></a>1502 <span class="k">sub </span><span class="m">GetValence</span> <span class="s">{</span> | |
| 1516 1503 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1517 1504 | |
| 1518 1505 <span class="c"># Is this atom in a molecule?</span> | |
| 1519 1506 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1520 1507 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1521 1508 <span class="s">}</span> | |
| 1522 1509 | |
| 1523 1510 <span class="c"># Is Valence property explicitly set?</span> | |
| 1524 1511 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Valence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1525 1512 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Valence'</span><span class="s">)</span><span class="sc">;</span> | |
| 1526 1513 <span class="s">}</span> | |
| 1527 1514 <span class="k">my</span><span class="s">(</span><span class="i">$Valence</span><span class="s">)</span><span class="sc">;</span> | |
| 1528 1515 | |
| 1529 1516 <span class="i">$Valence</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1530 1517 | |
| 1531 1518 <span class="k">return</span> <span class="i">$Valence</span> > <span class="n">0</span> ? <span class="i">$Valence</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 1532 1519 <span class="s">}</span> | |
| 1533 1520 | |
| 1534 1521 <span class="c"># Get free non-bodning valence electrons left on atom after taking into account</span> | |
| 1535 1522 <span class="c"># sum of bond orders, missing hydrogens and formal charged on the atom. Free</span> | |
| 1536 1523 <span class="c"># radical electrons are included in the valence free electrons count by default.</span> | |
| 1537 1524 <span class="c">#</span> | |
| 1538 1525 <span class="c"># Valence corresponds to number of electrons used by atom in bonding:</span> | |
| 1539 1526 <span class="c">#</span> | |
| 1540 1527 <span class="c"># Valence = ValenceElectrons - ValenceFreeElectrons</span> | |
| 1541 1528 <span class="c">#</span> | |
| 1542 1529 <span class="c"># Additionally, valence can also be calculated by:</span> | |
| 1543 1530 <span class="c">#</span> | |
| 1544 1531 <span class="c"># Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</span> | |
| 1545 1532 <span class="c">#</span> | |
| 1546 1533 <span class="c"># Valence and SumOfBondOrders are equal for neutral molecules.</span> | |
| 1547 1534 <span class="c">#</span> | |
| 1548 1535 <span class="c"># From two formulas for Valence described above, non-bonding free electrons</span> | |
| 1549 1536 <span class="c"># left can be computed by:</span> | |
| 1550 1537 <span class="c">#</span> | |
| 1551 1538 <span class="c"># ValenceFreeElectrons = ValenceElectrons - Valence</span> | |
| 1552 1539 <span class="c"># = ValenceElectrons - SumOfBondOrders -</span> | |
| 1553 1540 <span class="c"># NumOfMissingHydrogens - FormalCharge</span> | |
| 1554 1541 <span class="c">#</span> | |
| 1555 1542 <span class="c"># . Notes:</span> | |
| 1556 1543 <span class="c"># . Missing hydrogens are excluded from the valence free electrons.</span> | |
| 1557 1544 <span class="c"># . Any free radical electrons are considered part of the valence free electrons</span> | |
| 1558 1545 <span class="c"># by default.</span> | |
| 1559 1546 <span class="c">#</span> | |
| 1560 1547 <span class="c"># Examples:</span> | |
| 1561 1548 <span class="c">#</span> | |
| 1562 1549 <span class="c"># o NH3: ValenceFreeElectrons = 5 - 3 = 5 - 3 - 0 - 0 = 2</span> | |
| 1563 1550 <span class="c"># o NH2: ValenceFreeElectrons = 5 - 3 = 5 - 2 - 1 - 0 = 2</span> | |
| 1564 1551 <span class="c"># o NH4+; ValenceFreeElectrons = 5 - 5 = 5 - 4 - 0 - 1 = 0</span> | |
| 1565 1552 <span class="c"># o NH3+; ValenceFreeElectrons = 5 - 5 = 5 - 3 - 1 - 1 = 0</span> | |
| 1566 1553 <span class="c"># o C(=O)O- : ValenceFreeElectrons on O- = 6 - 0 = 6 - 1 - 0 - (-1) = 6</span> | |
| 1567 1554 <span class="c"># o C(=O)O- : ValenceFreeElectrons on =O = 6 - 2 = 6 - 2 - 0 - 0 = 4</span> | |
| 1568 1555 <span class="c">#</span> | |
| 1569 1556 <span class="c">#</span> | |
| 1570 <a name="GetValenceFreeElectrons-"></a>1557 <span class="k">sub </span><span class="m">GetValenceFreeElectrons</span> <span class="s">{</span> | |
| 1571 1558 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1572 1559 | |
| 1573 1560 <span class="c"># Is this atom in a molecule?</span> | |
| 1574 1561 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1575 1562 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1576 1563 <span class="s">}</span> | |
| 1577 1564 | |
| 1578 1565 <span class="c"># Is ValenceFreeElectrons property explicitly set?</span> | |
| 1579 1566 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceFreeElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1580 1567 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceFreeElectrons'</span><span class="s">)</span><span class="sc">;</span> | |
| 1581 1568 <span class="s">}</span> | |
| 1582 1569 | |
| 1583 1570 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1584 1571 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1585 1572 <span class="s">}</span> | |
| 1586 1573 | |
| 1587 1574 <span class="k">my</span><span class="s">(</span><span class="i">$ValenceFreeElectrons</span><span class="s">)</span><span class="sc">;</span> | |
| 1588 1575 | |
| 1589 1576 <span class="i">$ValenceFreeElectrons</span> = <span class="i">$This</span><span class="i">->GetValenceElectrons</span><span class="s">(</span><span class="s">)</span> - <span class="i">$This</span><span class="i">->GetValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1590 1577 <span class="k">if</span> <span class="s">(</span><span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span> | |
| 1591 1578 <span class="i">$ValenceFreeElectrons</span> -= <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1592 1579 <span class="s">}</span> | |
| 1593 1580 | |
| 1594 1581 <span class="k">return</span> <span class="i">$ValenceFreeElectrons</span> > <span class="n">0</span> ? <span class="i">$ValenceFreeElectrons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 1595 1582 <span class="s">}</span> | |
| 1596 1583 | |
| 1597 1584 <span class="c"># Get potential total common valence for calculating the number of implicit hydrogens</span> | |
| 1598 1585 <span class="c"># using the specified common valence model or default internal model for a molecule...</span> | |
| 1599 1586 <span class="c">#</span> | |
| 1600 <a name="GetPotentialTotalCommonValence-"></a>1587 <span class="k">sub </span><span class="m">GetPotentialTotalCommonValence</span> <span class="s">{</span> | |
| 1601 1588 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1602 1589 | |
| 1603 1590 <span class="c"># Is this atom in a molecule?</span> | |
| 1604 1591 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1605 1592 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1606 1593 <span class="s">}</span> | |
| 1607 1594 <span class="k">my</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$ValenceModel</span><span class="s">)</span><span class="sc">;</span> | |
| 1608 1595 | |
| 1609 1596 <span class="i">$PotentialTotalValence</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1610 1597 <span class="i">$ValenceModel</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="i">->GetValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1611 1598 | |
| 1612 1599 <span class="j">VALENCEMODEL:</span> <span class="s">{</span> | |
| 1613 1600 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> =~ <span class="q">/^MDLValenceModel$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1614 1601 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingMDLValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1615 1602 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span> | |
| 1616 1603 <span class="s">}</span> | |
| 1617 1604 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> =~ <span class="q">/^DaylightValenceModel$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1618 1605 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingDaylightValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1619 1606 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span> | |
| 1620 1607 <span class="s">}</span> | |
| 1621 1608 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> !~ <span class="q">/^(InternalValenceModel|MayaChemToolsValenceModel)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1622 1609 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetPotentialTotalCommonValence: The current release of MayaChemTools doesn't support the specified valence model $ValenceModel. Supported valence models: MDLValenceModel, DaylightValenceModel, InternalValenceModel. Using internal valence model..."</span><span class="sc">;</span> | |
| 1623 1610 <span class="s">}</span> | |
| 1624 1611 <span class="c"># Use internal valence model as the default valence model...</span> | |
| 1625 1612 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1626 1613 <span class="s">}</span> | |
| 1627 1614 | |
| 1628 1615 <span class="k">return</span> <span class="i">$PotentialTotalValence</span><span class="sc">;</span> | |
| 1629 1616 <span class="s">}</span> | |
| 1630 1617 | |
| 1631 1618 <span class="c"># Get potential total common valence using data for MDL valence model available in file,</span> | |
| 1632 1619 <span class="c"># lib/data/MDLValenceModelData.csv, distributed with the package...</span> | |
| 1633 1620 <span class="c">#</span> | |
| 1634 <a name="_GetPotentialTotalCommonValenceUsingMDLValenceModel-"></a>1621 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingMDLValenceModel</span> <span class="s">{</span> | |
| 1635 1622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1636 1623 | |
| 1637 1624 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingValenceModelData</span><span class="s">(</span>\<span class="i">%MDLValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 1638 1625 | |
| 1639 1626 <span class="s">}</span> | |
| 1640 1627 | |
| 1641 1628 <span class="c"># Get potential total common valence using data for Daylight valence model available in file,</span> | |
| 1642 1629 <span class="c"># lib/data/DaylightValenceModelData.csv, distributed with the release...</span> | |
| 1643 1630 <span class="c">#</span> | |
| 1644 <a name="_GetPotentialTotalCommonValenceUsingDaylightValenceModel-"></a>1631 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingDaylightValenceModel</span> <span class="s">{</span> | |
| 1645 1632 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1646 1633 | |
| 1647 1634 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingValenceModelData</span><span class="s">(</span>\<span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 1648 1635 <span class="s">}</span> | |
| 1649 1636 | |
| 1650 1637 <span class="c"># Get potential total common valence using data for a specific valence model...</span> | |
| 1651 1638 <span class="c">#</span> | |
| 1652 <a name="_GetPotentialTotalCommonValenceUsingValenceModelData-"></a>1639 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingValenceModelData</span> <span class="s">{</span> | |
| 1653 1640 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ValenceModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1654 1641 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> | |
| 1655 1642 | |
| 1656 1643 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 1657 1644 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 1658 1645 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1659 1646 <span class="s">}</span> | |
| 1660 1647 | |
| 1661 1648 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1662 1649 | |
| 1663 1650 <span class="c"># Is any valence model data available for atomic number and formal charge?</span> | |
| 1664 1651 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ValenceModelDataRef</span>->{<span class="i">$AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1665 1652 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1666 1653 <span class="s">}</span> | |
| 1667 1654 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ValenceModelDataRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1668 1655 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1669 1656 <span class="s">}</span> | |
| 1670 1657 | |
| 1671 1658 <span class="k">my</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="cm">,</span> <span class="i">$CurrentEffectiveValence</span><span class="cm">,</span> <span class="i">$AvailableCommonValence</span><span class="s">)</span><span class="sc">;</span> | |
| 1672 1659 | |
| 1673 1660 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1674 1661 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span> | |
| 1675 1662 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1676 1663 <span class="s">}</span> | |
| 1677 1664 <span class="i">$CurrentEffectiveValence</span> = <span class="i">$SumOfBondOrders</span> + <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1678 1665 | |
| 1679 1666 <span class="i">$PotentialTotalValence</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1680 1667 <span class="j">VALENCE:</span> <span class="k">for</span> <span class="i">$AvailableCommonValence</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ValenceModelDataRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 1681 1668 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentEffectiveValence</span> <= <span class="i">$AvailableCommonValence</span><span class="s">)</span> <span class="s">{</span> | |
| 1682 1669 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValence</span><span class="sc">;</span> | |
| 1683 1670 <span class="k">last</span> <span class="j">VALENCE</span><span class="sc">;</span> | |
| 1684 1671 <span class="s">}</span> | |
| 1685 1672 <span class="s">}</span> | |
| 1686 1673 | |
| 1687 1674 <span class="k">return</span> <span class="i">$PotentialTotalValence</span><span class="sc">;</span> | |
| 1688 1675 <span class="s">}</span> | |
| 1689 1676 | |
| 1690 1677 <span class="c">#</span> | |
| 1691 1678 <span class="c"># For elements with one one common valence, potential total common valence used</span> | |
| 1692 1679 <span class="c"># during the calculation for number of implicit hydrogens during InternalValenceMode</span> | |
| 1693 1680 <span class="c"># corresponds to:</span> | |
| 1694 1681 <span class="c">#</span> | |
| 1695 1682 <span class="c"># CommonValence + FormalCharge - FreeRadicalElectrons</span> | |
| 1696 1683 <span class="c">#</span> | |
| 1697 1684 <span class="c"># For elements with multiple common valences, each common valence is used to</span> | |
| 1698 1685 <span class="c"># calculate total potential common valence as shown above, and the first total potential</span> | |
| 1699 1686 <span class="c"># common valence gerater than the sum of bond orderes is selected as the final total</span> | |
| 1700 1687 <span class="c"># common valence.</span> | |
| 1701 1688 <span class="c">#</span> | |
| 1702 1689 <span class="c"># Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He)</span> | |
| 1703 1690 <span class="c">#</span> | |
| 1704 1691 <span class="c"># Formal charge sign is not adjusted. Positive and negative values result in the</span> | |
| 1705 1692 <span class="c"># increase and decrease of valence.</span> | |
| 1706 1693 <span class="c">#</span> | |
| 1707 1694 <span class="c"># Group 14 containing C, Si, Ge, Sn, Pb...</span> | |
| 1708 1695 <span class="c">#</span> | |
| 1709 1696 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> | |
| 1710 1697 <span class="c"># values result in the decrease of valence.</span> | |
| 1711 1698 <span class="c">#</span> | |
| 1712 1699 <span class="c"># Group 13 containing B, Al, Ga, In, Tl...</span> | |
| 1713 1700 <span class="c">#</span> | |
| 1714 1701 <span class="c"># Formal charge sign is always reversed. Positive and negative values result in the</span> | |
| 1715 1702 <span class="c"># decrease and increase of valence.</span> | |
| 1716 1703 <span class="c">#</span> | |
| 1717 1704 <span class="c"># Groups 1 (H) through 12 (Zn)...</span> | |
| 1718 1705 <span class="c">#</span> | |
| 1719 1706 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> | |
| 1720 1707 <span class="c"># values result in the decrease of valence.</span> | |
| 1721 1708 <span class="c">#</span> | |
| 1722 1709 <span class="c"># Lanthanides and actinides...</span> | |
| 1723 1710 <span class="c">#</span> | |
| 1724 1711 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> | |
| 1725 1712 <span class="c"># values result in the decrease of valence.</span> | |
| 1726 1713 <span class="c">#</span> | |
| 1727 1714 <span class="c"># Notes:</span> | |
| 1728 1715 <span class="c"># . CommonValence and HighestCommonValence available from PeriodicTable module</span> | |
| 1729 1716 <span class="c"># are equivalent to most common and highest sum of bond orders for an element. For</span> | |
| 1730 1717 <span class="c"># neutral atoms involved only in single bonds, it corresponds to highest number of</span> | |
| 1731 1718 <span class="c"># allowed bonds for the atom.</span> | |
| 1732 1719 <span class="c"># . FormalCharge sign is reversed for electropositive elements with positive formal charge</span> | |
| 1733 1720 <span class="c"># during common valence calculations. Electropositive elements, metals and transition elements,</span> | |
| 1734 1721 <span class="c"># have usually plus formal charge and it leads to decrease in common valence; the negative</span> | |
| 1735 1722 <span class="c"># formal charge should result in the decrease of common valence.</span> | |
| 1736 1723 <span class="c"># . For carbon, both plus/minus formal charge cause decrease in common valence</span> | |
| 1737 1724 <span class="c"># . For elements on the right of carbon in periodic table, electronegative elements, plus formal</span> | |
| 1738 1725 <span class="c"># charge causes common valence to increase and minus formal charge cause it to decrease.</span> | |
| 1739 1726 <span class="c">#</span> | |
| 1740 <a name="_GetPotentialTotalCommonValenceUsingInternalValenceModel-"></a>1727 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingInternalValenceModel</span> <span class="s">{</span> | |
| 1741 1728 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1742 1729 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="s">)</span><span class="sc">;</span> | |
| 1743 1730 | |
| 1744 1731 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 1745 1732 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 1746 1733 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1747 1734 <span class="s">}</span> | |
| 1748 1735 | |
| 1749 1736 <span class="i">$CommonValences</span> = <span class="i">PeriodicTable::GetElementCommonValences</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 1750 1737 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CommonValences</span><span class="s">)</span> <span class="s">{</span> | |
| 1751 1738 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1752 1739 <span class="s">}</span> | |
| 1753 1740 | |
| 1754 1741 <span class="k">my</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$AdjustedFormalCharge</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="cm">,</span> <span class="i">$AvailableCommonValence</span><span class="cm">,</span> <span class="i">@AvailableCommonValences</span><span class="s">)</span><span class="sc">;</span> | |
| 1755 1742 | |
| 1756 1743 <span class="i">$AdjustedFormalCharge</span> = <span class="i">$This</span><span class="i">->_GetFormalChargeAdjustedForInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1757 1744 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1758 1745 | |
| 1759 1746 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1760 1747 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span> | |
| 1761 1748 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1762 1749 <span class="s">}</span> | |
| 1763 1750 | |
| 1764 1751 <span class="i">@AvailableCommonValences</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="sc">;</span> | |
| 1765 1752 | |
| 1766 1753 <span class="k">if</span> <span class="s">(</span><span class="i">@AvailableCommonValences</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 1767 1754 <span class="c"># Calculate potential total valence using the only available common valence...</span> | |
| 1768 1755 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValences</span>[<span class="n">0</span>] + <span class="i">$AdjustedFormalCharge</span> - <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span> | |
| 1769 1756 <span class="s">}</span> | |
| 1770 1757 <span class="k">else</span> <span class="s">{</span> | |
| 1771 1758 <span class="c"># Calculate potential total valence using common valence from a list of available valences</span> | |
| 1772 1759 <span class="c"># that makes it higher than sum of bond orders or using the highest common valence...</span> | |
| 1773 1760 <span class="j">VALENCE:</span> <span class="k">for</span> <span class="i">$AvailableCommonValence</span> <span class="s">(</span><span class="i">@AvailableCommonValences</span><span class="s">)</span> <span class="s">{</span> | |
| 1774 1761 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValence</span> + <span class="i">$AdjustedFormalCharge</span> - <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span> | |
| 1775 1762 | |
| 1776 1763 <span class="k">if</span> <span class="s">(</span><span class="i">$PotentialTotalValence</span> < <span class="n">0</span> || <span class="i">$PotentialTotalValence</span> >= <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span> | |
| 1777 1764 <span class="k">last</span> <span class="j">VALENCE</span><span class="sc">;</span> | |
| 1778 1765 <span class="s">}</span> | |
| 1779 1766 <span class="s">}</span> | |
| 1780 1767 <span class="s">}</span> | |
| 1781 1768 | |
| 1782 1769 <span class="k">return</span> <span class="i">$PotentialTotalValence</span> > <span class="n">0</span> ? <span class="i">$PotentialTotalValence</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 1783 1770 <span class="s">}</span> | |
| 1784 1771 | |
| 1785 1772 <span class="c"># Adjust sign of the formal charge for potential total common valence calculation</span> | |
| 1786 1773 <span class="c"># used during internal valence model to figure out number of implicit hydrogens.</span> | |
| 1787 1774 <span class="c">#</span> | |
| 1788 <a name="_GetFormalChargeAdjustedForInternalValenceModel-"></a>1775 <span class="k">sub </span><span class="m">_GetFormalChargeAdjustedForInternalValenceModel</span> <span class="s">{</span> | |
| 1789 1776 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1790 1777 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$GroupNumber</span><span class="cm">,</span> <span class="i">$SwitchSign</span><span class="s">)</span><span class="sc">;</span> | |
| 1791 1778 | |
| 1792 1779 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1793 1780 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 1794 1781 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1795 1782 <span class="s">}</span> | |
| 1796 1783 | |
| 1797 1784 <span class="i">$GroupNumber</span> = <span class="i">$This</span><span class="i">->GetGroupNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1798 1785 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$GroupNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 1799 1786 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span> | |
| 1800 1787 <span class="s">}</span> | |
| 1801 1788 | |
| 1802 1789 <span class="c"># Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He)</span> | |
| 1803 1790 <span class="c">#</span> | |
| 1804 1791 <span class="c"># Formal charge sign is not adjusted. Positive and negative values result in the</span> | |
| 1805 1792 <span class="c"># increase and decrease of valence.</span> | |
| 1806 1793 <span class="c">#</span> | |
| 1807 1794 <span class="c"># Group 14 containing C, Si, Ge, Sn, Pb...</span> | |
| 1808 1795 <span class="c">#</span> | |
| 1809 1796 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> | |
| 1810 1797 <span class="c"># values result in the decrease of valence.</span> | |
| 1811 1798 <span class="c">#</span> | |
| 1812 1799 <span class="c"># Group 13 containing B, Al, Ga, In, Tl...</span> | |
| 1813 1800 <span class="c">#</span> | |
| 1814 1801 <span class="c"># Formal charge sign is always reversed. Positive and negative values result in the</span> | |
| 1815 1802 <span class="c"># decrease and increase of valence.</span> | |
| 1816 1803 <span class="c">#</span> | |
| 1817 1804 <span class="c"># Groups 1 (H) through 12 (Zn)...</span> | |
| 1818 1805 <span class="c">#</span> | |
| 1819 1806 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> | |
| 1820 1807 <span class="c"># values result in the decrease of valence.</span> | |
| 1821 1808 <span class="c">#</span> | |
| 1822 1809 <span class="c"># Lanthanides and actinides...</span> | |
| 1823 1810 <span class="c">#</span> | |
| 1824 1811 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> | |
| 1825 1812 <span class="c"># values result in the decrease of valence.</span> | |
| 1826 1813 <span class="c">#</span> | |
| 1827 1814 | |
| 1828 1815 <span class="i">$SwitchSign</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1829 1816 <span class="k">if</span> <span class="s">(</span><span class="k">length</span> <span class="i">$GroupNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 1830 1817 <span class="j">GROUPNUMBER:</span> <span class="s">{</span> | |
| 1831 1818 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> > <span class="n">14</span><span class="s">)</span> <span class="s">{</span> | |
| 1832 1819 <span class="c"># Groups on the right side of C group in the periodic table...</span> | |
| 1833 1820 <span class="i">$SwitchSign</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1834 1821 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span> | |
| 1835 1822 <span class="s">}</span> | |
| 1836 1823 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> == <span class="n">14</span><span class="s">)</span> <span class="s">{</span> | |
| 1837 1824 <span class="c"># Group containing C, Si, Ge, Sn, Pb...</span> | |
| 1838 1825 <span class="i">$SwitchSign</span> = <span class="s">(</span><span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 1839 1826 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span> | |
| 1840 1827 <span class="s">}</span> | |
| 1841 1828 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> == <span class="n">13</span><span class="s">)</span> <span class="s">{</span> | |
| 1842 1829 <span class="c"># Group containing B, Al, Ga, In, Tl...</span> | |
| 1843 1830 <span class="i">$SwitchSign</span> = <span class="n">1</span><span class="sc">;</span> | |
| 1844 1831 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span> | |
| 1845 1832 <span class="s">}</span> | |
| 1846 1833 <span class="c"># Groups 1 (H) through 12 (Zn)...</span> | |
| 1847 1834 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> >=<span class="n">1</span> && <span class="i">$GroupNumber</span> <= <span class="n">12</span><span class="s">)</span> <span class="s">{</span> | |
| 1848 1835 <span class="c"># Groups 1 (H) through 12 (Zn)...</span> | |
| 1849 1836 <span class="i">$SwitchSign</span> = <span class="s">(</span><span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 1850 1837 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span> | |
| 1851 1838 <span class="s">}</span> | |
| 1852 1839 <span class="s">}</span> | |
| 1853 1840 <span class="s">}</span> | |
| 1854 1841 <span class="k">else</span> <span class="s">{</span> | |
| 1855 1842 <span class="c"># Lanthanides and actinides...</span> | |
| 1856 1843 <span class="i">$SwitchSign</span> = <span class="s">(</span><span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 1857 1844 <span class="s">}</span> | |
| 1858 1845 | |
| 1859 1846 <span class="k">if</span> <span class="s">(</span><span class="i">$SwitchSign</span><span class="s">)</span> <span class="s">{</span> | |
| 1860 1847 <span class="i">$FormalCharge</span> *= <span class="n">-1.0</span><span class="sc">;</span> | |
| 1861 1848 <span class="s">}</span> | |
| 1862 1849 | |
| 1863 1850 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span> | |
| 1864 1851 <span class="s">}</span> | |
| 1865 1852 | |
| 1866 1853 <span class="c"># Get lowest common valence...</span> | |
| 1867 <a name="GetLowestCommonValence-"></a>1854 <span class="k">sub </span><span class="m">GetLowestCommonValence</span> <span class="s">{</span> | |
| 1868 1855 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1869 1856 | |
| 1870 1857 <span class="c"># Is LowestCommonValence property explicitly set?</span> | |
| 1871 1858 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'LowestCommonValence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1872 1859 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'LowestCommonValence'</span><span class="s">)</span><span class="sc">;</span> | |
| 1873 1860 <span class="s">}</span> | |
| 1874 1861 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$LowestCommonValence</span><span class="s">)</span><span class="sc">;</span> | |
| 1875 1862 | |
| 1876 1863 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 1877 1864 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 1878 1865 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1879 1866 <span class="s">}</span> | |
| 1880 1867 <span class="c"># Any need to differentiate between internal and other valence models...</span> | |
| 1881 1868 | |
| 1882 1869 <span class="c"># LowestCommonValence is not set for all elements...</span> | |
| 1883 1870 <span class="i">$LowestCommonValence</span> = <span class="i">PeriodicTable::GetElementLowestCommonValence</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 1884 1871 <span class="k">if</span> <span class="s">(</span>!<span class="i">$LowestCommonValence</span><span class="s">)</span> <span class="s">{</span> | |
| 1885 1872 <span class="i">$LowestCommonValence</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 1886 1873 <span class="s">}</span> | |
| 1887 1874 | |
| 1888 1875 <span class="k">return</span> <span class="i">$LowestCommonValence</span><span class="sc">;</span> | |
| 1889 1876 <span class="s">}</span> | |
| 1890 1877 | |
| 1891 1878 <span class="c"># Get highest common valence...</span> | |
| 1892 <a name="GetHighestCommonValence-"></a>1879 <span class="k">sub </span><span class="m">GetHighestCommonValence</span> <span class="s">{</span> | |
| 1893 1880 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1894 1881 | |
| 1895 1882 <span class="c"># Is HighestCommonValence property explicitly set?</span> | |
| 1896 1883 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'HighestCommonValence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1897 1884 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'HighestCommonValence'</span><span class="s">)</span><span class="sc">;</span> | |
| 1898 1885 <span class="s">}</span> | |
| 1899 1886 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$HighestCommonValence</span><span class="s">)</span><span class="sc">;</span> | |
| 1900 1887 | |
| 1901 1888 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 1902 1889 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 1903 1890 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1904 1891 <span class="s">}</span> | |
| 1905 1892 | |
| 1906 1893 <span class="c"># Any need to differentiate between internal and other valence models...</span> | |
| 1907 1894 | |
| 1908 1895 <span class="c"># HighestCommonValence is not set for all elements...</span> | |
| 1909 1896 <span class="i">$HighestCommonValence</span> = <span class="i">PeriodicTable::GetElementHighestCommonValence</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 1910 1897 <span class="k">if</span> <span class="s">(</span>!<span class="i">$HighestCommonValence</span><span class="s">)</span> <span class="s">{</span> | |
| 1911 1898 <span class="i">$HighestCommonValence</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 1912 1899 <span class="s">}</span> | |
| 1913 1900 | |
| 1914 1901 <span class="k">return</span> <span class="i">$HighestCommonValence</span><span class="sc">;</span> | |
| 1915 1902 <span class="s">}</span> | |
| 1916 1903 | |
| 1917 1904 <span class="c"># Get valence electrons...</span> | |
| 1918 <a name="GetValenceElectrons-"></a>1905 <span class="k">sub </span><span class="m">GetValenceElectrons</span> <span class="s">{</span> | |
| 1919 1906 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1920 1907 | |
| 1921 1908 <span class="c"># Is ValenceElectrons property explicitly set?</span> | |
| 1922 1909 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1923 1910 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceElectrons'</span><span class="s">)</span><span class="sc">;</span> | |
| 1924 1911 <span class="s">}</span> | |
| 1925 1912 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$ValenceElectrons</span><span class="s">)</span><span class="sc">;</span> | |
| 1926 1913 | |
| 1927 1914 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 1928 1915 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 1929 1916 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1930 1917 <span class="s">}</span> | |
| 1931 1918 | |
| 1932 1919 <span class="i">$ValenceElectrons</span> = <span class="i">PeriodicTable::GetElementValenceElectrons</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 1933 1920 | |
| 1934 1921 <span class="k">return</span> <span class="i">$ValenceElectrons</span><span class="sc">;</span> | |
| 1935 1922 <span class="s">}</span> | |
| 1936 1923 | |
| 1937 1924 <span class="c"># Add hydrogens to specified atom in molecule and return number of hydrogens added:</span> | |
| 1938 1925 <span class="c">#</span> | |
| 1939 1926 <span class="c"># o HydrogensToAdd = ImplicitHydrogenCount - ExplicitHydrogenCount</span> | |
| 1940 1927 <span class="c">#</span> | |
| 1941 1928 <span class="c"># o XYZ are set to ZeroVector</span> | |
| 1942 1929 <span class="c">#</span> | |
| 1943 <a name="AddHydrogens-"></a>1930 <span class="k">sub </span><span class="m">AddHydrogens</span> <span class="s">{</span> | |
| 1944 1931 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1945 1932 | |
| 1946 1933 <span class="c"># Is this atom in a molecule?</span> | |
| 1947 1934 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1948 1935 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1949 1936 <span class="s">}</span> | |
| 1950 1937 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> <span class="s">{</span> | |
| 1951 1938 <span class="i">$HydrogenPositionsWarning</span> = <span class="n">1</span><span class="sc">;</span> | |
| 1952 1939 <span class="s">}</span> | |
| 1953 1940 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> <span class="s">{</span> | |
| 1954 1941 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddHydrogens: The current release of MayaChemTools doesn't assign any hydrogen positions..."</span><span class="sc">;</span> | |
| 1955 1942 <span class="s">}</span> | |
| 1956 1943 | |
| 1957 1944 <span class="c"># Is it an element symbol?</span> | |
| 1958 1945 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1959 1946 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1960 1947 <span class="s">}</span> | |
| 1961 1948 | |
| 1962 1949 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$HydrogensAdded</span><span class="cm">,</span> <span class="i">$HydrogensToAdd</span><span class="s">)</span><span class="sc">;</span> | |
| 1963 1950 | |
| 1964 1951 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 1965 1952 <span class="i">$HydrogensAdded</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1966 1953 <span class="i">$HydrogensToAdd</span> = <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1967 1954 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogensToAdd</span> <= <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 1968 1955 <span class="k">return</span> <span class="i">$HydrogensAdded</span><span class="sc">;</span> | |
| 1969 1956 <span class="s">}</span> | |
| 1970 1957 | |
| 1971 1958 <span class="k">my</span><span class="s">(</span><span class="i">$Count</span><span class="cm">,</span> <span class="i">$Hydrogen</span><span class="s">)</span><span class="sc">;</span> | |
| 1972 1959 | |
| 1973 1960 <span class="k">for</span> <span class="i">$Count</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$HydrogensToAdd</span><span class="s">)</span> <span class="s">{</span> | |
| 1974 1961 <span class="i">$HydrogensAdded</span>++<span class="sc">;</span> | |
| 1975 1962 | |
| 1976 1963 <span class="i">$Hydrogen</span> = <span class="i">$Molecule</span><span class="i">->NewAtom</span><span class="s">(</span><span class="q">'AtomSymbol'</span> <span class="cm">=></span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'XYZ'</span> <span class="cm">=></span> <span class="s">[</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
| 1977 1964 <span class="i">$Molecule</span><span class="i">->NewBond</span><span class="s">(</span><span class="q">'Atoms'</span> <span class="cm">=></span> <span class="s">[</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Hydrogen</span><span class="s">]</span><span class="cm">,</span> <span class="q">'BondOrder'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 1978 1965 <span class="s">}</span> | |
| 1979 1966 | |
| 1980 1967 <span class="k">return</span> <span class="i">$HydrogensAdded</span><span class="sc">;</span> | |
| 1981 1968 <span class="s">}</span> | |
| 1982 1969 | |
| 1983 1970 <span class="c"># Delete hydrogens attached to atom in molecule and return total number of hydrogens deleted...</span> | |
| 1984 <a name="DeleteHydrogens-"></a>1971 <span class="k">sub </span><span class="m">DeleteHydrogens</span> <span class="s">{</span> | |
| 1985 1972 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1986 1973 | |
| 1987 1974 <span class="c"># Is this atom in a molecule?</span> | |
| 1988 1975 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1989 1976 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1990 1977 <span class="s">}</span> | |
| 1991 1978 | |
| 1992 1979 <span class="c"># Is it an element symbol?</span> | |
| 1993 1980 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1994 1981 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1995 1982 <span class="s">}</span> | |
| 1996 1983 | |
| 1997 1984 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">$HydrogensDeleted</span><span class="cm">,</span> <span class="i">@Neighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 1998 1985 | |
| 1999 1986 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 2000 1987 <span class="i">$HydrogensDeleted</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2001 1988 <span class="i">@Neighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2002 1989 | |
| 2003 1990 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">@Neighbors</span><span class="s">)</span> <span class="s">{</span> | |
| 2004 1991 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Neighbor</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2005 1992 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> | |
| 2006 1993 <span class="s">}</span> | |
| 2007 1994 <span class="i">$Molecule</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$Neighbor</span><span class="s">)</span><span class="sc">;</span> | |
| 2008 1995 <span class="i">$HydrogensDeleted</span>++<span class="sc">;</span> | |
| 2009 1996 <span class="s">}</span> | |
| 2010 1997 | |
| 2011 1998 <span class="k">return</span> <span class="i">$HydrogensDeleted</span><span class="sc">;</span> | |
| 2012 1999 <span class="s">}</span> | |
| 2013 2000 | |
| 2014 2001 <span class="c"># Copy atom and all its associated data...</span> | |
| 2015 <a name="Copy-"></a>2002 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span> | |
| 2016 2003 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2017 2004 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 2018 2005 | |
| 2019 2006 <span class="i">$Atom</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 2020 2007 | |
| 2021 2008 <span class="k">return</span> <span class="i">$Atom</span><span class="sc">;</span> | |
| 2022 2009 <span class="s">}</span> | |
| 2023 2010 | |
| 2024 2011 <span class="c"># Get atomic invariant value...</span> | |
| 2025 2012 <span class="c">#</span> | |
| 2026 <a name="GetAtomicInvariantValue-"></a>2013 <span class="k">sub </span><span class="m">GetAtomicInvariantValue</span> <span class="s">{</span> | |
| 2027 2014 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2028 2015 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 2029 2016 | |
| 2030 2017 <span class="i">$Value</span> = <span class="q">""</span><span class="sc">;</span> | |
| 2031 2018 | |
| 2032 2019 <span class="j">ATOMICVARIANT:</span> <span class="s">{</span> | |
| 2033 2020 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AS|AtomSymbol|ElementSymbol)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2034 2021 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2035 2022 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2036 2023 <span class="s">}</span> | |
| 2037 2024 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(X|NumOfNonHydrogenAtomNeighbors|NumOfHeavyAtomNeighbors)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2038 2025 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2039 2026 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2040 2027 <span class="s">}</span> | |
| 2041 2028 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(BO|SumOfBondOrdersToNonHydrogenAtoms|SumOfBondOrdersToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2042 2029 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2043 2030 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2044 2031 <span class="s">}</span> | |
| 2045 2032 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(LBO|LargestBondOrderToNonHydrogenAtoms|LargestBondOrderToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2046 2033 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2047 2034 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2048 2035 <span class="s">}</span> | |
| 2049 2036 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(H|NumOfImplicitAndExplicitHydrogens)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2050 2037 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2051 2038 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2052 2039 <span class="s">}</span> | |
| 2053 2040 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(SB|NumOfSingleBondsToNonHydrogenAtoms|NumOfSingleBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2054 2041 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2055 2042 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2056 2043 <span class="s">}</span> | |
| 2057 2044 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(DB|NumOfDoubleBondsToNonHydrogenAtoms|NumOfDoubleBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2058 2045 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2059 2046 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2060 2047 <span class="s">}</span> | |
| 2061 2048 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(TB|NumOfTripleBondsToNonHydrogenAtoms|NumOfTripleBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2062 2049 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2063 2050 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2064 2051 <span class="s">}</span> | |
| 2065 2052 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AB|NumOfAromaticBondsToNonHydrogenAtoms|NumOfAromaticBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2066 2053 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2067 2054 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2068 2055 <span class="s">}</span> | |
| 2069 2056 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(FC|FormalCharge)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2070 2057 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2071 2058 <span class="i">$Value</span> = <span class="k">defined</span> <span class="i">$Value</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2072 2059 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2073 2060 <span class="s">}</span> | |
| 2074 2061 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(T|TotalNumOfAtomNeighbors)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2075 2062 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2076 2063 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2077 2064 <span class="s">}</span> | |
| 2078 2065 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(TSB|TotalNumOfSingleBonds)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2079 2066 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2080 2067 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2081 2068 <span class="s">}</span> | |
| 2082 2069 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2083 2070 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2084 2071 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2085 2072 <span class="s">}</span> | |
| 2086 2073 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(RA|RingAtom)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2087 2074 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2088 2075 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2089 2076 <span class="s">}</span> | |
| 2090 2077 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(Str|Stereochemistry)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2091 2078 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2092 2079 <span class="i">$Value</span>= <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Value</span> =~ <span class="q">/^(R|S)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> | |
| 2093 2080 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2094 2081 <span class="s">}</span> | |
| 2095 2082 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AN|AtomicNumber)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2096 2083 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2097 2084 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2098 2085 <span class="s">}</span> | |
| 2099 2086 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AM|AtomicMass)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2100 2087 <span class="i">$Value</span> = <span class="i">round</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="n">4</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> | |
| 2101 2088 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2102 2089 <span class="s">}</span> | |
| 2103 2090 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(MN|MassNumber)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2104 2091 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2105 2092 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2106 2093 <span class="s">}</span> | |
| 2107 2094 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(SM|SpinMultiplicity)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2108 2095 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2109 2096 <span class="i">$Value</span> = <span class="k">defined</span> <span class="i">$Value</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> | |
| 2110 2097 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
| 2111 2098 <span class="s">}</span> | |
| 2112 2099 <span class="i">$Value</span> = <span class="q">""</span><span class="sc">;</span> | |
| 2113 2100 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetAtomicInvariantValue: Unknown atomic invariant $AtomicInvariant..."</span><span class="sc">;</span> | |
| 2114 2101 <span class="s">}</span> | |
| 2115 2102 | |
| 2116 2103 <span class="k">return</span> <span class="i">$Value</span><span class="sc">;</span> | |
| 2117 2104 <span class="s">}</span> | |
| 2118 2105 | |
| 2119 2106 <span class="c"># Get period number of the atom..</span> | |
| 2120 2107 <span class="c">#</span> | |
| 2121 <a name="GetPeriodNumber-"></a>2108 <span class="k">sub </span><span class="m">GetPeriodNumber</span> <span class="s">{</span> | |
| 2122 2109 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2123 2110 | |
| 2124 2111 <span class="c"># Is PeriodNumber property explicitly set?</span> | |
| 2125 2112 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'PeriodNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2126 2113 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'PeriodNumber'</span><span class="s">)</span><span class="sc">;</span> | |
| 2127 2114 <span class="s">}</span> | |
| 2128 2115 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$PeriodNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 2129 2116 | |
| 2130 2117 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 2131 2118 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 2132 2119 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2133 2120 <span class="s">}</span> | |
| 2134 2121 | |
| 2135 2122 <span class="i">$PeriodNumber</span> = <span class="i">PeriodicTable::GetElementPeriodNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 2136 2123 | |
| 2137 2124 <span class="k">return</span> <span class="i">$PeriodNumber</span><span class="sc">;</span> | |
| 2138 2125 <span class="s">}</span> | |
| 2139 2126 | |
| 2140 2127 <span class="c"># Get group number of the atom..</span> | |
| 2141 2128 <span class="c">#</span> | |
| 2142 <a name="GetGroupNumber-"></a>2129 <span class="k">sub </span><span class="m">GetGroupNumber</span> <span class="s">{</span> | |
| 2143 2130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2144 2131 | |
| 2145 2132 <span class="c"># Is GroupNumber property explicitly set?</span> | |
| 2146 2133 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'GroupNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2147 2134 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'GroupNumber'</span><span class="s">)</span><span class="sc">;</span> | |
| 2148 2135 <span class="s">}</span> | |
| 2149 2136 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$GroupNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 2150 2137 | |
| 2151 2138 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 2152 2139 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 2153 2140 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2154 2141 <span class="s">}</span> | |
| 2155 2142 | |
| 2156 2143 <span class="i">$GroupNumber</span> = <span class="i">PeriodicTable::GetElementGroupNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 2157 2144 | |
| 2158 2145 <span class="k">return</span> <span class="i">$GroupNumber</span><span class="sc">;</span> | |
| 2159 2146 <span class="s">}</span> | |
| 2160 2147 | |
| 2161 2148 <span class="c"># Is it a specified topological pharmacophore atom type?</span> | |
| 2162 2149 <span class="c">#</span> | |
| 2163 <a name="IsTopologicalPharmacophoreType-"></a>2150 <span class="k">sub </span><span class="m">IsTopologicalPharmacophoreType</span> <span class="s">{</span> | |
| 2164 2151 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2165 2152 | |
| 2166 2153 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsFunctionalClassType</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span><span class="sc">;</span> | |
| 2167 2154 <span class="s">}</span> | |
| 2168 2155 | |
| 2169 2156 <span class="c"># Is it a specified functional class atom type?</span> | |
| 2170 2157 <span class="c">#</span> | |
| 2171 <a name="IsFunctionalClassType-"></a>2158 <span class="k">sub </span><span class="m">IsFunctionalClassType</span> <span class="s">{</span> | |
| 2172 2159 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2173 2160 | |
| 2174 2161 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsFunctionalClassType</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span><span class="sc">;</span> | |
| 2175 2162 <span class="s">}</span> | |
| 2176 2163 | |
| 2177 2164 <span class="c"># Is it a specified functional/topological pharmacophore atom type?</span> | |
| 2178 2165 <span class="c">#</span> | |
| 2179 <a name="_IsFunctionalClassType-"></a>2166 <span class="k">sub </span><span class="m">_IsFunctionalClassType</span> <span class="s">{</span> | |
| 2180 2167 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2181 2168 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 2182 2169 | |
| 2183 2170 <span class="i">$Value</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2184 2171 | |
| 2185 2172 <span class="j">TYPE:</span> <span class="s">{</span> | |
| 2186 2173 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(HBD|HydrogenBondDonor)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2187 2174 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsHydrogenBondDonor</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2188 2175 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> | |
| 2189 2176 <span class="s">}</span> | |
| 2190 2177 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(HBA|HydrogenBondAcceptor)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2191 2178 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsHydrogenBondAcceptor</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2192 2179 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> | |
| 2193 2180 <span class="s">}</span> | |
| 2194 2181 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(PI|PositivelyIonizable)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2195 2182 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsPositivelyIonizable</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2196 2183 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> | |
| 2197 2184 <span class="s">}</span> | |
| 2198 2185 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(NI|NegativelyIonizable)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2199 2186 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsNegativelyIonizable</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2200 2187 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> | |
| 2201 2188 <span class="s">}</span> | |
| 2202 2189 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(H|Hydrophobic)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2203 2190 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsHydrophobic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2204 2191 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> | |
| 2205 2192 <span class="s">}</span> | |
| 2206 2193 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2207 2194 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2208 2195 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> | |
| 2209 2196 <span class="s">}</span> | |
| 2210 2197 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(Hal|Halogen)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2211 2198 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsHalogen</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2212 2199 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> | |
| 2213 2200 <span class="s">}</span> | |
| 2214 2201 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(RA|RingAtom)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2215 2202 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2216 2203 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> | |
| 2217 2204 <span class="s">}</span> | |
| 2218 2205 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(CA|ChainAtom)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2219 2206 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsNotInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2220 2207 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> | |
| 2221 2208 <span class="s">}</span> | |
| 2222 2209 <span class="i">$Value</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2223 2210 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_IsType: Unknown functional/pharmacohore type $Type..."</span><span class="sc">;</span> | |
| 2224 2211 <span class="s">}</span> | |
| 2225 2212 <span class="k">return</span> <span class="i">$Value</span><span class="sc">;</span> | |
| 2226 2213 <span class="s">}</span> | |
| 2227 2214 | |
| 2228 2215 <span class="c"># Is it a Hydrogen atom?</span> | |
| 2229 <a name="IsHydrogen-"></a>2216 <span class="k">sub </span><span class="m">IsHydrogen</span> <span class="s">{</span> | |
| 2230 2217 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2231 2218 | |
| 2232 2219 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">1</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2233 2220 <span class="s">}</span> | |
| 2234 2221 | |
| 2235 2222 <span class="c"># Is it a Carbon atom?</span> | |
| 2236 <a name="IsCarbon-"></a>2223 <span class="k">sub </span><span class="m">IsCarbon</span> <span class="s">{</span> | |
| 2237 2224 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2238 2225 | |
| 2239 2226 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">6</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2240 2227 <span class="s">}</span> | |
| 2241 2228 | |
| 2242 2229 <span class="c"># Is it a Nitrogen atom?</span> | |
| 2243 <a name="IsNitrogen-"></a>2230 <span class="k">sub </span><span class="m">IsNitrogen</span> <span class="s">{</span> | |
| 2244 2231 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2245 2232 | |
| 2246 2233 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">7</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2247 2234 <span class="s">}</span> | |
| 2248 2235 | |
| 2249 2236 <span class="c"># Is it a Oxygen atom?</span> | |
| 2250 <a name="IsOxygen-"></a>2237 <span class="k">sub </span><span class="m">IsOxygen</span> <span class="s">{</span> | |
| 2251 2238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2252 2239 | |
| 2253 2240 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">8</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2254 2241 <span class="s">}</span> | |
| 2255 2242 | |
| 2256 2243 <span class="c"># Is it a Fluorine atom?</span> | |
| 2257 <a name="IsFluorine-"></a>2244 <span class="k">sub </span><span class="m">IsFluorine</span> <span class="s">{</span> | |
| 2258 2245 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2259 2246 | |
| 2260 2247 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">9</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2261 2248 <span class="s">}</span> | |
| 2262 2249 | |
| 2263 2250 <span class="c"># Is it a Silicon atom?</span> | |
| 2264 <a name="IsSilicon-"></a>2251 <span class="k">sub </span><span class="m">IsSilicon</span> <span class="s">{</span> | |
| 2265 2252 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2266 2253 | |
| 2267 2254 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">14</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2268 2255 <span class="s">}</span> | |
| 2269 2256 | |
| 2270 2257 <span class="c"># Is it a Phosphorus atom?</span> | |
| 2271 <a name="IsPhosphorus-"></a>2258 <span class="k">sub </span><span class="m">IsPhosphorus</span> <span class="s">{</span> | |
| 2272 2259 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2273 2260 | |
| 2274 2261 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">15</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2275 2262 <span class="s">}</span> | |
| 2276 2263 | |
| 2277 2264 <span class="c"># Is it a Sulphur atom?</span> | |
| 2278 <a name="IsSulphur-"></a>2265 <span class="k">sub </span><span class="m">IsSulphur</span> <span class="s">{</span> | |
| 2279 2266 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2280 2267 | |
| 2281 2268 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsSulfur</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2282 2269 <span class="s">}</span> | |
| 2283 2270 | |
| 2284 2271 <span class="c"># Is it a Sulfur atom?</span> | |
| 2285 <a name="IsSulfur-"></a>2272 <span class="k">sub </span><span class="m">IsSulfur</span> <span class="s">{</span> | |
| 2286 2273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2287 2274 | |
| 2288 2275 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">16</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2289 2276 <span class="s">}</span> | |
| 2290 2277 | |
| 2291 2278 <span class="c"># Is it a Chlorine atom?</span> | |
| 2292 <a name="IsChlorine-"></a>2279 <span class="k">sub </span><span class="m">IsChlorine</span> <span class="s">{</span> | |
| 2293 2280 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2294 2281 | |
| 2295 2282 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">17</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2296 2283 <span class="s">}</span> | |
| 2297 2284 | |
| 2298 2285 <span class="c"># Is it a Arsenic atom?</span> | |
| 2299 <a name="IsArsenic-"></a>2286 <span class="k">sub </span><span class="m">IsArsenic</span> <span class="s">{</span> | |
| 2300 2287 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2301 2288 | |
| 2302 2289 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">33</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2303 2290 <span class="s">}</span> | |
| 2304 2291 | |
| 2305 2292 <span class="c"># Is it a Selenium atom?</span> | |
| 2306 <a name="IsSelenium-"></a>2293 <span class="k">sub </span><span class="m">IsSelenium</span> <span class="s">{</span> | |
| 2307 2294 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2308 2295 | |
| 2309 2296 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">34</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2310 2297 <span class="s">}</span> | |
| 2311 2298 | |
| 2312 2299 <span class="c"># Is it a Bromine atom?</span> | |
| 2313 <a name="IsBromine-"></a>2300 <span class="k">sub </span><span class="m">IsBromine</span> <span class="s">{</span> | |
| 2314 2301 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2315 2302 | |
| 2316 2303 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">35</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2317 2304 <span class="s">}</span> | |
| 2318 2305 | |
| 2319 2306 <span class="c"># Is it a Tellurium atom?</span> | |
| 2320 <a name="IsTellurium-"></a>2307 <span class="k">sub </span><span class="m">IsTellurium</span> <span class="s">{</span> | |
| 2321 2308 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2322 2309 | |
| 2323 2310 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">52</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2324 2311 <span class="s">}</span> | |
| 2325 2312 | |
| 2326 2313 <span class="c"># Is it a Iodine atom?</span> | |
| 2327 <a name="IsIodine-"></a>2314 <span class="k">sub </span><span class="m">IsIodine</span> <span class="s">{</span> | |
| 2328 2315 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2329 2316 | |
| 2330 2317 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">53</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2331 2318 <span class="s">}</span> | |
| 2332 2319 | |
| 2333 2320 <span class="c"># Is it a hetro atom? (N, O, F, P, S, Cl, Br, I)</span> | |
| 2334 <a name="IsHeteroAtom-"></a>2321 <span class="k">sub </span><span class="m">IsHeteroAtom</span> <span class="s">{</span> | |
| 2335 2322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2336 2323 | |
| 2337 2324 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8|9|15|16|17|35|53)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2338 2325 <span class="s">}</span> | |
| 2339 2326 | |
| 2340 2327 <span class="c"># Is it a halogen atom? (F, Cl, Br, I)</span> | |
| 2341 <a name="IsHalogen-"></a>2328 <span class="k">sub </span><span class="m">IsHalogen</span> <span class="s">{</span> | |
| 2342 2329 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2343 2330 | |
| 2344 2331 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(9|17|35|53)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2345 2332 <span class="s">}</span> | |
| 2346 2333 | |
| 2347 2334 <span class="c"># Is it classified as metallic?</span> | |
| 2348 <a name="IsMetallic-"></a>2335 <span class="k">sub </span><span class="m">IsMetallic</span> <span class="s">{</span> | |
| 2349 2336 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2350 2337 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="s">)</span><span class="sc">;</span> | |
| 2351 2338 | |
| 2352 2339 <span class="i">$Classification</span> = <span class="i">PeriodicTable::GetElementClassification</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span><span class="sc">;</span> | |
| 2353 2340 | |
| 2354 2341 <span class="k">return</span> <span class="s">(</span><span class="i">$Classification</span> =~ <span class="q">/^Metallic$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2355 2342 <span class="s">}</span> | |
| 2356 2343 | |
| 2357 2344 <span class="c"># Is it a non carbon or hydrogen atom? (C, H)</span> | |
| 2358 <a name="IsNonCarbonOrHydrogen-"></a>2345 <span class="k">sub </span><span class="m">IsNonCarbonOrHydrogen</span> <span class="s">{</span> | |
| 2359 2346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2360 2347 | |
| 2361 2348 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(1|6)$/</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 2362 2349 <span class="s">}</span> | |
| 2363 2350 | |
| 2364 2351 <span class="c"># Is it a polar atom? ( N, O, P, S)</span> | |
| 2365 <a name="IsPolarAtom-"></a>2352 <span class="k">sub </span><span class="m">IsPolarAtom</span> <span class="s">{</span> | |
| 2366 2353 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2367 2354 | |
| 2368 2355 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8|15|16)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2369 2356 <span class="s">}</span> | |
| 2370 2357 | |
| 2371 2358 <span class="c"># Is it an isotope?</span> | |
| 2372 <a name="IsIsotope-"></a>2359 <span class="k">sub </span><span class="m">IsIsotope</span> <span class="s">{</span> | |
| 2373 2360 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2374 2361 | |
| 2375 2362 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
| 2376 2363 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 2377 2364 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2378 2365 <span class="s">}</span> | |
| 2379 2366 | |
| 2380 2367 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2381 2368 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2382 2369 <span class="s">}</span> | |
| 2383 2370 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$MostAbundantMassNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 2384 2371 | |
| 2385 2372 <span class="i">$MassNumber</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span> | |
| 2386 2373 <span class="i">$MostAbundantMassNumber</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 2387 2374 | |
| 2388 2375 <span class="k">return</span> <span class="s">(</span><span class="i">$MassNumber</span> == <span class="i">$MostAbundantMassNumber</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 2389 2376 <span class="s">}</span> | |
| 2390 2377 | |
| 2391 2378 <span class="c"># Is it a terminal atom?</span> | |
| 2392 <a name="IsTerminal-"></a>2379 <span class="k">sub </span><span class="m">IsTerminal</span> <span class="s">{</span> | |
| 2393 2380 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2394 2381 | |
| 2395 2382 <span class="c"># Is this atom in a molecule?</span> | |
| 2396 2383 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2397 2384 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 2398 2385 <span class="s">}</span> | |
| 2399 2386 | |
| 2400 2387 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> <= <span class="n">1</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span> | |
| 2401 2388 | |
| 2402 2389 <span class="s">}</span> | |
| 2403 2390 | |
| 2404 2391 <span class="c"># Is aromatic property set for the atom?</span> | |
| 2405 <a name="IsAromatic-"></a>2392 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span> | |
| 2406 2393 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2407 2394 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span> | |
| 2408 2395 | |
| 2409 2396 <span class="i">$Aromatic</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2410 2397 | |
| 2411 2398 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span> && <span class="i">$Aromatic</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2412 2399 <span class="s">}</span> | |
| 2413 2400 | |
| 2414 2401 <span class="c"># Is this a hydrogen atom and attached to one of these atoms: N, O, P, S</span> | |
| 2415 <a name="IsPolarHydrogen-"></a>2402 <span class="k">sub </span><span class="m">IsPolarHydrogen</span> <span class="s">{</span> | |
| 2416 2403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2417 2404 | |
| 2418 2405 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2419 2406 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2420 2407 <span class="s">}</span> | |
| 2421 2408 | |
| 2422 2409 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 2423 2410 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2424 2411 <span class="k">if</span> <span class="s">(</span><span class="i">@Bonds</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 2425 2412 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2426 2413 <span class="s">}</span> | |
| 2427 2414 | |
| 2428 2415 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="s">)</span><span class="sc">;</span> | |
| 2429 2416 <span class="s">(</span><span class="i">$Bond</span><span class="s">)</span> = <span class="i">@Bonds</span><span class="sc">;</span> | |
| 2430 2417 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 2431 2418 | |
| 2432 2419 <span class="k">return</span> <span class="i">$BondedAtom</span><span class="i">->IsPolarAtom</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> | |
| 2433 2420 <span class="s">}</span> | |
| 2434 2421 | |
| 2435 2422 <span class="c"># Is it a hydrogen bond donor atom?</span> | |
| 2436 2423 <span class="c">#</span> | |
| 2437 <a name="IsHBondDonor-"></a>2424 <span class="k">sub </span><span class="m">IsHBondDonor</span> <span class="s">{</span> | |
| 2438 2425 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2439 2426 | |
| 2440 2427 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsHydrogenBondDonor</span><span class="s">(</span><span class="i">$HydrogenBondsType</span><span class="s">)</span><span class="sc">;</span> | |
| 2441 2428 <span class="s">}</span> | |
| 2442 2429 | |
| 2443 2430 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span> | |
| 2444 2431 <span class="c"># hydrogen bond donor and acceptor atoms with these names:</span> | |
| 2445 2432 <span class="c">#</span> | |
| 2446 2433 <span class="c"># HBondsType1 or HydrogenBondsType1</span> | |
| 2447 2434 <span class="c"># HBondsType2 or HydrogenBondsType2</span> | |
| 2448 2435 <span class="c">#</span> | |
| 2449 2436 <span class="c"># The names of these hydrogen bond types are rather arbitrary. However, their</span> | |
| 2450 2437 <span class="c"># definitions have specific meaning and are as follows:</span> | |
| 2451 2438 <span class="c">#</span> | |
| 2452 2439 <span class="c"># HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</span> | |
| 2453 2440 <span class="c"># . Donor: NH, NH2, NH3, OH - Any N and O with available H</span> | |
| 2454 2441 <span class="c"># . Acceptor: N[!H], O - Any N without available H and any O</span> | |
| 2455 2442 <span class="c">#</span> | |
| 2456 2443 <span class="c"># HydrogenBondsType2 [ Ref 91 ]:</span> | |
| 2457 2444 <span class="c"># . Donor: NH, NH2, NH3, OH - Any N and O with availabe H</span> | |
| 2458 2445 <span class="c"># . Acceptor: N, O - Any N and O</span> | |
| 2459 2446 <span class="c">#</span> | |
| 2460 2447 <span class="c"># Note:</span> | |
| 2461 2448 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span> | |
| 2462 2449 <span class="c">#</span> | |
| 2463 2450 | |
| 2464 2451 <span class="c"># Is it a hydrogen bond donor atom?</span> | |
| 2465 2452 <span class="c">#</span> | |
| 2466 2453 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span> | |
| 2467 <a name="IsHydrogenBondDonor-"></a>2454 <span class="k">sub </span><span class="m">IsHydrogenBondDonor</span> <span class="s">{</span> | |
| 2468 2455 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2469 2456 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 2470 2457 | |
| 2471 2458 <span class="i">$HydrogenBondsType</span> = <span class="k">defined</span> <span class="i">$HydrogenBondsType</span> ? <span class="i">$HydrogenBondsType</span> <span class="co">:</span> <span class="q">'HBondsType1'</span><span class="sc">;</span> | |
| 2472 2459 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2473 2460 | |
| 2474 2461 <span class="j">HYDROGENBONDSTYPE:</span> <span class="s">{</span> | |
| 2475 2462 | |
| 2476 2463 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType1|HydrogenBondsType1)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2477 2464 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2478 2465 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> | |
| 2479 2466 <span class="s">}</span> | |
| 2480 2467 | |
| 2481 2468 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2482 2469 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2483 2470 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> | |
| 2484 2471 <span class="s">}</span> | |
| 2485 2472 | |
| 2486 2473 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2487 2474 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->IsHydrogenBondDonor: The current release of MayaChemTools doesn't support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ..."</span><span class="sc">;</span> | |
| 2488 2475 <span class="s">}</span> | |
| 2489 2476 | |
| 2490 2477 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 2491 2478 <span class="s">}</span> | |
| 2492 2479 | |
| 2493 2480 <span class="c"># Is it a MayaChemTools HBondType1 hydrogen bond donor atom?</span> | |
| 2494 2481 <span class="c">#</span> | |
| 2495 <a name="_IsHydrogenBondDonorOfType1-"></a>2482 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType1</span> <span class="s">{</span> | |
| 2496 2483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2497 2484 | |
| 2498 2485 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType1OrType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2499 2486 <span class="s">}</span> | |
| 2500 2487 | |
| 2501 2488 <span class="c"># Is it a MayaChemTools HBondType2 hydrogen bond donor atom?</span> | |
| 2502 2489 <span class="c">#</span> | |
| 2503 <a name="_IsHydrogenBondDonorOfType2-"></a>2490 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType2</span> <span class="s">{</span> | |
| 2504 2491 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2505 2492 | |
| 2506 2493 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType1OrType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2507 2494 <span class="s">}</span> | |
| 2508 2495 | |
| 2509 2496 <span class="c"># Is it a hydrogen bond donor atom of MayaChemTools Type1 or Type2?</span> | |
| 2510 2497 <span class="c">#</span> | |
| 2511 2498 <span class="c"># HydrogenBondDonor definition [ Ref 60-61, Ref 65-66, Ref 91 ]: NH, NH2, OH</span> | |
| 2512 2499 <span class="c">#</span> | |
| 2513 2500 <span class="c"># In other words:</span> | |
| 2514 2501 <span class="c"># . NH, NH2 - Nitrogen atom with available hydrogen</span> | |
| 2515 2502 <span class="c"># . OH - Oxygen atom with avilable hydrogen</span> | |
| 2516 2503 <span class="c">#</span> | |
| 2517 <a name="_IsHydrogenBondDonorOfType1OrType2-"></a>2504 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType1OrType2</span> <span class="s">{</span> | |
| 2518 2505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2519 2506 | |
| 2520 2507 <span class="c"># Is this atom in a molecule?</span> | |
| 2521 2508 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2522 2509 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2523 2510 <span class="s">}</span> | |
| 2524 2511 | |
| 2525 2512 <span class="c"># Is it N or O?</span> | |
| 2526 2513 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(7|8)$/</span><span class="s">)</span> <span class="s">{</span> | |
| 2527 2514 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2528 2515 <span class="s">}</span> | |
| 2529 2516 | |
| 2530 2517 <span class="c"># Any explicitly attached hydrogens?</span> | |
| 2531 2518 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2532 2519 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2533 2520 <span class="s">}</span> | |
| 2534 2521 | |
| 2535 2522 <span class="c"># Any missing hydrogens?</span> | |
| 2536 2523 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</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> | |
| 2537 2524 <span class="s">}</span> | |
| 2538 2525 | |
| 2539 2526 <span class="c"># Is it a hydrogen bond acceptor atom?</span> | |
| 2540 2527 <span class="c">#</span> | |
| 2541 <a name="IsHBondAcceptor-"></a>2528 <span class="k">sub </span><span class="m">IsHBondAcceptor</span> <span class="s">{</span> | |
| 2542 2529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2543 2530 | |
| 2544 2531 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsHydrogenBondAcceptor</span><span class="s">(</span><span class="i">$HydrogenBondsType</span><span class="s">)</span><span class="sc">;</span> | |
| 2545 2532 <span class="s">}</span> | |
| 2546 2533 | |
| 2547 2534 <span class="c"># Is it a hydrogen bond acceptor atom?</span> | |
| 2548 2535 <span class="c">#</span> | |
| 2549 <a name="IsHydrogenBondAcceptor-"></a>2536 <span class="k">sub </span><span class="m">IsHydrogenBondAcceptor</span> <span class="s">{</span> | |
| 2550 2537 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2551 2538 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 2552 2539 | |
| 2553 2540 <span class="i">$HydrogenBondsType</span> = <span class="k">defined</span> <span class="i">$HydrogenBondsType</span> ? <span class="i">$HydrogenBondsType</span> <span class="co">:</span> <span class="q">'HBondsType1'</span><span class="sc">;</span> | |
| 2554 2541 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2555 2542 | |
| 2556 2543 <span class="j">HYDROGENBONDSTYPE:</span> <span class="s">{</span> | |
| 2557 2544 | |
| 2558 2545 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType1|HydrogenBondsType1)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2559 2546 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondAcceptorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2560 2547 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> | |
| 2561 2548 <span class="s">}</span> | |
| 2562 2549 | |
| 2563 2550 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2564 2551 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondAcceptorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2565 2552 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> | |
| 2566 2553 <span class="s">}</span> | |
| 2567 2554 | |
| 2568 2555 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2569 2556 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->IsHydrogenBondAcceptor: The current release of MayaChemTools doesn't support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ..."</span><span class="sc">;</span> | |
| 2570 2557 <span class="s">}</span> | |
| 2571 2558 | |
| 2572 2559 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 2573 2560 <span class="s">}</span> | |
| 2574 2561 | |
| 2575 2562 <span class="c"># Is it a MayaChemTools HBondType1 hydrogen bond acceptor atom?</span> | |
| 2576 2563 <span class="c">#</span> | |
| 2577 2564 <span class="c"># HydrogenBondAcceptor definition [ Ref 60-61, Ref 65-66 ]: N[!H], O</span> | |
| 2578 2565 <span class="c">#</span> | |
| 2579 2566 <span class="c"># In other words:</span> | |
| 2580 2567 <span class="c"># . N[!H] - Nitrogen atom with no hydrogen</span> | |
| 2581 2568 <span class="c"># . O - Oxygen atom</span> | |
| 2582 2569 <span class="c">#</span> | |
| 2583 <a name="_IsHydrogenBondAcceptorOfType1-"></a>2570 <span class="k">sub </span><span class="m">_IsHydrogenBondAcceptorOfType1</span> <span class="s">{</span> | |
| 2584 2571 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2585 2572 | |
| 2586 2573 <span class="c"># Is this atom in a molecule?</span> | |
| 2587 2574 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2588 2575 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2589 2576 <span class="s">}</span> | |
| 2590 2577 | |
| 2591 2578 <span class="c"># Is it N or O?</span> | |
| 2592 2579 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(7|8)$/</span><span class="s">)</span> <span class="s">{</span> | |
| 2593 2580 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2594 2581 <span class="s">}</span> | |
| 2595 2582 | |
| 2596 2583 <span class="c"># Is it O?</span> | |
| 2597 2584 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">8</span> <span class="s">)</span> <span class="s">{</span> | |
| 2598 2585 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2599 2586 <span class="s">}</span> | |
| 2600 2587 | |
| 2601 2588 <span class="c"># Any explicitly attached hydrogens?</span> | |
| 2602 2589 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2603 2590 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2604 2591 <span class="s">}</span> | |
| 2605 2592 | |
| 2606 2593 <span class="c"># Any missing hydrogens?</span> | |
| 2607 2594 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 2608 2595 <span class="s">}</span> | |
| 2609 2596 | |
| 2610 2597 <span class="c"># Is it a MayaChemTools HBondType2 hydrogen bond acceptor atom?</span> | |
| 2611 2598 <span class="c">#</span> | |
| 2612 2599 <span class="c"># HydrogenBondAcceptor definition [ Ref 91 ]: N, O</span> | |
| 2613 2600 <span class="c">#</span> | |
| 2614 2601 <span class="c"># In other words:</span> | |
| 2615 2602 <span class="c"># . Any Nitrogen or Oxygen atom</span> | |
| 2616 2603 <span class="c">#</span> | |
| 2617 2604 <span class="c"># Note:</span> | |
| 2618 2605 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span> | |
| 2619 2606 <span class="c">#</span> | |
| 2620 <a name="_IsHydrogenBondAcceptorOfType2-"></a>2607 <span class="k">sub </span><span class="m">_IsHydrogenBondAcceptorOfType2</span> <span class="s">{</span> | |
| 2621 2608 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2622 2609 | |
| 2623 2610 <span class="c"># Is this atom in a molecule?</span> | |
| 2624 2611 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2625 2612 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2626 2613 <span class="s">}</span> | |
| 2627 2614 | |
| 2628 2615 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2629 2616 <span class="s">}</span> | |
| 2630 2617 | |
| 2631 2618 <span class="c"># Is it a positively ionizable atom?</span> | |
| 2632 2619 <span class="c">#</span> | |
| 2633 2620 <span class="c"># PositivelyIonizable defintion [ Ref 60-61, Ref 65-66 ]: +, NH2</span> | |
| 2634 2621 <span class="c">#</span> | |
| 2635 2622 <span class="c"># In other words:</span> | |
| 2636 2623 <span class="c"># . Any atom with positve formal charge</span> | |
| 2637 2624 <span class="c"># . NH2 - Nitogen atom in amino group</span> | |
| 2638 2625 <span class="c">#</span> | |
| 2639 <a name="IsPositivelyIonizable-"></a>2626 <span class="k">sub </span><span class="m">IsPositivelyIonizable</span> <span class="s">{</span> | |
| 2640 2627 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2641 2628 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> | |
| 2642 2629 | |
| 2643 2630 <span class="c"># Is this atom in a molecule?</span> | |
| 2644 2631 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2645 2632 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2646 2633 <span class="s">}</span> | |
| 2647 2634 | |
| 2648 2635 <span class="c"># Any explicit positive formal charge?</span> | |
| 2649 2636 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2650 2637 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> && <span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 2651 2638 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2652 2639 <span class="s">}</span> | |
| 2653 2640 | |
| 2654 2641 <span class="c"># Is it N?</span> | |
| 2655 2642 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} != <span class="n">7</span> <span class="s">)</span> <span class="s">{</span> | |
| 2656 2643 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2657 2644 <span class="s">}</span> | |
| 2658 2645 | |
| 2659 2646 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span> == <span class="n">2</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2660 2647 <span class="s">}</span> | |
| 2661 2648 | |
| 2662 2649 <span class="c"># Is it a negatively ionizable atom?</span> | |
| 2663 2650 <span class="c">#</span> | |
| 2664 2651 <span class="c"># NegativelyIonizable definition [ Ref 60-61, Ref 65-66 ]: -, C(=O)OH, S(=O)OH, P(=O)OH</span> | |
| 2665 2652 <span class="c">#</span> | |
| 2666 2653 <span class="c"># In other words:</span> | |
| 2667 2654 <span class="c"># . Any atom with negative formal charge</span> | |
| 2668 2655 <span class="c"># . Carbon atom in C(=O)OH group</span> | |
| 2669 2656 <span class="c"># . Phosphorous in P(=O)OH group</span> | |
| 2670 2657 <span class="c"># . Sulfur atom in S(=O)OH group</span> | |
| 2671 2658 <span class="c">#</span> | |
| 2672 <a name="IsNegativelyIonizable-"></a>2659 <span class="k">sub </span><span class="m">IsNegativelyIonizable</span> <span class="s">{</span> | |
| 2673 2660 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2674 2661 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> | |
| 2675 2662 | |
| 2676 2663 <span class="c"># Is this atom in a molecule?</span> | |
| 2677 2664 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2678 2665 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2679 2666 <span class="s">}</span> | |
| 2680 2667 | |
| 2681 2668 <span class="c"># Any explicit negative formal charge?</span> | |
| 2682 2669 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2683 2670 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> && <span class="i">$FormalCharge</span> < <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 2684 2671 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2685 2672 <span class="s">}</span> | |
| 2686 2673 | |
| 2687 2674 <span class="c"># Is it C, P or S?</span> | |
| 2688 2675 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(6|15|16)$/</span> <span class="s">)</span> <span class="s">{</span> | |
| 2689 2676 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2690 2677 <span class="s">}</span> | |
| 2691 2678 | |
| 2692 2679 <span class="c"># Collect oxygens connected to C, P or S with single or double bonds and not connected to</span> | |
| 2693 2680 <span class="c"># any other heavy atom...</span> | |
| 2694 2681 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">$NeighborOxygenBondOrder</span><span class="cm">,</span> <span class="i">$NumOfNeighborOxygensWithSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 2695 2682 | |
| 2696 2683 <span class="i">$NumOfNeighborOxygensWithSingleBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2697 2684 | |
| 2698 2685 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2699 2686 <span class="c"># Is it an oxygen?</span> | |
| 2700 2687 <span class="k">if</span> <span class="s">(</span><span class="i">$Neighbor</span>->{<span class="w">AtomicNumber</span>} != <span class="n">8</span><span class="s">)</span> <span class="s">{</span> | |
| 2701 2688 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> | |
| 2702 2689 <span class="s">}</span> | |
| 2703 2690 <span class="c"># Is oxygent connected to only heavy atom?</span> | |
| 2704 2691 <span class="k">if</span> <span class="s">(</span><span class="i">$Neighbor</span><span class="i">->GetNumOfHeavyAtomNeighbors</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 2705 2692 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> | |
| 2706 2693 <span class="s">}</span> | |
| 2707 2694 <span class="i">$NeighborOxygenBondOrder</span> = <span class="i">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="i">$Neighbor</span><span class="s">)</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2708 2695 | |
| 2709 2696 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborOxygenBondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 2710 2697 <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span>++<span class="sc">;</span> | |
| 2711 2698 <span class="s">}</span> | |
| 2712 2699 <span class="k">elsif</span> <span class="s">(</span><span class="i">$NeighborOxygenBondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 2713 2700 <span class="i">$NumOfNeighborOxygensWithSingleBonds</span>++<span class="sc">;</span> | |
| 2714 2701 <span class="s">}</span> | |
| 2715 2702 <span class="s">}</span> | |
| 2716 2703 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfNeighborOxygensWithDoubleBonds</span> >= <span class="n">1</span> && <span class="i">$NumOfNeighborOxygensWithSingleBonds</span> >= <span class="n">1</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2717 2704 <span class="s">}</span> | |
| 2718 2705 | |
| 2719 2706 <span class="c"># Is it a liphophilic atom?</span> | |
| 2720 2707 <span class="c">#</span> | |
| 2721 2708 <span class="c"># Lipophilic definition [ Ref 60-61, Ref 65-66 ]: C(C)(C)(C)(C), Cl, Br, I, S(C)(C)</span> | |
| 2722 2709 <span class="c">#</span> | |
| 2723 2710 <span class="c"># In other words:</span> | |
| 2724 2711 <span class="c"># . C(C)(C)(C)(C) - Carbon atom connected to only other carbons</span> | |
| 2725 2712 <span class="c"># . Chlorine, Bromine or Iodine atom</span> | |
| 2726 2713 <span class="c"># . S(C)(C) - Sulfur connected to two carbons</span> | |
| 2727 2714 <span class="c">#</span> | |
| 2728 <a name="IsLipophilic-"></a>2715 <span class="k">sub </span><span class="m">IsLipophilic</span> <span class="s">{</span> | |
| 2729 2716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2730 2717 | |
| 2731 2718 <span class="c"># Is this atom in a molecule?</span> | |
| 2732 2719 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2733 2720 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2734 2721 <span class="s">}</span> | |
| 2735 2722 | |
| 2736 2723 <span class="c"># Is it Cl, Br, I?</span> | |
| 2737 2724 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(17|35|53)$/</span><span class="s">)</span> <span class="s">{</span> | |
| 2738 2725 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2739 2726 <span class="s">}</span> | |
| 2740 2727 | |
| 2741 2728 <span class="c"># Is it C, S?</span> | |
| 2742 2729 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(6|16)$/</span><span class="s">)</span> <span class="s">{</span> | |
| 2743 2730 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2744 2731 <span class="s">}</span> | |
| 2745 2732 | |
| 2746 2733 <span class="c"># Are all heavy atom neighbors Carbons?</span> | |
| 2747 2734 <span class="k">my</span><span class="s">(</span><span class="i">$HeavyAtomNeighbor</span><span class="cm">,</span> <span class="i">@HeavyAtomNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
| 2748 2735 <span class="i">@HeavyAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2749 2736 <span class="i">@HeavyAtomNeighbors</span> = <span class="i">$This</span><span class="i">->GetHeavyAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2750 2737 | |
| 2751 2738 <span class="k">for</span> <span class="i">$HeavyAtomNeighbor</span> <span class="s">(</span><span class="i">@HeavyAtomNeighbors</span><span class="s">)</span> <span class="s">{</span> | |
| 2752 2739 <span class="k">if</span> <span class="s">(</span><span class="i">$HeavyAtomNeighbor</span>->{<span class="w">AtomicNumber</span>} != <span class="n">6</span><span class="s">)</span> <span class="s">{</span> | |
| 2753 2740 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2754 2741 <span class="s">}</span> | |
| 2755 2742 <span class="s">}</span> | |
| 2756 2743 | |
| 2757 2744 <span class="c"># Does sulfur has two carbon neighbors?</span> | |
| 2758 2745 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">16</span><span class="s">)</span> <span class="s">{</span> | |
| 2759 2746 <span class="k">if</span> <span class="s">(</span><span class="i">@HeavyAtomNeighbors</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 2760 2747 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2761 2748 <span class="s">}</span> | |
| 2762 2749 <span class="s">}</span> | |
| 2763 2750 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2764 2751 <span class="s">}</span> | |
| 2765 2752 | |
| 2766 2753 <span class="c"># Is it hydrophobic?</span> | |
| 2767 2754 <span class="c">#</span> | |
| 2768 <a name="IsHydrophobic-"></a>2755 <span class="k">sub </span><span class="m">IsHydrophobic</span> <span class="s">{</span> | |
| 2769 2756 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2770 2757 | |
| 2771 2758 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsLipophilic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2772 2759 <span class="s">}</span> | |
| 2773 2760 | |
| 2774 2761 <span class="c"># Is it a Nitrogen atom in Guadinium group?</span> | |
| 2775 2762 <span class="c">#</span> | |
| 2776 <a name="IsGuadiniumNitrogen-"></a>2763 <span class="k">sub </span><span class="m">IsGuadiniumNitrogen</span> <span class="s">{</span> | |
| 2777 2764 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2778 2765 | |
| 2779 2766 <span class="c"># Is it Nitrogen?</span> | |
| 2780 2767 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2781 2768 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2782 2769 <span class="s">}</span> | |
| 2783 2770 | |
| 2784 2771 <span class="c"># Is it connected to a Guadinium Carbon?</span> | |
| 2785 2772 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span> | |
| 2786 2773 | |
| 2787 2774 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2788 2775 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->IsGuadiniumCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2789 2776 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2790 2777 <span class="s">}</span> | |
| 2791 2778 <span class="s">}</span> | |
| 2792 2779 | |
| 2793 2780 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2794 2781 <span class="s">}</span> | |
| 2795 2782 | |
| 2796 2783 <span class="c"># Is it a Carbon atom in Guadinium group?</span> | |
| 2797 2784 <span class="c">#</span> | |
| 2798 2785 <span class="c"># Guadinium group definition:</span> | |
| 2799 2786 <span class="c">#</span> | |
| 2800 2787 <span class="c"># R2N-C(=NR)-(NR2) or R2N-C(=NR2+)-(NR2)</span> | |
| 2801 2788 <span class="c">#</span> | |
| 2802 2789 <span class="c"># where:</span> | |
| 2803 2790 <span class="c"># . R = Hydrogens or group of atoms attached through Carbon</span> | |
| 2804 2791 <span class="c"># . Only one of the three Nitrogens has a double bond to Carbon and has optional</span> | |
| 2805 2792 <span class="c"># formal charge allowing it to be neutral or charged state</span> | |
| 2806 2793 <span class="c">#</span> | |
| 2807 <a name="IsGuadiniumCarbon-"></a>2794 <span class="k">sub </span><span class="m">IsGuadiniumCarbon</span> <span class="s">{</span> | |
| 2808 2795 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2809 2796 | |
| 2810 2797 <span class="c"># Is it Carbon?</span> | |
| 2811 2798 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2812 2799 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2813 2800 <span class="s">}</span> | |
| 2814 2801 | |
| 2815 2802 <span class="c"># Match atom neighborhood...</span> | |
| 2816 2803 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2817 2804 | |
| 2818 2805 <span class="i">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4'</span><span class="sc">;</span> | |
| 2819 2806 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'N.FC0'</span><span class="cm">,</span> <span class="q">'N.FC0'</span><span class="cm">,</span> <span class="q">'N.FC0,N.FC+1'</span><span class="s">)</span><span class="sc">;</span> | |
| 2820 2807 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="s">)</span><span class="sc">;</span> | |
| 2821 2808 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="s">)</span><span class="sc">;</span> | |
| 2822 2809 | |
| 2823 2810 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2824 2811 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2825 2812 <span class="s">}</span> | |
| 2826 2813 | |
| 2827 2814 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2828 2815 <span class="s">}</span> | |
| 2829 2816 | |
| 2830 2817 <span class="c"># Is it a Nitrogen atom in Amide group?</span> | |
| 2831 2818 <span class="c">#</span> | |
| 2832 <a name="IsAmideNitrogen-"></a>2819 <span class="k">sub </span><span class="m">IsAmideNitrogen</span> <span class="s">{</span> | |
| 2833 2820 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2834 2821 | |
| 2835 2822 <span class="c"># Is it Nitrogen?</span> | |
| 2836 2823 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2837 2824 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2838 2825 <span class="s">}</span> | |
| 2839 2826 | |
| 2840 2827 <span class="c"># Is it connected to a Amide Carbon?</span> | |
| 2841 2828 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span> | |
| 2842 2829 | |
| 2843 2830 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2844 2831 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->IsAmideCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2845 2832 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2846 2833 <span class="s">}</span> | |
| 2847 2834 <span class="s">}</span> | |
| 2848 2835 | |
| 2849 2836 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2850 2837 <span class="s">}</span> | |
| 2851 2838 | |
| 2852 2839 <span class="c"># Is it a Carbon atom in Amide group?</span> | |
| 2853 2840 <span class="c">#</span> | |
| 2854 2841 <span class="c"># Amide group definition: R-C(=O)-N(-R')-R''</span> | |
| 2855 2842 <span class="c">#</span> | |
| 2856 2843 <span class="c"># where:</span> | |
| 2857 2844 <span class="c"># . R = Hydrogen or groups of atoms attached through Carbon</span> | |
| 2858 2845 <span class="c"># . R' = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span> | |
| 2859 2846 <span class="c"># . R'' = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span> | |
| 2860 2847 <span class="c">#</span> | |
| 2861 <a name="IsAmideCarbon-"></a>2848 <span class="k">sub </span><span class="m">IsAmideCarbon</span> <span class="s">{</span> | |
| 2862 2849 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2863 2850 | |
| 2864 2851 <span class="c"># Is this atom in a molecule?</span> | |
| 2865 2852 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2866 2853 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2867 2854 <span class="s">}</span> | |
| 2868 2855 | |
| 2869 2856 <span class="c"># Is it Carbon?</span> | |
| 2870 2857 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2871 2858 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2872 2859 <span class="s">}</span> | |
| 2873 2860 | |
| 2874 2861 <span class="c"># Match atom neighborhood...</span> | |
| 2875 2862 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2876 2863 | |
| 2877 2864 <span class="i">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4,C.X2.BO3'</span><span class="sc">;</span> | |
| 2878 2865 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'N'</span><span class="s">)</span><span class="sc">;</span> | |
| 2879 2866 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">)</span><span class="sc">;</span> | |
| 2880 2867 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C'</span><span class="cm">,</span> <span class="q">'C,H,N,O,S,P,F,Cl,Br,I'</span><span class="s">)</span><span class="sc">;</span> | |
| 2881 2868 | |
| 2882 2869 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2883 2870 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2884 2871 <span class="s">}</span> | |
| 2885 2872 | |
| 2886 2873 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2887 2874 <span class="s">}</span> | |
| 2888 2875 | |
| 2889 2876 <span class="c"># Is it a Oxygen atom in Carboxylate group?</span> | |
| 2890 2877 <span class="c">#</span> | |
| 2891 <a name="IsCarboxylateOxygen-"></a>2878 <span class="k">sub </span><span class="m">IsCarboxylateOxygen</span> <span class="s">{</span> | |
| 2892 2879 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2893 2880 | |
| 2894 2881 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">'Carboxylate'</span><span class="s">)</span><span class="sc">;</span> | |
| 2895 2882 <span class="s">}</span> | |
| 2896 2883 | |
| 2897 2884 <span class="c"># Is it a Carbon atom in Carboxylate group?</span> | |
| 2898 2885 <span class="c">#</span> | |
| 2899 2886 <span class="c"># Carboxyl group definition: R-C(=O)-O-</span> | |
| 2900 2887 <span class="c">#</span> | |
| 2901 <a name="IsCarboxylateCarbon-"></a>2888 <span class="k">sub </span><span class="m">IsCarboxylateCarbon</span> <span class="s">{</span> | |
| 2902 2889 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2903 2890 | |
| 2904 2891 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">'Carboxylate'</span><span class="s">)</span><span class="sc">;</span> | |
| 2905 2892 <span class="s">}</span> | |
| 2906 2893 | |
| 2907 2894 <span class="c"># Is it a Oxygen atom in Carboxyl group?</span> | |
| 2908 2895 <span class="c">#</span> | |
| 2909 <a name="IsCarboxylOxygen-"></a>2896 <span class="k">sub </span><span class="m">IsCarboxylOxygen</span> <span class="s">{</span> | |
| 2910 2897 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2911 2898 | |
| 2912 2899 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">'Carboxyl'</span><span class="s">)</span><span class="sc">;</span> | |
| 2913 2900 <span class="s">}</span> | |
| 2914 2901 | |
| 2915 2902 <span class="c"># Is it a Carbon atom in Carboxyl group?</span> | |
| 2916 2903 <span class="c">#</span> | |
| 2917 2904 <span class="c"># Carboxyl group definition: R-C(=O)-OH</span> | |
| 2918 2905 <span class="c">#</span> | |
| 2919 <a name="IsCarboxylCarbon-"></a>2906 <span class="k">sub </span><span class="m">IsCarboxylCarbon</span> <span class="s">{</span> | |
| 2920 2907 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2921 2908 | |
| 2922 2909 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">'Carboxyl'</span><span class="s">)</span><span class="sc">;</span> | |
| 2923 2910 <span class="s">}</span> | |
| 2924 2911 | |
| 2925 2912 <span class="c"># Match Carboxylate and/or Carboxyl oxygen...</span> | |
| 2926 2913 <span class="c">#</span> | |
| 2927 <a name="_MatchCarboxylateAndOrCarboxylOxygen-"></a>2914 <span class="k">sub </span><span class="m">_MatchCarboxylateAndOrCarboxylOxygen</span> <span class="s">{</span> | |
| 2928 2915 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2929 2916 | |
| 2930 2917 <span class="c"># Is it Oxygen?</span> | |
| 2931 2918 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2932 2919 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2933 2920 <span class="s">}</span> | |
| 2934 2921 | |
| 2935 2922 <span class="c"># Is it connected to a Carboxylate Carbon?</span> | |
| 2936 2923 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span> | |
| 2937 2924 | |
| 2938 2925 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2939 2926 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2940 2927 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2941 2928 <span class="s">}</span> | |
| 2942 2929 <span class="s">}</span> | |
| 2943 2930 | |
| 2944 2931 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2945 2932 <span class="s">}</span> | |
| 2946 2933 | |
| 2947 2934 <span class="c"># Match Carboxylate and Carboxyl Carbon</span> | |
| 2948 2935 <span class="c">#</span> | |
| 2949 2936 <span class="c"># Carboxylate group definition: R-C(=O)-O-</span> | |
| 2950 2937 <span class="c"># Carboxyl group definition: R-C(=O)-OH</span> | |
| 2951 2938 <span class="c">#</span> | |
| 2952 2939 <span class="c"># where:</span> | |
| 2953 2940 <span class="c"># . R = Hydrogens or groups of atoms attached through Carbon</span> | |
| 2954 2941 <span class="c">#</span> | |
| 2955 <a name="_MatchCarboxylateAndOrCarboxylCarbon-"></a>2942 <span class="k">sub </span><span class="m">_MatchCarboxylateAndOrCarboxylCarbon</span> <span class="s">{</span> | |
| 2956 2943 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2957 2944 | |
| 2958 2945 <span class="c"># Is this atom in a molecule?</span> | |
| 2959 2946 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2960 2947 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2961 2948 <span class="s">}</span> | |
| 2962 2949 | |
| 2963 2950 <span class="c"># Is it Carbon?</span> | |
| 2964 2951 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2965 2952 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2966 2953 <span class="s">}</span> | |
| 2967 2954 | |
| 2968 2955 <span class="c"># Match atom neighborhood...</span> | |
| 2969 2956 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2970 2957 | |
| 2971 2958 <span class="i">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4,C.X2.BO3'</span><span class="sc">;</span> | |
| 2972 2959 <span class="j">MODE:</span> <span class="s">{</span> | |
| 2973 2960 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Carboxylate$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2974 2961 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O.X1.FC-1'</span><span class="s">)</span><span class="sc">;</span> | |
| 2975 2962 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> | |
| 2976 2963 <span class="s">}</span> | |
| 2977 2964 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Carboxyl$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2978 2965 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O.X1.FC0'</span><span class="s">)</span><span class="sc">;</span> | |
| 2979 2966 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> | |
| 2980 2967 <span class="s">}</span> | |
| 2981 2968 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^CarboxylateOrCarboxyl$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2982 2969 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O.X1.FC-1,O.X1.FC0'</span><span class="s">)</span><span class="sc">;</span> | |
| 2983 2970 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> | |
| 2984 2971 <span class="s">}</span> | |
| 2985 2972 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_MatchCarboxylateAndCarboxylCarbon.: Unknown mode $Mode..."</span><span class="sc">;</span> | |
| 2986 2973 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2987 2974 <span class="s">}</span> | |
| 2988 2975 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">)</span><span class="sc">;</span> | |
| 2989 2976 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C'</span><span class="cm">,</span> <span class="q">'C'</span><span class="s">)</span><span class="sc">;</span> | |
| 2990 2977 | |
| 2991 2978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2992 2979 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2993 2980 <span class="s">}</span> | |
| 2994 2981 | |
| 2995 2982 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2996 2983 <span class="s">}</span> | |
| 2997 2984 | |
| 2998 2985 <span class="c"># Is it a Oxygen atom in Phosphate group?</span> | |
| 2999 2986 <span class="c">#</span> | |
| 3000 <a name="IsPhosphateOxygen-"></a>2987 <span class="k">sub </span><span class="m">IsPhosphateOxygen</span> <span class="s">{</span> | |
| 3001 2988 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3002 2989 | |
| 3003 2990 <span class="c"># Is it Oxygen?</span> | |
| 3004 2991 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3005 2992 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3006 2993 <span class="s">}</span> | |
| 3007 2994 | |
| 3008 2995 <span class="c"># Is it connected to a Phosphate Phosphorus?</span> | |
| 3009 2996 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span> | |
| 3010 2997 | |
| 3011 2998 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3012 2999 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->IsPhosphatePhosphorus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3013 3000 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3014 3001 <span class="s">}</span> | |
| 3015 3002 <span class="s">}</span> | |
| 3016 3003 | |
| 3017 3004 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3018 3005 <span class="s">}</span> | |
| 3019 3006 | |
| 3020 3007 <span class="c"># Is it a Phosphorus atom in Phosphate group?</span> | |
| 3021 3008 <span class="c">#</span> | |
| 3022 3009 <span class="c"># Phosphate group definition: AO-(O=)P(-OA)-OA</span> | |
| 3023 3010 <span class="c">#</span> | |
| 3024 3011 <span class="c"># where:</span> | |
| 3025 3012 <span class="c"># . A = Any Groups of atoms including hydrogens</span> | |
| 3026 3013 <span class="c">#</span> | |
| 3027 <a name="IsPhosphatePhosphorus-"></a>3014 <span class="k">sub </span><span class="m">IsPhosphatePhosphorus</span> <span class="s">{</span> | |
| 3028 3015 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3029 3016 | |
| 3030 3017 <span class="c"># Is this atom in a molecule?</span> | |
| 3031 3018 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3032 3019 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3033 3020 <span class="s">}</span> | |
| 3034 3021 | |
| 3035 3022 <span class="c"># Is it Phosphorus?</span> | |
| 3036 3023 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsPhosphorus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3037 3024 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3038 3025 <span class="s">}</span> | |
| 3039 3026 | |
| 3040 3027 <span class="c"># Match atom neighborhood...</span> | |
| 3041 3028 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 3042 3029 | |
| 3043 3030 <span class="i">$CentralAtomSpec</span> = <span class="q">'P.X4.BO5'</span><span class="sc">;</span> | |
| 3044 3031 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="s">)</span><span class="sc">;</span> | |
| 3045 3032 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">)</span><span class="sc">;</span> | |
| 3046 3033 <span class="i">@NbrOfNbrAtomSpecsRef</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="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 3047 3034 | |
| 3048 3035 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3049 3036 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3050 3037 <span class="s">}</span> | |
| 3051 3038 | |
| 3052 3039 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3053 3040 <span class="s">}</span> | |
| 3054 3041 | |
| 3055 3042 | |
| 3056 3043 <span class="c"># Match central atom and its neighborhood using specified atom and bonds specifications...</span> | |
| 3057 3044 <span class="c">#</span> | |
| 3058 3045 <span class="c"># Let:</span> | |
| 3059 3046 <span class="c"># AS = Atom symbol corresponding to element symbol, atomic number (#n) or any</span> | |
| 3060 3047 <span class="c"># atom (A)</span> | |
| 3061 3048 <span class="c">#</span> | |
| 3062 3049 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 3063 3050 <span class="c"># T<n> = Total number of atom neighbors including implcit and explicit hydrogens</span> | |
| 3064 3051 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 3065 3052 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 3066 3053 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 3067 3054 <span class="c"># TSB<n> = Total number of single bonds to atom neighbors including implcit and explicit hydrogens</span> | |
| 3068 3055 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 3069 3056 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 3070 3057 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> | |
| 3071 3058 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> | |
| 3072 3059 <span class="c"># RA or RA<n> = Ring atom annotation indicating whether atom is a ring</span> | |
| 3073 3060 <span class="c"># TR<n> = Total number of rings containing atom</span> | |
| 3074 3061 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> | |
| 3075 3062 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> | |
| 3076 3063 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> | |
| 3077 3064 <span class="c">#</span> | |
| 3078 3065 <span class="c"># Then:</span> | |
| 3079 3066 <span class="c">#</span> | |
| 3080 3067 <span class="c"># Atom specification corresponds to:</span> | |
| 3081 3068 <span class="c">#</span> | |
| 3082 3069 <span class="c"># AS.X<n>.T<n>.BO<n>.LBO<n>.<SB><n>.TSB<n>.<DB><n>.<TB><n>.H<n>.Ar.RA<n>.TR<n>FC<+n/-n>.MN<n>.SM<n></span> | |
| 3083 3070 <span class="c">#</span> | |
| 3084 3071 <span class="c"># Except for AS which is a required atomic invariant in atom specification, all other atomic invariants are</span> | |
| 3085 3072 <span class="c"># optional. For an atom specification to match an atom, the values of all specified atomic invariants must</span> | |
| 3086 3073 <span class="c"># match. Exclamation in from of atomic invariant can be used to negate its effect during the match.</span> | |
| 3087 3074 <span class="c">#</span> | |
| 3088 3075 <span class="c"># A comma delimited atom specification string is used to match any one of the specifed atom specification.</span> | |
| 3089 3076 <span class="c">#</span> | |
| 3090 3077 <span class="c"># Notes:</span> | |
| 3091 3078 <span class="c"># . During atom specification match to an atom, the first atomic invariant is always assumed to</span> | |
| 3092 3079 <span class="c"># atom symbol.</span> | |
| 3093 3080 <span class="c"># . Atom match specfication is based on AtomicInvariantAtomTypes implemented in</span> | |
| 3094 3081 <span class="c"># AotmTypes::AtomicInvariantAtomType.pm module</span> | |
| 3095 3082 <span class="c">#</span> | |
| 3096 3083 <span class="c"># Examples:</span> | |
| 3097 3084 <span class="c"># . ('N', 'N', 'N')</span> | |
| 3098 3085 <span class="c"># . ('N.FC0', 'N.FC0', 'N,N.FC+1.H1')</span> | |
| 3099 3086 <span class="c"># . ('N.H2', 'N.H2', 'N.H1')</span> | |
| 3100 3087 <span class="c"># . ('C,N', '!N', '!H')</span> | |
| 3101 3088 <span class="c"># . ('C,N', 'N.Ar', 'N.R5')</span> | |
| 3102 3089 <span class="c">#</span> | |
| 3103 3090 <span class="c"># Let:</span> | |
| 3104 3091 <span class="c"># -|1|s|Single = Single bond</span> | |
| 3105 3092 <span class="c"># =|2|d|Double = Double bond</span> | |
| 3106 3093 <span class="c"># #|3|t|Triple = Triple bond</span> | |
| 3107 3094 <span class="c"># :|1.5|a|Ar|Aromatic = Aromatic bond</span> | |
| 3108 3095 <span class="c">#</span> | |
| 3109 3096 <span class="c"># @|RB|Ring = Ring bond</span> | |
| 3110 3097 <span class="c"># ~|*|Any = Any bond</span> | |
| 3111 3098 <span class="c">#</span> | |
| 3112 3099 <span class="c"># Then:</span> | |
| 3113 3100 <span class="c">#</span> | |
| 3114 3101 <span class="c"># Bond specification corresponds to:</span> | |
| 3115 3102 <span class="c">#</span> | |
| 3116 3103 <span class="c"># -.:</span> | |
| 3117 3104 <span class="c"># =.@</span> | |
| 3118 3105 <span class="c"># Double.Aromatic</span> | |
| 3119 3106 <span class="c">#</span> | |
| 3120 3107 <span class="c"># For a bond specification to match bond between two atoms, the values of all specified bond symbols must</span> | |
| 3121 3108 <span class="c"># match. Exclamation in from of bond symbol can be used to negate its effect during the match.</span> | |
| 3122 3109 <span class="c">#</span> | |
| 3123 3110 <span class="c"># A comma delimited bond specification string is used to match any one of the specifed atom specification.</span> | |
| 3124 3111 <span class="c">#</span> | |
| 3125 <a name="DoesAtomNeighborhoodMatch-"></a>3112 <span class="k">sub </span><span class="m">DoesAtomNeighborhoodMatch</span> <span class="s">{</span> | |
| 3126 3113 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="cm">,</span> <span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3127 3114 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NumOfNbrBondSpecs</span><span class="cm">,</span> <span class="i">$NumOfNbrOfNbrAtomSpecs</span><span class="s">)</span><span class="sc">;</span> | |
| 3128 3115 | |
| 3129 3116 <span class="c"># Is this atom in a molecule?</span> | |
| 3130 3117 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3131 3118 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3132 3119 <span class="s">}</span> | |
| 3133 3120 | |
| 3134 3121 <span class="i">$NumOfNbrAtomSpecs</span> = <span class="k">defined</span> <span class="i">$NbrAtomSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3135 3122 <span class="i">$NumOfNbrBondSpecs</span> = <span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrBondSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3136 3123 <span class="i">$NumOfNbrOfNbrAtomSpecs</span> = <span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrOfNbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3137 3124 | |
| 3138 3125 <span class="c"># Validate number of specifications...</span> | |
| 3139 3126 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrBondSpecs</span> && <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> != <span class="i">$NumOfNbrBondSpecs</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3140 3127 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and bond, $NumOfNbrBondSpecs, specifications must be same; No neighborhood match performed ..."</span><span class="sc">;</span> | |
| 3141 3128 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3142 3129 <span class="s">}</span> | |
| 3143 3130 | |
| 3144 3131 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrOfNbrAtomSpecs</span> && <span class="s">(</span><span class="i">$NumOfNbrOfNbrAtomSpecs</span> != <span class="i">$NumOfNbrAtomSpecs</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3145 3132 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and neighbor of neighbor atoms specifications, $NumOfNbrOfNbrAtomSpecs, must be same; No neighborhood match performed ..."</span><span class="sc">;</span> | |
| 3146 3133 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3147 3134 <span class="s">}</span> | |
| 3148 3135 | |
| 3149 3136 <span class="c"># Sort atom and bond specifications in terms of being most specific to least specific..</span> | |
| 3150 3137 <span class="s">(</span><span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">$CentralAtom</span><span class="i">->_SortSpecificationsForAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 3151 3138 | |
| 3152 3139 <span class="c"># Does central atom specification match?</span> | |
| 3153 3140 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3154 3141 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3155 3142 <span class="s">}</span> | |
| 3156 3143 | |
| 3157 3144 <span class="c"># No neighbors to match...</span> | |
| 3158 3145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfNbrAtomSpecs</span><span class="s">)</span> <span class="s">{</span> | |
| 3159 3146 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3160 3147 <span class="s">}</span> | |
| 3161 3148 | |
| 3162 3149 <span class="c"># Match neighbors...</span> | |
| 3163 3150 <span class="k">my</span><span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> <span class="i">%NbrSpecAlreadyMatchedMap</span><span class="s">)</span><span class="sc">;</span> | |
| 3164 3151 | |
| 3165 3152 <span class="i">$NbrSpecCount</span> = <span class="i">$NumOfNbrAtomSpecs</span><span class="sc">;</span> | |
| 3166 3153 <span class="i">$NbrSpecMatchCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3167 3154 | |
| 3168 3155 <span class="i">%NbrSpecAlreadyMatchedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3169 3156 <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span> = <span class="i">$CentralAtom</span><span class="i">->_MatchAtomNeighborhoodUsingAtomBondSpecs</span><span class="s">(</span><span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> \<span class="i">%NbrSpecAlreadyMatchedMap</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 3170 3157 | |
| 3171 3158 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="s">)</span> <span class="s">{</span> | |
| 3172 3159 <span class="c"># It's match...</span> | |
| 3173 3160 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3174 3161 <span class="s">}</span> | |
| 3175 3162 | |
| 3176 3163 <span class="c"># Match central atom's missing hydrogens with any unmatched atom</span> | |
| 3177 3164 <span class="c"># and bond specifications...</span> | |
| 3178 3165 <span class="c">#</span> | |
| 3179 3166 <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span> = <span class="i">$CentralAtom</span><span class="i">->_MatchAtomNeighborhoodUsingMissingHydrogens</span><span class="s">(</span><span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> \<span class="i">%NbrSpecAlreadyMatchedMap</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 3180 3167 | |
| 3181 3168 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="s">)</span> <span class="s">{</span> | |
| 3182 3169 <span class="c"># It's match...</span> | |
| 3183 3170 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3184 3171 <span class="s">}</span> | |
| 3185 3172 | |
| 3186 3173 <span class="c"># No match...</span> | |
| 3187 3174 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3188 3175 <span class="s">}</span> | |
| 3189 3176 | |
| 3190 3177 <span class="c"># Match central atom neighborhood atom and bond specifications...</span> | |
| 3191 3178 <span class="c">#</span> | |
| 3192 <a name="_MatchAtomNeighborhoodUsingAtomBondSpecs-"></a>3179 <span class="k">sub </span><span class="m">_MatchAtomNeighborhoodUsingAtomBondSpecs</span> <span class="s">{</span> | |
| 3193 3180 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="cm">,</span> <span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> <span class="i">$NbrSpecAlreadyMatchedRef</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3194 3181 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$NbrAtom</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="cm">,</span> <span class="i">$NbrBondSpec</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtom</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpec</span><span class="cm">,</span> <span class="i">$MatchNbrOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrSpecsMatched</span><span class="s">)</span><span class="sc">;</span> | |
| 3195 3182 | |
| 3196 3183 <span class="i">$MatchNbrOfNbrAtomSpecs</span> = <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span> && <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrOfNbrAtomSpecsRef</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3197 3184 | |
| 3198 3185 <span class="i">$NbrSpecsMatched</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3199 3186 | |
| 3200 3187 <span class="c"># Match central atom's immediate neighbors atom and bond specifications...</span> | |
| 3201 3188 <span class="j">NBRATOM:</span> <span class="k">for</span> <span class="i">$NbrAtom</span> <span class="s">(</span><span class="i">$CentralAtom</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3202 3189 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3203 3190 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>}<span class="s">)</span> <span class="s">{</span> | |
| 3204 3191 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> | |
| 3205 3192 <span class="s">}</span> | |
| 3206 3193 <span class="i">$NbrAtomSpec</span> = <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 3207 3194 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 3208 3195 | |
| 3209 3196 <span class="i">$NbrOfNbrAtomSpec</span> = <span class="i">$MatchNbrOfNbrAtomSpecs</span> ? <span class="i">$NbrOfNbrAtomSpecsRef</span>->[<span class="i">$Index</span>] <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3210 3197 | |
| 3211 3198 <span class="c"># Match neighbor atom specification...</span> | |
| 3212 3199 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NbrAtom</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$NbrAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3213 3200 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> | |
| 3214 3201 <span class="s">}</span> | |
| 3215 3202 | |
| 3216 3203 <span class="c"># Match central atom to neighbor atom bond specification...</span> | |
| 3217 3204 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">->_DoesBondSpecificationMatch</span><span class="s">(</span><span class="i">$NbrAtom</span><span class="cm">,</span> <span class="i">$NbrBondSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3218 3205 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> | |
| 3219 3206 <span class="s">}</span> | |
| 3220 3207 | |
| 3221 3208 <span class="c"># Match any neighbor of neighbor atom specifications...</span> | |
| 3222 3209 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span> | |
| 3223 3210 <span class="c"># Go over the neighbors of central atom skipping the central atom...</span> | |
| 3224 3211 <span class="k">for</span> <span class="i">$NbrOfNbrAtom</span> <span class="s">(</span><span class="i">$NbrAtom</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3225 3212 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NbrOfNbrAtom</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$NbrOfNbrAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3226 3213 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> | |
| 3227 3214 <span class="s">}</span> | |
| 3228 3215 <span class="s">}</span> | |
| 3229 3216 <span class="s">}</span> | |
| 3230 3217 | |
| 3231 3218 <span class="c"># It's a match for a neighbor atom specification...</span> | |
| 3232 3219 <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>} = <span class="i">$Index</span><span class="sc">;</span> | |
| 3233 3220 <span class="i">$NbrSpecMatchCount</span>++<span class="sc">;</span> | |
| 3234 3221 | |
| 3235 3222 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecMatchCount</span> == <span class="i">$NbrSpecCount</span><span class="s">)</span> <span class="s">{</span> | |
| 3236 3223 <span class="c"># It's match...</span> | |
| 3237 3224 <span class="i">$NbrSpecsMatched</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3238 3225 <span class="k">last</span> <span class="j">NBRATOM</span><span class="sc">;</span> | |
| 3239 3226 <span class="s">}</span> | |
| 3240 3227 <span class="c"># Match next neighbor atom...</span> | |
| 3241 3228 <span class="k">next</span> <span class="j">NBRATOM</span><span class="sc">;</span> | |
| 3242 3229 <span class="s">}</span> | |
| 3243 3230 <span class="s">}</span> | |
| 3244 3231 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span> | |
| 3245 3232 <span class="s">}</span> | |
| 3246 3233 | |
| 3247 3234 <span class="c"># Match central atom's missing hydrogens with any unmatched atom and bond</span> | |
| 3248 3235 <span class="c"># specifications...</span> | |
| 3249 3236 <span class="c">#</span> | |
| 3250 <a name="_MatchAtomNeighborhoodUsingMissingHydrogens-"></a>3237 <span class="k">sub </span><span class="m">_MatchAtomNeighborhoodUsingMissingHydrogens</span> <span class="s">{</span> | |
| 3251 3238 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="cm">,</span> <span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> <span class="i">$NbrSpecAlreadyMatchedRef</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3252 3239 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$NbrAtom</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="cm">,</span> <span class="i">$NbrBondSpec</span><span class="cm">,</span> <span class="i">$NumOfMissingHydrogens</span><span class="cm">,</span> <span class="i">$MissingHydrogensIndex</span><span class="cm">,</span> <span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$AtomSpecMatched</span><span class="cm">,</span> <span class="i">$AtomSpec</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span> | |
| 3253 3240 | |
| 3254 3241 <span class="i">$NbrSpecsMatched</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3255 3242 | |
| 3256 3243 <span class="i">$NumOfMissingHydrogens</span> = <span class="i">$CentralAtom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3257 3244 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="i">$NbrSpecMatchCount</span><span class="s">)</span> > <span class="i">$NumOfMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
| 3258 3245 <span class="c"># It won't match...</span> | |
| 3259 3246 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span> | |
| 3260 3247 <span class="s">}</span> | |
| 3261 3248 | |
| 3262 3249 <span class="j">MISSINGHYDROGENNBR:</span> <span class="k">for</span> <span class="i">$MissingHydrogensIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfMissingHydrogens</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3263 3250 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3264 3251 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>}<span class="s">)</span> <span class="s">{</span> | |
| 3265 3252 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> | |
| 3266 3253 <span class="s">}</span> | |
| 3267 3254 <span class="i">$NbrAtomSpec</span> = <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 3268 3255 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 3269 3256 | |
| 3270 3257 <span class="i">$NbrAtomSpec</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 3271 3258 | |
| 3272 3259 <span class="c"># Match neighbor atom specification hydrogen atom symbol...</span> | |
| 3273 3260 <span class="i">$AtomSpecMatched</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3274 3261 <span class="j">ATOMSPEC:</span> <span class="k">for</span> <span class="i">$AtomSpec</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="s">)</span> <span class="s">{</span> | |
| 3275 3262 <span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomSpec</span><span class="sc">;</span> | |
| 3276 3263 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomSymbol</span> =~ <span class="q">/^(H|A|\*)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3277 3264 <span class="i">$AtomSpecMatched</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3278 3265 <span class="k">last</span> <span class="j">ATOMSPEC</span><span class="sc">;</span> | |
| 3279 3266 <span class="s">}</span> | |
| 3280 3267 <span class="s">}</span> | |
| 3281 3268 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSpecMatched</span><span class="s">)</span> <span class="s">{</span> | |
| 3282 3269 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> | |
| 3283 3270 <span class="s">}</span> | |
| 3284 3271 | |
| 3285 3272 <span class="c"># Match neighbor atom bond specification to singal bond...</span> | |
| 3286 3273 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrBondSpec</span><span class="s">)</span> <span class="s">{</span> | |
| 3287 3274 <span class="i">$NbrBondSpec</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 3288 3275 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrBondSpec</span> !~ <span class="q">/^(-|1|s|Single|\~|\*|Any)/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3289 3276 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> | |
| 3290 3277 <span class="s">}</span> | |
| 3291 3278 <span class="s">}</span> | |
| 3292 3279 | |
| 3293 3280 <span class="c"># It's a match for a neighbor atom specification...</span> | |
| 3294 3281 <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>} = <span class="i">$Index</span><span class="sc">;</span> | |
| 3295 3282 <span class="i">$NbrSpecMatchCount</span>++<span class="sc">;</span> | |
| 3296 3283 | |
| 3297 3284 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecMatchCount</span> == <span class="i">$NbrSpecCount</span><span class="s">)</span> <span class="s">{</span> | |
| 3298 3285 <span class="c"># It's match...</span> | |
| 3299 3286 <span class="i">$NbrSpecsMatched</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3300 3287 <span class="k">last</span> <span class="j">MISSINGHYDROGENNBR</span><span class="sc">;</span> | |
| 3301 3288 <span class="s">}</span> | |
| 3302 3289 <span class="c"># Match next missing hydrogen neighbor...</span> | |
| 3303 3290 <span class="k">next</span> <span class="j">MISSINGHYDROGENNBR</span><span class="sc">;</span> | |
| 3304 3291 <span class="s">}</span> | |
| 3305 3292 <span class="s">}</span> | |
| 3306 3293 | |
| 3307 3294 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span> | |
| 3308 3295 <span class="s">}</span> | |
| 3309 3296 | |
| 3310 3297 <span class="c"># Sort atom and bond specifications base on neighbor atom specifications going</span> | |
| 3311 3298 <span class="c"># from most to least specific atom specifications.</span> | |
| 3312 3299 <span class="c">#</span> | |
| 3313 3300 <span class="c"># Atom specifications are sorted at the following two levels:</span> | |
| 3314 3301 <span class="c">#</span> | |
| 3315 3302 <span class="c"># o By atom specification count with in each specification going from most specific</span> | |
| 3316 3303 <span class="c"># to least specific, where count is determined by the number of "," in each</span> | |
| 3317 3304 <span class="c"># specification. Wild card containing specifications are considered least specific</span> | |
| 3318 3305 <span class="c"># and end up at the end of the sorted list.</span> | |
| 3319 3306 <span class="c"># o By atomic invariant count with in each sorted list going from most specific to</span> | |
| 3320 3307 <span class="c"># least specific, where count is determined by the number of "." in each atom</span> | |
| 3321 3308 <span class="c"># specification.</span> | |
| 3322 3309 <span class="c">#</span> | |
| 3323 3310 <span class="c">#A single atom specification,</span> | |
| 3324 3311 <span class="c"># without any commas in atom specification, is is considered most specific...</span> | |
| 3325 3312 <span class="c">#</span> | |
| 3326 <a name="_SortSpecificationsForAtomNeighborhoodMatch-"></a>3313 <span class="k">sub </span><span class="m">_SortSpecificationsForAtomNeighborhoodMatch</span> <span class="s">{</span> | |
| 3327 3314 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3328 3315 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$NeedToSort</span><span class="cm">,</span> <span class="i">$NumOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrAtomSpecCount</span><span class="cm">,</span> <span class="i">$NbrAtomSpecAtomicInvarintCount</span><span class="cm">,</span> <span class="i">$NbrAtomSpecToMatch</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="cm">,</span> <span class="i">$FirstAtomicInvariant</span><span class="cm">,</span> <span class="i">$WildCardInNbrAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecs</span><span class="cm">,</span> <span class="i">@NbrAtomSpecAtomicInvariants</span><span class="cm">,</span> <span class="i">@SortedNbrAtomSpecs</span><span class="cm">,</span> <span class="i">@SortedNbrBondSpecs</span><span class="cm">,</span> <span class="i">@SortedNbrOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">%NbrAtomSpecDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 3329 3316 | |
| 3330 3317 <span class="i">$NumOfNbrAtomSpecs</span> = <span class="k">defined</span> <span class="i">$NbrAtomSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3331 3318 | |
| 3332 3319 <span class="c"># Figure out whether sorting is necessary...</span> | |
| 3333 3320 <span class="i">$NeedToSort</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3334 3321 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 3335 3322 <span class="j">ATOMSPEC:</span> <span class="k">for</span> <span class="i">$NbrAtomSpecToMatch</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 3336 3323 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">/(,|\.|A|\*)/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3337 3324 <span class="i">$NeedToSort</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3338 3325 <span class="k">last</span> <span class="j">ATOMSPEC</span><span class="sc">;</span> | |
| 3339 3326 <span class="s">}</span> | |
| 3340 3327 <span class="s">}</span> | |
| 3341 3328 <span class="s">}</span> | |
| 3342 3329 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NeedToSort</span><span class="s">)</span> <span class="s">{</span> | |
| 3343 3330 <span class="c"># Nothing to do...</span> | |
| 3344 3331 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 3345 3332 <span class="s">}</span> | |
| 3346 3333 | |
| 3347 3334 <span class="i">%NbrAtomSpecDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3348 3335 | |
| 3349 3336 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3350 3337 <span class="i">$NbrAtomSpecToMatch</span> = <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 3351 3338 <span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 3352 3339 | |
| 3353 3340 <span class="i">@NbrAtomSpecs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NbrAtomSpecToMatch</span><span class="sc">;</span> | |
| 3354 3341 <span class="i">$NbrAtomSpecCount</span> = <span class="k">scalar</span> <span class="i">@NbrAtomSpecs</span><span class="sc">;</span> | |
| 3355 3342 | |
| 3356 3343 <span class="c"># Does neighbor specification contains a wild card in atom symbol specification?</span> | |
| 3357 3344 <span class="c">#</span> | |
| 3358 3345 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">/(A|\*)/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3359 3346 <span class="i">$WildCardInNbrAtomSpec</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3360 3347 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$NbrAtomSpec</span> <span class="s">(</span><span class="i">@NbrAtomSpecs</span><span class="s">)</span> <span class="s">{</span> | |
| 3361 3348 <span class="s">(</span><span class="i">$FirstAtomicInvariant</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="sc">;</span> | |
| 3362 3349 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span> | |
| 3363 3350 <span class="i">$FirstAtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span> | |
| 3364 3351 <span class="s">}</span> | |
| 3365 3352 <span class="i">$WildCardInNbrAtomSpec</span> = <span class="i">$This</span><span class="i">->_IsWildCardAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$FirstAtomicInvariant</span><span class="s">)</span><span class="sc">;</span> | |
| 3366 3353 <span class="k">if</span> <span class="s">(</span><span class="i">$WildCardInNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span> | |
| 3367 3354 <span class="k">last</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> | |
| 3368 3355 <span class="s">}</span> | |
| 3369 3356 <span class="s">}</span> | |
| 3370 3357 <span class="k">if</span> <span class="s">(</span><span class="i">$WildCardInNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span> | |
| 3371 3358 <span class="c"># Set NbrAtomSpecCount arbitrarily high to make the spec containing wild</span> | |
| 3372 3359 <span class="c"># card last on the sorted list while maintaining its original order in the list...</span> | |
| 3373 3360 <span class="i">$NbrAtomSpecCount</span> = <span class="n">999</span><span class="sc">;</span> | |
| 3374 3361 <span class="s">}</span> | |
| 3375 3362 <span class="s">}</span> | |
| 3376 3363 | |
| 3377 3364 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}<span class="s">)</span> <span class="s">{</span> | |
| 3378 3365 <span class="i">%</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3379 3366 <span class="s">}</span> | |
| 3380 3367 | |
| 3381 3368 <span class="c"># Use first NbrAtomSpec available in @NbrAtomSpecs to determine atomic invariant count</span> | |
| 3382 3369 <span class="c"># with in each NbrAtomSpecToMatch, as @NbrAtomSpecs derived from $NbrAtomSpecToMatch</span> | |
| 3383 3370 <span class="c"># simply corresponds to a list of possible matches...</span> | |
| 3384 3371 <span class="c">#</span> | |
| 3385 3372 <span class="s">(</span><span class="i">$NbrAtomSpec</span><span class="s">)</span> = <span class="i">@NbrAtomSpecs</span><span class="sc">;</span> | |
| 3386 3373 <span class="i">@NbrAtomSpecAtomicInvariants</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="sc">;</span> | |
| 3387 3374 <span class="i">$NbrAtomSpecAtomicInvarintCount</span> = <span class="k">scalar</span> <span class="i">@NbrAtomSpecAtomicInvariants</span><span class="sc">;</span> | |
| 3388 3375 | |
| 3389 3376 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}<span class="s">)</span> <span class="s">{</span> | |
| 3390 3377 <span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3391 3378 <span class="s">}</span> | |
| 3392 3379 <span class="k">push</span> <span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}}<span class="cm">,</span> <span class="i">$Index</span><span class="sc">;</span> | |
| 3393 3380 | |
| 3394 3381 <span class="s">}</span> | |
| 3395 3382 | |
| 3396 3383 <span class="i">@SortedNbrAtomSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@SortedNbrBondSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3397 3384 <span class="i">@SortedNbrOfNbrAtomSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3398 3385 | |
| 3399 3386 <span class="k">for</span> <span class="i">$NbrAtomSpecCount</span> <span class="s">(</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%NbrAtomSpecDataMap</span><span class="s">)</span> <span class="s">{</span> | |
| 3400 3387 <span class="k">for</span> <span class="i">$NbrAtomSpecAtomicInvarintCount</span> <span class="s">(</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$b</span> <=> <span class="i">$a</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 3401 3388 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 3402 3389 <span class="k">push</span> <span class="i">@SortedNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 3403 3390 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span><span class="s">)</span> <span class="s">{</span> | |
| 3404 3391 <span class="k">push</span> <span class="i">@SortedNbrBondSpecs</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 3405 3392 <span class="s">}</span> | |
| 3406 3393 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> <span class="s">{</span> | |
| 3407 3394 <span class="k">push</span> <span class="i">@SortedNbrOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 3408 3395 <span class="s">}</span> | |
| 3409 3396 <span class="s">}</span> | |
| 3410 3397 <span class="s">}</span> | |
| 3411 3398 <span class="s">}</span> | |
| 3412 3399 | |
| 3413 3400 <span class="k">return</span> <span class="s">(</span>\<span class="i">@SortedNbrAtomSpecs</span><span class="cm">,</span> <span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span> ? \<span class="i">@SortedNbrBondSpecs</span> <span class="co">:</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span> ? \<span class="i">@SortedNbrOfNbrAtomSpecs</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 3414 3401 <span class="s">}</span> | |
| 3415 3402 | |
| 3416 3403 <span class="c"># Check whether atom matches supported atom specification...</span> | |
| 3417 3404 <span class="c">#</span> | |
| 3418 <a name="_DoesAtomSpecificationMatch-"></a>3405 <span class="k">sub </span><span class="m">_DoesAtomSpecificationMatch</span> <span class="s">{</span> | |
| 3419 3406 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3420 3407 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomSpecificationMatched</span><span class="cm">,</span> <span class="i">$AtomicInvariantMatched</span><span class="cm">,</span> <span class="i">$FirstMatch</span><span class="s">)</span><span class="sc">;</span> | |
| 3421 3408 | |
| 3422 3409 <span class="c"># Anything to match...</span> | |
| 3423 3410 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> && <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3424 3411 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3425 3412 <span class="s">}</span> | |
| 3426 3413 | |
| 3427 3414 <span class="c"># Take out any spaces...</span> | |
| 3428 3415 <span class="i">$AtomSpecificationToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 3429 3416 | |
| 3430 3417 <span class="c"># Match specified atom specifications. For multiple atom specifications in a comma delimited string,</span> | |
| 3431 3418 <span class="c"># only one atom specification needs to match for a successful match. It's up to the caller to make</span> | |
| 3432 3419 <span class="c"># sure that the specificaton list is ordered from least to most specific atom specification...</span> | |
| 3433 3420 <span class="c">#</span> | |
| 3434 3421 <span class="k">for</span> <span class="i">$AtomSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> <span class="s">{</span> | |
| 3435 3422 <span class="i">$AtomSpecificationMatched</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3436 3423 <span class="i">$FirstMatch</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3437 3424 | |
| 3438 3425 <span class="c"># Match all atom symbol atomic invariants...</span> | |
| 3439 3426 <span class="j">ATOMICINVARIANT:</span> <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomSpecification</span><span class="s">)</span> <span class="s">{</span> | |
| 3440 3427 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstMatch</span><span class="s">)</span> <span class="s">{</span> | |
| 3441 3428 <span class="c"># Match atom symbol atomic invariant...</span> | |
| 3442 3429 <span class="i">$FirstMatch</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3443 3430 <span class="i">$AtomicInvariantMatched</span> = <span class="i">$This</span><span class="i">->_MatchAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="sc">;</span> | |
| 3444 3431 <span class="s">}</span> | |
| 3445 3432 <span class="k">else</span> <span class="s">{</span> | |
| 3446 3433 <span class="c"># Match non atom symbol atomic invariant...</span> | |
| 3447 3434 <span class="i">$AtomicInvariantMatched</span> = <span class="i">$This</span><span class="i">->_MatchNonAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="sc">;</span> | |
| 3448 3435 <span class="s">}</span> | |
| 3449 3436 | |
| 3450 3437 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicInvariantMatched</span><span class="s">)</span> <span class="s">{</span> | |
| 3451 3438 <span class="c"># No need to match other atomic invariants...</span> | |
| 3452 3439 <span class="i">$AtomSpecificationMatched</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3453 3440 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span> | |
| 3454 3441 <span class="s">}</span> | |
| 3455 3442 <span class="s">}</span> | |
| 3456 3443 | |
| 3457 3444 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomSpecificationMatched</span><span class="s">)</span> <span class="s">{</span> | |
| 3458 3445 <span class="c"># No need to match other atom specifications...</span> | |
| 3459 3446 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3460 3447 <span class="s">}</span> | |
| 3461 3448 <span class="s">}</span> | |
| 3462 3449 | |
| 3463 3450 <span class="c"># Nothing matched...</span> | |
| 3464 3451 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3465 3452 <span class="s">}</span> | |
| 3466 3453 | |
| 3467 3454 <span class="c"># Check whether atom matches atom symbol atomic invariant...</span> | |
| 3468 3455 <span class="c">#</span> | |
| 3469 <a name="_MatchAtomSymbolAtomicInvariant-"></a>3456 <span class="k">sub </span><span class="m">_MatchAtomSymbolAtomicInvariant</span> <span class="s">{</span> | |
| 3470 3457 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3471 3458 <span class="k">my</span><span class="s">(</span><span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 3472 3459 | |
| 3473 3460 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3474 3461 <span class="i">$NegateMatch</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3475 3462 | |
| 3476 3463 <span class="c"># Does match needs to be negated?</span> | |
| 3477 3464 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span> | |
| 3478 3465 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3479 3466 <span class="i">$AtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span> | |
| 3480 3467 <span class="s">}</span> | |
| 3481 3468 | |
| 3482 3469 <span class="j">ATOMICINVARIANT:</span> <span class="s">{</span> | |
| 3483 3470 <span class="c"># Any atom match...</span> | |
| 3484 3471 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_IsWildCardAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3485 3472 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3486 3473 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span> | |
| 3487 3474 <span class="s">}</span> | |
| 3488 3475 | |
| 3489 3476 <span class="c"># Atomic number match...</span> | |
| 3490 3477 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> | |
| 3491 3478 <span class="i">$AtomicNumber</span> = <span class="i">$AtomicInvariant</span><span class="sc">;</span> <span class="i">$AtomicNumber</span> =~ <span class="q">s/^#//</span><span class="sc">;</span> | |
| 3492 3479 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="i">$AtomicNumber</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3493 3480 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span> | |
| 3494 3481 <span class="s">}</span> | |
| 3495 3482 | |
| 3496 3483 <span class="c"># Atom symbol match...</span> | |
| 3497 3484 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomSymbol</span>} =~ <span class="q">/^$AtomicInvariant$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3498 3485 <span class="s">}</span> | |
| 3499 3486 | |
| 3500 3487 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span> | |
| 3501 3488 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 3502 3489 <span class="s">}</span> | |
| 3503 3490 | |
| 3504 3491 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 3505 3492 <span class="s">}</span> | |
| 3506 3493 | |
| 3507 3494 <span class="c"># Is it a wild card atom symbol atomic invariant?</span> | |
| 3508 3495 <span class="c">#</span> | |
| 3509 <a name="_IsWildCardAtomSymbolAtomicInvariant-"></a>3496 <span class="k">sub </span><span class="m">_IsWildCardAtomSymbolAtomicInvariant</span> <span class="s">{</span> | |
| 3510 3497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3511 3498 | |
| 3512 3499 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(A|\*)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3513 3500 <span class="s">}</span> | |
| 3514 3501 | |
| 3515 3502 <span class="c"># Check whether atom matches non atom symbol atomic invariants...</span> | |
| 3516 3503 <span class="c">#</span> | |
| 3517 <a name="_MatchNonAtomSymbolAtomicInvariant-"></a>3504 <span class="k">sub </span><span class="m">_MatchNonAtomSymbolAtomicInvariant</span> <span class="s">{</span> | |
| 3518 3505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3519 3506 <span class="k">my</span><span class="s">(</span><span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$UnknownName</span><span class="s">)</span><span class="sc">;</span> | |
| 3520 3507 | |
| 3521 3508 <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$UnknownName</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> | |
| 3522 3509 | |
| 3523 3510 <span class="c"># Does match needs to be negated?</span> | |
| 3524 3511 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span> | |
| 3525 3512 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3526 3513 <span class="i">$AtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span> | |
| 3527 3514 <span class="s">}</span> | |
| 3528 3515 | |
| 3529 3516 <span class="c"># Extract atomic invariant name and any value...</span> | |
| 3530 3517 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/[0-9\*]+/</span><span class="s">)</span> <span class="s">{</span> | |
| 3531 3518 <span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">$AtomicInvariant</span> =~ <span class="q">/^([a-zA-Z]+)([0-9\-\+\*\>\<\=]+)$/</span><span class="sc">;</span> | |
| 3532 3519 <span class="s">}</span> | |
| 3533 3520 <span class="k">else</span> <span class="s">{</span> | |
| 3534 3521 <span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 3535 3522 <span class="s">}</span> | |
| 3536 3523 | |
| 3537 3524 <span class="j">NAME:</span> <span class="s">{</span> | |
| 3538 3525 <span class="c"># Match number of non-hydrogen atom neighbors</span> | |
| 3539 3526 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^X$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3540 3527 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3541 3528 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3542 3529 <span class="s">}</span> | |
| 3543 3530 | |
| 3544 3531 <span class="c"># Match total number of atom neighbors including missing hydrogens...</span> | |
| 3545 3532 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^T$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3546 3533 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3547 3534 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3548 3535 <span class="s">}</span> | |
| 3549 3536 | |
| 3550 3537 <span class="c"># Match formal charge...</span> | |
| 3551 3538 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^FC$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3552 3539 <span class="k">my</span> <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3553 3540 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_MatchNonAtomSymbolAtomicInvariantValue</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 3554 3541 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3555 3542 <span class="s">}</span> | |
| 3556 3543 | |
| 3557 3544 <span class="c"># Match aromatic annotation indicating whether atom is aromatic...</span> | |
| 3558 3545 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^Ar$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3559 3546 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3560 3547 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3561 3548 <span class="s">}</span> | |
| 3562 3549 | |
| 3563 3550 <span class="c"># Match number of implicit and explicit hydrogens...</span> | |
| 3564 3551 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^H$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3565 3552 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3566 3553 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3567 3554 <span class="s">}</span> | |
| 3568 3555 | |
| 3569 3556 <span class="c"># Match ring atom annotation indicating whether atom is in ring...</span> | |
| 3570 3557 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^RA$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3571 3558 <span class="i">$Status</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> ? <span class="i">$This</span><span class="i">->IsInRingOfSize</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$This</span><span class="i">->IsInRing</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="s">)</span><span class="sc">;</span> | |
| 3572 3559 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3573 3560 <span class="s">}</span> | |
| 3574 3561 | |
| 3575 3562 <span class="c"># Match number of rings for atom..</span> | |
| 3576 3563 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TR$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3577 3564 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Value</span> == <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</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> | |
| 3578 3565 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3579 3566 <span class="s">}</span> | |
| 3580 3567 | |
| 3581 3568 <span class="c"># Match sum of bond orders to non-hydrogen atom neighbors...</span> | |
| 3582 3569 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^BO$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3583 3570 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3584 3571 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3585 3572 <span class="s">}</span> | |
| 3586 3573 | |
| 3587 3574 <span class="c"># Match largest bond order of non-hydrogen atom neighbors...</span> | |
| 3588 3575 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^LBO$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3589 3576 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3590 3577 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3591 3578 <span class="s">}</span> | |
| 3592 3579 | |
| 3593 3580 <span class="c"># Match number of single bonds to non-hydrogen atom neighbors...</span> | |
| 3594 3581 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^SB$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3595 3582 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3596 3583 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3597 3584 <span class="s">}</span> | |
| 3598 3585 | |
| 3599 3586 <span class="c"># Match total number of single bonds to atom neighbors including missing and explicit hydrogens...</span> | |
| 3600 3587 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TSB$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3601 3588 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3602 3589 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3603 3590 <span class="s">}</span> | |
| 3604 3591 | |
| 3605 3592 <span class="c"># Match number of double bonds to non-hydrogen atom neighbors...</span> | |
| 3606 3593 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^DB$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3607 3594 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3608 3595 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3609 3596 <span class="s">}</span> | |
| 3610 3597 | |
| 3611 3598 <span class="c"># Match number of triple bonds to non-hydrogen atom neighbors...</span> | |
| 3612 3599 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TB$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3613 3600 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3614 3601 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3615 3602 <span class="s">}</span> | |
| 3616 3603 | |
| 3617 3604 <span class="c"># Match number of aromatic bonds to non-hydrogen atom neighbors...</span> | |
| 3618 3605 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^AB$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3619 3606 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3620 3607 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3621 3608 <span class="s">}</span> | |
| 3622 3609 | |
| 3623 3610 | |
| 3624 3611 <span class="c"># Match mass number indicating isotope other than most abundant isotope...</span> | |
| 3625 3612 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^MN$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3626 3613 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3627 3614 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3628 3615 <span class="s">}</span> | |
| 3629 3616 | |
| 3630 3617 <span class="c"># Match spin multiplicity...</span> | |
| 3631 3618 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^SM$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3632 3619 <span class="k">my</span> <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3633 3620 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">}</span> | |
| 3634 3621 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span> && <span class="i">$Value</span> == <span class="i">$SpinMultiplicity</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3635 3622 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 3636 3623 <span class="s">}</span> | |
| 3637 3624 | |
| 3638 3625 <span class="i">$UnknownName</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3639 3626 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_MatchNonAtomSymbolAtomicInvariant: Unknown atomic invariant $AtomicInvariant..."</span><span class="sc">;</span> | |
| 3640 3627 <span class="s">}</span> | |
| 3641 3628 | |
| 3642 3629 <span class="k">if</span> <span class="s">(</span>!<span class="i">$UnknownName</span><span class="s">)</span> <span class="s">{</span> | |
| 3643 3630 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span> | |
| 3644 3631 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 3645 3632 <span class="s">}</span> | |
| 3646 3633 <span class="s">}</span> | |
| 3647 3634 | |
| 3648 3635 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 3649 3636 <span class="s">}</span> | |
| 3650 3637 | |
| 3651 3638 <span class="c"># Match atomic invariant value...</span> | |
| 3652 3639 <span class="c">#</span> | |
| 3653 3640 <span class="c"># Specified value format:</span> | |
| 3654 3641 <span class="c"># . +* : Any positive value</span> | |
| 3655 3642 <span class="c"># . -* : Any negative value</span> | |
| 3656 3643 <span class="c"># . >ValidNumber or >=ValidNumber</span> | |
| 3657 3644 <span class="c"># . <ValidNumber or <=ValidNumber</span> | |
| 3658 3645 <span class="c"># . Any valid number</span> | |
| 3659 3646 <span class="c">#</span> | |
| 3660 <a name="_MatchNonAtomSymbolAtomicInvariantValue-"></a>3647 <span class="k">sub </span><span class="m">_MatchNonAtomSymbolAtomicInvariantValue</span> <span class="s">{</span> | |
| 3661 3648 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$TargetValue</span><span class="cm">,</span> <span class="i">$SpecifiedValue</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3662 3649 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 3663 3650 | |
| 3664 3651 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3665 3652 | |
| 3666 3653 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$TargetValue</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SpecifiedValue</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3667 3654 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 3668 3655 <span class="s">}</span> | |
| 3669 3656 | |
| 3670 3657 <span class="j">VALUE:</span> <span class="s">{</span> | |
| 3671 3658 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^\+\*/</span><span class="s">)</span> <span class="s">{</span> | |
| 3672 3659 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$TargetValue</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3673 3660 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> | |
| 3674 3661 <span class="s">}</span> | |
| 3675 3662 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^\-\*/</span><span class="s">)</span> <span class="s">{</span> | |
| 3676 3663 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$TargetValue</span> < <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3677 3664 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> | |
| 3678 3665 <span class="s">}</span> | |
| 3679 3666 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^>/</span><span class="s">)</span> <span class="s">{</span> | |
| 3680 3667 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^>=/</span><span class="s">)</span> <span class="s">{</span> | |
| 3681 3668 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^>=//</span><span class="sc">;</span> | |
| 3682 3669 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> >= <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3683 3670 <span class="s">}</span> | |
| 3684 3671 <span class="k">else</span> <span class="s">{</span> | |
| 3685 3672 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^>//</span><span class="sc">;</span> | |
| 3686 3673 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> > <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3687 3674 <span class="s">}</span> | |
| 3688 3675 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> | |
| 3689 3676 <span class="s">}</span> | |
| 3690 3677 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^</</span><span class="s">)</span> <span class="s">{</span> | |
| 3691 3678 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^<=/</span><span class="s">)</span> <span class="s">{</span> | |
| 3692 3679 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^<=//</span><span class="sc">;</span> | |
| 3693 3680 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> <= <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3694 3681 <span class="s">}</span> | |
| 3695 3682 <span class="k">else</span> <span class="s">{</span> | |
| 3696 3683 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^<//</span><span class="sc">;</span> | |
| 3697 3684 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> < <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3698 3685 <span class="s">}</span> | |
| 3699 3686 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> | |
| 3700 3687 <span class="s">}</span> | |
| 3701 3688 <span class="c"># Default is do perform an equality match...</span> | |
| 3702 3689 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> == <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3703 3690 <span class="s">}</span> | |
| 3704 3691 | |
| 3705 3692 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 3706 3693 <span class="s">}</span> | |
| 3707 3694 | |
| 3708 3695 <span class="c"># Check whether atoms match bond specifications...</span> | |
| 3709 3696 <span class="c">#</span> | |
| 3710 <a name="_DoesBondSpecificationMatch-"></a>3697 <span class="k">sub </span><span class="m">_DoesBondSpecificationMatch</span> <span class="s">{</span> | |
| 3711 3698 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondSpecificationToMatch</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3712 3699 <span class="k">my</span><span class="s">(</span><span class="i">$BondSpecification</span><span class="cm">,</span> <span class="i">$BondSymbolSpecification</span><span class="cm">,</span> <span class="i">$BondSpecificationMatched</span><span class="s">)</span><span class="sc">;</span> | |
| 3713 3700 | |
| 3714 3701 <span class="c"># Anything to match...</span> | |
| 3715 3702 <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">$BondSpecificationToMatch</span><span class="s">)</span> && <span class="i">$BondSpecificationToMatch</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3716 3703 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3717 3704 <span class="s">}</span> | |
| 3718 3705 | |
| 3719 3706 <span class="c"># Take out any spaces...</span> | |
| 3720 3707 <span class="i">$BondSpecificationToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 3721 3708 | |
| 3722 3709 <span class="c"># Match specified bond specifications. For multiple bond specifications in a comma delimited string,</span> | |
| 3723 3710 <span class="c"># only one bond specification needs to match for a successful match...</span> | |
| 3724 3711 <span class="c">#</span> | |
| 3725 3712 <span class="k">for</span> <span class="i">$BondSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$BondSpecificationToMatch</span><span class="s">)</span> <span class="s">{</span> | |
| 3726 3713 <span class="i">$BondSpecificationMatched</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3727 3714 | |
| 3728 3715 <span class="c"># Match all specified bond symbol specifications...</span> | |
| 3729 3716 <span class="j">BONDSYMBOL:</span> <span class="k">for</span> <span class="i">$BondSymbolSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$BondSpecification</span><span class="s">)</span> <span class="s">{</span> | |
| 3730 3717 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_MatchBondSymbolSpecification</span><span class="s">(</span><span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondSymbolSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3731 3718 <span class="c"># No need to match other bond symbol specifications...</span> | |
| 3732 3719 <span class="i">$BondSpecificationMatched</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3733 3720 <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> | |
| 3734 3721 <span class="s">}</span> | |
| 3735 3722 <span class="s">}</span> | |
| 3736 3723 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSpecificationMatched</span><span class="s">)</span> <span class="s">{</span> | |
| 3737 3724 <span class="c"># No need to try matching other bond specifications...</span> | |
| 3738 3725 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3739 3726 <span class="s">}</span> | |
| 3740 3727 <span class="s">}</span> | |
| 3741 3728 | |
| 3742 3729 <span class="c"># Nothing matched...</span> | |
| 3743 3730 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3744 3731 <span class="s">}</span> | |
| 3745 3732 | |
| 3746 3733 <span class="c"># Check whether atoms match bond symbol specification...</span> | |
| 3747 3734 <span class="c">#</span> | |
| 3748 <a name="_MatchBondSymbolSpecification-"></a>3735 <span class="k">sub </span><span class="m">_MatchBondSymbolSpecification</span> <span class="s">{</span> | |
| 3749 3736 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondSymbolSpecification</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3750 3737 <span class="k">my</span><span class="s">(</span><span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondSymbol</span><span class="cm">,</span> <span class="i">$UnknownBondSymbol</span><span class="s">)</span><span class="sc">;</span> | |
| 3751 3738 | |
| 3752 3739 <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$UnknownBondSymbol</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> | |
| 3753 3740 | |
| 3754 3741 <span class="c"># Does match needs to be negated?</span> | |
| 3755 3742 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbolSpecification</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span> | |
| 3756 3743 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3757 3744 <span class="i">$BondSymbolSpecification</span> =~ <span class="q">s/^!//</span><span class="sc">;</span> | |
| 3758 3745 <span class="s">}</span> | |
| 3759 3746 <span class="i">$BondSymbol</span> = <span class="i">$BondSymbolSpecification</span><span class="sc">;</span> | |
| 3760 3747 <span class="i">$Bond</span> = <span class="i">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="i">$BondedAtom</span><span class="s">)</span><span class="sc">;</span> | |
| 3761 3748 | |
| 3762 3749 <span class="j">BONDSYMBOL:</span> <span class="s">{</span> | |
| 3763 3750 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(-|1|s|Single)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsSingle</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span> | |
| 3764 3751 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(=|2|d|Double)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsDouble</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span> | |
| 3765 3752 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(#|3|t|Triple)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsTriple</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span> | |
| 3766 3753 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(:|a|Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsAromatic</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span> | |
| 3767 3754 | |
| 3768 3755 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(\@|RB|Ring)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsInRing</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span> | |
| 3769 3756 | |
| 3770 3757 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(\~|\*|Any)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span> | |
| 3771 3758 | |
| 3772 3759 <span class="i">$UnknownBondSymbol</span> = <span class="n">1</span><span class="sc">;</span> | |
| 3773 3760 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_MatchBondSpecification: Unknown bond specification $BondSymbolSpecification..."</span><span class="sc">;</span> | |
| 3774 3761 <span class="s">}</span> | |
| 3775 3762 | |
| 3776 3763 <span class="k">if</span> <span class="s">(</span>!<span class="i">$UnknownBondSymbol</span><span class="s">)</span> <span class="s">{</span> | |
| 3777 3764 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span> | |
| 3778 3765 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 3779 3766 <span class="s">}</span> | |
| 3780 3767 <span class="s">}</span> | |
| 3781 3768 | |
| 3782 3769 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 3783 3770 <span class="s">}</span> | |
| 3784 3771 | |
| 3785 3772 <span class="c"># Is it a saturated atom?</span> | |
| 3786 3773 <span class="c">#</span> | |
| 3787 <a name="IsSaturated-"></a>3774 <span class="k">sub </span><span class="m">IsSaturated</span> <span class="s">{</span> | |
| 3788 3775 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3789 3776 | |
| 3790 3777 <span class="k">return</span> !<span class="i">$This</span><span class="i">->IsUnsaturated</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3791 3778 <span class="s">}</span> | |
| 3792 3779 | |
| 3793 3780 <span class="c"># Is it an unsaturated atom containing at least one non-single bond?</span> | |
| 3794 3781 <span class="c">#</span> | |
| 3795 <a name="IsUnsaturated-"></a>3782 <span class="k">sub </span><span class="m">IsUnsaturated</span> <span class="s">{</span> | |
| 3796 3783 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3797 3784 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 3798 3785 | |
| 3799 3786 <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3800 3787 | |
| 3801 3788 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfDoubleBonds</span> || <span class="i">$NumOfTripleBonds</span> || <span class="i">$NumOfAromaticBonds</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3802 3789 <span class="s">}</span> | |
| 3803 3790 | |
| 3804 3791 <span class="c"># Is atom in a ring?</span> | |
| 3805 3792 <span class="c">#</span> | |
| 3806 <a name="IsInRing-"></a>3793 <span class="k">sub </span><span class="m">IsInRing</span> <span class="s">{</span> | |
| 3807 3794 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3808 3795 | |
| 3809 3796 <span class="c"># Is this atom in a molecule?</span> | |
| 3810 3797 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3811 3798 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3812 3799 <span class="s">}</span> | |
| 3813 3800 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3814 3801 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3815 3802 | |
| 3816 3803 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 3817 3804 <span class="s">}</span> | |
| 3818 3805 | |
| 3819 3806 <span class="c"># Is atom not in a ring?</span> | |
| 3820 3807 <span class="c">#</span> | |
| 3821 <a name="IsNotInRing-"></a>3808 <span class="k">sub </span><span class="m">IsNotInRing</span> <span class="s">{</span> | |
| 3822 3809 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3823 3810 | |
| 3824 3811 <span class="c"># Is this atom in a molecule?</span> | |
| 3825 3812 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3826 3813 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3827 3814 <span class="s">}</span> | |
| 3828 3815 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3829 3816 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3830 3817 | |
| 3831 3818 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomNotInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 3832 3819 <span class="s">}</span> | |
| 3833 3820 | |
| 3834 3821 <span class="c"># Is atom only in one ring?</span> | |
| 3835 3822 <span class="c">#</span> | |
| 3836 <a name="IsOnlyInOneRing-"></a>3823 <span class="k">sub </span><span class="m">IsOnlyInOneRing</span> <span class="s">{</span> | |
| 3837 3824 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3838 3825 | |
| 3839 3826 <span class="c"># Is this atom in a molecule?</span> | |
| 3840 3827 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3841 3828 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3842 3829 <span class="s">}</span> | |
| 3843 3830 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3844 3831 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3845 3832 | |
| 3846 3833 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomInOnlyOneRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 3847 3834 <span class="s">}</span> | |
| 3848 3835 | |
| 3849 3836 <span class="c"># Is atom in a ring of specific size?</span> | |
| 3850 3837 <span class="c">#</span> | |
| 3851 <a name="IsInRingOfSize-"></a>3838 <span class="k">sub </span><span class="m">IsInRingOfSize</span> <span class="s">{</span> | |
| 3852 3839 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3853 3840 | |
| 3854 3841 <span class="c"># Is this atom in a molecule?</span> | |
| 3855 3842 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3856 3843 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3857 3844 <span class="s">}</span> | |
| 3858 3845 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3859 3846 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3860 3847 | |
| 3861 3848 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomInRingOfSize</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3862 3849 <span class="s">}</span> | |
| 3863 3850 | |
| 3864 3851 <span class="c"># Get size of smallest ring containing the atom...</span> | |
| 3865 3852 <span class="c">#</span> | |
| 3866 <a name="GetSizeOfSmallestRing-"></a>3853 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span> | |
| 3867 3854 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3868 3855 | |
| 3869 3856 <span class="c"># Is this atom in a molecule?</span> | |
| 3870 3857 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3871 3858 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3872 3859 <span class="s">}</span> | |
| 3873 3860 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3874 3861 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3875 3862 | |
| 3876 3863 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfSmallestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 3877 3864 <span class="s">}</span> | |
| 3878 3865 | |
| 3879 3866 <span class="c"># Get size of largest ring containing the atom...</span> | |
| 3880 3867 <span class="c">#</span> | |
| 3881 <a name="GetSizeOfLargestRing-"></a>3868 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span> | |
| 3882 3869 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3883 3870 | |
| 3884 3871 <span class="c"># Is this atom in a molecule?</span> | |
| 3885 3872 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3886 3873 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3887 3874 <span class="s">}</span> | |
| 3888 3875 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3889 3876 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3890 3877 | |
| 3891 3878 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfLargestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 3892 3879 <span class="s">}</span> | |
| 3893 3880 | |
| 3894 3881 <span class="c"># Get number of rings containing the atom...</span> | |
| 3895 3882 <span class="c">#</span> | |
| 3896 <a name="GetNumOfRings-"></a>3883 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span> | |
| 3897 3884 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3898 3885 | |
| 3899 3886 <span class="c"># Is this atom in a molecule?</span> | |
| 3900 3887 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3901 3888 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3902 3889 <span class="s">}</span> | |
| 3903 3890 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3904 3891 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3905 3892 | |
| 3906 3893 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 3907 3894 <span class="s">}</span> | |
| 3908 3895 | |
| 3909 3896 <span class="c"># Get number of rings with odd size containing the atom...</span> | |
| 3910 3897 <span class="c">#</span> | |
| 3911 <a name="GetNumOfRingsWithOddSize-"></a>3898 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span> | |
| 3912 3899 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3913 3900 | |
| 3914 3901 <span class="c"># Is this atom in a molecule?</span> | |
| 3915 3902 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3916 3903 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3917 3904 <span class="s">}</span> | |
| 3918 3905 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3919 3906 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3920 3907 | |
| 3921 3908 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 3922 3909 <span class="s">}</span> | |
| 3923 3910 | |
| 3924 3911 <span class="c"># Get number of rings with even size containing the atom...</span> | |
| 3925 3912 <span class="c">#</span> | |
| 3926 <a name="GetNumOfRingsWithEvenSize-"></a>3913 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span> | |
| 3927 3914 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3928 3915 | |
| 3929 3916 <span class="c"># Is this atom in a molecule?</span> | |
| 3930 3917 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3931 3918 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3932 3919 <span class="s">}</span> | |
| 3933 3920 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3934 3921 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3935 3922 | |
| 3936 3923 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 3937 3924 <span class="s">}</span> | |
| 3938 3925 | |
| 3939 3926 <span class="c"># Get number of rings with specified size containing the atom...</span> | |
| 3940 3927 <span class="c">#</span> | |
| 3941 <a name="GetNumOfRingsWithSize-"></a>3928 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span> | |
| 3942 3929 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3943 3930 | |
| 3944 3931 <span class="c"># Is this atom in a molecule?</span> | |
| 3945 3932 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3946 3933 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3947 3934 <span class="s">}</span> | |
| 3948 3935 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3949 3936 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3950 3937 | |
| 3951 3938 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithSize</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3952 3939 | |
| 3953 3940 <span class="s">}</span> | |
| 3954 3941 | |
| 3955 3942 <span class="c"># Get number of rings with size less than specified containing the atom...</span> | |
| 3956 3943 <span class="c">#</span> | |
| 3957 <a name="GetNumOfRingsWithSizeLessThan-"></a>3944 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 3958 3945 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3959 3946 | |
| 3960 3947 <span class="c"># Is this atom in a molecule?</span> | |
| 3961 3948 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3962 3949 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3963 3950 <span class="s">}</span> | |
| 3964 3951 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3965 3952 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3966 3953 | |
| 3967 3954 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3968 3955 <span class="s">}</span> | |
| 3969 3956 | |
| 3970 3957 <span class="c"># Get number of rings with size greater than specified size containing the atom...</span> | |
| 3971 3958 <span class="c">#</span> | |
| 3972 <a name="GetNumOfRingsWithSizeGreaterThan-"></a>3959 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 3973 3960 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3974 3961 | |
| 3975 3962 <span class="c"># Is this atom in a molecule?</span> | |
| 3976 3963 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3977 3964 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3978 3965 <span class="s">}</span> | |
| 3979 3966 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3980 3967 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3981 3968 | |
| 3982 3969 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithSizeGreaterThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3983 3970 <span class="s">}</span> | |
| 3984 3971 | |
| 3985 3972 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span> | |
| 3986 3973 <span class="c">#</span> | |
| 3987 <a name="GetRings-"></a>3974 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span> | |
| 3988 3975 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3989 3976 | |
| 3990 3977 <span class="c"># Is this atom in a molecule?</span> | |
| 3991 3978 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3992 3979 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 3993 3980 <span class="s">}</span> | |
| 3994 3981 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 3995 3982 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 3996 3983 | |
| 3997 3984 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 3998 3985 <span class="s">}</span> | |
| 3999 3986 | |
| 4000 3987 <span class="c"># Get smallest ring as an array containing ring atoms...</span> | |
| 4001 3988 <span class="c">#</span> | |
| 4002 <a name="GetSmallestRing-"></a>3989 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span> | |
| 4003 3990 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4004 3991 | |
| 4005 3992 <span class="c"># Is this atom in a molecule?</span> | |
| 4006 3993 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 4007 3994 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 4008 3995 <span class="s">}</span> | |
| 4009 3996 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 4010 3997 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 4011 3998 | |
| 4012 3999 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSmallestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 4013 4000 <span class="s">}</span> | |
| 4014 4001 | |
| 4015 4002 <span class="c"># Get largest ring as an array containing ring atoms...</span> | |
| 4016 4003 <span class="c">#</span> | |
| 4017 <a name="GetLargestRing-"></a>4004 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span> | |
| 4018 4005 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4019 4006 | |
| 4020 4007 <span class="c"># Is this atom in a molecule?</span> | |
| 4021 4008 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 4022 4009 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 4023 4010 <span class="s">}</span> | |
| 4024 4011 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 4025 4012 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 4026 4013 | |
| 4027 4014 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetLargestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 4028 4015 <span class="s">}</span> | |
| 4029 4016 | |
| 4030 4017 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> | |
| 4031 4018 <span class="c">#</span> | |
| 4032 <a name="GetRingsWithOddSize-"></a>4019 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span> | |
| 4033 4020 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4034 4021 | |
| 4035 4022 <span class="c"># Is this atom in a molecule?</span> | |
| 4036 4023 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 4037 4024 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 4038 4025 <span class="s">}</span> | |
| 4039 4026 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 4040 4027 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 4041 4028 | |
| 4042 4029 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 4043 4030 <span class="s">}</span> | |
| 4044 4031 | |
| 4045 4032 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span> | |
| 4046 4033 <span class="c">#</span> | |
| 4047 <a name="GetRingsWithEvenSize-"></a>4034 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span> | |
| 4048 4035 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4049 4036 | |
| 4050 4037 <span class="c"># Is this atom in a molecule?</span> | |
| 4051 4038 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 4052 4039 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 4053 4040 <span class="s">}</span> | |
| 4054 4041 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 4055 4042 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 4056 4043 | |
| 4057 4044 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 4058 4045 <span class="s">}</span> | |
| 4059 4046 | |
| 4060 4047 <span class="c"># Get rings with specified size as an array of references to arrays containing ring atoms...</span> | |
| 4061 4048 <span class="c">#</span> | |
| 4062 <a name="GetRingsWithSize-"></a>4049 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span> | |
| 4063 4050 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4064 4051 | |
| 4065 4052 <span class="c"># Is this atom in a molecule?</span> | |
| 4066 4053 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 4067 4054 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 4068 4055 <span class="s">}</span> | |
| 4069 4056 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 4070 4057 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 4071 4058 | |
| 4072 4059 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithSize</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 4073 4060 <span class="s">}</span> | |
| 4074 4061 | |
| 4075 4062 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> | |
| 4076 4063 <span class="c">#</span> | |
| 4077 <a name="GetRingsWithSizeLessThan-"></a>4064 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 4078 4065 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4079 4066 | |
| 4080 4067 <span class="c"># Is this atom in a molecule?</span> | |
| 4081 4068 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 4082 4069 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 4083 4070 <span class="s">}</span> | |
| 4084 4071 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 4085 4072 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 4086 4073 | |
| 4087 4074 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 4088 4075 <span class="s">}</span> | |
| 4089 4076 | |
| 4090 4077 <span class="c"># Get rings with size greater than specfied size as an array of references to arrays containing ring atoms...</span> | |
| 4091 4078 <span class="c">#</span> | |
| 4092 <a name="GetRingsWithSizeGreaterThan-"></a>4079 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 4093 4080 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4094 4081 | |
| 4095 4082 <span class="c"># Is this atom in a molecule?</span> | |
| 4096 4083 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 4097 4084 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 4098 4085 <span class="s">}</span> | |
| 4099 4086 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 4100 4087 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 4101 4088 | |
| 4102 4089 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithSizeGreaterThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 4103 4090 <span class="s">}</span> | |
| 4104 4091 | |
| 4105 4092 <span class="c"># Get next object ID...</span> | |
| 4106 <a name="_GetNewObjectID-"></a>4093 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span> | |
| 4107 4094 <span class="i">$ObjectID</span>++<span class="sc">;</span> | |
| 4108 4095 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span> | |
| 4109 4096 <span class="s">}</span> | |
| 4110 4097 | |
| 4111 4098 <span class="c"># Return a string containing vertices, edges and other properties...</span> | |
| 4112 <a name="StringifyAtom-"></a>4099 <span class="k">sub </span><span class="m">StringifyAtom</span> <span class="s">{</span> | |
| 4113 4100 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4114 4101 <span class="k">my</span><span class="s">(</span><span class="i">$AtomString</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$XYZVector</span><span class="cm">,</span> <span class="i">$AtomicWeight</span><span class="cm">,</span> <span class="i">$ExactMass</span><span class="cm">,</span> <span class="i">$NumOfNeighbors</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$Valence</span><span class="cm">,</span> <span class="i">$MissingHydrogens</span><span class="cm">,</span> <span class="i">$TotalHydrogens</span><span class="cm">,</span> <span class="i">$ImplicitHydrogens</span><span class="cm">,</span> <span class="i">$ExplicitHydrogens</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$StereoCenter</span><span class="cm">,</span> <span class="i">$StereoCenterStatus</span><span class="cm">,</span> <span class="i">$StereoChemistry</span><span class="cm">,</span> <span class="i">$StereochemistryString</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$NumOfRings</span><span class="cm">,</span> <span class="i">$AromaticAtom</span><span class="s">)</span><span class="sc">;</span> | |
| 4115 4102 | |
| 4116 4103 <span class="i">$ID</span> = <span class="i">$This</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4117 4104 <span class="i">$Name</span> = <span class="i">$This</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4118 4105 <span class="i">$AtomSymbol</span> = <span class="i">$This</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4119 4106 <span class="i">$AtomicNumber</span> = <span class="i">$This</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4120 4107 <span class="i">$XYZVector</span> = <span class="i">$This</span><span class="i">->GetXYZVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4121 4108 | |
| 4122 4109 <span class="i">$AtomicWeight</span> = <span class="i">$This</span><span class="i">->GetAtomicWeight</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4123 4110 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$AtomicWeight</span><span class="s">)</span> <span class="s">{</span> | |
| 4124 4111 <span class="i">$AtomicWeight</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4125 4112 <span class="s">}</span> | |
| 4126 4113 <span class="i">$ExactMass</span> = <span class="i">$This</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4127 4114 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExactMass</span><span class="s">)</span> <span class="s">{</span> | |
| 4128 4115 <span class="i">$ExactMass</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4129 4116 <span class="s">}</span> | |
| 4130 4117 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetNumOfNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4131 4118 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> <span class="s">{</span> | |
| 4132 4119 <span class="i">$NumOfNeighbors</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4133 4120 <span class="s">}</span> | |
| 4134 4121 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4135 4122 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> <span class="s">{</span> | |
| 4136 4123 <span class="i">$NumOfBonds</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4137 4124 <span class="s">}</span> | |
| 4138 4125 <span class="i">$Valence</span> = <span class="i">$This</span><span class="i">->GetValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4139 4126 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Valence</span><span class="s">)</span> <span class="s">{</span> | |
| 4140 4127 <span class="i">$Valence</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4141 4128 <span class="s">}</span> | |
| 4142 4129 | |
| 4143 4130 <span class="i">$MissingHydrogens</span> = <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4144 4131 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$MissingHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
| 4145 4132 <span class="i">$MissingHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4146 4133 <span class="s">}</span> | |
| 4147 4134 <span class="i">$TotalHydrogens</span> = <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4148 4135 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$TotalHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
| 4149 4136 <span class="i">$TotalHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4150 4137 <span class="s">}</span> | |
| 4151 4138 <span class="i">$ImplicitHydrogens</span> = <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4152 4139 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ImplicitHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
| 4153 4140 <span class="i">$ImplicitHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4154 4141 <span class="s">}</span> | |
| 4155 4142 <span class="i">$ExplicitHydrogens</span> = <span class="i">$This</span><span class="i">->GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4156 4143 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExplicitHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
| 4157 4144 <span class="i">$ExplicitHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4158 4145 <span class="s">}</span> | |
| 4159 4146 | |
| 4160 4147 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4161 4148 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span> | |
| 4162 4149 <span class="i">$FormalCharge</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4163 4150 <span class="s">}</span> | |
| 4164 4151 <span class="i">$Charge</span> = <span class="i">$This</span><span class="i">->GetCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4165 4152 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span> | |
| 4166 4153 <span class="i">$Charge</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4167 4154 <span class="s">}</span> | |
| 4168 4155 | |
| 4169 4156 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4170 4157 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span> <span class="s">{</span> | |
| 4171 4158 <span class="i">$SpinMultiplicity</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4172 4159 <span class="s">}</span> | |
| 4173 4160 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4174 4161 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span> | |
| 4175 4162 <span class="i">$FreeRadicalElectrons</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4176 4163 <span class="s">}</span> | |
| 4177 4164 | |
| 4178 4165 <span class="i">$RingAtom</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4179 4166 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$RingAtom</span><span class="s">)</span> <span class="s">{</span> | |
| 4180 4167 <span class="i">$RingAtom</span> = <span class="i">$RingAtom</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> | |
| 4181 4168 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4182 4169 <span class="s">}</span> | |
| 4183 4170 <span class="k">else</span> <span class="s">{</span> | |
| 4184 4171 <span class="i">$RingAtom</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4185 4172 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4186 4173 <span class="s">}</span> | |
| 4187 4174 | |
| 4188 4175 <span class="i">$AromaticAtom</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4189 4176 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticAtom</span><span class="s">)</span> <span class="s">{</span> | |
| 4190 4177 <span class="i">$AromaticAtom</span> = <span class="i">$AromaticAtom</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> | |
| 4191 4178 <span class="s">}</span> | |
| 4192 4179 <span class="k">else</span> <span class="s">{</span> | |
| 4193 4180 <span class="i">$AromaticAtom</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4194 4181 <span class="s">}</span> | |
| 4195 4182 | |
| 4196 4183 <span class="i">$StereochemistryString</span> = <span class="q">''</span><span class="sc">;</span> | |
| 4197 4184 <span class="i">$StereoCenter</span> = <span class="i">$This</span><span class="i">->GetStereoCenter</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4198 4185 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$StereoCenter</span><span class="s">)</span> <span class="s">{</span> | |
| 4199 4186 <span class="i">$StereoCenterStatus</span> = <span class="i">$This</span><span class="i">->IsStereoCenter</span><span class="s">(</span><span class="s">)</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> | |
| 4200 4187 <span class="i">$StereoChemistry</span> = <span class="i">$This</span><span class="i">->GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4201 4188 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$StereoChemistry</span><span class="s">)</span> <span class="s">{</span> | |
| 4202 4189 <span class="i">$StereoChemistry</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4203 4190 <span class="s">}</span> | |
| 4204 4191 <span class="i">$StereochemistryString</span> = <span class="q">"StereoCenter: $StereoCenterStatus; Stereochemistry: $StereoChemistry"</span><span class="sc">;</span> | |
| 4205 4192 <span class="s">}</span> | |
| 4206 4193 | |
| 4207 4194 <span class="i">$AtomString</span> = <span class="q">"Atom: ID: $ID; Name: \"$Name\"; AtomSymbol: \"$AtomSymbol\"; AtomicNumber: $AtomicNumber; XYZ: $XYZVector; AtomicWeight: $AtomicWeight; ExactMass: $ExactMass; NumOfNeighbors: $NumOfNeighbors; NumOfBonds: $NumOfBonds; Valence: $Valence; MissingHydrogens: $MissingHydrogens; TotalHydrogens: $TotalHydrogens; ImplicitHydrogens: $ImplicitHydrogens; ExplicitHydrogens: $ExplicitHydrogens; FormalCharge: $FormalCharge; Charge: $Charge; SpinMultiplicity: $SpinMultiplicity; FreeRadicalElectrons: $FreeRadicalElectrons; RingAtom: $RingAtom; NumOfAtomRings: $NumOfRings; AromaticAtom: $AromaticAtom"</span><span class="sc">;</span> | |
| 4208 4195 | |
| 4209 4196 <span class="k">if</span> <span class="s">(</span><span class="i">$StereochemistryString</span><span class="s">)</span> <span class="s">{</span> | |
| 4210 4197 <span class="i">$AtomString</span> .= <span class="q">"; $StereochemistryString"</span><span class="sc">;</span> | |
| 4211 4198 <span class="s">}</span> | |
| 4212 4199 | |
| 4213 4200 <span class="k">return</span> <span class="i">$AtomString</span><span class="sc">;</span> | |
| 4214 4201 <span class="s">}</span> | |
| 4215 4202 | |
| 4216 4203 <span class="c"># Load appropriate atom data files from <MayaChemTools>/lib directory used by various</span> | |
| 4217 4204 <span class="c"># object methods in the current class...</span> | |
| 4218 4205 <span class="c">#</span> | |
| 4219 <a name="_LoadAtomClassData-"></a>4206 <span class="k">sub </span><span class="m">_LoadAtomClassData</span> <span class="s">{</span> | |
| 4220 4207 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> | |
| 4221 4208 | |
| 4222 4209 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4223 4210 | |
| 4224 4211 <span class="i">_LoadAtomValenceModelData</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> | |
| 4225 4212 | |
| 4226 4213 <span class="s">}</span> | |
| 4227 4214 | |
| 4228 4215 <span class="c">#</span> | |
| 4229 4216 <span class="c"># Load data for supported valence models...</span> | |
| 4230 4217 <span class="c">#</span> | |
| 4231 <a name="_LoadAtomValenceModelData-"></a>4218 <span class="k">sub </span><span class="m">_LoadAtomValenceModelData</span> <span class="s">{</span> | |
| 4232 4219 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4233 4220 <span class="k">my</span><span class="s">(</span><span class="i">$MDLValenceModelDataFile</span><span class="cm">,</span> <span class="i">$DaylightValenceModelDataFile</span><span class="s">)</span><span class="sc">;</span> | |
| 4234 4221 | |
| 4235 4222 <span class="i">%MDLValenceModelDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4236 4223 <span class="i">%DaylightValenceModelDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4237 4224 | |
| 4238 4225 <span class="i">$MDLValenceModelDataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/MDLValenceModelData.csv"</span><span class="sc">;</span> | |
| 4239 4226 <span class="i">$DaylightValenceModelDataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/DaylightValenceModelData.csv"</span><span class="sc">;</span> | |
| 4240 4227 | |
| 4241 4228 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$MDLValenceModelDataFile"</span><span class="s">)</span> <span class="s">{</span> | |
| 4242 4229 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $MDLValenceModelDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> | |
| 4243 4230 <span class="s">}</span> | |
| 4244 4231 | |
| 4245 4232 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$DaylightValenceModelDataFile"</span><span class="s">)</span> <span class="s">{</span> | |
| 4246 4233 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $DaylightValenceModelDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> | |
| 4247 4234 <span class="s">}</span> | |
| 4248 4235 | |
| 4249 4236 <span class="i">_LoadValenceModelDataFile</span><span class="s">(</span><span class="i">$MDLValenceModelDataFile</span><span class="cm">,</span> \<span class="i">%MDLValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 4250 4237 <span class="i">_LoadValenceModelDataFile</span><span class="s">(</span><span class="i">$DaylightValenceModelDataFile</span><span class="cm">,</span> \<span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 4251 4238 | |
| 4252 4239 <span class="s">}</span> | |
| 4253 4240 | |
| 4254 4241 <span class="c">#</span> | |
| 4255 4242 <span class="c"># Load valence model data file...</span> | |
| 4256 4243 <span class="c">#</span> | |
| 4257 <a name="_LoadValenceModelDataFile-"></a>4244 <span class="k">sub </span><span class="m">_LoadValenceModelDataFile</span> <span class="s">{</span> | |
| 4258 4245 <span class="k">my</span><span class="s">(</span><span class="i">$DataFile</span><span class="cm">,</span> <span class="i">$DataMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4259 4246 | |
| 4260 4247 <span class="c"># File format:</span> | |
| 4261 4248 <span class="c">#</span> | |
| 4262 4249 <span class="c"># "AtomicNumber","ElementSymbol","FormalCharge","CommomValences"</span> | |
| 4263 4250 <span class="c">#</span> | |
| 4264 4251 <span class="k">my</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span> | |
| 4265 4252 | |
| 4266 4253 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span> | |
| 4267 4254 <span class="k">open</span> <span class="w">DATAFILE</span><span class="cm">,</span> <span class="q">"$DataFile"</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">"Couldn't open $DataFile: $! ..."</span><span class="sc">;</span> | |
| 4268 4255 | |
| 4269 4256 <span class="c"># Skip lines up to column labels...</span> | |
| 4270 4257 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 4271 4258 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> | |
| 4272 4259 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 4273 4260 <span class="s">}</span> | |
| 4274 4261 <span class="s">}</span> | |
| 4275 4262 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 4276 4263 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span> | |
| 4277 4264 | |
| 4278 4265 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="s">)</span><span class="sc">;</span> | |
| 4279 4266 | |
| 4280 4267 <span class="c"># Process element data...</span> | |
| 4281 4268 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 4282 4269 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> | |
| 4283 4270 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 4284 4271 <span class="s">}</span> | |
| 4285 4272 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4286 4273 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 4287 4274 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span> | |
| 4288 4275 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadValenceModelDataFile: The number of data fields, @LineWords, in $DataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span> | |
| 4289 4276 <span class="s">}</span> | |
| 4290 4277 | |
| 4291 4278 <span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="s">)</span> = <span class="i">@LineWords</span><span class="sc">;</span> | |
| 4292 4279 | |
| 4293 4280 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> | |
| 4294 4281 <span class="c"># Additional data for an element...</span> | |
| 4295 4282 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}<span class="s">)</span> <span class="s">{</span> | |
| 4296 4283 <span class="c"># Duplicate data entries for an element...</span> | |
| 4297 4284 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}::_LoadValenceModelDataFile: Ignoring valence data for element with atomic number $AtomicNumber and formal charge $FormalCharge in data file $DataFile: It has already been loaded.\nLine: $Line..."</span><span class="sc">;</span> | |
| 4298 4285 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 4299 4286 <span class="s">}</span> | |
| 4300 4287 <span class="s">}</span> | |
| 4301 4288 <span class="k">else</span> <span class="s">{</span> | |
| 4302 4289 <span class="c"># Data for a new element...</span> | |
| 4303 4290 <span class="i">%</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4304 4291 <span class="s">}</span> | |
| 4305 4292 | |
| 4306 4293 <span class="i">%</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4307 4294 <span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">ElementSymbol</span>} = <span class="i">$ElementSymbol</span><span class="sc">;</span> | |
| 4308 4295 | |
| 4309 4296 <span class="i">@</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4310 4297 <span class="i">@</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}} = <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="sc">;</span> | |
| 4311 4298 <span class="s">}</span> | |
| 4312 4299 <span class="k">close</span> <span class="w">DATAFILE</span><span class="sc">;</span> | |
| 4313 4300 <span class="s">}</span> | |
| 4314 4301 | |
| 4315 <a name="EOF-"></a></pre> | |
| 4316 <p> </p> | |
| 4317 <br /> | |
| 4318 <center> | |
| 4319 <img src="../../../images/h2o2.png"> | |
| 4320 </center> | |
| 4321 </body> | |
| 4322 </html> |