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<html> <head> <title>MayaChemTools:Code:Atom.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-Atom-"></a> 1 <span class="k">package </span><span class="i">Atom</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: Atom.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span> 5 <span class="c"># $Revision: 1.62 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Storable</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">PeriodicTable</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">Vector</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">MathUtil</span><span class="sc">;</span> 38 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 39 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> 40 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 41 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> 43 44 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> 45 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 46 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> 47 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> 49 50 <span class="c"># Setup class variables...</span> 51 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="cm">,</span> <span class="i">%MDLValenceModelDataMap</span><span class="cm">,</span> <span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> 52 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 53 54 <span class="c"># Overload Perl functions...</span> 55 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyAtom'</span><span class="sc">;</span> 56 57 <span class="c"># Class constructor...</span> <a name="new-"></a> 58 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 59 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 60 61 <span class="c"># Initialize object...</span> 62 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> 63 <span class="k">bless</span> <span class="i">$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> 64 <span class="i">$This</span><span class="i">->_InitializeAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 65 66 <span class="i">$This</span><span class="i">->_InitializeAtomProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 67 68 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 69 <span class="s">}</span> 70 71 <span class="c"># Initialize object data...</span> <a name="_InitializeAtom-"></a> 72 <span class="k">sub </span><span class="m">_InitializeAtom</span> <span class="s">{</span> 73 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 74 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 75 76 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> 77 <span class="c"># are implemented on-demand using ObjectProperty class.</span> 78 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span> 79 <span class="i">$This</span>->{<span class="w">Name</span>} = <span class="q">"Atom ${ObjectID}"</span><span class="sc">;</span> 80 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="q">''</span><span class="sc">;</span> 81 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="n">0</span><span class="sc">;</span> 82 <span class="i">$This</span>->{<span class="w">XYZ</span>} = <span class="w">Vector::ZeroVector</span><span class="sc">;</span> 83 <span class="s">}</span> 84 85 <span class="c"># Initialize atom properties...</span> <a name="_InitializeAtomProperties-"></a> 86 <span class="k">sub </span><span class="m">_InitializeAtomProperties</span> <span class="s">{</span> 87 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 88 89 <span class="k">my</span><span class="s">(</span><span class="i">$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> 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> 91 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 92 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 93 <span class="s">}</span> 94 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'AtomSymbol'</span>}<span class="s">)</span> <span class="s">{</span> 95 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Atom object instantiated without setting atom symbol..."</span><span class="sc">;</span> 96 <span class="s">}</span> 97 98 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 99 <span class="s">}</span> 100 101 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 102 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 103 <span class="c">#Class name...</span> 104 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 105 106 <span class="c"># ID to keep track of objects...</span> 107 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span> 108 109 <span class="c"># Load atom class data...</span> 110 <span class="i">_LoadAtomClassData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 111 <span class="s">}</span> 112 113 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span> <a name="SetID-"></a> 114 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span> 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> 116 117 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> 118 119 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 120 <span class="s">}</span> 121 122 <span class="c"># Setup an explicit SetMolecule method to block setting of ID by AUTOLOAD function...</span> <a name="SetMolecule-"></a> 123 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> 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> 125 126 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMolecule: Molecule property can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> 127 128 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 129 <span class="s">}</span> 130 131 <span class="c"># Assign atom to molecule...</span> <a name="_SetMolecule-"></a> 132 <span class="k">sub </span><span class="m">_SetMolecule</span> <span class="s">{</span> 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> 134 135 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> 136 137 <span class="c"># Weaken the reference to disable increment of reference count; otherwise,</span> 138 <span class="c"># it it becomes a circular reference and destruction of Molecule object doesn't</span> 139 <span class="c"># get initiated which in turn disables destruction of atom object.</span> 140 <span class="c">#</span> 141 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> 142 143 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 144 <span class="s">}</span> 145 146 <span class="c"># Setup atom symbol and atomic number for the element...</span> 147 <span class="c">#</span> 148 <span class="c"># Possible atom symbol values:</span> 149 <span class="c"># . An element symbol or some other type of atom: L - Atom list; LP - Lone pair; R# - R group;</span> 150 <span class="c"># A, Q, * - unknown atom; or something else?</span> 151 <span class="c">#</span> 152 <span class="c"># Default mass number corresponds to the most abundant natural isotope unless it's explicity</span> 153 <span class="c"># set using "MassNumber" property.</span> 154 <span class="c">#</span> <a name="SetAtomSymbol-"></a> 155 <span class="k">sub </span><span class="m">SetAtomSymbol</span> <span class="s">{</span> 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> 157 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> 158 159 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="i">$AtomSymbol</span><span class="sc">;</span> 160 161 <span class="i">$AtomicNumber</span> = <span class="i">PeriodicTable::GetElementAtomicNumber</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span> 162 <span class="i">$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> 163 164 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 165 <span class="s">}</span> 166 167 <span class="c"># Setup atom symbol and atomic number for the element...</span> <a name="SetAtomicNumber-"></a> 168 <span class="k">sub </span><span class="m">SetAtomicNumber</span> <span class="s">{</span> 169 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 170 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span> 171 172 <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> 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> 174 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicNumber: Didn't set atomic number: Invalid atomic number, $AtomicNumber, specified..."</span><span class="sc">;</span> 175 <span class="k">return</span><span class="sc">;</span> 176 <span class="s">}</span> 177 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="i">$AtomicNumber</span><span class="sc">;</span> 178 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="i">$AtomSymbol</span><span class="sc">;</span> 179 180 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 181 <span class="s">}</span> 182 183 <span class="c"># Set atom as stereo center...</span> 184 <span class="c">#</span> <a name="SetStereoCenter-"></a> 185 <span class="k">sub </span><span class="m">SetStereoCenter</span> <span class="s">{</span> 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> 187 188 <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> 189 190 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 191 <span class="s">}</span> 192 193 <span class="c"># Is it a stereo center?</span> 194 <span class="c">#</span> <a name="IsStereoCenter-"></a> 195 <span class="k">sub </span><span class="m">IsStereoCenter</span> <span class="s">{</span> 196 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 197 <span class="k">my</span><span class="s">(</span><span class="i">$StereoCenter</span><span class="s">)</span><span class="sc">;</span> 198 199 <span class="i">$StereoCenter</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="s">)</span><span class="sc">;</span> 200 201 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StereoCenter</span><span class="s">)</span> && <span class="i">$StereoCenter</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 202 <span class="s">}</span> 203 204 <span class="c"># Set atom stereochemistry.</span> 205 <span class="c">#</span> 206 <span class="c"># Supported values are: R, S.</span> 207 <span class="c">#</span> 208 <span class="c"># Notes:</span> 209 <span class="c">#</span> 210 <span class="c"># . After the ligands around a central stereocenter has been ranked using CIP priority scheme and</span> 211 <span class="c"># the lowest ranked ligand lies behind the center atom, then R and S values correspond to:</span> 212 <span class="c">#</span> 213 <span class="c"># R: Clockwise arrangement of remaining ligands around the central atom going from highest to lowest ranked ligand</span> 214 <span class="c"># S: CounterClockwise arrangement of remaining ligands around the central atom going from highest to lowest ranked ligand</span> 215 <span class="c">#</span> 216 <span class="c"># . Assignment of any other arbitray values besides R and S is also allowed; however, a warning is printed.</span> 217 <span class="c">#</span> <a name="SetStereochemistry-"></a> 218 <span class="k">sub </span><span class="m">SetStereochemistry</span> <span class="s">{</span> 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 220 221 <span class="k">if</span> <span class="s">(</span><span class="i">$Stereochemistry</span> !~ <span class="q">/^(R|S)$/i</span><span class="s">)</span> <span class="s">{</span> 222 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetStereochemistry: Assigning non-supported Stereochemistry value of $Stereochemistry. Supported values: R, S..."</span><span class="sc">;</span> 223 <span class="s">}</span> 224 225 <span class="i">$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> 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> 227 228 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 229 <span class="s">}</span> 230 231 <span class="c"># Setup mass number for atom...</span> <a name="SetMassNumber-"></a> 232 <span class="k">sub </span><span class="m">SetMassNumber</span> <span class="s">{</span> 233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 234 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span> 235 236 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 237 <span class="i">$AtomSymbol</span> = <span class="i">$This</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span> 238 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 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, $AtomSymbol..."</span><span class="sc">;</span> 240 <span class="k">return</span><span class="sc">;</span> 241 <span class="s">}</span> 242 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 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, $AtomSymbol. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope..."</span><span class="sc">;</span> 244 <span class="s">}</span> 245 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span> 246 247 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 248 <span class="s">}</span> 249 250 <span class="c"># Get mass number...</span> 251 <span class="c">#</span> <a name="GetMassNumber-"></a> 252 <span class="k">sub </span><span class="m">GetMassNumber</span> <span class="s">{</span> 253 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 254 255 <span class="c"># Is mass number explicity set?</span> 256 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 257 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span> 258 <span class="s">}</span> 259 260 <span class="c"># Is it an element symbol?</span> 261 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 262 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 263 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 264 <span class="s">}</span> 265 266 <span class="c"># Return most abundant mass number...</span> 267 <span class="k">return</span> <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> 268 <span class="s">}</span> 269 270 <span class="c"># Get atomic weight:</span> 271 <span class="c"># . Explicitly set by the caller</span> 272 <span class="c"># . Using atomic number</span> 273 <span class="c">#</span> <a name="GetAtomicWeight-"></a> 274 <span class="k">sub </span><span class="m">GetAtomicWeight</span> <span class="s">{</span> 275 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 276 277 <span class="c"># Is atomic weight explicity set?</span> 278 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AtomicWeight'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 279 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'AtomicWeight'</span><span class="s">)</span><span class="sc">;</span> 280 <span class="s">}</span> 281 282 <span class="c"># Is it an element symbol?</span> 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> 284 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 285 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 286 <span class="s">}</span> 287 288 <span class="c"># Return its atomic weight...</span> 289 <span class="k">return</span> <span class="i">PeriodicTable::GetElementAtomicWeight</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> 290 <span class="s">}</span> 291 292 <span class="c"># Get exact mass weight:</span> 293 <span class="c"># . Explicitly set by the caller</span> 294 <span class="c"># . Using atomic number and mass number explicity set by the caller</span> 295 <span class="c"># . Using atomic number and most abundant isotope</span> 296 <span class="c">#</span> <a name="GetExactMass-"></a> 297 <span class="k">sub </span><span class="m">GetExactMass</span> <span class="s">{</span> 298 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 299 300 <span class="c"># Is exact mass explicity set?</span> 301 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 302 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ExactMass'</span><span class="s">)</span><span class="sc">;</span> 303 <span class="s">}</span> 304 305 <span class="c"># Is it an element symbol?</span> 306 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 307 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 308 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 309 <span class="s">}</span> 310 311 <span class="c"># Is mass number explicitly set?</span> 312 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 313 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span> 314 <span class="k">if</span> <span class="s">(</span><span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 315 <span class="k">return</span> <span class="i">PeriodicTable::GetElementNaturalIsotopeMass</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span> 316 <span class="s">}</span> 317 <span class="s">}</span> 318 319 <span class="c"># Return most abundant isotope mass...</span> 320 <span class="k">return</span> <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMass</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> 321 <span class="s">}</span> 322 323 <span class="c"># Get formal charge:</span> 324 <span class="c"># . Explicitly set by the caller</span> 325 <span class="c"># . Or return zero insetad of undef</span> 326 <span class="c">#</span> <a name="GetFormalCharge-"></a> 327 <span class="k">sub </span><span class="m">GetFormalCharge</span> <span class="s">{</span> 328 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 329 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> 330 331 <span class="i">$FormalCharge</span> = <span class="n">0</span><span class="sc">;</span> 332 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 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> 334 <span class="s">}</span> 335 336 <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> 337 <span class="s">}</span> 338 339 <span class="c"># Get spin multiplicity:</span> 340 <span class="c"># . Explicitly set by the caller</span> 341 <span class="c"># . From FreeRadicalElectrons value explicitly set by the caller</span> 342 <span class="c"># . Or return zero insetad of undef</span> 343 <span class="c">#</span> <a name="GetSpinMultiplicity-"></a> 344 <span class="k">sub </span><span class="m">GetSpinMultiplicity</span> <span class="s">{</span> 345 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 346 <span class="k">my</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span> 347 348 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> 349 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 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> 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> 352 <span class="s">}</span> 353 354 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 355 <span class="k">my</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span><span class="sc">;</span> 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> 357 358 <span class="j">SPINMULTIPLICITY:</span> <span class="s">{</span> 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> 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> 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, $FreeRadicalElectrons. It has been set to 0..."</span><span class="sc">;</span> 362 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> 363 <span class="s">}</span> 364 <span class="s">}</span> 365 366 <span class="k">return</span> <span class="i">$SpinMultiplicity</span><span class="sc">;</span> 367 <span class="s">}</span> 368 369 <span class="c"># Get number of free radical electrons:</span> 370 <span class="c"># . Explicitly set by the caller</span> 371 <span class="c"># . From SpinMultiplicity value explicitly set by the caller</span> 372 <span class="c"># . Or return zero insetad of undef</span> 373 <span class="c">#</span> 374 <span class="c"># Notes:</span> 375 <span class="c"># . For atoms with explicit assignment of SpinMultiplicity property values corresponding to</span> 376 <span class="c"># Singlet (two unpaired electrons corresponding to one spin state), Doublet (free radical; an unpaired</span> 377 <span class="c"># electron corresponding to two spin states), and Triplet (two unparied electrons corresponding to</span> 378 <span class="c"># three spin states; divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</span> 379 <span class="c">#</span> 380 <span class="c"># SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1</span> 381 <span class="c"># SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2</span> 382 <span class="c">#</span> <a name="GetFreeRadicalElectrons-"></a> 383 <span class="k">sub </span><span class="m">GetFreeRadicalElectrons</span> <span class="s">{</span> 384 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 385 <span class="k">my</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span><span class="sc">;</span> 386 387 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span> 388 389 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 390 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="sc">;</span> 391 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span> ? <span class="i">$FreeRadicalElectrons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 392 <span class="s">}</span> 393 394 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 395 <span class="k">my</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span> 396 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span> 397 398 <span class="j">SPINMULTIPLICITY:</span> <span class="s">{</span> 399 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span> 400 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span> 401 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 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, $FreeRadicalElectrons. It has been set to 0..."</span><span class="sc">;</span> 403 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span> 404 <span class="s">}</span> 405 <span class="s">}</span> 406 407 <span class="k">return</span> <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span> 408 <span class="s">}</span> 409 410 <span class="c"># Set atom coordinates using:</span> 411 <span class="c"># . An array reference with three values</span> 412 <span class="c"># . An array containg three values</span> 413 <span class="c"># . A 3D vector</span> 414 <span class="c">#</span> <a name="SetXYZ-"></a> 415 <span class="k">sub </span><span class="m">SetXYZ</span> <span class="s">{</span> 416 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 417 418 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 419 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetXYZ: No values specified..."</span><span class="sc">;</span> 420 <span class="k">return</span><span class="sc">;</span> 421 <span class="s">}</span> 422 423 <span class="i">$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> 424 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 425 <span class="s">}</span> 426 427 <span class="c"># Set X value...</span> <a name="SetX-"></a> 428 <span class="k">sub </span><span class="m">SetX</span> <span class="s">{</span> 429 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 430 431 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span> 432 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetX: Undefined X value..."</span><span class="sc">;</span> 433 <span class="k">return</span><span class="sc">;</span> 434 <span class="s">}</span> 435 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetX</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 437 <span class="s">}</span> 438 439 <span class="c"># Set Y value...</span> <a name="SetY-"></a> 440 <span class="k">sub </span><span class="m">SetY</span> <span class="s">{</span> 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> 442 443 <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> 444 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetY: Undefined Y value..."</span><span class="sc">;</span> 445 <span class="k">return</span><span class="sc">;</span> 446 <span class="s">}</span> 447 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetY</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 448 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 449 <span class="s">}</span> 450 451 <span class="c"># Set Z value...</span> <a name="SetZ-"></a> 452 <span class="k">sub </span><span class="m">SetZ</span> <span class="s">{</span> 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> 454 455 <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> 456 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetZ: Undefined Z value..."</span><span class="sc">;</span> 457 <span class="k">return</span><span class="sc">;</span> 458 <span class="s">}</span> 459 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetZ</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 460 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 461 <span class="s">}</span> 462 463 <span class="c"># Return XYZ as:</span> 464 <span class="c"># . Reference to an array</span> 465 <span class="c"># . An array</span> 466 <span class="c">#</span> <a name="GetXYZ-"></a> 467 <span class="k">sub </span><span class="m">GetXYZ</span> <span class="s">{</span> 468 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 469 470 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetXYZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 471 <span class="s">}</span> 472 473 <span class="c"># Return XYZ as a vector object...</span> 474 <span class="c">#</span> <a name="GetXYZVector-"></a> 475 <span class="k">sub </span><span class="m">GetXYZVector</span> <span class="s">{</span> 476 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 477 478 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="sc">;</span> 479 <span class="s">}</span> 480 481 <span class="c"># Get X value...</span> <a name="GetX-"></a> 482 <span class="k">sub </span><span class="m">GetX</span> <span class="s">{</span> 483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 484 485 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetX</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 486 <span class="s">}</span> 487 488 <span class="c"># Get Y value...</span> <a name="GetY-"></a> 489 <span class="k">sub </span><span class="m">GetY</span> <span class="s">{</span> 490 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 491 492 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetY</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 493 <span class="s">}</span> 494 495 <span class="c"># Get Z value...</span> <a name="GetZ-"></a> 496 <span class="k">sub </span><span class="m">GetZ</span> <span class="s">{</span> 497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 498 499 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 500 <span class="s">}</span> 501 502 <span class="c"># Delete atom...</span> <a name="DeleteAtom-"></a> 503 <span class="k">sub </span><span class="m">DeleteAtom</span> <span class="s">{</span> 504 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 505 506 <span class="c"># Is this atom in a molecule?</span> 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 508 <span class="c"># Nothing to do...</span> 509 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 510 <span class="s">}</span> 511 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 512 513 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 514 <span class="s">}</span> 515 516 <span class="c"># Get atom neighbor objects as array. In scalar conetxt, return number of neighbors...</span> <a name="GetNeighbors-"></a> 517 <span class="k">sub </span><span class="m">GetNeighbors</span> <span class="s">{</span> 518 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 519 520 <span class="c"># Is this atom in a molecule?</span> 521 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 522 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 523 <span class="s">}</span> 524 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 525 526 <span class="k">if</span> <span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span> 527 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span><span class="sc">;</span> 528 <span class="s">}</span> 529 <span class="k">else</span> <span class="s">{</span> 530 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 531 <span class="s">}</span> 532 <span class="s">}</span> 533 534 <span class="c"># Get atom neighbor objects as array. In scalar conetxt, return number of neighbors...</span> <a name="_GetAtomNeighbors-"></a> 535 <span class="k">sub </span><span class="m">_GetAtomNeighbors</span> <span class="s">{</span> 536 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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> 538 539 <span class="k">if</span> <span class="s">(</span>!<span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span> 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> 541 <span class="s">}</span> 542 543 <span class="c"># Setup a map for neigbhors to exclude...</span> 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> 545 546 <span class="i">%ExcludeNeighborsIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 547 <span class="k">for</span> <span class="i">$ExcludeNeighbor</span> <span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span> 548 <span class="i">$ExcludeNeighborID</span> = <span class="i">$ExcludeNeighbor</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 549 <span class="i">$ExcludeNeighborsIDsMap</span>{<span class="i">$ExcludeNeighborID</span>} = <span class="i">$ExcludeNeighborID</span><span class="sc">;</span> 550 <span class="s">}</span> 551 552 <span class="c"># Generate a filtered neighbors list...</span> 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> 554 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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">$This</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 556 <span class="i">$NeighborID</span> = <span class="i">$Neighbor</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 557 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ExcludeNeighborsIDsMap</span>{<span class="i">$NeighborID</span>}<span class="s">)</span> <span class="s">{</span> 558 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> 559 <span class="s">}</span> 560 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="sc">;</span> 561 <span class="s">}</span> 562 563 <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> 564 <span class="s">}</span> 565 566 <span class="c"># Get specific atom neighbor objects as array. In scalar conetxt, return number of neighbors.</span> 567 <span class="c">#</span> 568 <span class="c"># Notes:</span> 569 <span class="c"># . AtomSpecification correspond to any valid AtomicInvariant based atomic specifications</span> 570 <span class="c"># as implemented in DoesAtomNeighborhoodMatch method.</span> 571 <span class="c"># . Multiple atom specifications can be used in a string delimited by comma.</span> 572 <span class="c">#</span> <a name="GetNeighborsUsingAtomSpecification-"></a> 573 <span class="k">sub </span><span class="m">GetNeighborsUsingAtomSpecification</span> <span class="s">{</span> 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> 575 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span><span class="sc">;</span> 576 577 <span class="i">@AtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 578 <span class="i">@AtomNeighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span><span class="sc">;</span> 579 580 <span class="c"># Does atom has any neighbors and do they need to be filtered?</span> 581 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@AtomNeighbors</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="s">)</span> && <span class="i">$AtomSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 582 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@AtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@AtomNeighbors</span><span class="sc">;</span> 583 <span class="s">}</span> 584 585 <span class="c"># Filter neighbors using atom specification...</span> 586 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span> 587 588 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 589 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span> <span class="s">{</span> 590 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNeighbor</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 591 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> 592 <span class="s">}</span> 593 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$AtomNeighbor</span><span class="sc">;</span> 594 <span class="s">}</span> 595 596 <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> 597 <span class="s">}</span> 598 599 600 <span class="c"># Get non-hydrogen atom neighbor objects as array. In scalar context, return number of neighbors...</span> <a name="GetHeavyAtomNeighbors-"></a> 601 <span class="k">sub </span><span class="m">GetHeavyAtomNeighbors</span> <span class="s">{</span> 602 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 603 604 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 605 <span class="s">}</span> 606 607 <span class="c"># Get non-hydrogen atom neighbor objects as array. In scalar context, return number of neighbors...</span> <a name="GetNonHydrogenAtomNeighbors-"></a> 608 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighbors</span> <span class="s">{</span> 609 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 610 611 <span class="c"># Is this atom in a molecule?</span> 612 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 613 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 614 <span class="s">}</span> 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> 616 617 <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">$HydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> 618 <span class="s">}</span> 619 620 <span class="c"># Get hydrogen atom neighbor objects as array. In scalar context, return numbe of neighbors...</span> <a name="GetHydrogenAtomNeighbors-"></a> 621 <span class="k">sub </span><span class="m">GetHydrogenAtomNeighbors</span> <span class="s">{</span> 622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 623 624 <span class="c"># Is this atom in a molecule?</span> 625 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 626 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 627 <span class="s">}</span> 628 <span class="k">my</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> 629 630 <span class="k">return</span> <span class="i">$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> 631 <span class="s">}</span> 632 633 <span class="c"># Get non-hydrogen neighbor of hydrogen atom...</span> 634 <span class="c">#</span> <a name="GetNonHydrogenNeighborOfHydrogenAtom-"></a> 635 <span class="k">sub </span><span class="m">GetNonHydrogenNeighborOfHydrogenAtom</span> <span class="s">{</span> 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 637 638 <span class="c"># Is it Hydrogen?</span> 639 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 640 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 641 <span class="s">}</span> 642 <span class="k">my</span><span class="s">(</span><span class="i">@Neighbors</span><span class="s">)</span><span class="sc">;</span> 643 644 <span class="i">@Neighbors</span> = <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 645 646 <span class="k">return</span> <span class="s">(</span><span class="i">@Neighbors</span> == <span class="n">1</span><span class="s">)</span> ? <span class="i">$Neighbors</span>[<span class="n">0</span>] <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> 647 <span class="s">}</span> 648 649 <span class="c"># Get filtered atom atom neighbors</span> <a name="_GetFilteredAtomNeighbors-"></a> 650 <span class="k">sub </span><span class="m">_GetFilteredAtomNeighbors</span> <span class="s">{</span> 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">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 652 653 <span class="c"># Check flags...</span> 654 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 655 <span class="i">$NonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> 656 <span class="s">}</span> 657 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 658 <span class="i">$HydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> 659 <span class="s">}</span> 660 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span> 661 662 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 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> 665 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> 666 <span class="s">}</span> 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> 668 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> 669 <span class="s">}</span> 670 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="sc">;</span> 671 <span class="s">}</span> 672 673 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span> 674 <span class="s">}</span> 675 676 <span class="c"># Get number of neighbors...</span> 677 <span class="c">#</span> <a name="GetNumOfNeighbors-"></a> 678 <span class="k">sub </span><span class="m">GetNumOfNeighbors</span> <span class="s">{</span> 679 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 680 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span> 681 682 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 683 684 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> 685 <span class="s">}</span> 686 687 <span class="c"># Get number of neighbors which are non-hydrogen atoms...</span> <a name="GetNumOfHeavyAtomNeighbors-"></a> 688 <span class="k">sub </span><span class="m">GetNumOfHeavyAtomNeighbors</span> <span class="s">{</span> 689 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 690 691 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 692 <span class="s">}</span> 693 694 <span class="c"># Get number of neighbors which are non-hydrogen atoms...</span> <a name="GetNumOfNonHydrogenAtomNeighbors-"></a> 695 <span class="k">sub </span><span class="m">GetNumOfNonHydrogenAtomNeighbors</span> <span class="s">{</span> 696 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 697 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span> 698 699 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 700 701 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> 702 <span class="s">}</span> 703 704 <span class="c"># Get number of neighbors which are hydrogen atoms...</span> <a name="GetNumOfHydrogenAtomNeighbors-"></a> 705 <span class="k">sub </span><span class="m">GetNumOfHydrogenAtomNeighbors</span> <span class="s">{</span> 706 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 707 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span> 708 709 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 710 711 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> 712 <span class="s">}</span> 713 714 <span class="c"># Get bond objects as array. In scalar context, return number of bonds...</span> <a name="GetBonds-"></a> 715 <span class="k">sub </span><span class="m">GetBonds</span> <span class="s">{</span> 716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 717 718 <span class="c"># Is this atom in a molecule?</span> 719 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 720 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 721 <span class="s">}</span> 722 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 723 724 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomBonds</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 725 <span class="s">}</span> 726 727 <span class="c"># Get bond to specified atom...</span> <a name="GetBondToAtom-"></a> 728 <span class="k">sub </span><span class="m">GetBondToAtom</span> <span class="s">{</span> 729 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 730 731 <span class="c"># Is this atom in a molecule?</span> 732 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 733 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 734 <span class="s">}</span> 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> 736 737 <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">$Other</span><span class="s">)</span><span class="sc">;</span> 738 <span class="s">}</span> 739 740 <span class="c"># It it bonded to a specified atom?</span> <a name="IsBondedToAtom-"></a> 741 <span class="k">sub </span><span class="m">IsBondedToAtom</span> <span class="s">{</span> 742 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 743 744 <span class="c"># Is this atom in a molecule?</span> 745 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 746 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 747 <span class="s">}</span> 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> 749 750 <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">$Other</span><span class="s">)</span><span class="sc">;</span> 751 <span class="s">}</span> 752 753 <span class="c"># Get bond objects to non-hydrogen atoms as array. In scalar context, return number of bonds...</span> <a name="GetBondsToHeavyAtoms-"></a> 754 <span class="k">sub </span><span class="m">GetBondsToHeavyAtoms</span> <span class="s">{</span> 755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 756 757 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 758 <span class="s">}</span> 759 760 <span class="c"># Get bond objects to non-hydrogen atoms as array. In scalar context, return number of bonds...</span> <a name="GetBondsToNonHydrogenAtoms-"></a> 761 <span class="k">sub </span><span class="m">GetBondsToNonHydrogenAtoms</span> <span class="s">{</span> 762 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 763 764 <span class="c"># Is this atom in a molecule?</span> 765 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 766 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 767 <span class="s">}</span> 768 <span class="k">my</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> 769 770 <span class="k">return</span> <span class="i">$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> 771 <span class="s">}</span> 772 773 <span class="c"># Get bond objects to hydrogen atoms as array. In scalar context, return number of bonds...</span> <a name="GetBondsToHydrogenAtoms-"></a> 774 <span class="k">sub </span><span class="m">GetBondsToHydrogenAtoms</span> <span class="s">{</span> 775 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 776 777 <span class="c"># Is this atom in a molecule?</span> 778 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 779 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 780 <span class="s">}</span> 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> 782 783 <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">$BondsToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> 784 <span class="s">}</span> 785 786 <span class="c"># Get filtered bonds...</span> <a name="_GetFilteredBonds-"></a> 787 <span class="k">sub </span><span class="m">_GetFilteredBonds</span> <span class="s">{</span> 788 <span class="k">my</span><span class="s">(</span><span class="i">$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> 789 790 <span class="c"># Check flags...</span> 791 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 792 <span class="i">$BondsToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> 793 <span class="s">}</span> 794 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 795 <span class="i">$BondsToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> 796 <span class="s">}</span> 797 798 <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> 799 800 <span class="i">@FilteredBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 802 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 803 <span class="k">if</span> <span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span> && <span class="i">$BondedAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 804 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 805 <span class="s">}</span> 806 <span class="k">if</span> <span class="s">(</span><span class="i">$BondsToHydrogenAtomsOnly</span> && <span class="s">(</span>!<span class="i">$BondedAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 807 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 808 <span class="s">}</span> 809 <span class="k">push</span> <span class="i">@FilteredBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="sc">;</span> 810 <span class="s">}</span> 811 812 <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> 813 <span class="s">}</span> 814 815 <span class="c"># Get number of bonds...</span> 816 <span class="c">#</span> <a name="GetNumOfBonds-"></a> 817 <span class="k">sub </span><span class="m">GetNumOfBonds</span> <span class="s">{</span> 818 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 819 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span> 820 821 <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> 822 823 <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> 824 <span class="s">}</span> 825 826 <span class="c"># Get number of bonds to non-hydrogen atoms...</span> <a name="GetNumOfBondsToHeavyAtoms-"></a> 827 <span class="k">sub </span><span class="m">GetNumOfBondsToHeavyAtoms</span> <span class="s">{</span> 828 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 829 830 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 831 <span class="s">}</span> 832 833 <span class="c"># Get number of bonds to non-hydrogen atoms...</span> <a name="GetNumOfBondsToNonHydrogenAtoms-"></a> 834 <span class="k">sub </span><span class="m">GetNumOfBondsToNonHydrogenAtoms</span> <span class="s">{</span> 835 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 836 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span> 837 838 <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> 839 840 <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> 841 <span class="s">}</span> 842 843 <span class="c"># Get number of single bonds to heavy atoms...</span> <a name="GetNumOfSingleBondsToHeavyAtoms-"></a> 844 <span class="k">sub </span><span class="m">GetNumOfSingleBondsToHeavyAtoms</span> <span class="s">{</span> 845 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 846 847 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 848 <span class="s">}</span> 849 850 <span class="c"># Get number of single bonds to non-hydrogen atoms...</span> <a name="GetNumOfSingleBondsToNonHydrogenAtoms-"></a> 851 <span class="k">sub </span><span class="m">GetNumOfSingleBondsToNonHydrogenAtoms</span> <span class="s">{</span> 852 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 853 854 <span class="c"># Is this atom in a molecule?</span> 855 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 856 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 857 <span class="s">}</span> 858 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> 859 <span class="s">}</span> 860 861 <span class="c"># Get number of double bonds to heavy atoms...</span> <a name="GetNumOfDoubleBondsToHeavyAtoms-"></a> 862 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToHeavyAtoms</span> <span class="s">{</span> 863 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 864 865 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 866 <span class="s">}</span> 867 868 <span class="c"># Get number of double bonds to non-hydrogen atoms...</span> <a name="GetNumOfDoubleBondsToNonHydrogenAtoms-"></a> 869 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToNonHydrogenAtoms</span> <span class="s">{</span> 870 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 871 872 <span class="c"># Is this atom in a molecule?</span> 873 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 874 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 875 <span class="s">}</span> 876 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">2</span><span class="s">)</span><span class="sc">;</span> 877 <span class="s">}</span> 878 879 <span class="c"># Get number of triple bonds to heavy atoms...</span> <a name="GetNumOfTripleBondsToHeavyAtoms-"></a> 880 <span class="k">sub </span><span class="m">GetNumOfTripleBondsToHeavyAtoms</span> <span class="s">{</span> 881 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 882 883 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 884 <span class="s">}</span> 885 886 <span class="c"># Get number of triple bonds to non-hydrogen atoms...</span> <a name="GetNumOfTripleBondsToNonHydrogenAtoms-"></a> 887 <span class="k">sub </span><span class="m">GetNumOfTripleBondsToNonHydrogenAtoms</span> <span class="s">{</span> 888 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 889 890 <span class="c"># Is this atom in a molecule?</span> 891 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 892 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 893 <span class="s">}</span> 894 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">3</span><span class="s">)</span><span class="sc">;</span> 895 <span class="s">}</span> 896 897 <span class="c"># Get number of bonds of specified bond order to non-hydrogen atoms...</span> <a name="_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms-"></a> 898 <span class="k">sub </span><span class="m">_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span> <span class="s">{</span> 899 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$SpecifiedBondOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 900 <span class="k">my</span><span class="s">(</span><span class="i">$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> 901 902 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span> 903 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 904 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 905 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 906 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedBondOrder</span> == <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span> 907 <span class="i">$NumOfBonds</span>++<span class="sc">;</span> 908 <span class="s">}</span> 909 <span class="s">}</span> 910 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span> 911 <span class="s">}</span> 912 913 <span class="c"># Get number of aromatic bonds to heavy atoms...</span> <a name="GetNumOfAromaticBondsToHeavyAtoms-"></a> 914 <span class="k">sub </span><span class="m">GetNumOfAromaticBondsToHeavyAtoms</span> <span class="s">{</span> 915 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 916 917 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 918 <span class="s">}</span> 919 920 <span class="c"># Get number of aromatic bonds to non-hydrogen atoms...</span> <a name="GetNumOfAromaticBondsToNonHydrogenAtoms-"></a> 921 <span class="k">sub </span><span class="m">GetNumOfAromaticBondsToNonHydrogenAtoms</span> <span class="s">{</span> 922 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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> 924 925 <span class="c"># Is this atom in a molecule?</span> 926 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 927 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 928 <span class="s">}</span> 929 930 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span> 931 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 932 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 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> 934 <span class="s">}</span> 935 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span> 936 <span class="s">}</span> 937 938 <span class="c"># Get number of different bond types to non-hydrogen atoms...</span> 939 <span class="c">#</span> <a name="GetNumOfBondTypesToHeavyAtoms-"></a> 940 <span class="k">sub </span><span class="m">GetNumOfBondTypesToHeavyAtoms</span> <span class="s">{</span> 941 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CountAromaticBonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 942 943 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span><span class="sc">;</span> 944 <span class="s">}</span> 945 946 <span class="c"># Get number of single, double, triple, and aromatic bonds from an atom to all other</span> 947 <span class="c"># non-hydrogen atoms. Value of CountAtomaticBonds parameter controls whether</span> 948 <span class="c"># number of aromatic bonds is returned; default is not to count aromatic bonds. During</span> 949 <span class="c"># counting of aromatic bonds, the bond marked aromatic is not included in the count</span> 950 <span class="c"># of other bond types.</span> 951 <span class="c">#</span> <a name="GetNumOfBondTypesToNonHydrogenAtoms-"></a> 952 <span class="k">sub </span><span class="m">GetNumOfBondTypesToNonHydrogenAtoms</span> <span class="s">{</span> 953 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CountAromaticBonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 954 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> 955 956 <span class="i">$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> 957 958 <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">$NumOfTripleBonds</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> 959 <span class="i">$NumOfAromaticBonds</span> = <span class="i">$CountAromaticBonds</span> ? <span class="n">0</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> 960 961 <span class="c"># Is this atom in a molecule?</span> 962 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 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> 964 <span class="s">}</span> 965 966 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 967 968 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 969 <span class="j">BONDTYPE:</span> <span class="s">{</span> 970 <span class="k">if</span> <span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span> <span class="s">{</span> 971 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$NumOfAromaticBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span> 972 <span class="s">}</span> 973 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$NumOfSingleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span> 974 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$NumOfDoubleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span> 975 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$NumOfTripleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span> 976 <span class="i">$None</span> = <span class="n">1</span><span class="sc">;</span> 977 <span class="s">}</span> 978 <span class="s">}</span> 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> 980 <span class="s">}</span> 981 982 <span class="c"># Get number of sigma and pi bonds to heavy atoms...</span> 983 <span class="c">#</span> <a name="GetNumOfSigmaAndPiBondsToHeavyAtoms-"></a> 984 <span class="k">sub </span><span class="m">GetNumOfSigmaAndPiBondsToHeavyAtoms</span> <span class="s">{</span> 985 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 986 987 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 988 <span class="s">}</span> 989 990 <span class="c"># Get number of sigma and pi bonds from an atom to all other non-hydrogen atoms.</span> 991 <span class="c"># Sigma and pi bonds are counted using the following methodology: a single bond</span> 992 <span class="c"># correspond to one sigma bond; a double bond contributes one to sigma bond count</span> 993 <span class="c"># and one to pi bond count; a triple bond contributes one to sigma bond count and</span> 994 <span class="c"># two to pi bond count.</span> 995 <span class="c">#</span> <a name="GetNumOfSigmaAndPiBondsToNonHydrogenAtoms-"></a> 996 <span class="k">sub </span><span class="m">GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</span> <span class="s">{</span> 997 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 998 <span class="k">my</span><span class="s">(</span><span class="i">$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> 999 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> 1001 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> 1003 <span class="i">$NumOfPiBonds</span> = <span class="i">$NumOfDoubleBonds</span> + <span class="n">2</span>*<span class="i">$NumOfTripleBonds</span><span class="sc">;</span> 1004 1005 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSigmaBonds</span><span class="cm">,</span> <span class="i">$NumOfPiBonds</span><span class="s">)</span><span class="sc">;</span> 1006 <span class="s">}</span> 1007 1008 <span class="c"># Get information related to atoms for all heavy atoms attached to an atom..</span> 1009 <span class="c">#</span> <a name="GetHeavyAtomNeighborsAtomInformation-"></a>1010 <span class="k">sub </span><span class="m">GetHeavyAtomNeighborsAtomInformation</span> <span class="s">{</span> 1011 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1012 1013 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighborsAtomInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1014 <span class="s">}</span> 1015 1016 <span class="c"># Get information related to atoms for all non-hydrogen atoms attached to an atom..</span> 1017 <span class="c">#</span> 1018 <span class="c"># The following values are returned:</span> 1019 <span class="c"># . Number of non-hydrogen atom neighbors</span> 1020 <span class="c"># . A reference to an array containing atom objects correpsonding to non-hydrogen</span> 1021 <span class="c"># atom neighbors</span> 1022 <span class="c"># . Number of different types of non-hydrogen atom neighbors</span> 1023 <span class="c"># . A reference to a hash containing atom symbol as key with value corresponding</span> 1024 <span class="c"># to its count for non-hydrogen atom neighbors</span> 1025 <span class="c">#</span> <a name="GetNonHydrogenAtomNeighborsAtomInformation-"></a>1026 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsAtomInformation</span> <span class="s">{</span> 1027 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1028 1029 <span class="c"># Is this atom in a molecule?</span> 1030 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1031 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> 1032 <span class="s">}</span> 1033 <span class="k">my</span><span class="s">(</span><span class="i">$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">$NumOfAtomNeighborsType</span><span class="cm">,</span> <span class="i">@AtomNeighbors</span><span class="cm">,</span> <span class="i">%AtomNeighborsTypeMap</span><span class="s">)</span><span class="sc">;</span> 1034 1035 <span class="i">$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> 1036 <span class="i">$NumOfAtomNeighborsType</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">%AtomNeighborsTypeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1037 1038 <span class="i">@AtomNeighbors</span> = <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1039 <span class="i">$NumOfAtomNeighbors</span> = <span class="k">scalar</span> <span class="i">@AtomNeighbors</span><span class="sc">;</span> 1040 1041 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span> <span class="s">{</span> 1042 <span class="i">$AtomSymbol</span> = <span class="i">$AtomNeighbor</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span> 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> 1044 <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span> 1045 <span class="s">}</span> 1046 <span class="k">else</span> <span class="s">{</span> 1047 <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span> 1048 <span class="i">$NumOfAtomNeighborsType</span>++<span class="sc">;</span> 1049 <span class="s">}</span> 1050 <span class="s">}</span> 1051 1052 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfAtomNeighbors</span><span class="cm">,</span> \<span class="i">@AtomNeighbors</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighborsType</span><span class="cm">,</span> \<span class="i">%AtomNeighborsTypeMap</span><span class="s">)</span><span class="sc">;</span> 1053 <span class="s">}</span> 1054 1055 <span class="c"># Get information related to bonds for all heavy atoms attached to an atom..</span> 1056 <span class="c">#</span> <a name="GetHeavyAtomNeighborsBondformation-"></a>1057 <span class="k">sub </span><span class="m">GetHeavyAtomNeighborsBondformation</span> <span class="s">{</span> 1058 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1059 1060 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighborsBondInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1061 <span class="s">}</span> 1062 1063 <span class="c"># Get information related to bonds for all non-hydrogen atoms attached to an atom..</span> 1064 <span class="c">#</span> 1065 <span class="c"># The following values are returned:</span> 1066 <span class="c"># . Number of bonds to non-hydrogen atom neighbors</span> 1067 <span class="c"># . A reference to an array containing bond objects correpsonding to non-hydrogen</span> 1068 <span class="c"># atom neighbors</span> 1069 <span class="c"># . A reference to a hash containing bond type as key with value corresponding</span> 1070 <span class="c"># to its count for non-hydrogen atom neighbors. Bond types are: Single, Double or Triple</span> 1071 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span> 1072 <span class="c"># key with values correponding to count of bond types for atom symbol for non-hydrogen</span> 1073 <span class="c"># atom neighbors</span> 1074 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span> 1075 <span class="c"># key with values correponding to atom objects array involved in corresponding bond type for</span> 1076 <span class="c"># atom symbol for non-hydrogen atom neighbors</span> 1077 <span class="c">#</span> <a name="GetNonHydrogenAtomNeighborsBondInformation-"></a>1078 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsBondInformation</span> <span class="s">{</span> 1079 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1080 1081 <span class="c"># Is this atom in a molecule?</span> 1082 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1083 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> 1084 <span class="s">}</span> 1085 <span class="k">my</span><span class="s">(</span><span class="i">$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">$NumOfBonds</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="cm">,</span> <span class="i">%BondTypeCountMap</span><span class="cm">,</span> <span class="i">%AtomsBondTypesCountMap</span><span class="cm">,</span> <span class="i">%AtomsBondTypeAtomsMap</span><span class="s">)</span><span class="sc">;</span> 1086 1087 <span class="i">$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> 1088 <span class="i">%BondTypeCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 1090 1091 <span class="i">$BondTypeCountMap</span>{<span class="w">Single</span>} = <span class="n">0</span><span class="sc">;</span> 1092 <span class="i">$BondTypeCountMap</span>{<span class="w">Double</span>} = <span class="n">0</span><span class="sc">;</span> 1093 <span class="i">$BondTypeCountMap</span>{<span class="w">Triple</span>} = <span class="n">0</span><span class="sc">;</span> 1094 1095 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1096 <span class="i">$NumOfBonds</span> = <span class="k">scalar</span> <span class="i">@Bonds</span><span class="sc">;</span> 1097 1098 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 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> 1100 <span class="k">if</span> <span class="s">(</span>!<span class="i">$BondType</span><span class="s">)</span> <span class="s">{</span> 1101 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 1102 <span class="s">}</span> 1103 1104 <span class="c"># Track bond types...</span> 1105 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span> 1106 <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>} += <span class="n">1</span><span class="sc">;</span> 1107 <span class="s">}</span> 1108 <span class="k">else</span> <span class="s">{</span> 1109 <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>} = <span class="n">1</span><span class="sc">;</span> 1110 <span class="s">}</span> 1111 1112 <span class="i">$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> 1113 <span class="i">$BondedAtomSymbol</span> = <span class="i">$BondedAtom</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span> 1114 1115 <span class="c"># Track bond types count for atom types involved in specific bond types...</span> 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> 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> 1118 <span class="s">}</span> 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">$BondType</span>}<span class="s">)</span> <span class="s">{</span> 1120 <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>} += <span class="n">1</span><span class="sc">;</span> 1121 <span class="s">}</span> 1122 <span class="k">else</span> <span class="s">{</span> 1123 <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>} = <span class="n">1</span><span class="sc">;</span> 1124 <span class="s">}</span> 1125 1126 <span class="c"># Track atoms involved in specific bond types for specific atom types...</span> 1127 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> 1128 <span class="i">%</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1129 <span class="s">}</span> 1130 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span> 1131 <span class="i">@</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1132 <span class="s">}</span> 1133 <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}}<span class="cm">,</span> <span class="i">$BondedAtom</span><span class="sc">;</span> 1134 <span class="s">}</span> 1135 1136 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 1137 <span class="s">}</span> 1138 1139 <span class="c"># Get number of bonds to hydrogen atoms...</span> <a name="GetNumOfBondsToHydrogenAtoms-"></a>1140 <span class="k">sub </span><span class="m">GetNumOfBondsToHydrogenAtoms</span> <span class="s">{</span> 1141 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1142 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span> 1143 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> 1145 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> 1147 <span class="s">}</span> 1148 1149 <span class="c"># Get sum of bond orders to all bonded atoms...</span> 1150 <span class="c">#</span> <a name="GetSumOfBondOrders-"></a>1151 <span class="k">sub </span><span class="m">GetSumOfBondOrders</span> <span class="s">{</span> 1152 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1153 1154 <span class="c"># Is this atom in a molecule?</span> 1155 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 1156 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1157 <span class="s">}</span> 1158 1159 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1160 <span class="s">}</span> 1161 1162 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span> 1163 <span class="c">#</span> <a name="GetSumOfBondOrdersToHeavyAtoms-"></a>1164 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToHeavyAtoms</span> <span class="s">{</span> 1165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1166 1167 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1168 <span class="s">}</span> 1169 1170 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span> 1171 <span class="c">#</span> <a name="GetSumOfBondOrdersToNonHydrogenAtoms-"></a>1172 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToNonHydrogenAtoms</span> <span class="s">{</span> 1173 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1174 1175 <span class="c"># Is this atom in a molecule?</span> 1176 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1177 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1178 <span class="s">}</span> 1179 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> 1180 1181 <span class="k">return</span> <span class="i">$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> 1182 <span class="s">}</span> 1183 1184 <span class="c"># Get sum of bond orders to hydrogen atoms only...</span> 1185 <span class="c">#</span> <a name="GetSumOfBondOrdersToHydrogenAtoms-"></a>1186 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToHydrogenAtoms</span> <span class="s">{</span> 1187 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1188 1189 <span class="c"># Is this atom in a molecule?</span> 1190 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 1191 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1192 <span class="s">}</span> 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> 1194 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">$ToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> 1196 <span class="s">}</span> 1197 1198 <span class="c"># Get sum of bond orders to all bonded atoms, non-hydrogen or hydrogen bonded atoms...</span> 1199 <span class="c">#</span> <a name="_GetSumOfBondOrders-"></a>1200 <span class="k">sub </span><span class="m">_GetSumOfBondOrders</span> <span class="s">{</span> 1201 <span class="k">my</span><span class="s">(</span><span class="i">$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> 1202 1203 <span class="c"># Check flags...</span> 1204 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 1205 <span class="i">$ToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> 1206 <span class="s">}</span> 1207 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 1208 <span class="i">$ToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> 1209 <span class="s">}</span> 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> 1211 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1212 1213 <span class="k">if</span> <span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 1214 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1215 <span class="s">}</span> 1216 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 1217 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1218 <span class="s">}</span> 1219 <span class="k">else</span> <span class="s">{</span> 1220 <span class="c"># All bonds...</span> 1221 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1222 <span class="s">}</span> 1223 1224 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span> 1225 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 1226 <span class="i">$SumOfBondOrders</span> += <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1227 <span class="s">}</span> 1228 1229 <span class="k">if</span> <span class="s">(</span><span class="i">$SumOfBondOrders</span> =~ <span class="q">/\./</span><span class="s">)</span> <span class="s">{</span> 1230 <span class="c">#</span> 1231 <span class="c"># Change any fractional bond order to next largest integer...</span> 1232 <span class="c">#</span> 1233 <span class="c"># As long as aromatic bond orders in a ring are correctly using using 4n + 2 Huckel rule</span> 1234 <span class="c"># (BondOrder: 1.5) or explicity set as Kekule bonds (alternate single/double),</span> 1235 <span class="c"># SumOfBondOrders should add up to an integer.</span> 1236 <span class="c">#</span> 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> 1238 <span class="s">}</span> 1239 1240 <span class="k">return</span> <span class="i">$SumOfBondOrders</span><span class="sc">;</span> 1241 <span class="s">}</span> 1242 1243 <span class="c"># Get largest bond order to any bonded atoms...</span> 1244 <span class="c">#</span> <a name="GetLargestBondOrder-"></a>1245 <span class="k">sub </span><span class="m">GetLargestBondOrder</span> <span class="s">{</span> 1246 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1247 1248 <span class="c"># Is this atom in a molecule?</span> 1249 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1250 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1251 <span class="s">}</span> 1252 1253 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetLargestBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1254 <span class="s">}</span> 1255 1256 <span class="c"># Get largest bond order to bonded non-hydrogen atoms...</span> 1257 <span class="c">#</span> <a name="GetLargestBondOrderToHeavyAtoms-"></a>1258 <span class="k">sub </span><span class="m">GetLargestBondOrderToHeavyAtoms</span> <span class="s">{</span> 1259 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1260 1261 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1262 <span class="s">}</span> 1263 1264 <span class="c"># Get largest bond order to bonded non-hydrogen atoms...</span> 1265 <span class="c">#</span> <a name="GetLargestBondOrderToNonHydrogenAtoms-"></a>1266 <span class="k">sub </span><span class="m">GetLargestBondOrderToNonHydrogenAtoms</span> <span class="s">{</span> 1267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1268 1269 <span class="c"># Is this atom in a molecule?</span> 1270 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 1271 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1272 <span class="s">}</span> 1273 1274 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> 1275 1276 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetLargestBondOrder</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span> 1277 <span class="s">}</span> 1278 1279 <span class="c"># Get largest bond order to all bonded atoms, non-hydrogen or hydrogen bonded atoms...</span> 1280 <span class="c">#</span> <a name="_GetLargestBondOrder-"></a>1281 <span class="k">sub </span><span class="m">_GetLargestBondOrder</span> <span class="s">{</span> 1282 <span class="k">my</span><span class="s">(</span><span class="i">$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> 1283 1284 <span class="c"># Check flags...</span> 1285 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 1286 <span class="i">$ToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> 1287 <span class="s">}</span> 1288 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 1289 <span class="i">$ToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span> 1290 <span class="s">}</span> 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">$BondOrder</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> 1292 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1293 1294 <span class="k">if</span> <span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 1295 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1296 <span class="s">}</span> 1297 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> 1298 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1299 <span class="s">}</span> 1300 <span class="k">else</span> <span class="s">{</span> 1301 <span class="c"># All bonds...</span> 1302 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1303 <span class="s">}</span> 1304 1305 <span class="i">$LargestBondOrder</span> = <span class="n">0</span><span class="sc">;</span> 1306 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 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> 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> 1309 <span class="i">$LargestBondOrder</span> = <span class="i">$BondOrder</span><span class="sc">;</span> 1310 <span class="s">}</span> 1311 <span class="s">}</span> 1312 1313 <span class="k">return</span> <span class="i">$LargestBondOrder</span><span class="sc">;</span> 1314 <span class="s">}</span> 1315 1316 <span class="c"># Get number of implicit hydrogen for atom...</span> 1317 <span class="c">#</span> <a name="GetImplicitHydrogens-"></a>1318 <span class="k">sub </span><span class="m">GetImplicitHydrogens</span> <span class="s">{</span> 1319 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1320 1321 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1322 <span class="s">}</span> 1323 1324 <span class="c"># Get number of implicit hydrogen for atom...</span> 1325 <span class="c">#</span> <a name="GetNumOfImplicitHydrogens-"></a>1326 <span class="k">sub </span><span class="m">GetNumOfImplicitHydrogens</span> <span class="s">{</span> 1327 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1328 1329 <span class="c"># Is this atom in a molecule?</span> 1330 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1331 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1332 <span class="s">}</span> 1333 1334 <span class="c"># Is ImplicitHydrogens property explicitly set?</span> 1335 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 1336 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="sc">;</span> 1337 <span class="s">}</span> 1338 1339 <span class="c"># Is it an element symbol?</span> 1340 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> 1341 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1342 <span class="s">}</span> 1343 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">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span> 1345 1346 <span class="i">$ImplicitHydrogens</span> = <span class="n">0</span><span class="sc">;</span> 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> 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> 1349 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> 1351 <span class="c"># Subtract sum of bond orders to non-hydrogen and hydrogen atom neighbors...</span> 1352 <span class="i">$ImplicitHydrogens</span> = <span class="i">$PotentialTotalValence</span> - <span class="i">$SumOfBondOrders</span><span class="sc">;</span> 1353 <span class="s">}</span> 1354 1355 <span class="k">return</span> <span class="i">$ImplicitHydrogens</span> > <span class="n">0</span> ? <span class="i">$ImplicitHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 1356 <span class="s">}</span> 1357 1358 <span class="c"># Get number of bonds available to form additional bonds with heavy atoms, excluding</span> 1359 <span class="c"># any implicit bonds to hydrogens set using ImplicitHydrogens property.</span> 1360 <span class="c">#</span> 1361 <span class="c"># It's different from number of implicit or missing hydrogens, both of which are equivalent.</span> 1362 <span class="c">#</span> 1363 <span class="c"># For example, in a SMILES string, [nH] ring atom corresponds to an aromatic nitrogen.</span> 1364 <span class="c"># Although the hydrogen specified for n is treated internally as implicit hydrogen and shows</span> 1365 <span class="c"># up in missing hydrogen count, it's not available to participate in double bonds to additional</span> 1366 <span class="c"># heavy atoms.</span> 1367 <span class="c">#</span> <a name="GetNumOfBondsAvailableForHeavyAtoms-"></a>1368 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForHeavyAtoms</span> <span class="s">{</span> 1369 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1370 1371 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfBondsAvailableForNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1372 <span class="s">}</span> 1373 1374 <span class="c"># It's another name for GetNumOfBondsAvailableForHeavyAtoms</span> 1375 <span class="c">#</span> <a name="GetNumOfBondsAvailableForNonHydrogenAtoms-"></a>1376 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForNonHydrogenAtoms</span> <span class="s">{</span> 1377 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span> 1379 1380 <span class="i">$NumOfAvailableBonds</span> = <span class="n">0</span><span class="sc">;</span> 1381 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> 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> 1384 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> 1386 <span class="c"># Subtract sum of bond orders to non-hydrogen and hydrogen atom neighbors...</span> 1387 <span class="i">$NumOfAvailableBonds</span> = <span class="i">$PotentialTotalValence</span> - <span class="i">$SumOfBondOrders</span><span class="sc">;</span> 1388 <span class="s">}</span> 1389 1390 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 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> 1392 <span class="s">}</span> 1393 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> 1395 <span class="s">}</span> 1396 1397 <span class="c"># Disable setting of explicit hydrogens property...</span> <a name="SetExplicitHydrogens-"></a>1398 <span class="k">sub </span><span class="m">SetExplicitHydrogens</span> <span class="s">{</span> 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> 1400 1401 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetExplicitHydrogens: Setting of explicit hydrogens is not supported..."</span><span class="sc">;</span> 1402 1403 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1404 <span class="s">}</span> 1405 1406 <span class="c"># Get number of explicit hydrogens for atom...</span> 1407 <span class="c">#</span> <a name="GetExplicitHydrogens-"></a>1408 <span class="k">sub </span><span class="m">GetExplicitHydrogens</span> <span class="s">{</span> 1409 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1410 1411 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1412 <span class="s">}</span> 1413 1414 <span class="c"># Get number of explicit hydrogens for atom...</span> 1415 <span class="c">#</span> <a name="GetNumOfExplicitHydrogens-"></a>1416 <span class="k">sub </span><span class="m">GetNumOfExplicitHydrogens</span> <span class="s">{</span> 1417 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1418 <span class="k">my</span><span class="s">(</span><span class="i">$HydrogenAtomNbrs</span><span class="s">)</span><span class="sc">;</span> 1419 1420 <span class="c"># Is this atom in a molecule?</span> 1421 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1422 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1423 <span class="s">}</span> 1424 1425 <span class="i">$HydrogenAtomNbrs</span> = <span class="i">$This</span><span class="i">->GetNumOfHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1426 1427 <span class="k">return</span> <span class="k">defined</span> <span class="i">$HydrogenAtomNbrs</span> ? <span class="i">$HydrogenAtomNbrs</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 1428 <span class="s">}</span> 1429 1430 <span class="c"># Get num of missing hydrogens...</span> 1431 <span class="c">#</span> <a name="GetMissingHydrogens-"></a>1432 <span class="k">sub </span><span class="m">GetMissingHydrogens</span> <span class="s">{</span> 1433 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1434 1435 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1436 <span class="s">}</span> 1437 1438 <span class="c"># Get num of missing hydrogens...</span> 1439 <span class="c">#</span> <a name="GetNumOfMissingHydrogens-"></a>1440 <span class="k">sub </span><span class="m">GetNumOfMissingHydrogens</span> <span class="s">{</span> 1441 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1442 1443 <span class="c"># Is this atom in a molecule?</span> 1444 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1445 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1446 <span class="s">}</span> 1447 1448 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1449 <span class="s">}</span> 1450 1451 <span class="c"># Get total number of hydrogens...</span> 1452 <span class="c">#</span> <a name="GetHydrogens-"></a>1453 <span class="k">sub </span><span class="m">GetHydrogens</span> <span class="s">{</span> 1454 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1455 1456 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1457 <span class="s">}</span> 1458 1459 <span class="c"># Get total number of hydrogens...</span> 1460 <span class="c">#</span> <a name="GetNumOfHydrogens-"></a>1461 <span class="k">sub </span><span class="m">GetNumOfHydrogens</span> <span class="s">{</span> 1462 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1463 1464 <span class="c"># Is this atom in a molecule?</span> 1465 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 1466 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1467 <span class="s">}</span> 1468 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> 1470 <span class="s">}</span> 1471 1472 <span class="c"># Valence corresponds to the number of electrons used by an atom in bonding:</span> 1473 <span class="c">#</span> 1474 <span class="c"># Valence = ValenceElectrons - ValenceFreeElectrons = BondingElectrons</span> 1475 <span class="c">#</span> 1476 <span class="c"># Single, double, triple bonds with bond orders of 1, 2 and 3 correspond to contribution of</span> 1477 <span class="c"># 1, 2, and 3 bonding electrons. So Valence can be computed using:</span> 1478 <span class="c">#</span> 1479 <span class="c"># Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</span> 1480 <span class="c">#</span> 1481 <span class="c"># where positive and negative values of FormalCharge increase and decrease the number</span> 1482 <span class="c"># of bonding electrons respectively.</span> 1483 <span class="c">#</span> 1484 <span class="c"># The current release of MayaChemTools supports the following three valence models, which</span> 1485 <span class="c"># are used during calculation of implicit hydrogens: MDLValenceModel, DaylightValenceModel,</span> 1486 <span class="c"># InternalValenceModel or MayaChemToolsValenceModel.</span> 1487 <span class="c">#</span> 1488 <span class="c"># Notes:</span> 1489 <span class="c"># . This doesn't always corresponds to explicit valence.</span> 1490 <span class="c"># . Missing hydrogens are included in the valence.</span> 1491 <span class="c"># . For neutral molecules, valence and sum of bond order are equal.</span> 1492 <span class="c"># . For molecules containing only single bonds, SumOfBondOrders and NumOfBonds are equal.</span> 1493 <span class="c"># . Free radical electrons lead to the decrease in valence. For atoms with explicit assignment</span> 1494 <span class="c"># of SpinMultiplicity property values corresponding to Singlet (two unparied electrons</span> 1495 <span class="c"># corresponding to one spin state), Doublet (free radical; an unpaired electron corresponding</span> 1496 <span class="c"># to two spin states), and Triplet (two unparied electrons corresponding to three spin states;</span> 1497 <span class="c"># divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</span> 1498 <span class="c">#</span> 1499 <span class="c"># SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1 (one valence electron not available for bonding)</span> 1500 <span class="c"># SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2 (two valence electrons not available for bonding)</span> 1501 <span class="c">#</span> <a name="GetValence-"></a>1502 <span class="k">sub </span><span class="m">GetValence</span> <span class="s">{</span> 1503 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1504 1505 <span class="c"># Is this atom in a molecule?</span> 1506 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 1507 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1508 <span class="s">}</span> 1509 1510 <span class="c"># Is Valence property explicitly set?</span> 1511 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Valence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1512 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Valence'</span><span class="s">)</span><span class="sc">;</span> 1513 <span class="s">}</span> 1514 <span class="k">my</span><span class="s">(</span><span class="i">$Valence</span><span class="s">)</span><span class="sc">;</span> 1515 1516 <span class="i">$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">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1517 1518 <span class="k">return</span> <span class="i">$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> 1519 <span class="s">}</span> 1520 1521 <span class="c"># Get free non-bodning valence electrons left on atom after taking into account</span> 1522 <span class="c"># sum of bond orders, missing hydrogens and formal charged on the atom. Free</span> 1523 <span class="c"># radical electrons are included in the valence free electrons count by default.</span> 1524 <span class="c">#</span> 1525 <span class="c"># Valence corresponds to number of electrons used by atom in bonding:</span> 1526 <span class="c">#</span> 1527 <span class="c"># Valence = ValenceElectrons - ValenceFreeElectrons</span> 1528 <span class="c">#</span> 1529 <span class="c"># Additionally, valence can also be calculated by:</span> 1530 <span class="c">#</span> 1531 <span class="c"># Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</span> 1532 <span class="c">#</span> 1533 <span class="c"># Valence and SumOfBondOrders are equal for neutral molecules.</span> 1534 <span class="c">#</span> 1535 <span class="c"># From two formulas for Valence described above, non-bonding free electrons</span> 1536 <span class="c"># left can be computed by:</span> 1537 <span class="c">#</span> 1538 <span class="c"># ValenceFreeElectrons = ValenceElectrons - Valence</span> 1539 <span class="c"># = ValenceElectrons - SumOfBondOrders -</span> 1540 <span class="c"># NumOfMissingHydrogens - FormalCharge</span> 1541 <span class="c">#</span> 1542 <span class="c"># . Notes:</span> 1543 <span class="c"># . Missing hydrogens are excluded from the valence free electrons.</span> 1544 <span class="c"># . Any free radical electrons are considered part of the valence free electrons</span> 1545 <span class="c"># by default.</span> 1546 <span class="c">#</span> 1547 <span class="c"># Examples:</span> 1548 <span class="c">#</span> 1549 <span class="c"># o NH3: ValenceFreeElectrons = 5 - 3 = 5 - 3 - 0 - 0 = 2</span> 1550 <span class="c"># o NH2: ValenceFreeElectrons = 5 - 3 = 5 - 2 - 1 - 0 = 2</span> 1551 <span class="c"># o NH4+; ValenceFreeElectrons = 5 - 5 = 5 - 4 - 0 - 1 = 0</span> 1552 <span class="c"># o NH3+; ValenceFreeElectrons = 5 - 5 = 5 - 3 - 1 - 1 = 0</span> 1553 <span class="c"># o C(=O)O- : ValenceFreeElectrons on O- = 6 - 0 = 6 - 1 - 0 - (-1) = 6</span> 1554 <span class="c"># o C(=O)O- : ValenceFreeElectrons on =O = 6 - 2 = 6 - 2 - 0 - 0 = 4</span> 1555 <span class="c">#</span> 1556 <span class="c">#</span> <a name="GetValenceFreeElectrons-"></a>1557 <span class="k">sub </span><span class="m">GetValenceFreeElectrons</span> <span class="s">{</span> 1558 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1559 1560 <span class="c"># Is this atom in a molecule?</span> 1561 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 1562 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1563 <span class="s">}</span> 1564 1565 <span class="c"># Is ValenceFreeElectrons property explicitly set?</span> 1566 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceFreeElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1567 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceFreeElectrons'</span><span class="s">)</span><span class="sc">;</span> 1568 <span class="s">}</span> 1569 1570 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> 1571 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1572 <span class="s">}</span> 1573 1574 <span class="k">my</span><span class="s">(</span><span class="i">$ValenceFreeElectrons</span><span class="s">)</span><span class="sc">;</span> 1575 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">$This</span><span class="i">->GetValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1577 <span class="k">if</span> <span class="s">(</span><span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span> 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> 1579 <span class="s">}</span> 1580 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> 1582 <span class="s">}</span> 1583 1584 <span class="c"># Get potential total common valence for calculating the number of implicit hydrogens</span> 1585 <span class="c"># using the specified common valence model or default internal model for a molecule...</span> 1586 <span class="c">#</span> <a name="GetPotentialTotalCommonValence-"></a>1587 <span class="k">sub </span><span class="m">GetPotentialTotalCommonValence</span> <span class="s">{</span> 1588 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1589 1590 <span class="c"># Is this atom in a molecule?</span> 1591 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 1592 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1593 <span class="s">}</span> 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> 1595 1596 <span class="i">$PotentialTotalValence</span> = <span class="n">0</span><span class="sc">;</span> 1597 <span class="i">$ValenceModel</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="i">->GetValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1598 1599 <span class="j">VALENCEMODEL:</span> <span class="s">{</span> 1600 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> =~ <span class="q">/^MDLValenceModel$/i</span><span class="s">)</span> <span class="s">{</span> 1601 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingMDLValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1602 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span> 1603 <span class="s">}</span> 1604 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> =~ <span class="q">/^DaylightValenceModel$/i</span><span class="s">)</span> <span class="s">{</span> 1605 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingDaylightValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1606 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span> 1607 <span class="s">}</span> 1608 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> !~ <span class="q">/^(InternalValenceModel|MayaChemToolsValenceModel)$/i</span><span class="s">)</span> <span class="s">{</span> 1609 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetPotentialTotalCommonValence: The current release of MayaChemTools doesn't support the specified valence model $ValenceModel. Supported valence models: MDLValenceModel, DaylightValenceModel, InternalValenceModel. Using internal valence model..."</span><span class="sc">;</span> 1610 <span class="s">}</span> 1611 <span class="c"># Use internal valence model as the default valence model...</span> 1612 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1613 <span class="s">}</span> 1614 1615 <span class="k">return</span> <span class="i">$PotentialTotalValence</span><span class="sc">;</span> 1616 <span class="s">}</span> 1617 1618 <span class="c"># Get potential total common valence using data for MDL valence model available in file,</span> 1619 <span class="c"># lib/data/MDLValenceModelData.csv, distributed with the package...</span> 1620 <span class="c">#</span> <a name="_GetPotentialTotalCommonValenceUsingMDLValenceModel-"></a>1621 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingMDLValenceModel</span> <span class="s">{</span> 1622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1623 1624 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingValenceModelData</span><span class="s">(</span>\<span class="i">%MDLValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> 1625 1626 <span class="s">}</span> 1627 1628 <span class="c"># Get potential total common valence using data for Daylight valence model available in file,</span> 1629 <span class="c"># lib/data/DaylightValenceModelData.csv, distributed with the release...</span> 1630 <span class="c">#</span> <a name="_GetPotentialTotalCommonValenceUsingDaylightValenceModel-"></a>1631 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingDaylightValenceModel</span> <span class="s">{</span> 1632 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1633 1634 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingValenceModelData</span><span class="s">(</span>\<span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> 1635 <span class="s">}</span> 1636 1637 <span class="c"># Get potential total common valence using data for a specific valence model...</span> 1638 <span class="c">#</span> <a name="_GetPotentialTotalCommonValenceUsingValenceModelData-"></a>1639 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingValenceModelData</span> <span class="s">{</span> 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> 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> 1642 1643 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 1644 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 1645 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1646 <span class="s">}</span> 1647 1648 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1649 1650 <span class="c"># Is any valence model data available for atomic number and formal charge?</span> 1651 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ValenceModelDataRef</span>->{<span class="i">$AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> 1652 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1653 <span class="s">}</span> 1654 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ValenceModelDataRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}<span class="s">)</span> <span class="s">{</span> 1655 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1656 <span class="s">}</span> 1657 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> 1659 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> 1661 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span> 1662 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span> 1663 <span class="s">}</span> 1664 <span class="i">$CurrentEffectiveValence</span> = <span class="i">$SumOfBondOrders</span> + <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1665 1666 <span class="i">$PotentialTotalValence</span> = <span class="n">0</span><span class="sc">;</span> 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> 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> 1669 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValence</span><span class="sc">;</span> 1670 <span class="k">last</span> <span class="j">VALENCE</span><span class="sc">;</span> 1671 <span class="s">}</span> 1672 <span class="s">}</span> 1673 1674 <span class="k">return</span> <span class="i">$PotentialTotalValence</span><span class="sc">;</span> 1675 <span class="s">}</span> 1676 1677 <span class="c">#</span> 1678 <span class="c"># For elements with one one common valence, potential total common valence used</span> 1679 <span class="c"># during the calculation for number of implicit hydrogens during InternalValenceMode</span> 1680 <span class="c"># corresponds to:</span> 1681 <span class="c">#</span> 1682 <span class="c"># CommonValence + FormalCharge - FreeRadicalElectrons</span> 1683 <span class="c">#</span> 1684 <span class="c"># For elements with multiple common valences, each common valence is used to</span> 1685 <span class="c"># calculate total potential common valence as shown above, and the first total potential</span> 1686 <span class="c"># common valence gerater than the sum of bond orderes is selected as the final total</span> 1687 <span class="c"># common valence.</span> 1688 <span class="c">#</span> 1689 <span class="c"># Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He)</span> 1690 <span class="c">#</span> 1691 <span class="c"># Formal charge sign is not adjusted. Positive and negative values result in the</span> 1692 <span class="c"># increase and decrease of valence.</span> 1693 <span class="c">#</span> 1694 <span class="c"># Group 14 containing C, Si, Ge, Sn, Pb...</span> 1695 <span class="c">#</span> 1696 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> 1697 <span class="c"># values result in the decrease of valence.</span> 1698 <span class="c">#</span> 1699 <span class="c"># Group 13 containing B, Al, Ga, In, Tl...</span> 1700 <span class="c">#</span> 1701 <span class="c"># Formal charge sign is always reversed. Positive and negative values result in the</span> 1702 <span class="c"># decrease and increase of valence.</span> 1703 <span class="c">#</span> 1704 <span class="c"># Groups 1 (H) through 12 (Zn)...</span> 1705 <span class="c">#</span> 1706 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> 1707 <span class="c"># values result in the decrease of valence.</span> 1708 <span class="c">#</span> 1709 <span class="c"># Lanthanides and actinides...</span> 1710 <span class="c">#</span> 1711 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> 1712 <span class="c"># values result in the decrease of valence.</span> 1713 <span class="c">#</span> 1714 <span class="c"># Notes:</span> 1715 <span class="c"># . CommonValence and HighestCommonValence available from PeriodicTable module</span> 1716 <span class="c"># are equivalent to most common and highest sum of bond orders for an element. For</span> 1717 <span class="c"># neutral atoms involved only in single bonds, it corresponds to highest number of</span> 1718 <span class="c"># allowed bonds for the atom.</span> 1719 <span class="c"># . FormalCharge sign is reversed for electropositive elements with positive formal charge</span> 1720 <span class="c"># during common valence calculations. Electropositive elements, metals and transition elements,</span> 1721 <span class="c"># have usually plus formal charge and it leads to decrease in common valence; the negative</span> 1722 <span class="c"># formal charge should result in the decrease of common valence.</span> 1723 <span class="c"># . For carbon, both plus/minus formal charge cause decrease in common valence</span> 1724 <span class="c"># . For elements on the right of carbon in periodic table, electronegative elements, plus formal</span> 1725 <span class="c"># charge causes common valence to increase and minus formal charge cause it to decrease.</span> 1726 <span class="c">#</span> <a name="_GetPotentialTotalCommonValenceUsingInternalValenceModel-"></a>1727 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingInternalValenceModel</span> <span class="s">{</span> 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> 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> 1730 1731 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 1732 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 1733 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1734 <span class="s">}</span> 1735 1736 <span class="i">$CommonValences</span> = <span class="i">PeriodicTable::GetElementCommonValences</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> 1737 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CommonValences</span><span class="s">)</span> <span class="s">{</span> 1738 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1739 <span class="s">}</span> 1740 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">$AvailableCommonValence</span><span class="cm">,</span> <span class="i">@AvailableCommonValences</span><span class="s">)</span><span class="sc">;</span> 1742 1743 <span class="i">$AdjustedFormalCharge</span> = <span class="i">$This</span><span class="i">->_GetFormalChargeAdjustedForInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1744 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1745 1746 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1747 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span> 1748 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span> 1749 <span class="s">}</span> 1750 1751 <span class="i">@AvailableCommonValences</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="sc">;</span> 1752 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> 1754 <span class="c"># Calculate potential total valence using the only available common valence...</span> 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> 1756 <span class="s">}</span> 1757 <span class="k">else</span> <span class="s">{</span> 1758 <span class="c"># Calculate potential total valence using common valence from a list of available valences</span> 1759 <span class="c"># that makes it higher than sum of bond orders or using the highest common valence...</span> 1760 <span class="j">VALENCE:</span> <span class="k">for</span> <span class="i">$AvailableCommonValence</span> <span class="s">(</span><span class="i">@AvailableCommonValences</span><span class="s">)</span> <span class="s">{</span> 1761 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValence</span> + <span class="i">$AdjustedFormalCharge</span> - <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span> 1762 1763 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 1764 <span class="k">last</span> <span class="j">VALENCE</span><span class="sc">;</span> 1765 <span class="s">}</span> 1766 <span class="s">}</span> 1767 <span class="s">}</span> 1768 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> 1770 <span class="s">}</span> 1771 1772 <span class="c"># Adjust sign of the formal charge for potential total common valence calculation</span> 1773 <span class="c"># used during internal valence model to figure out number of implicit hydrogens.</span> 1774 <span class="c">#</span> <a name="_GetFormalChargeAdjustedForInternalValenceModel-"></a>1775 <span class="k">sub </span><span class="m">_GetFormalChargeAdjustedForInternalValenceModel</span> <span class="s">{</span> 1776 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1777 <span class="k">my</span><span class="s">(</span><span class="i">$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> 1778 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> 1780 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 1781 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1782 <span class="s">}</span> 1783 1784 <span class="i">$GroupNumber</span> = <span class="i">$This</span><span class="i">->GetGroupNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1785 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$GroupNumber</span><span class="s">)</span> <span class="s">{</span> 1786 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span> 1787 <span class="s">}</span> 1788 1789 <span class="c"># Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He)</span> 1790 <span class="c">#</span> 1791 <span class="c"># Formal charge sign is not adjusted. Positive and negative values result in the</span> 1792 <span class="c"># increase and decrease of valence.</span> 1793 <span class="c">#</span> 1794 <span class="c"># Group 14 containing C, Si, Ge, Sn, Pb...</span> 1795 <span class="c">#</span> 1796 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> 1797 <span class="c"># values result in the decrease of valence.</span> 1798 <span class="c">#</span> 1799 <span class="c"># Group 13 containing B, Al, Ga, In, Tl...</span> 1800 <span class="c">#</span> 1801 <span class="c"># Formal charge sign is always reversed. Positive and negative values result in the</span> 1802 <span class="c"># decrease and increase of valence.</span> 1803 <span class="c">#</span> 1804 <span class="c"># Groups 1 (H) through 12 (Zn)...</span> 1805 <span class="c">#</span> 1806 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> 1807 <span class="c"># values result in the decrease of valence.</span> 1808 <span class="c">#</span> 1809 <span class="c"># Lanthanides and actinides...</span> 1810 <span class="c">#</span> 1811 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> 1812 <span class="c"># values result in the decrease of valence.</span> 1813 <span class="c">#</span> 1814 1815 <span class="i">$SwitchSign</span> = <span class="n">0</span><span class="sc">;</span> 1816 <span class="k">if</span> <span class="s">(</span><span class="k">length</span> <span class="i">$GroupNumber</span><span class="s">)</span> <span class="s">{</span> 1817 <span class="j">GROUPNUMBER:</span> <span class="s">{</span> 1818 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> > <span class="n">14</span><span class="s">)</span> <span class="s">{</span> 1819 <span class="c"># Groups on the right side of C group in the periodic table...</span> 1820 <span class="i">$SwitchSign</span> = <span class="n">0</span><span class="sc">;</span> 1821 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span> 1822 <span class="s">}</span> 1823 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> == <span class="n">14</span><span class="s">)</span> <span class="s">{</span> 1824 <span class="c"># Group containing C, Si, Ge, Sn, Pb...</span> 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> 1826 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span> 1827 <span class="s">}</span> 1828 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> == <span class="n">13</span><span class="s">)</span> <span class="s">{</span> 1829 <span class="c"># Group containing B, Al, Ga, In, Tl...</span> 1830 <span class="i">$SwitchSign</span> = <span class="n">1</span><span class="sc">;</span> 1831 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span> 1832 <span class="s">}</span> 1833 <span class="c"># Groups 1 (H) through 12 (Zn)...</span> 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> 1835 <span class="c"># Groups 1 (H) through 12 (Zn)...</span> 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> 1837 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span> 1838 <span class="s">}</span> 1839 <span class="s">}</span> 1840 <span class="s">}</span> 1841 <span class="k">else</span> <span class="s">{</span> 1842 <span class="c"># Lanthanides and actinides...</span> 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> 1844 <span class="s">}</span> 1845 1846 <span class="k">if</span> <span class="s">(</span><span class="i">$SwitchSign</span><span class="s">)</span> <span class="s">{</span> 1847 <span class="i">$FormalCharge</span> *= <span class="n">-1.0</span><span class="sc">;</span> 1848 <span class="s">}</span> 1849 1850 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span> 1851 <span class="s">}</span> 1852 1853 <span class="c"># Get lowest common valence...</span> <a name="GetLowestCommonValence-"></a>1854 <span class="k">sub </span><span class="m">GetLowestCommonValence</span> <span class="s">{</span> 1855 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1856 1857 <span class="c"># Is LowestCommonValence property explicitly set?</span> 1858 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'LowestCommonValence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1859 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'LowestCommonValence'</span><span class="s">)</span><span class="sc">;</span> 1860 <span class="s">}</span> 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> 1862 1863 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 1864 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 1865 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1866 <span class="s">}</span> 1867 <span class="c"># Any need to differentiate between internal and other valence models...</span> 1868 1869 <span class="c"># LowestCommonValence is not set for all elements...</span> 1870 <span class="i">$LowestCommonValence</span> = <span class="i">PeriodicTable::GetElementLowestCommonValence</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> 1871 <span class="k">if</span> <span class="s">(</span>!<span class="i">$LowestCommonValence</span><span class="s">)</span> <span class="s">{</span> 1872 <span class="i">$LowestCommonValence</span> = <span class="k">undef</span><span class="sc">;</span> 1873 <span class="s">}</span> 1874 1875 <span class="k">return</span> <span class="i">$LowestCommonValence</span><span class="sc">;</span> 1876 <span class="s">}</span> 1877 1878 <span class="c"># Get highest common valence...</span> <a name="GetHighestCommonValence-"></a>1879 <span class="k">sub </span><span class="m">GetHighestCommonValence</span> <span class="s">{</span> 1880 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1881 1882 <span class="c"># Is HighestCommonValence property explicitly set?</span> 1883 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 1884 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'HighestCommonValence'</span><span class="s">)</span><span class="sc">;</span> 1885 <span class="s">}</span> 1886 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$HighestCommonValence</span><span class="s">)</span><span class="sc">;</span> 1887 1888 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 1889 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 1890 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1891 <span class="s">}</span> 1892 1893 <span class="c"># Any need to differentiate between internal and other valence models...</span> 1894 1895 <span class="c"># HighestCommonValence is not set for all elements...</span> 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> 1897 <span class="k">if</span> <span class="s">(</span>!<span class="i">$HighestCommonValence</span><span class="s">)</span> <span class="s">{</span> 1898 <span class="i">$HighestCommonValence</span> = <span class="k">undef</span><span class="sc">;</span> 1899 <span class="s">}</span> 1900 1901 <span class="k">return</span> <span class="i">$HighestCommonValence</span><span class="sc">;</span> 1902 <span class="s">}</span> 1903 1904 <span class="c"># Get valence electrons...</span> <a name="GetValenceElectrons-"></a>1905 <span class="k">sub </span><span class="m">GetValenceElectrons</span> <span class="s">{</span> 1906 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1907 1908 <span class="c"># Is ValenceElectrons property explicitly set?</span> 1909 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1910 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceElectrons'</span><span class="s">)</span><span class="sc">;</span> 1911 <span class="s">}</span> 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> 1913 1914 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 1915 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 1916 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1917 <span class="s">}</span> 1918 1919 <span class="i">$ValenceElectrons</span> = <span class="i">PeriodicTable::GetElementValenceElectrons</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> 1920 1921 <span class="k">return</span> <span class="i">$ValenceElectrons</span><span class="sc">;</span> 1922 <span class="s">}</span> 1923 1924 <span class="c"># Add hydrogens to specified atom in molecule and return number of hydrogens added:</span> 1925 <span class="c">#</span> 1926 <span class="c"># o HydrogensToAdd = ImplicitHydrogenCount - ExplicitHydrogenCount</span> 1927 <span class="c">#</span> 1928 <span class="c"># o XYZ are set to ZeroVector</span> 1929 <span class="c">#</span> <a name="AddHydrogens-"></a>1930 <span class="k">sub </span><span class="m">AddHydrogens</span> <span class="s">{</span> 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> 1932 1933 <span class="c"># Is this atom in a molecule?</span> 1934 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1935 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1936 <span class="s">}</span> 1937 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> <span class="s">{</span> 1938 <span class="i">$HydrogenPositionsWarning</span> = <span class="n">1</span><span class="sc">;</span> 1939 <span class="s">}</span> 1940 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> <span class="s">{</span> 1941 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddHydrogens: The current release of MayaChemTools doesn't assign any hydrogen positions..."</span><span class="sc">;</span> 1942 <span class="s">}</span> 1943 1944 <span class="c"># Is it an element symbol?</span> 1945 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> 1946 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1947 <span class="s">}</span> 1948 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">$HydrogensToAdd</span><span class="s">)</span><span class="sc">;</span> 1950 1951 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 1952 <span class="i">$HydrogensAdded</span> = <span class="n">0</span><span class="sc">;</span> 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> 1954 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogensToAdd</span> <= <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 1955 <span class="k">return</span> <span class="i">$HydrogensAdded</span><span class="sc">;</span> 1956 <span class="s">}</span> 1957 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> 1959 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> 1961 <span class="i">$HydrogensAdded</span>++<span class="sc">;</span> 1962 1963 <span class="i">$Hydrogen</span> = <span class="i">$Molecule</span><span class="i">->NewAtom</span><span class="s">(</span><span class="q">'AtomSymbol'</span> <span class="cm">=></span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'XYZ'</span> <span class="cm">=></span> <span class="s">[</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> 1964 <span class="i">$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> 1965 <span class="s">}</span> 1966 1967 <span class="k">return</span> <span class="i">$HydrogensAdded</span><span class="sc">;</span> 1968 <span class="s">}</span> 1969 1970 <span class="c"># Delete hydrogens attached to atom in molecule and return total number of hydrogens deleted...</span> <a name="DeleteHydrogens-"></a>1971 <span class="k">sub </span><span class="m">DeleteHydrogens</span> <span class="s">{</span> 1972 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1973 1974 <span class="c"># Is this atom in a molecule?</span> 1975 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1976 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1977 <span class="s">}</span> 1978 1979 <span class="c"># Is it an element symbol?</span> 1980 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> 1981 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1982 <span class="s">}</span> 1983 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">$HydrogensDeleted</span><span class="cm">,</span> <span class="i">@Neighbors</span><span class="s">)</span><span class="sc">;</span> 1985 1986 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 1987 <span class="i">$HydrogensDeleted</span> = <span class="n">0</span><span class="sc">;</span> 1988 <span class="i">@Neighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1989 1990 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">@Neighbors</span><span class="s">)</span> <span class="s">{</span> 1991 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Neighbor</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1992 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> 1993 <span class="s">}</span> 1994 <span class="i">$Molecule</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$Neighbor</span><span class="s">)</span><span class="sc">;</span> 1995 <span class="i">$HydrogensDeleted</span>++<span class="sc">;</span> 1996 <span class="s">}</span> 1997 1998 <span class="k">return</span> <span class="i">$HydrogensDeleted</span><span class="sc">;</span> 1999 <span class="s">}</span> 2000 2001 <span class="c"># Copy atom and all its associated data...</span> <a name="Copy-"></a>2002 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span> 2003 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2004 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 2005 2006 <span class="i">$Atom</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 2007 2008 <span class="k">return</span> <span class="i">$Atom</span><span class="sc">;</span> 2009 <span class="s">}</span> 2010 2011 <span class="c"># Get atomic invariant value...</span> 2012 <span class="c">#</span> <a name="GetAtomicInvariantValue-"></a>2013 <span class="k">sub </span><span class="m">GetAtomicInvariantValue</span> <span class="s">{</span> 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> 2015 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 2016 2017 <span class="i">$Value</span> = <span class="q">""</span><span class="sc">;</span> 2018 2019 <span class="j">ATOMICVARIANT:</span> <span class="s">{</span> 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> 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> 2022 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2023 <span class="s">}</span> 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> 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> 2026 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2027 <span class="s">}</span> 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> 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> 2030 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2031 <span class="s">}</span> 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> 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> 2034 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2035 <span class="s">}</span> 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> 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> 2038 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2039 <span class="s">}</span> 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> 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> 2042 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2043 <span class="s">}</span> 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> 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> 2046 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2047 <span class="s">}</span> 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> 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> 2050 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2051 <span class="s">}</span> 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> 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> 2054 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2055 <span class="s">}</span> 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> 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> 2058 <span class="i">$Value</span> = <span class="k">defined</span> <span class="i">$Value</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 2059 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2060 <span class="s">}</span> 2061 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(T|TotalNumOfAtomNeighbors)$/i</span><span class="s">)</span> <span class="s">{</span> 2062 <span class="i">$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> 2063 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2064 <span class="s">}</span> 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> 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">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2067 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2068 <span class="s">}</span> 2069 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span> 2070 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 2071 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2072 <span class="s">}</span> 2073 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(RA|RingAtom)$/i</span><span class="s">)</span> <span class="s">{</span> 2074 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 2075 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2076 <span class="s">}</span> 2077 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(Str|Stereochemistry)$/i</span><span class="s">)</span> <span class="s">{</span> 2078 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2079 <span class="i">$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> 2080 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2081 <span class="s">}</span> 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> 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> 2084 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2085 <span class="s">}</span> 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> 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> 2088 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2089 <span class="s">}</span> 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> 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> 2092 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2093 <span class="s">}</span> 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> 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> 2096 <span class="i">$Value</span> = <span class="k">defined</span> <span class="i">$Value</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> 2097 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> 2098 <span class="s">}</span> 2099 <span class="i">$Value</span> = <span class="q">""</span><span class="sc">;</span> 2100 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetAtomicInvariantValue: Unknown atomic invariant $AtomicInvariant..."</span><span class="sc">;</span> 2101 <span class="s">}</span> 2102 2103 <span class="k">return</span> <span class="i">$Value</span><span class="sc">;</span> 2104 <span class="s">}</span> 2105 2106 <span class="c"># Get period number of the atom..</span> 2107 <span class="c">#</span> <a name="GetPeriodNumber-"></a>2108 <span class="k">sub </span><span class="m">GetPeriodNumber</span> <span class="s">{</span> 2109 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2110 2111 <span class="c"># Is PeriodNumber property explicitly set?</span> 2112 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 2113 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'PeriodNumber'</span><span class="s">)</span><span class="sc">;</span> 2114 <span class="s">}</span> 2115 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$PeriodNumber</span><span class="s">)</span><span class="sc">;</span> 2116 2117 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 2118 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 2119 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2120 <span class="s">}</span> 2121 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> 2123 2124 <span class="k">return</span> <span class="i">$PeriodNumber</span><span class="sc">;</span> 2125 <span class="s">}</span> 2126 2127 <span class="c"># Get group number of the atom..</span> 2128 <span class="c">#</span> <a name="GetGroupNumber-"></a>2129 <span class="k">sub </span><span class="m">GetGroupNumber</span> <span class="s">{</span> 2130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2131 2132 <span class="c"># Is GroupNumber property explicitly set?</span> 2133 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'GroupNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2134 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'GroupNumber'</span><span class="s">)</span><span class="sc">;</span> 2135 <span class="s">}</span> 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> 2137 2138 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 2139 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 2140 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2141 <span class="s">}</span> 2142 2143 <span class="i">$GroupNumber</span> = <span class="i">PeriodicTable::GetElementGroupNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> 2144 2145 <span class="k">return</span> <span class="i">$GroupNumber</span><span class="sc">;</span> 2146 <span class="s">}</span> 2147 2148 <span class="c"># Is it a specified topological pharmacophore atom type?</span> 2149 <span class="c">#</span> <a name="IsTopologicalPharmacophoreType-"></a>2150 <span class="k">sub </span><span class="m">IsTopologicalPharmacophoreType</span> <span class="s">{</span> 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> 2152 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> 2154 <span class="s">}</span> 2155 2156 <span class="c"># Is it a specified functional class atom type?</span> 2157 <span class="c">#</span> <a name="IsFunctionalClassType-"></a>2158 <span class="k">sub </span><span class="m">IsFunctionalClassType</span> <span class="s">{</span> 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> 2160 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> 2162 <span class="s">}</span> 2163 2164 <span class="c"># Is it a specified functional/topological pharmacophore atom type?</span> 2165 <span class="c">#</span> <a name="_IsFunctionalClassType-"></a>2166 <span class="k">sub </span><span class="m">_IsFunctionalClassType</span> <span class="s">{</span> 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> 2168 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 2169 2170 <span class="i">$Value</span> = <span class="n">0</span><span class="sc">;</span> 2171 2172 <span class="j">TYPE:</span> <span class="s">{</span> 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> 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> 2175 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> 2176 <span class="s">}</span> 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> 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> 2179 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> 2180 <span class="s">}</span> 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> 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> 2183 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> 2184 <span class="s">}</span> 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> 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> 2187 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> 2188 <span class="s">}</span> 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> 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> 2191 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> 2192 <span class="s">}</span> 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> 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> 2195 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> 2196 <span class="s">}</span> 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> 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> 2199 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> 2200 <span class="s">}</span> 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> 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> 2203 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> 2204 <span class="s">}</span> 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> 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> 2207 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span> 2208 <span class="s">}</span> 2209 <span class="i">$Value</span> = <span class="n">0</span><span class="sc">;</span> 2210 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_IsType: Unknown functional/pharmacohore type $Type..."</span><span class="sc">;</span> 2211 <span class="s">}</span> 2212 <span class="k">return</span> <span class="i">$Value</span><span class="sc">;</span> 2213 <span class="s">}</span> 2214 2215 <span class="c"># Is it a Hydrogen atom?</span> <a name="IsHydrogen-"></a>2216 <span class="k">sub </span><span class="m">IsHydrogen</span> <span class="s">{</span> 2217 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2218 2219 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2220 <span class="s">}</span> 2221 2222 <span class="c"># Is it a Carbon atom?</span> <a name="IsCarbon-"></a>2223 <span class="k">sub </span><span class="m">IsCarbon</span> <span class="s">{</span> 2224 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2225 2226 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2227 <span class="s">}</span> 2228 2229 <span class="c"># Is it a Nitrogen atom?</span> <a name="IsNitrogen-"></a>2230 <span class="k">sub </span><span class="m">IsNitrogen</span> <span class="s">{</span> 2231 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2232 2233 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2234 <span class="s">}</span> 2235 2236 <span class="c"># Is it a Oxygen atom?</span> <a name="IsOxygen-"></a>2237 <span class="k">sub </span><span class="m">IsOxygen</span> <span class="s">{</span> 2238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2239 2240 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2241 <span class="s">}</span> 2242 2243 <span class="c"># Is it a Fluorine atom?</span> <a name="IsFluorine-"></a>2244 <span class="k">sub </span><span class="m">IsFluorine</span> <span class="s">{</span> 2245 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2246 2247 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2248 <span class="s">}</span> 2249 2250 <span class="c"># Is it a Silicon atom?</span> <a name="IsSilicon-"></a>2251 <span class="k">sub </span><span class="m">IsSilicon</span> <span class="s">{</span> 2252 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2253 2254 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2255 <span class="s">}</span> 2256 2257 <span class="c"># Is it a Phosphorus atom?</span> <a name="IsPhosphorus-"></a>2258 <span class="k">sub </span><span class="m">IsPhosphorus</span> <span class="s">{</span> 2259 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2260 2261 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2262 <span class="s">}</span> 2263 2264 <span class="c"># Is it a Sulphur atom?</span> <a name="IsSulphur-"></a>2265 <span class="k">sub </span><span class="m">IsSulphur</span> <span class="s">{</span> 2266 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2267 2268 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsSulfur</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2269 <span class="s">}</span> 2270 2271 <span class="c"># Is it a Sulfur atom?</span> <a name="IsSulfur-"></a>2272 <span class="k">sub </span><span class="m">IsSulfur</span> <span class="s">{</span> 2273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2274 2275 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2276 <span class="s">}</span> 2277 2278 <span class="c"># Is it a Chlorine atom?</span> <a name="IsChlorine-"></a>2279 <span class="k">sub </span><span class="m">IsChlorine</span> <span class="s">{</span> 2280 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2281 2282 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2283 <span class="s">}</span> 2284 2285 <span class="c"># Is it a Arsenic atom?</span> <a name="IsArsenic-"></a>2286 <span class="k">sub </span><span class="m">IsArsenic</span> <span class="s">{</span> 2287 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2288 2289 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2290 <span class="s">}</span> 2291 2292 <span class="c"># Is it a Selenium atom?</span> <a name="IsSelenium-"></a>2293 <span class="k">sub </span><span class="m">IsSelenium</span> <span class="s">{</span> 2294 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2295 2296 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2297 <span class="s">}</span> 2298 2299 <span class="c"># Is it a Bromine atom?</span> <a name="IsBromine-"></a>2300 <span class="k">sub </span><span class="m">IsBromine</span> <span class="s">{</span> 2301 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2302 2303 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2304 <span class="s">}</span> 2305 2306 <span class="c"># Is it a Tellurium atom?</span> <a name="IsTellurium-"></a>2307 <span class="k">sub </span><span class="m">IsTellurium</span> <span class="s">{</span> 2308 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2309 2310 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2311 <span class="s">}</span> 2312 2313 <span class="c"># Is it a Iodine atom?</span> <a name="IsIodine-"></a>2314 <span class="k">sub </span><span class="m">IsIodine</span> <span class="s">{</span> 2315 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2316 2317 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2318 <span class="s">}</span> 2319 2320 <span class="c"># Is it a hetro atom? (N, O, F, P, S, Cl, Br, I)</span> <a name="IsHeteroAtom-"></a>2321 <span class="k">sub </span><span class="m">IsHeteroAtom</span> <span class="s">{</span> 2322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2323 2324 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8|9|15|16|17|35|53)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 2325 <span class="s">}</span> 2326 2327 <span class="c"># Is it a halogen atom? (F, Cl, Br, I)</span> <a name="IsHalogen-"></a>2328 <span class="k">sub </span><span class="m">IsHalogen</span> <span class="s">{</span> 2329 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2330 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> 2332 <span class="s">}</span> 2333 2334 <span class="c"># Is it classified as metallic?</span> <a name="IsMetallic-"></a>2335 <span class="k">sub </span><span class="m">IsMetallic</span> <span class="s">{</span> 2336 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2337 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="s">)</span><span class="sc">;</span> 2338 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> 2340 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> 2342 <span class="s">}</span> 2343 2344 <span class="c"># Is it a non carbon or hydrogen atom? (C, H)</span> <a name="IsNonCarbonOrHydrogen-"></a>2345 <span class="k">sub </span><span class="m">IsNonCarbonOrHydrogen</span> <span class="s">{</span> 2346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2347 2348 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(1|6)$/</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 2349 <span class="s">}</span> 2350 2351 <span class="c"># Is it a polar atom? ( N, O, P, S)</span> <a name="IsPolarAtom-"></a>2352 <span class="k">sub </span><span class="m">IsPolarAtom</span> <span class="s">{</span> 2353 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2354 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> 2356 <span class="s">}</span> 2357 2358 <span class="c"># Is it an isotope?</span> <a name="IsIsotope-"></a>2359 <span class="k">sub </span><span class="m">IsIsotope</span> <span class="s">{</span> 2360 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2361 2362 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> 2363 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 2364 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2365 <span class="s">}</span> 2366 2367 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2368 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2369 <span class="s">}</span> 2370 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$MostAbundantMassNumber</span><span class="s">)</span><span class="sc">;</span> 2371 2372 <span class="i">$MassNumber</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span> 2373 <span class="i">$MostAbundantMassNumber</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> 2374 2375 <span class="k">return</span> <span class="s">(</span><span class="i">$MassNumber</span> == <span class="i">$MostAbundantMassNumber</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 2376 <span class="s">}</span> 2377 2378 <span class="c"># Is it a terminal atom?</span> <a name="IsTerminal-"></a>2379 <span class="k">sub </span><span class="m">IsTerminal</span> <span class="s">{</span> 2380 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2381 2382 <span class="c"># Is this atom in a molecule?</span> 2383 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2384 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 2385 <span class="s">}</span> 2386 2387 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2388 2389 <span class="s">}</span> 2390 2391 <span class="c"># Is aromatic property set for the atom?</span> <a name="IsAromatic-"></a>2392 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span> 2393 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2394 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span> 2395 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> 2397 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> 2399 <span class="s">}</span> 2400 2401 <span class="c"># Is this a hydrogen atom and attached to one of these atoms: N, O, P, S</span> <a name="IsPolarHydrogen-"></a>2402 <span class="k">sub </span><span class="m">IsPolarHydrogen</span> <span class="s">{</span> 2403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2404 2405 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2406 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2407 <span class="s">}</span> 2408 2409 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> 2410 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2411 <span class="k">if</span> <span class="s">(</span><span class="i">@Bonds</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 2412 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2413 <span class="s">}</span> 2414 2415 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="s">)</span><span class="sc">;</span> 2416 <span class="s">(</span><span class="i">$Bond</span><span class="s">)</span> = <span class="i">@Bonds</span><span class="sc">;</span> 2417 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 2418 2419 <span class="k">return</span> <span class="i">$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> 2420 <span class="s">}</span> 2421 2422 <span class="c"># Is it a hydrogen bond donor atom?</span> 2423 <span class="c">#</span> <a name="IsHBondDonor-"></a>2424 <span class="k">sub </span><span class="m">IsHBondDonor</span> <span class="s">{</span> 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> 2426 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> 2428 <span class="s">}</span> 2429 2430 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span> 2431 <span class="c"># hydrogen bond donor and acceptor atoms with these names:</span> 2432 <span class="c">#</span> 2433 <span class="c"># HBondsType1 or HydrogenBondsType1</span> 2434 <span class="c"># HBondsType2 or HydrogenBondsType2</span> 2435 <span class="c">#</span> 2436 <span class="c"># The names of these hydrogen bond types are rather arbitrary. However, their</span> 2437 <span class="c"># definitions have specific meaning and are as follows:</span> 2438 <span class="c">#</span> 2439 <span class="c"># HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</span> 2440 <span class="c"># . Donor: NH, NH2, NH3, OH - Any N and O with available H</span> 2441 <span class="c"># . Acceptor: N[!H], O - Any N without available H and any O</span> 2442 <span class="c">#</span> 2443 <span class="c"># HydrogenBondsType2 [ Ref 91 ]:</span> 2444 <span class="c"># . Donor: NH, NH2, NH3, OH - Any N and O with availabe H</span> 2445 <span class="c"># . Acceptor: N, O - Any N and O</span> 2446 <span class="c">#</span> 2447 <span class="c"># Note:</span> 2448 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span> 2449 <span class="c">#</span> 2450 2451 <span class="c"># Is it a hydrogen bond donor atom?</span> 2452 <span class="c">#</span> 2453 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span> <a name="IsHydrogenBondDonor-"></a>2454 <span class="k">sub </span><span class="m">IsHydrogenBondDonor</span> <span class="s">{</span> 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> 2456 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> 2457 2458 <span class="i">$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> 2459 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> 2460 2461 <span class="j">HYDROGENBONDSTYPE:</span> <span class="s">{</span> 2462 2463 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType1|HydrogenBondsType1)$/i</span><span class="s">)</span> <span class="s">{</span> 2464 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2465 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> 2466 <span class="s">}</span> 2467 2468 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span> 2469 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2470 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> 2471 <span class="s">}</span> 2472 2473 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> 2474 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->IsHydrogenBondDonor: The current release of MayaChemTools doesn't support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ..."</span><span class="sc">;</span> 2475 <span class="s">}</span> 2476 2477 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 2478 <span class="s">}</span> 2479 2480 <span class="c"># Is it a MayaChemTools HBondType1 hydrogen bond donor atom?</span> 2481 <span class="c">#</span> <a name="_IsHydrogenBondDonorOfType1-"></a>2482 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType1</span> <span class="s">{</span> 2483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2484 2485 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType1OrType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2486 <span class="s">}</span> 2487 2488 <span class="c"># Is it a MayaChemTools HBondType2 hydrogen bond donor atom?</span> 2489 <span class="c">#</span> <a name="_IsHydrogenBondDonorOfType2-"></a>2490 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType2</span> <span class="s">{</span> 2491 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2492 2493 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType1OrType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2494 <span class="s">}</span> 2495 2496 <span class="c"># Is it a hydrogen bond donor atom of MayaChemTools Type1 or Type2?</span> 2497 <span class="c">#</span> 2498 <span class="c"># HydrogenBondDonor definition [ Ref 60-61, Ref 65-66, Ref 91 ]: NH, NH2, OH</span> 2499 <span class="c">#</span> 2500 <span class="c"># In other words:</span> 2501 <span class="c"># . NH, NH2 - Nitrogen atom with available hydrogen</span> 2502 <span class="c"># . OH - Oxygen atom with avilable hydrogen</span> 2503 <span class="c">#</span> <a name="_IsHydrogenBondDonorOfType1OrType2-"></a>2504 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType1OrType2</span> <span class="s">{</span> 2505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2506 2507 <span class="c"># Is this atom in a molecule?</span> 2508 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 2509 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2510 <span class="s">}</span> 2511 2512 <span class="c"># Is it N or O?</span> 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> 2514 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2515 <span class="s">}</span> 2516 2517 <span class="c"># Any explicitly attached hydrogens?</span> 2518 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2519 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2520 <span class="s">}</span> 2521 2522 <span class="c"># Any missing hydrogens?</span> 2523 <span class="k">return</span> <span class="i">$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> 2524 <span class="s">}</span> 2525 2526 <span class="c"># Is it a hydrogen bond acceptor atom?</span> 2527 <span class="c">#</span> <a name="IsHBondAcceptor-"></a>2528 <span class="k">sub </span><span class="m">IsHBondAcceptor</span> <span class="s">{</span> 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> 2530 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> 2532 <span class="s">}</span> 2533 2534 <span class="c"># Is it a hydrogen bond acceptor atom?</span> 2535 <span class="c">#</span> <a name="IsHydrogenBondAcceptor-"></a>2536 <span class="k">sub </span><span class="m">IsHydrogenBondAcceptor</span> <span class="s">{</span> 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> 2538 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> 2539 2540 <span class="i">$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> 2541 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> 2542 2543 <span class="j">HYDROGENBONDSTYPE:</span> <span class="s">{</span> 2544 2545 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType1|HydrogenBondsType1)$/i</span><span class="s">)</span> <span class="s">{</span> 2546 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondAcceptorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2547 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> 2548 <span class="s">}</span> 2549 2550 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span> 2551 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondAcceptorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2552 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> 2553 <span class="s">}</span> 2554 2555 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> 2556 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->IsHydrogenBondAcceptor: The current release of MayaChemTools doesn't support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ..."</span><span class="sc">;</span> 2557 <span class="s">}</span> 2558 2559 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 2560 <span class="s">}</span> 2561 2562 <span class="c"># Is it a MayaChemTools HBondType1 hydrogen bond acceptor atom?</span> 2563 <span class="c">#</span> 2564 <span class="c"># HydrogenBondAcceptor definition [ Ref 60-61, Ref 65-66 ]: N[!H], O</span> 2565 <span class="c">#</span> 2566 <span class="c"># In other words:</span> 2567 <span class="c"># . N[!H] - Nitrogen atom with no hydrogen</span> 2568 <span class="c"># . O - Oxygen atom</span> 2569 <span class="c">#</span> <a name="_IsHydrogenBondAcceptorOfType1-"></a>2570 <span class="k">sub </span><span class="m">_IsHydrogenBondAcceptorOfType1</span> <span class="s">{</span> 2571 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2572 2573 <span class="c"># Is this atom in a molecule?</span> 2574 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 2575 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2576 <span class="s">}</span> 2577 2578 <span class="c"># Is it N or O?</span> 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> 2580 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2581 <span class="s">}</span> 2582 2583 <span class="c"># Is it O?</span> 2584 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">8</span> <span class="s">)</span> <span class="s">{</span> 2585 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2586 <span class="s">}</span> 2587 2588 <span class="c"># Any explicitly attached hydrogens?</span> 2589 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2590 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2591 <span class="s">}</span> 2592 2593 <span class="c"># Any missing hydrogens?</span> 2594 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 2595 <span class="s">}</span> 2596 2597 <span class="c"># Is it a MayaChemTools HBondType2 hydrogen bond acceptor atom?</span> 2598 <span class="c">#</span> 2599 <span class="c"># HydrogenBondAcceptor definition [ Ref 91 ]: N, O</span> 2600 <span class="c">#</span> 2601 <span class="c"># In other words:</span> 2602 <span class="c"># . Any Nitrogen or Oxygen atom</span> 2603 <span class="c">#</span> 2604 <span class="c"># Note:</span> 2605 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span> 2606 <span class="c">#</span> <a name="_IsHydrogenBondAcceptorOfType2-"></a>2607 <span class="k">sub </span><span class="m">_IsHydrogenBondAcceptorOfType2</span> <span class="s">{</span> 2608 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2609 2610 <span class="c"># Is this atom in a molecule?</span> 2611 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2612 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2613 <span class="s">}</span> 2614 2615 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 2616 <span class="s">}</span> 2617 2618 <span class="c"># Is it a positively ionizable atom?</span> 2619 <span class="c">#</span> 2620 <span class="c"># PositivelyIonizable defintion [ Ref 60-61, Ref 65-66 ]: +, NH2</span> 2621 <span class="c">#</span> 2622 <span class="c"># In other words:</span> 2623 <span class="c"># . Any atom with positve formal charge</span> 2624 <span class="c"># . NH2 - Nitogen atom in amino group</span> 2625 <span class="c">#</span> <a name="IsPositivelyIonizable-"></a>2626 <span class="k">sub </span><span class="m">IsPositivelyIonizable</span> <span class="s">{</span> 2627 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2628 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> 2629 2630 <span class="c"># Is this atom in a molecule?</span> 2631 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 2632 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2633 <span class="s">}</span> 2634 2635 <span class="c"># Any explicit positive formal charge?</span> 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> 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> 2638 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2639 <span class="s">}</span> 2640 2641 <span class="c"># Is it N?</span> 2642 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} != <span class="n">7</span> <span class="s">)</span> <span class="s">{</span> 2643 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2644 <span class="s">}</span> 2645 2646 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 2647 <span class="s">}</span> 2648 2649 <span class="c"># Is it a negatively ionizable atom?</span> 2650 <span class="c">#</span> 2651 <span class="c"># NegativelyIonizable definition [ Ref 60-61, Ref 65-66 ]: -, C(=O)OH, S(=O)OH, P(=O)OH</span> 2652 <span class="c">#</span> 2653 <span class="c"># In other words:</span> 2654 <span class="c"># . Any atom with negative formal charge</span> 2655 <span class="c"># . Carbon atom in C(=O)OH group</span> 2656 <span class="c"># . Phosphorous in P(=O)OH group</span> 2657 <span class="c"># . Sulfur atom in S(=O)OH group</span> 2658 <span class="c">#</span> <a name="IsNegativelyIonizable-"></a>2659 <span class="k">sub </span><span class="m">IsNegativelyIonizable</span> <span class="s">{</span> 2660 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2661 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> 2662 2663 <span class="c"># Is this atom in a molecule?</span> 2664 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2665 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2666 <span class="s">}</span> 2667 2668 <span class="c"># Any explicit negative formal charge?</span> 2669 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2670 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> && <span class="i">$FormalCharge</span> < <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 2671 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2672 <span class="s">}</span> 2673 2674 <span class="c"># Is it C, P or S?</span> 2675 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(6|15|16)$/</span> <span class="s">)</span> <span class="s">{</span> 2676 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2677 <span class="s">}</span> 2678 2679 <span class="c"># Collect oxygens connected to C, P or S with single or double bonds and not connected to</span> 2680 <span class="c"># any other heavy atom...</span> 2681 <span class="k">my</span><span class="s">(</span><span class="i">$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">$NumOfNeighborOxygensWithDoubleBonds</span><span class="s">)</span><span class="sc">;</span> 2682 2683 <span class="i">$NumOfNeighborOxygensWithSingleBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span> = <span class="n">0</span><span class="sc">;</span> 2684 2685 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2686 <span class="c"># Is it an oxygen?</span> 2687 <span class="k">if</span> <span class="s">(</span><span class="i">$Neighbor</span>->{<span class="w">AtomicNumber</span>} != <span class="n">8</span><span class="s">)</span> <span class="s">{</span> 2688 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> 2689 <span class="s">}</span> 2690 <span class="c"># Is oxygent connected to only heavy atom?</span> 2691 <span class="k">if</span> <span class="s">(</span><span class="i">$Neighbor</span><span class="i">->GetNumOfHeavyAtomNeighbors</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 2692 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> 2693 <span class="s">}</span> 2694 <span class="i">$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> 2695 2696 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborOxygenBondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 2697 <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span>++<span class="sc">;</span> 2698 <span class="s">}</span> 2699 <span class="k">elsif</span> <span class="s">(</span><span class="i">$NeighborOxygenBondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 2700 <span class="i">$NumOfNeighborOxygensWithSingleBonds</span>++<span class="sc">;</span> 2701 <span class="s">}</span> 2702 <span class="s">}</span> 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> 2704 <span class="s">}</span> 2705 2706 <span class="c"># Is it a liphophilic atom?</span> 2707 <span class="c">#</span> 2708 <span class="c"># Lipophilic definition [ Ref 60-61, Ref 65-66 ]: C(C)(C)(C)(C), Cl, Br, I, S(C)(C)</span> 2709 <span class="c">#</span> 2710 <span class="c"># In other words:</span> 2711 <span class="c"># . C(C)(C)(C)(C) - Carbon atom connected to only other carbons</span> 2712 <span class="c"># . Chlorine, Bromine or Iodine atom</span> 2713 <span class="c"># . S(C)(C) - Sulfur connected to two carbons</span> 2714 <span class="c">#</span> <a name="IsLipophilic-"></a>2715 <span class="k">sub </span><span class="m">IsLipophilic</span> <span class="s">{</span> 2716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2717 2718 <span class="c"># Is this atom in a molecule?</span> 2719 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 2720 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2721 <span class="s">}</span> 2722 2723 <span class="c"># Is it Cl, Br, I?</span> 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> 2725 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2726 <span class="s">}</span> 2727 2728 <span class="c"># Is it C, S?</span> 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> 2730 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2731 <span class="s">}</span> 2732 2733 <span class="c"># Are all heavy atom neighbors Carbons?</span> 2734 <span class="k">my</span><span class="s">(</span><span class="i">$HeavyAtomNeighbor</span><span class="cm">,</span> <span class="i">@HeavyAtomNeighbors</span><span class="s">)</span><span class="sc">;</span> 2735 <span class="i">@HeavyAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2736 <span class="i">@HeavyAtomNeighbors</span> = <span class="i">$This</span><span class="i">->GetHeavyAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2737 2738 <span class="k">for</span> <span class="i">$HeavyAtomNeighbor</span> <span class="s">(</span><span class="i">@HeavyAtomNeighbors</span><span class="s">)</span> <span class="s">{</span> 2739 <span class="k">if</span> <span class="s">(</span><span class="i">$HeavyAtomNeighbor</span>->{<span class="w">AtomicNumber</span>} != <span class="n">6</span><span class="s">)</span> <span class="s">{</span> 2740 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2741 <span class="s">}</span> 2742 <span class="s">}</span> 2743 2744 <span class="c"># Does sulfur has two carbon neighbors?</span> 2745 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">16</span><span class="s">)</span> <span class="s">{</span> 2746 <span class="k">if</span> <span class="s">(</span><span class="i">@HeavyAtomNeighbors</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 2747 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2748 <span class="s">}</span> 2749 <span class="s">}</span> 2750 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2751 <span class="s">}</span> 2752 2753 <span class="c"># Is it hydrophobic?</span> 2754 <span class="c">#</span> <a name="IsHydrophobic-"></a>2755 <span class="k">sub </span><span class="m">IsHydrophobic</span> <span class="s">{</span> 2756 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2757 2758 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsLipophilic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2759 <span class="s">}</span> 2760 2761 <span class="c"># Is it a Nitrogen atom in Guadinium group?</span> 2762 <span class="c">#</span> <a name="IsGuadiniumNitrogen-"></a>2763 <span class="k">sub </span><span class="m">IsGuadiniumNitrogen</span> <span class="s">{</span> 2764 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2765 2766 <span class="c"># Is it Nitrogen?</span> 2767 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2768 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2769 <span class="s">}</span> 2770 2771 <span class="c"># Is it connected to a Guadinium Carbon?</span> 2772 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span> 2773 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> 2775 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->IsGuadiniumCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2776 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2777 <span class="s">}</span> 2778 <span class="s">}</span> 2779 2780 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2781 <span class="s">}</span> 2782 2783 <span class="c"># Is it a Carbon atom in Guadinium group?</span> 2784 <span class="c">#</span> 2785 <span class="c"># Guadinium group definition:</span> 2786 <span class="c">#</span> 2787 <span class="c"># R2N-C(=NR)-(NR2) or R2N-C(=NR2+)-(NR2)</span> 2788 <span class="c">#</span> 2789 <span class="c"># where:</span> 2790 <span class="c"># . R = Hydrogens or group of atoms attached through Carbon</span> 2791 <span class="c"># . Only one of the three Nitrogens has a double bond to Carbon and has optional</span> 2792 <span class="c"># formal charge allowing it to be neutral or charged state</span> 2793 <span class="c">#</span> <a name="IsGuadiniumCarbon-"></a>2794 <span class="k">sub </span><span class="m">IsGuadiniumCarbon</span> <span class="s">{</span> 2795 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2796 2797 <span class="c"># Is it Carbon?</span> 2798 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2799 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2800 <span class="s">}</span> 2801 2802 <span class="c"># Match atom neighborhood...</span> 2803 <span class="k">my</span><span class="s">(</span><span class="i">$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> 2804 2805 <span class="i">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4'</span><span class="sc">;</span> 2806 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'N.FC0'</span><span class="cm">,</span> <span class="q">'N.FC0'</span><span class="cm">,</span> <span class="q">'N.FC0,N.FC+1'</span><span class="s">)</span><span class="sc">;</span> 2807 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="s">)</span><span class="sc">;</span> 2808 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="s">)</span><span class="sc">;</span> 2809 2810 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2811 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2812 <span class="s">}</span> 2813 2814 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2815 <span class="s">}</span> 2816 2817 <span class="c"># Is it a Nitrogen atom in Amide group?</span> 2818 <span class="c">#</span> <a name="IsAmideNitrogen-"></a>2819 <span class="k">sub </span><span class="m">IsAmideNitrogen</span> <span class="s">{</span> 2820 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2821 2822 <span class="c"># Is it Nitrogen?</span> 2823 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2824 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2825 <span class="s">}</span> 2826 2827 <span class="c"># Is it connected to a Amide Carbon?</span> 2828 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span> 2829 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> 2831 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->IsAmideCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2832 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2833 <span class="s">}</span> 2834 <span class="s">}</span> 2835 2836 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2837 <span class="s">}</span> 2838 2839 <span class="c"># Is it a Carbon atom in Amide group?</span> 2840 <span class="c">#</span> 2841 <span class="c"># Amide group definition: R-C(=O)-N(-R')-R''</span> 2842 <span class="c">#</span> 2843 <span class="c"># where:</span> 2844 <span class="c"># . R = Hydrogen or groups of atoms attached through Carbon</span> 2845 <span class="c"># . R' = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span> 2846 <span class="c"># . R'' = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span> 2847 <span class="c">#</span> <a name="IsAmideCarbon-"></a>2848 <span class="k">sub </span><span class="m">IsAmideCarbon</span> <span class="s">{</span> 2849 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2850 2851 <span class="c"># Is this atom in a molecule?</span> 2852 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2853 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2854 <span class="s">}</span> 2855 2856 <span class="c"># Is it Carbon?</span> 2857 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2858 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2859 <span class="s">}</span> 2860 2861 <span class="c"># Match atom neighborhood...</span> 2862 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> 2863 2864 <span class="i">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4,C.X2.BO3'</span><span class="sc">;</span> 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> 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> 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> 2868 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> 2870 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2871 <span class="s">}</span> 2872 2873 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2874 <span class="s">}</span> 2875 2876 <span class="c"># Is it a Oxygen atom in Carboxylate group?</span> 2877 <span class="c">#</span> <a name="IsCarboxylateOxygen-"></a>2878 <span class="k">sub </span><span class="m">IsCarboxylateOxygen</span> <span class="s">{</span> 2879 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2880 2881 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">'Carboxylate'</span><span class="s">)</span><span class="sc">;</span> 2882 <span class="s">}</span> 2883 2884 <span class="c"># Is it a Carbon atom in Carboxylate group?</span> 2885 <span class="c">#</span> 2886 <span class="c"># Carboxyl group definition: R-C(=O)-O-</span> 2887 <span class="c">#</span> <a name="IsCarboxylateCarbon-"></a>2888 <span class="k">sub </span><span class="m">IsCarboxylateCarbon</span> <span class="s">{</span> 2889 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2890 2891 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">'Carboxylate'</span><span class="s">)</span><span class="sc">;</span> 2892 <span class="s">}</span> 2893 2894 <span class="c"># Is it a Oxygen atom in Carboxyl group?</span> 2895 <span class="c">#</span> <a name="IsCarboxylOxygen-"></a>2896 <span class="k">sub </span><span class="m">IsCarboxylOxygen</span> <span class="s">{</span> 2897 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2898 2899 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">'Carboxyl'</span><span class="s">)</span><span class="sc">;</span> 2900 <span class="s">}</span> 2901 2902 <span class="c"># Is it a Carbon atom in Carboxyl group?</span> 2903 <span class="c">#</span> 2904 <span class="c"># Carboxyl group definition: R-C(=O)-OH</span> 2905 <span class="c">#</span> <a name="IsCarboxylCarbon-"></a>2906 <span class="k">sub </span><span class="m">IsCarboxylCarbon</span> <span class="s">{</span> 2907 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2908 2909 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">'Carboxyl'</span><span class="s">)</span><span class="sc">;</span> 2910 <span class="s">}</span> 2911 2912 <span class="c"># Match Carboxylate and/or Carboxyl oxygen...</span> 2913 <span class="c">#</span> <a name="_MatchCarboxylateAndOrCarboxylOxygen-"></a>2914 <span class="k">sub </span><span class="m">_MatchCarboxylateAndOrCarboxylOxygen</span> <span class="s">{</span> 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> 2916 2917 <span class="c"># Is it Oxygen?</span> 2918 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2919 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2920 <span class="s">}</span> 2921 2922 <span class="c"># Is it connected to a Carboxylate Carbon?</span> 2923 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span> 2924 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> 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> 2927 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2928 <span class="s">}</span> 2929 <span class="s">}</span> 2930 2931 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2932 <span class="s">}</span> 2933 2934 <span class="c"># Match Carboxylate and Carboxyl Carbon</span> 2935 <span class="c">#</span> 2936 <span class="c"># Carboxylate group definition: R-C(=O)-O-</span> 2937 <span class="c"># Carboxyl group definition: R-C(=O)-OH</span> 2938 <span class="c">#</span> 2939 <span class="c"># where:</span> 2940 <span class="c"># . R = Hydrogens or groups of atoms attached through Carbon</span> 2941 <span class="c">#</span> <a name="_MatchCarboxylateAndOrCarboxylCarbon-"></a>2942 <span class="k">sub </span><span class="m">_MatchCarboxylateAndOrCarboxylCarbon</span> <span class="s">{</span> 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> 2944 2945 <span class="c"># Is this atom in a molecule?</span> 2946 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2947 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2948 <span class="s">}</span> 2949 2950 <span class="c"># Is it Carbon?</span> 2951 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2952 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2953 <span class="s">}</span> 2954 2955 <span class="c"># Match atom neighborhood...</span> 2956 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> 2957 2958 <span class="i">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4,C.X2.BO3'</span><span class="sc">;</span> 2959 <span class="j">MODE:</span> <span class="s">{</span> 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> 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> 2962 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> 2963 <span class="s">}</span> 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> 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> 2966 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> 2967 <span class="s">}</span> 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> 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> 2970 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> 2971 <span class="s">}</span> 2972 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_MatchCarboxylateAndCarboxylCarbon.: Unknown mode $Mode..."</span><span class="sc">;</span> 2973 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2974 <span class="s">}</span> 2975 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">)</span><span class="sc">;</span> 2976 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C'</span><span class="cm">,</span> <span class="q">'C'</span><span class="s">)</span><span class="sc">;</span> 2977 2978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2979 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2980 <span class="s">}</span> 2981 2982 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2983 <span class="s">}</span> 2984 2985 <span class="c"># Is it a Oxygen atom in Phosphate group?</span> 2986 <span class="c">#</span> <a name="IsPhosphateOxygen-"></a>2987 <span class="k">sub </span><span class="m">IsPhosphateOxygen</span> <span class="s">{</span> 2988 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2989 2990 <span class="c"># Is it Oxygen?</span> 2991 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2992 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2993 <span class="s">}</span> 2994 2995 <span class="c"># Is it connected to a Phosphate Phosphorus?</span> 2996 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span> 2997 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> 2999 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->IsPhosphatePhosphorus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3000 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3001 <span class="s">}</span> 3002 <span class="s">}</span> 3003 3004 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3005 <span class="s">}</span> 3006 3007 <span class="c"># Is it a Phosphorus atom in Phosphate group?</span> 3008 <span class="c">#</span> 3009 <span class="c"># Phosphate group definition: AO-(O=)P(-OA)-OA</span> 3010 <span class="c">#</span> 3011 <span class="c"># where:</span> 3012 <span class="c"># . A = Any Groups of atoms including hydrogens</span> 3013 <span class="c">#</span> <a name="IsPhosphatePhosphorus-"></a>3014 <span class="k">sub </span><span class="m">IsPhosphatePhosphorus</span> <span class="s">{</span> 3015 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3016 3017 <span class="c"># Is this atom in a molecule?</span> 3018 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3019 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3020 <span class="s">}</span> 3021 3022 <span class="c"># Is it Phosphorus?</span> 3023 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsPhosphorus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3024 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3025 <span class="s">}</span> 3026 3027 <span class="c"># Match atom neighborhood...</span> 3028 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> 3029 3030 <span class="i">$CentralAtomSpec</span> = <span class="q">'P.X4.BO5'</span><span class="sc">;</span> 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> 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> 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> 3034 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> 3036 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3037 <span class="s">}</span> 3038 3039 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3040 <span class="s">}</span> 3041 3042 3043 <span class="c"># Match central atom and its neighborhood using specified atom and bonds specifications...</span> 3044 <span class="c">#</span> 3045 <span class="c"># Let:</span> 3046 <span class="c"># AS = Atom symbol corresponding to element symbol, atomic number (#n) or any</span> 3047 <span class="c"># atom (A)</span> 3048 <span class="c">#</span> 3049 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 3050 <span class="c"># T<n> = Total number of atom neighbors including implcit and explicit hydrogens</span> 3051 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 3052 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 3053 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 3054 <span class="c"># TSB<n> = Total number of single bonds to atom neighbors including implcit and explicit hydrogens</span> 3055 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 3056 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 3057 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> 3058 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> 3059 <span class="c"># RA or RA<n> = Ring atom annotation indicating whether atom is a ring</span> 3060 <span class="c"># TR<n> = Total number of rings containing atom</span> 3061 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> 3062 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> 3063 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> 3064 <span class="c">#</span> 3065 <span class="c"># Then:</span> 3066 <span class="c">#</span> 3067 <span class="c"># Atom specification corresponds to:</span> 3068 <span class="c">#</span> 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> 3070 <span class="c">#</span> 3071 <span class="c"># Except for AS which is a required atomic invariant in atom specification, all other atomic invariants are</span> 3072 <span class="c"># optional. For an atom specification to match an atom, the values of all specified atomic invariants must</span> 3073 <span class="c"># match. Exclamation in from of atomic invariant can be used to negate its effect during the match.</span> 3074 <span class="c">#</span> 3075 <span class="c"># A comma delimited atom specification string is used to match any one of the specifed atom specification.</span> 3076 <span class="c">#</span> 3077 <span class="c"># Notes:</span> 3078 <span class="c"># . During atom specification match to an atom, the first atomic invariant is always assumed to</span> 3079 <span class="c"># atom symbol.</span> 3080 <span class="c"># . Atom match specfication is based on AtomicInvariantAtomTypes implemented in</span> 3081 <span class="c"># AotmTypes::AtomicInvariantAtomType.pm module</span> 3082 <span class="c">#</span> 3083 <span class="c"># Examples:</span> 3084 <span class="c"># . ('N', 'N', 'N')</span> 3085 <span class="c"># . ('N.FC0', 'N.FC0', 'N,N.FC+1.H1')</span> 3086 <span class="c"># . ('N.H2', 'N.H2', 'N.H1')</span> 3087 <span class="c"># . ('C,N', '!N', '!H')</span> 3088 <span class="c"># . ('C,N', 'N.Ar', 'N.R5')</span> 3089 <span class="c">#</span> 3090 <span class="c"># Let:</span> 3091 <span class="c"># -|1|s|Single = Single bond</span> 3092 <span class="c"># =|2|d|Double = Double bond</span> 3093 <span class="c"># #|3|t|Triple = Triple bond</span> 3094 <span class="c"># :|1.5|a|Ar|Aromatic = Aromatic bond</span> 3095 <span class="c">#</span> 3096 <span class="c"># @|RB|Ring = Ring bond</span> 3097 <span class="c"># ~|*|Any = Any bond</span> 3098 <span class="c">#</span> 3099 <span class="c"># Then:</span> 3100 <span class="c">#</span> 3101 <span class="c"># Bond specification corresponds to:</span> 3102 <span class="c">#</span> 3103 <span class="c"># -.:</span> 3104 <span class="c"># =.@</span> 3105 <span class="c"># Double.Aromatic</span> 3106 <span class="c">#</span> 3107 <span class="c"># For a bond specification to match bond between two atoms, the values of all specified bond symbols must</span> 3108 <span class="c"># match. Exclamation in from of bond symbol can be used to negate its effect during the match.</span> 3109 <span class="c">#</span> 3110 <span class="c"># A comma delimited bond specification string is used to match any one of the specifed atom specification.</span> 3111 <span class="c">#</span> <a name="DoesAtomNeighborhoodMatch-"></a>3112 <span class="k">sub </span><span class="m">DoesAtomNeighborhoodMatch</span> <span class="s">{</span> 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">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3114 <span class="k">my</span><span class="s">(</span><span class="i">$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> 3115 3116 <span class="c"># Is this atom in a molecule?</span> 3117 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3118 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3119 <span class="s">}</span> 3120 3121 <span class="i">$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> 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">$NbrBondSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3123 <span class="i">$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> 3124 3125 <span class="c"># Validate number of specifications...</span> 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> 3127 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and bond, $NumOfNbrBondSpecs, specifications must be same; No neighborhood match performed ..."</span><span class="sc">;</span> 3128 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3129 <span class="s">}</span> 3130 3131 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 3132 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and neighbor of neighbor atoms specifications, $NumOfNbrOfNbrAtomSpecs, must be same; No neighborhood match performed ..."</span><span class="sc">;</span> 3133 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3134 <span class="s">}</span> 3135 3136 <span class="c"># Sort atom and bond specifications in terms of being most specific to least specific..</span> 3137 <span class="s">(</span><span class="i">$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> 3138 3139 <span class="c"># Does central atom specification match?</span> 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> 3141 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3142 <span class="s">}</span> 3143 3144 <span class="c"># No neighbors to match...</span> 3145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfNbrAtomSpecs</span><span class="s">)</span> <span class="s">{</span> 3146 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3147 <span class="s">}</span> 3148 3149 <span class="c"># Match neighbors...</span> 3150 <span class="k">my</span><span class="s">(</span><span class="i">$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> 3151 3152 <span class="i">$NbrSpecCount</span> = <span class="i">$NumOfNbrAtomSpecs</span><span class="sc">;</span> 3153 <span class="i">$NbrSpecMatchCount</span> = <span class="n">0</span><span class="sc">;</span> 3154 3155 <span class="i">%NbrSpecAlreadyMatchedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3156 <span class="s">(</span><span class="i">$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">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> 3157 3158 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="s">)</span> <span class="s">{</span> 3159 <span class="c"># It's match...</span> 3160 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3161 <span class="s">}</span> 3162 3163 <span class="c"># Match central atom's missing hydrogens with any unmatched atom</span> 3164 <span class="c"># and bond specifications...</span> 3165 <span class="c">#</span> 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> 3167 3168 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="s">)</span> <span class="s">{</span> 3169 <span class="c"># It's match...</span> 3170 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3171 <span class="s">}</span> 3172 3173 <span class="c"># No match...</span> 3174 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3175 <span class="s">}</span> 3176 3177 <span class="c"># Match central atom neighborhood atom and bond specifications...</span> 3178 <span class="c">#</span> <a name="_MatchAtomNeighborhoodUsingAtomBondSpecs-"></a>3179 <span class="k">sub </span><span class="m">_MatchAtomNeighborhoodUsingAtomBondSpecs</span> <span class="s">{</span> 3180 <span class="k">my</span><span class="s">(</span><span class="i">$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> 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> 3182 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">$NbrOfNbrAtomSpecsRef</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3184 3185 <span class="i">$NbrSpecsMatched</span> = <span class="n">0</span><span class="sc">;</span> 3186 3187 <span class="c"># Match central atom's immediate neighbors atom and bond specifications...</span> 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> 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> 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> 3191 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> 3192 <span class="s">}</span> 3193 <span class="i">$NbrAtomSpec</span> = <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 3194 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 3195 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> 3197 3198 <span class="c"># Match neighbor atom specification...</span> 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> 3200 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> 3201 <span class="s">}</span> 3202 3203 <span class="c"># Match central atom to neighbor atom bond specification...</span> 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">$NbrBondSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3205 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> 3206 <span class="s">}</span> 3207 3208 <span class="c"># Match any neighbor of neighbor atom specifications...</span> 3209 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span> 3210 <span class="c"># Go over the neighbors of central atom skipping the central atom...</span> 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">$CentralAtom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3212 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NbrOfNbrAtom</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$NbrOfNbrAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3213 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> 3214 <span class="s">}</span> 3215 <span class="s">}</span> 3216 <span class="s">}</span> 3217 3218 <span class="c"># It's a match for a neighbor atom specification...</span> 3219 <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>} = <span class="i">$Index</span><span class="sc">;</span> 3220 <span class="i">$NbrSpecMatchCount</span>++<span class="sc">;</span> 3221 3222 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecMatchCount</span> == <span class="i">$NbrSpecCount</span><span class="s">)</span> <span class="s">{</span> 3223 <span class="c"># It's match...</span> 3224 <span class="i">$NbrSpecsMatched</span> = <span class="n">1</span><span class="sc">;</span> 3225 <span class="k">last</span> <span class="j">NBRATOM</span><span class="sc">;</span> 3226 <span class="s">}</span> 3227 <span class="c"># Match next neighbor atom...</span> 3228 <span class="k">next</span> <span class="j">NBRATOM</span><span class="sc">;</span> 3229 <span class="s">}</span> 3230 <span class="s">}</span> 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> 3232 <span class="s">}</span> 3233 3234 <span class="c"># Match central atom's missing hydrogens with any unmatched atom and bond</span> 3235 <span class="c"># specifications...</span> 3236 <span class="c">#</span> <a name="_MatchAtomNeighborhoodUsingMissingHydrogens-"></a>3237 <span class="k">sub </span><span class="m">_MatchAtomNeighborhoodUsingMissingHydrogens</span> <span class="s">{</span> 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">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3239 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span> 3240 3241 <span class="i">$NbrSpecsMatched</span> = <span class="n">0</span><span class="sc">;</span> 3242 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> 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">$NumOfMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> 3245 <span class="c"># It won't match...</span> 3246 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span> 3247 <span class="s">}</span> 3248 3249 <span class="j">MISSINGHYDROGENNBR:</span> <span class="k">for</span> <span class="i">$MissingHydrogensIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfMissingHydrogens</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3250 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3251 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>}<span class="s">)</span> <span class="s">{</span> 3252 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> 3253 <span class="s">}</span> 3254 <span class="i">$NbrAtomSpec</span> = <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 3255 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 3256 3257 <span class="i">$NbrAtomSpec</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 3258 3259 <span class="c"># Match neighbor atom specification hydrogen atom symbol...</span> 3260 <span class="i">$AtomSpecMatched</span> = <span class="n">0</span><span class="sc">;</span> 3261 <span class="j">ATOMSPEC:</span> <span class="k">for</span> <span class="i">$AtomSpec</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="s">)</span> <span class="s">{</span> 3262 <span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomSpec</span><span class="sc">;</span> 3263 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomSymbol</span> =~ <span class="q">/^(H|A|\*)$/i</span><span class="s">)</span> <span class="s">{</span> 3264 <span class="i">$AtomSpecMatched</span> = <span class="n">1</span><span class="sc">;</span> 3265 <span class="k">last</span> <span class="j">ATOMSPEC</span><span class="sc">;</span> 3266 <span class="s">}</span> 3267 <span class="s">}</span> 3268 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSpecMatched</span><span class="s">)</span> <span class="s">{</span> 3269 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> 3270 <span class="s">}</span> 3271 3272 <span class="c"># Match neighbor atom bond specification to singal bond...</span> 3273 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrBondSpec</span><span class="s">)</span> <span class="s">{</span> 3274 <span class="i">$NbrBondSpec</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 3275 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrBondSpec</span> !~ <span class="q">/^(-|1|s|Single|\~|\*|Any)/i</span><span class="s">)</span> <span class="s">{</span> 3276 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> 3277 <span class="s">}</span> 3278 <span class="s">}</span> 3279 3280 <span class="c"># It's a match for a neighbor atom specification...</span> 3281 <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>} = <span class="i">$Index</span><span class="sc">;</span> 3282 <span class="i">$NbrSpecMatchCount</span>++<span class="sc">;</span> 3283 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> 3285 <span class="c"># It's match...</span> 3286 <span class="i">$NbrSpecsMatched</span> = <span class="n">1</span><span class="sc">;</span> 3287 <span class="k">last</span> <span class="j">MISSINGHYDROGENNBR</span><span class="sc">;</span> 3288 <span class="s">}</span> 3289 <span class="c"># Match next missing hydrogen neighbor...</span> 3290 <span class="k">next</span> <span class="j">MISSINGHYDROGENNBR</span><span class="sc">;</span> 3291 <span class="s">}</span> 3292 <span class="s">}</span> 3293 3294 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span> 3295 <span class="s">}</span> 3296 3297 <span class="c"># Sort atom and bond specifications base on neighbor atom specifications going</span> 3298 <span class="c"># from most to least specific atom specifications.</span> 3299 <span class="c">#</span> 3300 <span class="c"># Atom specifications are sorted at the following two levels:</span> 3301 <span class="c">#</span> 3302 <span class="c"># o By atom specification count with in each specification going from most specific</span> 3303 <span class="c"># to least specific, where count is determined by the number of "," in each</span> 3304 <span class="c"># specification. Wild card containing specifications are considered least specific</span> 3305 <span class="c"># and end up at the end of the sorted list.</span> 3306 <span class="c"># o By atomic invariant count with in each sorted list going from most specific to</span> 3307 <span class="c"># least specific, where count is determined by the number of "." in each atom</span> 3308 <span class="c"># specification.</span> 3309 <span class="c">#</span> 3310 <span class="c">#A single atom specification,</span> 3311 <span class="c"># without any commas in atom specification, is is considered most specific...</span> 3312 <span class="c">#</span> <a name="_SortSpecificationsForAtomNeighborhoodMatch-"></a>3313 <span class="k">sub </span><span class="m">_SortSpecificationsForAtomNeighborhoodMatch</span> <span class="s">{</span> 3314 <span class="k">my</span><span class="s">(</span><span class="i">$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">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3315 <span class="k">my</span><span class="s">(</span><span class="i">$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> 3316 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">$NbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3318 3319 <span class="c"># Figure out whether sorting is necessary...</span> 3320 <span class="i">$NeedToSort</span> = <span class="n">0</span><span class="sc">;</span> 3321 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 3322 <span class="j">ATOMSPEC:</span> <span class="k">for</span> <span class="i">$NbrAtomSpecToMatch</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>}<span class="s">)</span> <span class="s">{</span> 3323 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">/(,|\.|A|\*)/i</span><span class="s">)</span> <span class="s">{</span> 3324 <span class="i">$NeedToSort</span> = <span class="n">1</span><span class="sc">;</span> 3325 <span class="k">last</span> <span class="j">ATOMSPEC</span><span class="sc">;</span> 3326 <span class="s">}</span> 3327 <span class="s">}</span> 3328 <span class="s">}</span> 3329 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NeedToSort</span><span class="s">)</span> <span class="s">{</span> 3330 <span class="c"># Nothing to do...</span> 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">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span> 3332 <span class="s">}</span> 3333 3334 <span class="i">%NbrAtomSpecDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3335 3336 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3337 <span class="i">$NbrAtomSpecToMatch</span> = <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 3338 <span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 3339 3340 <span class="i">@NbrAtomSpecs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NbrAtomSpecToMatch</span><span class="sc">;</span> 3341 <span class="i">$NbrAtomSpecCount</span> = <span class="k">scalar</span> <span class="i">@NbrAtomSpecs</span><span class="sc">;</span> 3342 3343 <span class="c"># Does neighbor specification contains a wild card in atom symbol specification?</span> 3344 <span class="c">#</span> 3345 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">/(A|\*)/i</span><span class="s">)</span> <span class="s">{</span> 3346 <span class="i">$WildCardInNbrAtomSpec</span> = <span class="n">0</span><span class="sc">;</span> 3347 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$NbrAtomSpec</span> <span class="s">(</span><span class="i">@NbrAtomSpecs</span><span class="s">)</span> <span class="s">{</span> 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> 3349 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span> 3350 <span class="i">$FirstAtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span> 3351 <span class="s">}</span> 3352 <span class="i">$WildCardInNbrAtomSpec</span> = <span class="i">$This</span><span class="i">->_IsWildCardAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$FirstAtomicInvariant</span><span class="s">)</span><span class="sc">;</span> 3353 <span class="k">if</span> <span class="s">(</span><span class="i">$WildCardInNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span> 3354 <span class="k">last</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> 3355 <span class="s">}</span> 3356 <span class="s">}</span> 3357 <span class="k">if</span> <span class="s">(</span><span class="i">$WildCardInNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span> 3358 <span class="c"># Set NbrAtomSpecCount arbitrarily high to make the spec containing wild</span> 3359 <span class="c"># card last on the sorted list while maintaining its original order in the list...</span> 3360 <span class="i">$NbrAtomSpecCount</span> = <span class="n">999</span><span class="sc">;</span> 3361 <span class="s">}</span> 3362 <span class="s">}</span> 3363 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> 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> 3366 <span class="s">}</span> 3367 3368 <span class="c"># Use first NbrAtomSpec available in @NbrAtomSpecs to determine atomic invariant count</span> 3369 <span class="c"># with in each NbrAtomSpecToMatch, as @NbrAtomSpecs derived from $NbrAtomSpecToMatch</span> 3370 <span class="c"># simply corresponds to a list of possible matches...</span> 3371 <span class="c">#</span> 3372 <span class="s">(</span><span class="i">$NbrAtomSpec</span><span class="s">)</span> = <span class="i">@NbrAtomSpecs</span><span class="sc">;</span> 3373 <span class="i">@NbrAtomSpecAtomicInvariants</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="sc">;</span> 3374 <span class="i">$NbrAtomSpecAtomicInvarintCount</span> = <span class="k">scalar</span> <span class="i">@NbrAtomSpecAtomicInvariants</span><span class="sc">;</span> 3375 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">$NbrAtomSpecAtomicInvarintCount</span>}<span class="s">)</span> <span class="s">{</span> 3377 <span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3378 <span class="s">}</span> 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> 3380 3381 <span class="s">}</span> 3382 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> 3384 <span class="i">@SortedNbrOfNbrAtomSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3385 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">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%NbrAtomSpecDataMap</span><span class="s">)</span> <span class="s">{</span> 3387 <span class="k">for</span> <span class="i">$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> 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> 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> 3390 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span><span class="s">)</span> <span class="s">{</span> 3391 <span class="k">push</span> <span class="i">@SortedNbrBondSpecs</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 3392 <span class="s">}</span> 3393 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> <span class="s">{</span> 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> 3395 <span class="s">}</span> 3396 <span class="s">}</span> 3397 <span class="s">}</span> 3398 <span class="s">}</span> 3399 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> 3401 <span class="s">}</span> 3402 3403 <span class="c"># Check whether atom matches supported atom specification...</span> 3404 <span class="c">#</span> <a name="_DoesAtomSpecificationMatch-"></a>3405 <span class="k">sub </span><span class="m">_DoesAtomSpecificationMatch</span> <span class="s">{</span> 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> 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">$FirstMatch</span><span class="s">)</span><span class="sc">;</span> 3408 3409 <span class="c"># Anything to match...</span> 3410 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> && <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3411 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3412 <span class="s">}</span> 3413 3414 <span class="c"># Take out any spaces...</span> 3415 <span class="i">$AtomSpecificationToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 3416 3417 <span class="c"># Match specified atom specifications. For multiple atom specifications in a comma delimited string,</span> 3418 <span class="c"># only one atom specification needs to match for a successful match. It's up to the caller to make</span> 3419 <span class="c"># sure that the specificaton list is ordered from least to most specific atom specification...</span> 3420 <span class="c">#</span> 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> 3422 <span class="i">$AtomSpecificationMatched</span> = <span class="n">1</span><span class="sc">;</span> 3423 <span class="i">$FirstMatch</span> = <span class="n">1</span><span class="sc">;</span> 3424 3425 <span class="c"># Match all atom symbol atomic invariants...</span> 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> 3427 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstMatch</span><span class="s">)</span> <span class="s">{</span> 3428 <span class="c"># Match atom symbol atomic invariant...</span> 3429 <span class="i">$FirstMatch</span> = <span class="n">0</span><span class="sc">;</span> 3430 <span class="i">$AtomicInvariantMatched</span> = <span class="i">$This</span><span class="i">->_MatchAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="sc">;</span> 3431 <span class="s">}</span> 3432 <span class="k">else</span> <span class="s">{</span> 3433 <span class="c"># Match non atom symbol atomic invariant...</span> 3434 <span class="i">$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> 3435 <span class="s">}</span> 3436 3437 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicInvariantMatched</span><span class="s">)</span> <span class="s">{</span> 3438 <span class="c"># No need to match other atomic invariants...</span> 3439 <span class="i">$AtomSpecificationMatched</span> = <span class="n">0</span><span class="sc">;</span> 3440 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span> 3441 <span class="s">}</span> 3442 <span class="s">}</span> 3443 3444 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomSpecificationMatched</span><span class="s">)</span> <span class="s">{</span> 3445 <span class="c"># No need to match other atom specifications...</span> 3446 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3447 <span class="s">}</span> 3448 <span class="s">}</span> 3449 3450 <span class="c"># Nothing matched...</span> 3451 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3452 <span class="s">}</span> 3453 3454 <span class="c"># Check whether atom matches atom symbol atomic invariant...</span> 3455 <span class="c">#</span> <a name="_MatchAtomSymbolAtomicInvariant-"></a>3456 <span class="k">sub </span><span class="m">_MatchAtomSymbolAtomicInvariant</span> <span class="s">{</span> 3457 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3458 <span class="k">my</span><span class="s">(</span><span class="i">$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> 3459 3460 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> 3461 <span class="i">$NegateMatch</span> = <span class="n">0</span><span class="sc">;</span> 3462 3463 <span class="c"># Does match needs to be negated?</span> 3464 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span> 3465 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span> 3466 <span class="i">$AtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span> 3467 <span class="s">}</span> 3468 3469 <span class="j">ATOMICINVARIANT:</span> <span class="s">{</span> 3470 <span class="c"># Any atom match...</span> 3471 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_IsWildCardAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3472 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> 3473 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span> 3474 <span class="s">}</span> 3475 3476 <span class="c"># Atomic number match...</span> 3477 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> 3478 <span class="i">$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> 3479 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="i">$AtomicNumber</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3480 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span> 3481 <span class="s">}</span> 3482 3483 <span class="c"># Atom symbol match...</span> 3484 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomSymbol</span>} =~ <span class="q">/^$AtomicInvariant$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3485 <span class="s">}</span> 3486 3487 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span> 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> 3489 <span class="s">}</span> 3490 3491 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 3492 <span class="s">}</span> 3493 3494 <span class="c"># Is it a wild card atom symbol atomic invariant?</span> 3495 <span class="c">#</span> <a name="_IsWildCardAtomSymbolAtomicInvariant-"></a>3496 <span class="k">sub </span><span class="m">_IsWildCardAtomSymbolAtomicInvariant</span> <span class="s">{</span> 3497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3498 3499 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(A|\*)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3500 <span class="s">}</span> 3501 3502 <span class="c"># Check whether atom matches non atom symbol atomic invariants...</span> 3503 <span class="c">#</span> <a name="_MatchNonAtomSymbolAtomicInvariant-"></a>3504 <span class="k">sub </span><span class="m">_MatchNonAtomSymbolAtomicInvariant</span> <span class="s">{</span> 3505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3506 <span class="k">my</span><span class="s">(</span><span class="i">$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> 3507 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">$UnknownName</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> 3509 3510 <span class="c"># Does match needs to be negated?</span> 3511 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span> 3512 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span> 3513 <span class="i">$AtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span> 3514 <span class="s">}</span> 3515 3516 <span class="c"># Extract atomic invariant name and any value...</span> 3517 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/[0-9\*]+/</span><span class="s">)</span> <span class="s">{</span> 3518 <span class="s">(</span><span class="i">$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\-\+\*\>\<\=]+)$/</span><span class="sc">;</span> 3519 <span class="s">}</span> 3520 <span class="k">else</span> <span class="s">{</span> 3521 <span class="s">(</span><span class="i">$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> 3522 <span class="s">}</span> 3523 3524 <span class="j">NAME:</span> <span class="s">{</span> 3525 <span class="c"># Match number of non-hydrogen atom neighbors</span> 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> 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> 3528 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3529 <span class="s">}</span> 3530 3531 <span class="c"># Match total number of atom neighbors including missing hydrogens...</span> 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> 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">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3534 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3535 <span class="s">}</span> 3536 3537 <span class="c"># Match formal charge...</span> 3538 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^FC$/i</span><span class="s">)</span> <span class="s">{</span> 3539 <span class="k">my</span> <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3540 <span class="i">$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">$Value</span><span class="s">)</span><span class="sc">;</span> 3541 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3542 <span class="s">}</span> 3543 3544 <span class="c"># Match aromatic annotation indicating whether atom is aromatic...</span> 3545 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^Ar$/i</span><span class="s">)</span> <span class="s">{</span> 3546 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3547 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3548 <span class="s">}</span> 3549 3550 <span class="c"># Match number of implicit and explicit hydrogens...</span> 3551 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^H$/i</span><span class="s">)</span> <span class="s">{</span> 3552 <span class="i">$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">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3553 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3554 <span class="s">}</span> 3555 3556 <span class="c"># Match ring atom annotation indicating whether atom is in ring...</span> 3557 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^RA$/i</span><span class="s">)</span> <span class="s">{</span> 3558 <span class="i">$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> 3559 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3560 <span class="s">}</span> 3561 3562 <span class="c"># Match number of rings for atom..</span> 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> 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> 3565 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3566 <span class="s">}</span> 3567 3568 <span class="c"># Match sum of bond orders to non-hydrogen atom neighbors...</span> 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> 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> 3571 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3572 <span class="s">}</span> 3573 3574 <span class="c"># Match largest bond order of non-hydrogen atom neighbors...</span> 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> 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> 3577 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3578 <span class="s">}</span> 3579 3580 <span class="c"># Match number of single bonds to non-hydrogen atom neighbors...</span> 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> 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> 3583 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3584 <span class="s">}</span> 3585 3586 <span class="c"># Match total number of single bonds to atom neighbors including missing and explicit hydrogens...</span> 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> 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">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3589 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3590 <span class="s">}</span> 3591 3592 <span class="c"># Match number of double bonds to non-hydrogen atom neighbors...</span> 3593 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^DB$/i</span><span class="s">)</span> <span class="s">{</span> 3594 <span class="i">$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">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3595 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3596 <span class="s">}</span> 3597 3598 <span class="c"># Match number of triple bonds to non-hydrogen atom neighbors...</span> 3599 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TB$/i</span><span class="s">)</span> <span class="s">{</span> 3600 <span class="i">$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">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3601 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3602 <span class="s">}</span> 3603 3604 <span class="c"># Match number of aromatic bonds to non-hydrogen atom neighbors...</span> 3605 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^AB$/i</span><span class="s">)</span> <span class="s">{</span> 3606 <span class="i">$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">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3607 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3608 <span class="s">}</span> 3609 3610 3611 <span class="c"># Match mass number indicating isotope other than most abundant isotope...</span> 3612 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^MN$/i</span><span class="s">)</span> <span class="s">{</span> 3613 <span class="i">$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">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3614 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3615 <span class="s">}</span> 3616 3617 <span class="c"># Match spin multiplicity...</span> 3618 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^SM$/i</span><span class="s">)</span> <span class="s">{</span> 3619 <span class="k">my</span> <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3620 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">}</span> 3621 <span class="i">$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> 3622 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> 3623 <span class="s">}</span> 3624 3625 <span class="i">$UnknownName</span> = <span class="n">1</span><span class="sc">;</span> 3626 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_MatchNonAtomSymbolAtomicInvariant: Unknown atomic invariant $AtomicInvariant..."</span><span class="sc">;</span> 3627 <span class="s">}</span> 3628 3629 <span class="k">if</span> <span class="s">(</span>!<span class="i">$UnknownName</span><span class="s">)</span> <span class="s">{</span> 3630 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span> 3631 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 3632 <span class="s">}</span> 3633 <span class="s">}</span> 3634 3635 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 3636 <span class="s">}</span> 3637 3638 <span class="c"># Match atomic invariant value...</span> 3639 <span class="c">#</span> 3640 <span class="c"># Specified value format:</span> 3641 <span class="c"># . +* : Any positive value</span> 3642 <span class="c"># . -* : Any negative value</span> 3643 <span class="c"># . >ValidNumber or >=ValidNumber</span> 3644 <span class="c"># . <ValidNumber or <=ValidNumber</span> 3645 <span class="c"># . Any valid number</span> 3646 <span class="c">#</span> <a name="_MatchNonAtomSymbolAtomicInvariantValue-"></a>3647 <span class="k">sub </span><span class="m">_MatchNonAtomSymbolAtomicInvariantValue</span> <span class="s">{</span> 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">$SpecifiedValue</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3649 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> 3650 3651 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> 3652 3653 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$TargetValue</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SpecifiedValue</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3654 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 3655 <span class="s">}</span> 3656 3657 <span class="j">VALUE:</span> <span class="s">{</span> 3658 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^\+\*/</span><span class="s">)</span> <span class="s">{</span> 3659 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$TargetValue</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3660 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> 3661 <span class="s">}</span> 3662 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^\-\*/</span><span class="s">)</span> <span class="s">{</span> 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> 3664 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> 3665 <span class="s">}</span> 3666 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^>/</span><span class="s">)</span> <span class="s">{</span> 3667 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^>=/</span><span class="s">)</span> <span class="s">{</span> 3668 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^>=//</span><span class="sc">;</span> 3669 <span class="i">$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> 3670 <span class="s">}</span> 3671 <span class="k">else</span> <span class="s">{</span> 3672 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^>//</span><span class="sc">;</span> 3673 <span class="i">$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> 3674 <span class="s">}</span> 3675 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> 3676 <span class="s">}</span> 3677 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^</</span><span class="s">)</span> <span class="s">{</span> 3678 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^<=/</span><span class="s">)</span> <span class="s">{</span> 3679 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^<=//</span><span class="sc">;</span> 3680 <span class="i">$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> 3681 <span class="s">}</span> 3682 <span class="k">else</span> <span class="s">{</span> 3683 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^<//</span><span class="sc">;</span> 3684 <span class="i">$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> 3685 <span class="s">}</span> 3686 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> 3687 <span class="s">}</span> 3688 <span class="c"># Default is do perform an equality match...</span> 3689 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> == <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3690 <span class="s">}</span> 3691 3692 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 3693 <span class="s">}</span> 3694 3695 <span class="c"># Check whether atoms match bond specifications...</span> 3696 <span class="c">#</span> <a name="_DoesBondSpecificationMatch-"></a>3697 <span class="k">sub </span><span class="m">_DoesBondSpecificationMatch</span> <span class="s">{</span> 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">$BondSpecificationToMatch</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3699 <span class="k">my</span><span class="s">(</span><span class="i">$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> 3700 3701 <span class="c"># Anything to match...</span> 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> 3703 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3704 <span class="s">}</span> 3705 3706 <span class="c"># Take out any spaces...</span> 3707 <span class="i">$BondSpecificationToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 3708 3709 <span class="c"># Match specified bond specifications. For multiple bond specifications in a comma delimited string,</span> 3710 <span class="c"># only one bond specification needs to match for a successful match...</span> 3711 <span class="c">#</span> 3712 <span class="k">for</span> <span class="i">$BondSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$BondSpecificationToMatch</span><span class="s">)</span> <span class="s">{</span> 3713 <span class="i">$BondSpecificationMatched</span> = <span class="n">1</span><span class="sc">;</span> 3714 3715 <span class="c"># Match all specified bond symbol specifications...</span> 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> 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">$BondSymbolSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3718 <span class="c"># No need to match other bond symbol specifications...</span> 3719 <span class="i">$BondSpecificationMatched</span> = <span class="n">0</span><span class="sc">;</span> 3720 <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> 3721 <span class="s">}</span> 3722 <span class="s">}</span> 3723 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSpecificationMatched</span><span class="s">)</span> <span class="s">{</span> 3724 <span class="c"># No need to try matching other bond specifications...</span> 3725 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3726 <span class="s">}</span> 3727 <span class="s">}</span> 3728 3729 <span class="c"># Nothing matched...</span> 3730 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3731 <span class="s">}</span> 3732 3733 <span class="c"># Check whether atoms match bond symbol specification...</span> 3734 <span class="c">#</span> <a name="_MatchBondSymbolSpecification-"></a>3735 <span class="k">sub </span><span class="m">_MatchBondSymbolSpecification</span> <span class="s">{</span> 3736 <span class="k">my</span><span class="s">(</span><span class="i">$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> 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">$UnknownBondSymbol</span><span class="s">)</span><span class="sc">;</span> 3738 3739 <span class="s">(</span><span class="i">$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> 3740 3741 <span class="c"># Does match needs to be negated?</span> 3742 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbolSpecification</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span> 3743 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span> 3744 <span class="i">$BondSymbolSpecification</span> =~ <span class="q">s/^!//</span><span class="sc">;</span> 3745 <span class="s">}</span> 3746 <span class="i">$BondSymbol</span> = <span class="i">$BondSymbolSpecification</span><span class="sc">;</span> 3747 <span class="i">$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> 3748 3749 <span class="j">BONDSYMBOL:</span> <span class="s">{</span> 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> 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> 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> 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> 3754 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> 3756 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">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span> 3758 3759 <span class="i">$UnknownBondSymbol</span> = <span class="n">1</span><span class="sc">;</span> 3760 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_MatchBondSpecification: Unknown bond specification $BondSymbolSpecification..."</span><span class="sc">;</span> 3761 <span class="s">}</span> 3762 3763 <span class="k">if</span> <span class="s">(</span>!<span class="i">$UnknownBondSymbol</span><span class="s">)</span> <span class="s">{</span> 3764 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span> 3765 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 3766 <span class="s">}</span> 3767 <span class="s">}</span> 3768 3769 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 3770 <span class="s">}</span> 3771 3772 <span class="c"># Is it a saturated atom?</span> 3773 <span class="c">#</span> <a name="IsSaturated-"></a>3774 <span class="k">sub </span><span class="m">IsSaturated</span> <span class="s">{</span> 3775 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3776 3777 <span class="k">return</span> !<span class="i">$This</span><span class="i">->IsUnsaturated</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3778 <span class="s">}</span> 3779 3780 <span class="c"># Is it an unsaturated atom containing at least one non-single bond?</span> 3781 <span class="c">#</span> <a name="IsUnsaturated-"></a>3782 <span class="k">sub </span><span class="m">IsUnsaturated</span> <span class="s">{</span> 3783 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3784 <span class="k">my</span><span class="s">(</span><span class="i">$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">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span> 3785 3786 <span class="s">(</span><span class="i">$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> 3787 3788 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfDoubleBonds</span> || <span class="i">$NumOfTripleBonds</span> || <span class="i">$NumOfAromaticBonds</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3789 <span class="s">}</span> 3790 3791 <span class="c"># Is atom in a ring?</span> 3792 <span class="c">#</span> <a name="IsInRing-"></a>3793 <span class="k">sub </span><span class="m">IsInRing</span> <span class="s">{</span> 3794 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3795 3796 <span class="c"># Is this atom in a molecule?</span> 3797 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3798 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3799 <span class="s">}</span> 3800 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 3802 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> 3804 <span class="s">}</span> 3805 3806 <span class="c"># Is atom not in a ring?</span> 3807 <span class="c">#</span> <a name="IsNotInRing-"></a>3808 <span class="k">sub </span><span class="m">IsNotInRing</span> <span class="s">{</span> 3809 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3810 3811 <span class="c"># Is this atom in a molecule?</span> 3812 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 3813 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3814 <span class="s">}</span> 3815 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 3816 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 3817 3818 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomNotInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 3819 <span class="s">}</span> 3820 3821 <span class="c"># Is atom only in one ring?</span> 3822 <span class="c">#</span> <a name="IsOnlyInOneRing-"></a>3823 <span class="k">sub </span><span class="m">IsOnlyInOneRing</span> <span class="s">{</span> 3824 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3825 3826 <span class="c"># Is this atom in a molecule?</span> 3827 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3828 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3829 <span class="s">}</span> 3830 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 3832 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> 3834 <span class="s">}</span> 3835 3836 <span class="c"># Is atom in a ring of specific size?</span> 3837 <span class="c">#</span> <a name="IsInRingOfSize-"></a>3838 <span class="k">sub </span><span class="m">IsInRingOfSize</span> <span class="s">{</span> 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> 3840 3841 <span class="c"># Is this atom in a molecule?</span> 3842 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3843 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3844 <span class="s">}</span> 3845 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 3847 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">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3849 <span class="s">}</span> 3850 3851 <span class="c"># Get size of smallest ring containing the atom...</span> 3852 <span class="c">#</span> <a name="GetSizeOfSmallestRing-"></a>3853 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span> 3854 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3855 3856 <span class="c"># Is this atom in a molecule?</span> 3857 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3858 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3859 <span class="s">}</span> 3860 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 3862 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> 3864 <span class="s">}</span> 3865 3866 <span class="c"># Get size of largest ring containing the atom...</span> 3867 <span class="c">#</span> <a name="GetSizeOfLargestRing-"></a>3868 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span> 3869 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3870 3871 <span class="c"># Is this atom in a molecule?</span> 3872 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 3873 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3874 <span class="s">}</span> 3875 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 3876 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 3877 3878 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfLargestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 3879 <span class="s">}</span> 3880 3881 <span class="c"># Get number of rings containing the atom...</span> 3882 <span class="c">#</span> <a name="GetNumOfRings-"></a>3883 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span> 3884 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3885 3886 <span class="c"># Is this atom in a molecule?</span> 3887 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3888 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3889 <span class="s">}</span> 3890 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 3892 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> 3894 <span class="s">}</span> 3895 3896 <span class="c"># Get number of rings with odd size containing the atom...</span> 3897 <span class="c">#</span> <a name="GetNumOfRingsWithOddSize-"></a>3898 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span> 3899 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3900 3901 <span class="c"># Is this atom in a molecule?</span> 3902 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 3903 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3904 <span class="s">}</span> 3905 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 3906 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 3907 3908 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 3909 <span class="s">}</span> 3910 3911 <span class="c"># Get number of rings with even size containing the atom...</span> 3912 <span class="c">#</span> <a name="GetNumOfRingsWithEvenSize-"></a>3913 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span> 3914 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3915 3916 <span class="c"># Is this atom in a molecule?</span> 3917 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3918 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3919 <span class="s">}</span> 3920 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 3922 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> 3924 <span class="s">}</span> 3925 3926 <span class="c"># Get number of rings with specified size containing the atom...</span> 3927 <span class="c">#</span> <a name="GetNumOfRingsWithSize-"></a>3928 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span> 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> 3930 3931 <span class="c"># Is this atom in a molecule?</span> 3932 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3933 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3934 <span class="s">}</span> 3935 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 3937 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">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3939 3940 <span class="s">}</span> 3941 3942 <span class="c"># Get number of rings with size less than specified containing the atom...</span> 3943 <span class="c">#</span> <a name="GetNumOfRingsWithSizeLessThan-"></a>3944 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span> 3945 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3946 3947 <span class="c"># Is this atom in a molecule?</span> 3948 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 3949 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3950 <span class="s">}</span> 3951 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 3952 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 3953 3954 <span class="k">return</span> <span class="i">$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> 3955 <span class="s">}</span> 3956 3957 <span class="c"># Get number of rings with size greater than specified size containing the atom...</span> 3958 <span class="c">#</span> <a name="GetNumOfRingsWithSizeGreaterThan-"></a>3959 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span> 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> 3961 3962 <span class="c"># Is this atom in a molecule?</span> 3963 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3964 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3965 <span class="s">}</span> 3966 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 3968 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">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3970 <span class="s">}</span> 3971 3972 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span> 3973 <span class="c">#</span> <a name="GetRings-"></a>3974 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span> 3975 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3976 3977 <span class="c"># Is this atom in a molecule?</span> 3978 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3979 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3980 <span class="s">}</span> 3981 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 3983 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> 3985 <span class="s">}</span> 3986 3987 <span class="c"># Get smallest ring as an array containing ring atoms...</span> 3988 <span class="c">#</span> <a name="GetSmallestRing-"></a>3989 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span> 3990 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3991 3992 <span class="c"># Is this atom in a molecule?</span> 3993 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 3994 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 3995 <span class="s">}</span> 3996 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 3997 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 3998 3999 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSmallestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 4000 <span class="s">}</span> 4001 4002 <span class="c"># Get largest ring as an array containing ring atoms...</span> 4003 <span class="c">#</span> <a name="GetLargestRing-"></a>4004 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span> 4005 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4006 4007 <span class="c"># Is this atom in a molecule?</span> 4008 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4009 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 4010 <span class="s">}</span> 4011 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 4013 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> 4015 <span class="s">}</span> 4016 4017 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> 4018 <span class="c">#</span> <a name="GetRingsWithOddSize-"></a>4019 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span> 4020 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4021 4022 <span class="c"># Is this atom in a molecule?</span> 4023 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 4024 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 4025 <span class="s">}</span> 4026 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 4027 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 4028 4029 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 4030 <span class="s">}</span> 4031 4032 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span> 4033 <span class="c">#</span> <a name="GetRingsWithEvenSize-"></a>4034 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span> 4035 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4036 4037 <span class="c"># Is this atom in a molecule?</span> 4038 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4039 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 4040 <span class="s">}</span> 4041 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 4043 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> 4045 <span class="s">}</span> 4046 4047 <span class="c"># Get rings with specified size as an array of references to arrays containing ring atoms...</span> 4048 <span class="c">#</span> <a name="GetRingsWithSize-"></a>4049 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span> 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> 4051 4052 <span class="c"># Is this atom in a molecule?</span> 4053 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4054 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 4055 <span class="s">}</span> 4056 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 4058 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">$RingSize</span><span class="s">)</span><span class="sc">;</span> 4060 <span class="s">}</span> 4061 4062 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> 4063 <span class="c">#</span> <a name="GetRingsWithSizeLessThan-"></a>4064 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span> 4065 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4066 4067 <span class="c"># Is this atom in a molecule?</span> 4068 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 4069 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 4070 <span class="s">}</span> 4071 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 4072 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 4073 4074 <span class="k">return</span> <span class="i">$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> 4075 <span class="s">}</span> 4076 4077 <span class="c"># Get rings with size greater than specfied size as an array of references to arrays containing ring atoms...</span> 4078 <span class="c">#</span> <a name="GetRingsWithSizeGreaterThan-"></a>4079 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span> 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> 4081 4082 <span class="c"># Is this atom in a molecule?</span> 4083 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4084 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 4085 <span class="s">}</span> 4086 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 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> 4088 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">$RingSize</span><span class="s">)</span><span class="sc">;</span> 4090 <span class="s">}</span> 4091 4092 <span class="c"># Get next object ID...</span> <a name="_GetNewObjectID-"></a>4093 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span> 4094 <span class="i">$ObjectID</span>++<span class="sc">;</span> 4095 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span> 4096 <span class="s">}</span> 4097 4098 <span class="c"># Return a string containing vertices, edges and other properties...</span> <a name="StringifyAtom-"></a>4099 <span class="k">sub </span><span class="m">StringifyAtom</span> <span class="s">{</span> 4100 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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> 4102 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> 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> 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> 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> 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> 4108 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> 4110 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$AtomicWeight</span><span class="s">)</span> <span class="s">{</span> 4111 <span class="i">$AtomicWeight</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4112 <span class="s">}</span> 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> 4114 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExactMass</span><span class="s">)</span> <span class="s">{</span> 4115 <span class="i">$ExactMass</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4116 <span class="s">}</span> 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> 4118 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> <span class="s">{</span> 4119 <span class="i">$NumOfNeighbors</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4120 <span class="s">}</span> 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> 4122 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> <span class="s">{</span> 4123 <span class="i">$NumOfBonds</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4124 <span class="s">}</span> 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> 4126 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Valence</span><span class="s">)</span> <span class="s">{</span> 4127 <span class="i">$Valence</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4128 <span class="s">}</span> 4129 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> 4131 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$MissingHydrogens</span><span class="s">)</span> <span class="s">{</span> 4132 <span class="i">$MissingHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4133 <span class="s">}</span> 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> 4135 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$TotalHydrogens</span><span class="s">)</span> <span class="s">{</span> 4136 <span class="i">$TotalHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4137 <span class="s">}</span> 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> 4139 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ImplicitHydrogens</span><span class="s">)</span> <span class="s">{</span> 4140 <span class="i">$ImplicitHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4141 <span class="s">}</span> 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> 4143 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExplicitHydrogens</span><span class="s">)</span> <span class="s">{</span> 4144 <span class="i">$ExplicitHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4145 <span class="s">}</span> 4146 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> 4148 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span> 4149 <span class="i">$FormalCharge</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4150 <span class="s">}</span> 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> 4152 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span> 4153 <span class="i">$Charge</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4154 <span class="s">}</span> 4155 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> 4157 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span> <span class="s">{</span> 4158 <span class="i">$SpinMultiplicity</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4159 <span class="s">}</span> 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> 4161 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span> 4162 <span class="i">$FreeRadicalElectrons</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4163 <span class="s">}</span> 4164 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> 4166 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$RingAtom</span><span class="s">)</span> <span class="s">{</span> 4167 <span class="i">$RingAtom</span> = <span class="i">$RingAtom</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> 4168 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4169 <span class="s">}</span> 4170 <span class="k">else</span> <span class="s">{</span> 4171 <span class="i">$RingAtom</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4172 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4173 <span class="s">}</span> 4174 4175 <span class="i">$AromaticAtom</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4176 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticAtom</span><span class="s">)</span> <span class="s">{</span> 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> 4178 <span class="s">}</span> 4179 <span class="k">else</span> <span class="s">{</span> 4180 <span class="i">$AromaticAtom</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4181 <span class="s">}</span> 4182 4183 <span class="i">$StereochemistryString</span> = <span class="q">''</span><span class="sc">;</span> 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> 4185 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$StereoCenter</span><span class="s">)</span> <span class="s">{</span> 4186 <span class="i">$StereoCenterStatus</span> = <span class="i">$This</span><span class="i">->IsStereoCenter</span><span class="s">(</span><span class="s">)</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> 4187 <span class="i">$StereoChemistry</span> = <span class="i">$This</span><span class="i">->GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4188 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$StereoChemistry</span><span class="s">)</span> <span class="s">{</span> 4189 <span class="i">$StereoChemistry</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4190 <span class="s">}</span> 4191 <span class="i">$StereochemistryString</span> = <span class="q">"StereoCenter: $StereoCenterStatus; Stereochemistry: $StereoChemistry"</span><span class="sc">;</span> 4192 <span class="s">}</span> 4193 4194 <span class="i">$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: $AromaticAtom"</span><span class="sc">;</span> 4195 4196 <span class="k">if</span> <span class="s">(</span><span class="i">$StereochemistryString</span><span class="s">)</span> <span class="s">{</span> 4197 <span class="i">$AtomString</span> .= <span class="q">"; $StereochemistryString"</span><span class="sc">;</span> 4198 <span class="s">}</span> 4199 4200 <span class="k">return</span> <span class="i">$AtomString</span><span class="sc">;</span> 4201 <span class="s">}</span> 4202 4203 <span class="c"># Load appropriate atom data files from <MayaChemTools>/lib directory used by various</span> 4204 <span class="c"># object methods in the current class...</span> 4205 <span class="c">#</span> <a name="_LoadAtomClassData-"></a>4206 <span class="k">sub </span><span class="m">_LoadAtomClassData</span> <span class="s">{</span> 4207 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> 4208 4209 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4210 4211 <span class="i">_LoadAtomValenceModelData</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> 4212 4213 <span class="s">}</span> 4214 4215 <span class="c">#</span> 4216 <span class="c"># Load data for supported valence models...</span> 4217 <span class="c">#</span> <a name="_LoadAtomValenceModelData-"></a>4218 <span class="k">sub </span><span class="m">_LoadAtomValenceModelData</span> <span class="s">{</span> 4219 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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> 4221 4222 <span class="i">%MDLValenceModelDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4223 <span class="i">%DaylightValenceModelDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4224 4225 <span class="i">$MDLValenceModelDataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/MDLValenceModelData.csv"</span><span class="sc">;</span> 4226 <span class="i">$DaylightValenceModelDataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/DaylightValenceModelData.csv"</span><span class="sc">;</span> 4227 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> 4229 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $MDLValenceModelDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> 4230 <span class="s">}</span> 4231 4232 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$DaylightValenceModelDataFile"</span><span class="s">)</span> <span class="s">{</span> 4233 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $DaylightValenceModelDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> 4234 <span class="s">}</span> 4235 4236 <span class="i">_LoadValenceModelDataFile</span><span class="s">(</span><span class="i">$MDLValenceModelDataFile</span><span class="cm">,</span> \<span class="i">%MDLValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> 4237 <span class="i">_LoadValenceModelDataFile</span><span class="s">(</span><span class="i">$DaylightValenceModelDataFile</span><span class="cm">,</span> \<span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> 4238 4239 <span class="s">}</span> 4240 4241 <span class="c">#</span> 4242 <span class="c"># Load valence model data file...</span> 4243 <span class="c">#</span> <a name="_LoadValenceModelDataFile-"></a>4244 <span class="k">sub </span><span class="m">_LoadValenceModelDataFile</span> <span class="s">{</span> 4245 <span class="k">my</span><span class="s">(</span><span class="i">$DataFile</span><span class="cm">,</span> <span class="i">$DataMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4246 4247 <span class="c"># File format:</span> 4248 <span class="c">#</span> 4249 <span class="c"># "AtomicNumber","ElementSymbol","FormalCharge","CommomValences"</span> 4250 <span class="c">#</span> 4251 <span class="k">my</span><span class="s">(</span><span class="i">$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> 4252 4253 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span> 4254 <span class="k">open</span> <span class="w">DATAFILE</span><span class="cm">,</span> <span class="q">"$DataFile"</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">"Couldn't open $DataFile: $! ..."</span><span class="sc">;</span> 4255 4256 <span class="c"># Skip lines up to column labels...</span> 4257 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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> 4258 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> 4259 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> 4260 <span class="s">}</span> 4261 <span class="s">}</span> 4262 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> 4263 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span> 4264 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> 4266 4267 <span class="c"># Process element data...</span> 4268 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4269 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> 4270 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> 4271 <span class="s">}</span> 4272 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 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> 4275 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadValenceModelDataFile: The number of data fields, @LineWords, in $DataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span> 4276 <span class="s">}</span> 4277 4278 <span class="s">(</span><span class="i">$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">$CommonValences</span><span class="s">)</span> = <span class="i">@LineWords</span><span class="sc">;</span> 4279 4280 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> 4281 <span class="c"># Additional data for an element...</span> 4282 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}<span class="s">)</span> <span class="s">{</span> 4283 <span class="c"># Duplicate data entries for an element...</span> 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: $Line..."</span><span class="sc">;</span> 4285 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> 4286 <span class="s">}</span> 4287 <span class="s">}</span> 4288 <span class="k">else</span> <span class="s">{</span> 4289 <span class="c"># Data for a new element...</span> 4290 <span class="i">%</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4291 <span class="s">}</span> 4292 4293 <span class="i">%</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 4295 4296 <span class="i">@</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4297 <span class="i">@</span>{<span class="i">$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> 4298 <span class="s">}</span> 4299 <span class="k">close</span> <span class="w">DATAFILE</span><span class="sc">;</span> 4300 <span class="s">}</span> 4301 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>