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diff mayachemtools/docs/modules/html/code/Atom.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/Atom.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,4322 @@ +<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>