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<html> <head> <title>MayaChemTools:Code:Bond.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-Bond-"></a> 1 <span class="k">package </span><span class="i">Bond</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: Bond.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span> 5 <span class="c"># $Revision: 1.40 $</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 36 <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> 37 38 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> 41 42 <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> 43 44 <span class="c"># Setup class variables...</span> 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="s">)</span><span class="sc">;</span> 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 47 48 <span class="c"># Overload Perl functions...</span> 49 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyBond'</span><span class="sc">;</span> 50 51 <span class="c"># Class constructor...</span> <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 54 55 <span class="c"># Initialize object...</span> 56 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> 57 <span class="k">bless</span> <span class="i">$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> 58 <span class="i">$This</span><span class="i">->_InitializeBond</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 59 60 <span class="i">$This</span><span class="i">->_InitializeBondProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 61 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 63 <span class="s">}</span> 64 65 <span class="c"># Initialize object data...</span> 66 <span class="c">#</span> <a name="_InitializeBond-"></a> 67 <span class="k">sub </span><span class="m">_InitializeBond</span> <span class="s">{</span> 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 69 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 70 71 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> 72 <span class="c"># are implemented on-demand using ObjectProperty class.</span> 73 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span> 74 75 <span class="c"># Bond from and to atoms indicate begining and ending bond atoms...</span> 76 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="k">undef</span><span class="sc">;</span> 77 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="k">undef</span><span class="sc">;</span> 78 79 <span class="i">$This</span>->{<span class="w">BondOrder</span>} = <span class="q">''</span><span class="sc">;</span> 80 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="q">''</span><span class="sc">;</span> 81 <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} = <span class="q">''</span><span class="sc">;</span> 82 <span class="s">}</span> 83 84 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 85 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 86 <span class="c">#Class name...</span> 87 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 88 89 <span class="c"># ID to keep track of objects...</span> 90 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span> 91 <span class="s">}</span> 92 93 <span class="c"># Initialize bond properties...</span> <a name="_InitializeBondProperties-"></a> 94 <span class="k">sub </span><span class="m">_InitializeBondProperties</span> <span class="s">{</span> 95 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 96 97 <span class="k">my</span><span class="s">(</span><span class="i">$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> 98 <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> 99 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 100 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 101 <span class="s">}</span> 102 103 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'Atoms'</span>}<span class="s">)</span> <span class="s">{</span> 104 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Bond object instantiated without specifying atoms list..."</span><span class="sc">;</span> 105 <span class="s">}</span> 106 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'BondOrder'</span>}<span class="s">)</span> <span class="s">{</span> 107 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Bond object instantiated without setting bond order..."</span><span class="sc">;</span> 108 <span class="s">}</span> 109 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 110 <span class="s">}</span> 111 112 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span> <a name="SetID-"></a> 113 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span> 114 <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> 115 116 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> 117 118 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 119 <span class="s">}</span> 120 121 <span class="c"># Setup an explicit SetMolecule method to block setting of ID by AUTOLOAD function...</span> <a name="SetMolecule-"></a> 122 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> 123 <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> 124 125 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMolecule: Molecule property can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> 126 127 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 128 <span class="s">}</span> 129 130 <span class="c"># Assign bond to molecule...</span> <a name="_SetMolecule-"></a> 131 <span class="k">sub </span><span class="m">_SetMolecule</span> <span class="s">{</span> 132 <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> 133 134 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> 135 136 <span class="c"># Weaken the reference to disable increment of reference count; otherwise,</span> 137 <span class="c"># it it becomes a circular reference and destruction of Molecule object doesn't</span> 138 <span class="c"># get initiated which in turn disables destruction of bond object.</span> 139 <span class="c">#</span> 140 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> 141 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 143 <span class="s">}</span> 144 145 <span class="c"># Set bond atoms...</span> <a name="SetAtoms-"></a> 146 <span class="k">sub </span><span class="m">SetAtoms</span> <span class="s">{</span> 147 <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> 148 149 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 150 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtoms: No atoms specified..."</span><span class="sc">;</span> 151 <span class="s">}</span> 152 153 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 154 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 155 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 156 157 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 158 <span class="c"># Initialize using array refernce...</span> 159 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FirstValue</span>} != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 160 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Number of atoms specified in bond object is not equal to 2..."</span><span class="sc">;</span> 161 <span class="s">}</span> 162 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 163 <span class="s">}</span> 164 <span class="k">else</span> <span class="s">{</span> 165 <span class="c"># It's a list of values...</span> 166 <span class="k">if</span> <span class="s">(</span><span class="i">@Values</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 167 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Number of atoms specified in bond object is not equal to 2..."</span><span class="sc">;</span> 168 <span class="s">}</span> 169 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@Values</span><span class="sc">;</span> 170 <span class="s">}</span> 171 172 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 173 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$AtomID2</span><span class="s">)</span> <span class="s">{</span> 174 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Can't specify same atoms to create a bond..."</span><span class="sc">;</span> 175 <span class="s">}</span> 176 177 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="i">$Atom1</span><span class="sc">;</span> 178 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="i">$Atom2</span><span class="sc">;</span> 179 180 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 181 <span class="s">}</span> 182 183 <span class="c"># Get bond atoms as array. In scalar context, return number of atoms involved in</span> 184 <span class="c"># bond...</span> 185 <span class="c">#</span> <a name="GetAtoms-"></a> 186 <span class="k">sub </span><span class="m">GetAtoms</span> <span class="s">{</span> 187 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 188 189 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondFromAtom</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">BondToAtom</span>}<span class="s">)</span> <span class="co">:</span> <span class="n">2</span><span class="sc">;</span> 190 <span class="s">}</span> 191 192 <span class="c"># Get atom bonded to specified atom...</span> <a name="GetBondedAtom-"></a> 193 <span class="k">sub </span><span class="m">GetBondedAtom</span> <span class="s">{</span> 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 195 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 196 197 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 198 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 199 200 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$AtomID</span><span class="s">)</span> ? <span class="i">$Atom2</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomID2</span> == <span class="i">$AtomID</span><span class="s">)</span> ? <span class="i">$Atom1</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="sc">;</span> 201 <span class="s">}</span> 202 203 <span class="c"># Get common atom between two bonds...</span> <a name="GetCommonAtom-"></a> 204 <span class="k">sub </span><span class="m">GetCommonAtom</span> <span class="s">{</span> 205 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 206 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$OtherAtom1</span><span class="cm">,</span> <span class="i">$OtherAtom2</span><span class="cm">,</span> <span class="i">$OtherAtomID1</span><span class="cm">,</span> <span class="i">$OtherAtomID2</span><span class="s">)</span><span class="sc">;</span> 207 208 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 209 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 210 211 <span class="s">(</span><span class="i">$OtherAtom1</span><span class="cm">,</span> <span class="i">$OtherAtom2</span><span class="s">)</span> = <span class="i">$Other</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 212 <span class="i">$OtherAtomID1</span> = <span class="i">$OtherAtom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$OtherAtomID2</span> = <span class="i">$OtherAtom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 213 214 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$OtherAtomID1</span> || <span class="i">$AtomID1</span> == <span class="i">$OtherAtomID2</span><span class="s">)</span> ? <span class="i">$Atom1</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomID2</span> == <span class="i">$OtherAtomID1</span> || <span class="i">$AtomID2</span> == <span class="i">$OtherAtomID2</span><span class="s">)</span> ? <span class="i">$Atom2</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="sc">;</span> 215 <span class="s">}</span> 216 217 <span class="c"># Get bond from atom indicating begining atom of a bond...</span> <a name="GetBondFromAtom-"></a> 218 <span class="k">sub </span><span class="m">GetBondFromAtom</span> <span class="s">{</span> 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 220 221 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">BondFromAtom</span>}<span class="sc">;</span> 222 <span class="s">}</span> 223 224 <span class="c"># Get begin bond atom...</span> <a name="GetBondBeginAtom-"></a> 225 <span class="k">sub </span><span class="m">GetBondBeginAtom</span> <span class="s">{</span> 226 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 227 228 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondFromAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 229 <span class="s">}</span> 230 231 <span class="c"># Get bond to atom indicating ending atom of a bond...</span> <a name="GetBondToAtom-"></a> 232 <span class="k">sub </span><span class="m">GetBondToAtom</span> <span class="s">{</span> 233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 234 235 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">BondToAtom</span>}<span class="sc">;</span> 236 <span class="s">}</span> 237 238 <span class="c"># Get begin bond atom...</span> <a name="GetBondEndAtom-"></a> 239 <span class="k">sub </span><span class="m">GetBondEndAtom</span> <span class="s">{</span> 240 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 241 242 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 243 <span class="s">}</span> 244 245 <span class="c"># Switch bond from and to atoms...</span> <a name="SwitchBondFromAndToAtoms-"></a> 246 <span class="k">sub </span><span class="m">SwitchBondFromAndToAtoms</span> <span class="s">{</span> 247 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 248 <span class="k">my</span><span class="s">(</span><span class="i">$FromAtom</span><span class="cm">,</span> <span class="i">$ToAtom</span><span class="s">)</span><span class="sc">;</span> 249 250 <span class="s">(</span><span class="i">$FromAtom</span><span class="cm">,</span> <span class="i">$ToAtom</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 251 252 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="i">$ToAtom</span><span class="sc">;</span> 253 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="i">$FromAtom</span><span class="sc">;</span> 254 255 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 256 <span class="s">}</span> 257 258 <span class="c"># Set bond order...</span> 259 <span class="c">#</span> 260 <span class="c"># Possible BondOrder are: 0 = None, 1 = Single, 1.5 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple,</span> 261 <span class="c"># 5 = Quintuple, 6 = Sextuple, 7 = Septuple</span> 262 <span class="c">#</span> 263 <span class="c"># Possible BondType for different BondOrders are:</span> 264 <span class="c">#</span> 265 <span class="c"># 0 : None, Ionic, Unspecified</span> 266 <span class="c"># 1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric</span> 267 <span class="c"># 1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic</span> 268 <span class="c"># 2 : Double, Tautomeric, SingleOrDouble, DoubleOrAromatic</span> 269 <span class="c"># 3 : Triple</span> 270 <span class="c"># 4 : Quadruple</span> 271 <span class="c"># 5 : Quintuple</span> 272 <span class="c"># 6 : Sextuple</span> 273 <span class="c"># 7 : Septuple</span> 274 <span class="c">#</span> 275 <span class="c"># Note: BondType Any is valid for all BondOrders.</span> 276 <span class="c">#</span> 277 <span class="c"># Possible BondStereochemistry values for different BondOrders are:</span> 278 <span class="c">#</span> 279 <span class="c"># 0 : None, Unspecified</span> 280 <span class="c"># 1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, None, Unspecified</span> 281 <span class="c"># 2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified</span> 282 <span class="c">#</span> 283 <span class="c"># Notes:</span> 284 <span class="c"># . BondType property is automatically assigned using default BondType values for</span> 285 <span class="c"># specified BondOrder.</span> 286 <span class="c"># . BondType values can also be explicit set.</span> 287 <span class="c"># . To make bonds aromatic in a ring, explicitly set "Aromatic" property for bond/atoms and make sure</span> 288 <span class="c"># appropriate BondOrder values are assigned.</span> 289 <span class="c"># . Dative or coordinate bond types are treated as single bond types with explicit formal charge</span> 290 <span class="c"># of + and - on first and second bond atoms.</span> 291 <span class="c">#</span> <a name="SetBondOrder-"></a> 292 <span class="k">sub </span><span class="m">SetBondOrder</span> <span class="s">{</span> 293 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 294 295 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> !~ <span class="q">/^(0|1|1.5|2|3|4|5|6|7)$/</span><span class="s">)</span> <span class="s">{</span> 296 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondOrder: BondOrder value $BondOrder is not valid. Supported values: 0, 1, 1.5, 2, 3, 4, 5, 6, 7"</span><span class="sc">;</span> 297 <span class="s">}</span> 298 299 <span class="c"># Set bond order and type...</span> 300 <span class="k">my</span><span class="s">(</span><span class="i">$BondType</span><span class="s">)</span><span class="sc">;</span> 301 302 <span class="j">BONDORDER:</span> <span class="s">{</span> 303 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Single'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 304 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1.5</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Aromatic'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 305 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Double'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 306 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Triple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 307 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">4</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Quadruple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 308 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">5</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Quintuple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 309 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">6</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Sextuple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 310 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">7</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Septuple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 311 <span class="i">$BondType</span> = <span class="q">''</span><span class="sc">;</span> 312 <span class="i">$BondOrder</span> = <span class="n">0</span><span class="sc">;</span> 313 <span class="s">}</span> 314 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="i">$BondType</span><span class="sc">;</span> 315 <span class="i">$This</span>->{<span class="w">BondOrder</span>} = <span class="i">$BondOrder</span><span class="sc">;</span> 316 317 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 318 319 <span class="s">}</span> 320 321 <span class="c"># Set bond type for a specific bond...</span> 322 <span class="c">#</span> <a name="SetBondType-"></a> 323 <span class="k">sub </span><span class="m">SetBondType</span> <span class="s">{</span> 324 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 325 326 <span class="k">if</span> <span class="s">(</span><span class="i">$BondType</span> !~ <span class="q">/^(None|Ionic|Unspecified|Single|Dative|Coordinate|SingleOrDouble|SingleOrAromatic|Aromatic|Tautomeric|Resonance|DoubleOrAromatic|Double|Triple|Quadruple|Any)$/i</span><span class="s">)</span> <span class="s">{</span> 327 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondType: BondType value $BondType is not valid. Supported values: None, Ionic, Unspecified, Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Aromatic, Tautomeric, Resonance, DoubleOrAromatic, Double, Triple, Quadruple, Any..."</span><span class="sc">;</span> 328 <span class="s">}</span> 329 330 <span class="c"># Make sure its a valid BondType value for BondOrder...</span> 331 <span class="k">my</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$ValidBondType</span><span class="s">)</span><span class="sc">;</span> 332 333 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> 334 <span class="i">$BondOrder</span> = <span class="i">$This</span>->{<span class="w">BondOrder</span>}<span class="sc">;</span> 335 336 <span class="j">BONDORDER:</span> <span class="s">{</span> 337 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">0</span> && <span class="i">$BondType</span> =~ <span class="q">/^(None|Ionic|Unspecified|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 338 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Single|Dative|Coordinate|SingleOrDouble|SingleOrAromatic|Tautomeric|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 339 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1.5</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Aromatic|Resonance|SingleOrAromatic|DoubleOrAromatic|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 340 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Double|SingleOrDouble|DoubleOrAromatic|Tautomeric|Any)$/i</span> <span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 341 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">3</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Triple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 342 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">4</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Quadruple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 343 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">5</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Quintuple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 344 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">6</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Sextuple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 345 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">7</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Septuple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 346 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> 347 <span class="s">}</span> 348 349 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ValidBondType</span><span class="s">)</span> <span class="s">{</span> 350 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetBondType: Assigning invalid BondType value, $BondType, for BondOrder $BondOrder..."</span><span class="sc">;</span> 351 <span class="s">}</span> 352 353 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="i">$BondType</span><span class="sc">;</span> 354 355 <span class="c"># Set explicit formal charge for atoms involved in Dative or coordinate bonds...</span> 356 <span class="k">if</span> <span class="s">(</span><span class="i">$BondType</span> =~ <span class="q">/^(Dative|Coordinate)$/i</span><span class="s">)</span> <span class="s">{</span> 357 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 358 <span class="i">$Atom1</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="q">'1'</span><span class="s">)</span><span class="sc">;</span> 359 <span class="i">$Atom2</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="q">'-1'</span><span class="s">)</span><span class="sc">;</span> 360 <span class="s">}</span> 361 362 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 363 <span class="s">}</span> 364 365 <span class="c"># Set bond stereochemistry...</span> 366 <span class="c">#</span> 367 <span class="c"># Single bond stereochemistry:</span> 368 <span class="c">#</span> 369 <span class="c"># None, Unspecified: Not a stereo bond or unspecified</span> 370 <span class="c">#</span> 371 <span class="c"># Wedge, Up : Wedge end pointing up</span> 372 <span class="c"># Hash, Down: Wedge end pointing down</span> 373 <span class="c"># Wavy, WedgeOrHash, UpOrDown: Wedge end up or down</span> 374 <span class="c">#</span> 375 <span class="c"># Note: Wedge starts at begin atom of bond making wedge pointed end always at this</span> 376 <span class="c"># atom.</span> 377 <span class="c">#</span> 378 <span class="c"># Upward: Single bond around cis/trans double bonds pointing upward</span> 379 <span class="c"># Downward: Single bond around cis/trans double bonds pointing upward</span> 380 <span class="c">#</span> 381 <span class="c"># Note: Upward/downward bonds start at atoms involved in cis/trans double bond.</span> 382 <span class="c">#</span> 383 <span class="c"># Double bond stereochemistry:</span> 384 <span class="c">#</span> 385 <span class="c"># None, Unspecified: Not a stereo bond or unspecified</span> 386 <span class="c">#</span> 387 <span class="c"># Z, cis: Similar groups on same side of double bond</span> 388 <span class="c"># E, trans: Similar groups on different side of double bond</span> 389 <span class="c">#</span> 390 <span class="c"># CisOrTrans, DoubleCross: cis or trans</span> 391 <span class="c">#</span> <a name="SetBondStereochemistry-"></a> 392 <span class="k">sub </span><span class="m">SetBondStereochemistry</span> <span class="s">{</span> 393 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondStereochemistry</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 394 395 <span class="k">if</span> <span class="s">(</span><span class="i">$BondStereochemistry</span> !~ <span class="q">/^(None|Unspecified|Wedge|Hash|Up|Down|Wavy|WedgeOrHash|UpOrDown|Upward|Downward|Cis|Trans|Z|E|DoubleCross|CisOrTrans)$/i</span><span class="s">)</span> <span class="s">{</span> 396 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondStereochemistry: BondStereochemistry value $BondStereochemistry is not valid. Supported values: None, Unspecified, Wedge, Hash, Up, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, Cis, Trans, Z, E, DoubleCross, CisOrTrans..."</span><span class="sc">;</span> 397 <span class="s">}</span> 398 399 <span class="c"># Make sure its a valid BondStereochemistry value for BondOrder...</span> 400 <span class="k">my</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$ValidBondType</span><span class="s">)</span><span class="sc">;</span> 401 402 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> 403 <span class="i">$BondOrder</span> = <span class="i">$This</span>->{<span class="w">BondOrder</span>}<span class="sc">;</span> 404 405 <span class="j">BONDORDER:</span> <span class="s">{</span> 406 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">0</span> && <span class="i">$BondStereochemistry</span> =~ <span class="q">/^(None|Unspecified)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 407 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span> && <span class="i">$BondStereochemistry</span> =~ <span class="q">/^(Wedge|Hash|Up|Down|Wavy|WedgeOrHash|UpOrDown|Upward|Downward|None|Unspecified)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 408 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span> && <span class="i">$BondStereochemistry</span> =~ <span class="q">/^(Cis|Trans|Z|E|DoubleCross|CisOrTrans|None|Unspecified)$/i</span> <span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> 409 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> 410 <span class="s">}</span> 411 412 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ValidBondType</span><span class="s">)</span> <span class="s">{</span> 413 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetBondStereochemistry: Assigning invalid BondStereochemistry value, $BondStereochemistry, for BondOrder $BondOrder..."</span><span class="sc">;</span> 414 <span class="s">}</span> 415 416 <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} = <span class="i">$BondStereochemistry</span><span class="sc">;</span> 417 418 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 419 <span class="s">}</span> 420 421 <span class="c"># Is it a single bond?</span> <a name="IsSingle-"></a> 422 <span class="k">sub </span><span class="m">IsSingle</span> <span class="s">{</span> 423 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 424 425 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</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> 426 <span class="s">}</span> 427 428 <span class="c"># Is it a double bond?</span> <a name="IsDouble-"></a> 429 <span class="k">sub </span><span class="m">IsDouble</span> <span class="s">{</span> 430 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 431 432 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</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> 433 <span class="s">}</span> 434 435 <span class="c"># Is it a triple bond?</span> <a name="IsTriple-"></a> 436 <span class="k">sub </span><span class="m">IsTriple</span> <span class="s">{</span> 437 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 438 439 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">3</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 440 <span class="s">}</span> 441 442 <span class="c"># Is it a quadruple bond?</span> <a name="IsQuadruple-"></a> 443 <span class="k">sub </span><span class="m">IsQuadruple</span> <span class="s">{</span> 444 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 445 446 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">4</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 447 <span class="s">}</span> 448 449 <span class="c"># Is aromatic property set for the bond?</span> <a name="IsAromatic-"></a> 450 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span> 451 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 452 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span> 453 454 <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> 455 456 <span class="k">return</span> <span class="s">(</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="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">1.5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 457 <span class="s">}</span> 458 459 <span class="c"># Is it a quintuple bond?</span> <a name="IsQuintuple-"></a> 460 <span class="k">sub </span><span class="m">IsQuintuple</span> <span class="s">{</span> 461 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 462 463 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 464 <span class="s">}</span> 465 466 <span class="c"># Is it a sextuple bond?</span> <a name="IsSextuple-"></a> 467 <span class="k">sub </span><span class="m">IsSextuple</span> <span class="s">{</span> 468 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 469 470 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">6</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 471 <span class="s">}</span> 472 473 <span class="c"># Is bond type specified?</span> <a name="IsBondTypeSpecified-"></a> 474 <span class="k">sub </span><span class="m">IsBondTypeSpecified</span> <span class="s">{</span> 475 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 476 477 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} && <span class="i">$This</span>->{<span class="w">BondType</span>} !~ <span class="q">/^(None|Unspecified)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 478 <span class="s">}</span> 479 480 <span class="c"># Is it a dative or coordinate bond?</span> <a name="IsDative-"></a> 481 <span class="k">sub </span><span class="m">IsDative</span> <span class="s">{</span> 482 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 483 484 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^(Dative|Coordinate)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 485 <span class="s">}</span> 486 487 <span class="c"># Is it a dative or coordinate bond?</span> <a name="IsCoordinate-"></a> 488 <span class="k">sub </span><span class="m">IsCoordinate</span> <span class="s">{</span> 489 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 490 491 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsDative</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 492 <span class="s">}</span> 493 494 <span class="c"># Is it a ionic bond?</span> <a name="IsIonic-"></a> 495 <span class="k">sub </span><span class="m">IsIonic</span> <span class="s">{</span> 496 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 497 498 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^Ionic$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 499 <span class="s">}</span> 500 501 <span class="c"># Is it a tautomeric bond?</span> <a name="IsTautomeric-"></a> 502 <span class="k">sub </span><span class="m">IsTautomeric</span> <span class="s">{</span> 503 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 504 505 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^Tautomeric$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 506 <span class="s">}</span> 507 508 <span class="c"># Is bond stereochemistry specified?</span> <a name="IsBondStereochemistrySpecified-"></a> 509 <span class="k">sub </span><span class="m">IsBondStereochemistrySpecified</span> <span class="s">{</span> 510 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 511 512 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} && <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} !~ <span class="q">/^(None|Unspecified)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 513 <span class="s">}</span> 514 515 <span class="c"># Is it a Wedge or Up single bond?</span> <a name="IsWedge-"></a> 516 <span class="k">sub </span><span class="m">IsWedge</span> <span class="s">{</span> 517 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 518 519 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUp</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 520 <span class="s">}</span> 521 522 <span class="c"># Is it a Wedge or Up single bond?</span> <a name="IsUp-"></a> 523 <span class="k">sub </span><span class="m">IsUp</span> <span class="s">{</span> 524 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 525 526 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Wedge|Up)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 527 <span class="s">}</span> 528 529 <span class="c"># Is it a Hash or Down single bond?</span> <a name="IsHash-"></a> 530 <span class="k">sub </span><span class="m">IsHash</span> <span class="s">{</span> 531 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 532 533 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsDown</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 534 <span class="s">}</span> 535 536 <span class="c"># Is it a Hash or Down single bond?</span> <a name="IsDown-"></a> 537 <span class="k">sub </span><span class="m">IsDown</span> <span class="s">{</span> 538 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 539 540 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Hash|Down)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 541 <span class="s">}</span> 542 543 <span class="c"># Is it a Wavy, WedgeOrHash or UpOrDown single bond?</span> <a name="IsWedgeOrHash-"></a> 544 <span class="k">sub </span><span class="m">IsWedgeOrHash</span> <span class="s">{</span> 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 546 547 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUpOrDown</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 548 <span class="s">}</span> 549 550 <span class="c"># Is it a Wavy, WedgeOrHash or UpOrDown single bond?</span> <a name="IsUpOrDown-"></a> 551 <span class="k">sub </span><span class="m">IsUpOrDown</span> <span class="s">{</span> 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 553 554 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Wavy|WedgeOrHash|UpOrDown)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 555 <span class="s">}</span> 556 557 <span class="c"># Is it a upward single bond?</span> <a name="IsUpward-"></a> 558 <span class="k">sub </span><span class="m">IsUpward</span> <span class="s">{</span> 559 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 560 561 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^Upward$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 562 <span class="s">}</span> 563 564 <span class="c"># Is it a Downward single bond?</span> <a name="IsDownward-"></a> 565 <span class="k">sub </span><span class="m">IsDownward</span> <span class="s">{</span> 566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 567 568 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^Downward$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 569 <span class="s">}</span> 570 <span class="c"># Is it a cis or Z double bond?</span> <a name="IsCis-"></a> 571 <span class="k">sub </span><span class="m">IsCis</span> <span class="s">{</span> 572 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 573 574 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Cis|Z)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 575 <span class="s">}</span> 576 577 <span class="c"># Is it a trans or E double bond?</span> <a name="IsTrans-"></a> 578 <span class="k">sub </span><span class="m">IsTrans</span> <span class="s">{</span> 579 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 580 581 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Trans|E)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 582 <span class="s">}</span> 583 584 <span class="c"># Is it a cis or trans double bond?</span> <a name="IsCisOrTrans-"></a> 585 <span class="k">sub </span><span class="m">IsCisOrTrans</span> <span class="s">{</span> 586 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 587 588 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(CisOrTrans|DoubleCross)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 589 <span class="s">}</span> 590 591 <span class="c"># Delete bond...</span> <a name="DeleteBond-"></a> 592 <span class="k">sub </span><span class="m">DeleteBond</span> <span class="s">{</span> 593 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 594 595 <span class="c"># Is this atom in a molecule?</span> 596 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 597 <span class="c"># Nothing to do...</span> 598 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 599 <span class="s">}</span> 600 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 601 <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> 602 <span class="i">$Molecule</span><span class="i">->DeleteBond</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 603 604 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 605 <span class="s">}</span> 606 607 <span class="c"># Copy bond and all its associated data...</span> <a name="Copy-"></a> 608 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span> 609 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 610 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 611 612 <span class="i">$Bond</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 613 614 <span class="k">return</span> <span class="i">$Bond</span><span class="sc">;</span> 615 <span class="s">}</span> 616 617 <span class="c"># Is bond in a ring?</span> 618 <span class="c">#</span> <a name="IsInRing-"></a> 619 <span class="k">sub </span><span class="m">IsInRing</span> <span class="s">{</span> 620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 621 622 <span class="c"># Is this bond in a molecule?</span> 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 624 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 625 <span class="s">}</span> 626 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 627 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 628 629 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 630 <span class="s">}</span> 631 632 <span class="c"># Is bond not in a ring?</span> 633 <span class="c">#</span> <a name="IsNotInRing-"></a> 634 <span class="k">sub </span><span class="m">IsNotInRing</span> <span class="s">{</span> 635 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 636 637 <span class="c"># Is this bond in a molecule?</span> 638 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 639 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 640 <span class="s">}</span> 641 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 642 <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> 643 644 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondNotInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 645 <span class="s">}</span> 646 647 <span class="c"># Is bond only in one ring?</span> 648 <span class="c">#</span> <a name="IsOnlyInOneRing-"></a> 649 <span class="k">sub </span><span class="m">IsOnlyInOneRing</span> <span class="s">{</span> 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 651 652 <span class="c"># Is this bond in a molecule?</span> 653 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 654 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 655 <span class="s">}</span> 656 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 657 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 658 659 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInOnlyOneRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 660 <span class="s">}</span> 661 662 <span class="c"># Is bond in a ring of specific size?</span> 663 <span class="c">#</span> <a name="IsInRingOfSize-"></a> 664 <span class="k">sub </span><span class="m">IsInRingOfSize</span> <span class="s">{</span> 665 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 666 667 <span class="c"># Is this bond in a molecule?</span> 668 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 669 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 670 <span class="s">}</span> 671 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 672 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 673 674 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInRingOfSize</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> 675 <span class="s">}</span> 676 677 <span class="c"># Get size of smallest ring containing the bond...</span> 678 <span class="c">#</span> <a name="GetSizeOfSmallestRing-"></a> 679 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span> 680 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 681 682 <span class="c"># Is this bond in a molecule?</span> 683 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 684 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 685 <span class="s">}</span> 686 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 687 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 688 689 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfSmallestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 690 <span class="s">}</span> 691 692 <span class="c"># Get size of largest ring containing the bond...</span> 693 <span class="c">#</span> <a name="GetSizeOfLargestRing-"></a> 694 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span> 695 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 696 697 <span class="c"># Is this bond in a molecule?</span> 698 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 699 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 700 <span class="s">}</span> 701 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 702 <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> 703 704 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfLargestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 705 <span class="s">}</span> 706 707 <span class="c"># Get number of rings containing the bond...</span> 708 <span class="c">#</span> <a name="GetNumOfRings-"></a> 709 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span> 710 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 711 712 <span class="c"># Is this bond in a molecule?</span> 713 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 714 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 715 <span class="s">}</span> 716 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 717 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 718 719 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 720 <span class="s">}</span> 721 722 <span class="c"># Get number of rings with odd size containing the bond...</span> 723 <span class="c">#</span> <a name="GetNumOfRingsWithOddSize-"></a> 724 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span> 725 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 726 727 <span class="c"># Is this bond in a molecule?</span> 728 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 729 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 730 <span class="s">}</span> 731 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 732 <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> 733 734 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 735 <span class="s">}</span> 736 737 <span class="c"># Get number of rings with even size containing the bond...</span> 738 <span class="c">#</span> <a name="GetNumOfRingsWithEvenSize-"></a> 739 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span> 740 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 741 742 <span class="c"># Is this bond in a molecule?</span> 743 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 744 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 745 <span class="s">}</span> 746 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 747 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 748 749 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 750 <span class="s">}</span> 751 752 <span class="c"># Get number of rings with specified size containing the bond...</span> 753 <span class="c">#</span> <a name="GetNumOfRingsWithSize-"></a> 754 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span> 755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 756 757 <span class="c"># Is this bond in a molecule?</span> 758 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 759 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 760 <span class="s">}</span> 761 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 762 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 763 764 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithSize</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> 765 <span class="s">}</span> 766 767 <span class="c"># Get number of rings with size less than specified containing the bond...</span> 768 <span class="c">#</span> <a name="GetNumOfRingsWithSizeLessThan-"></a> 769 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span> 770 <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> 771 772 <span class="c"># Is this bond in a molecule?</span> 773 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 774 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 775 <span class="s">}</span> 776 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 777 <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> 778 779 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 780 <span class="s">}</span> 781 782 <span class="c"># Get number of rings with size greater than specified size containing the bond...</span> 783 <span class="c">#</span> <a name="GetNumOfRingsWithSizeGreaterThan-"></a> 784 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span> 785 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 786 787 <span class="c"># Is this bond in a molecule?</span> 788 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 789 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 790 <span class="s">}</span> 791 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 792 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 793 794 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithSizeGreaterThan</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> 795 <span class="s">}</span> 796 797 <span class="c"># Get all rings as an array of references to arrays containing ring atoms...</span> 798 <span class="c">#</span> <a name="GetRings-"></a> 799 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span> 800 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 801 802 <span class="c"># Is this bond in a molecule?</span> 803 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 804 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 805 <span class="s">}</span> 806 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 807 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 808 809 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 810 <span class="s">}</span> 811 812 <span class="c"># Get smallest ring as an array containing ring atoms...</span> 813 <span class="c">#</span> <a name="GetSmallestRing-"></a> 814 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span> 815 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 816 817 <span class="c"># Is this bond in a molecule?</span> 818 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 819 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 820 <span class="s">}</span> 821 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 822 <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> 823 824 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSmallestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 825 <span class="s">}</span> 826 827 <span class="c"># Get largest ring as an array containing ring atoms...</span> 828 <span class="c">#</span> <a name="GetLargestRing-"></a> 829 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span> 830 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 831 832 <span class="c"># Is this bond in a molecule?</span> 833 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 834 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 835 <span class="s">}</span> 836 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 837 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 838 839 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetLargestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 840 <span class="s">}</span> 841 842 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> 843 <span class="c">#</span> <a name="GetRingsWithOddSize-"></a> 844 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span> 845 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 846 847 <span class="c"># Is this bond in a molecule?</span> 848 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 849 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 850 <span class="s">}</span> 851 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 852 <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> 853 854 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 855 <span class="s">}</span> 856 857 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span> 858 <span class="c">#</span> <a name="GetRingsWithEvenSize-"></a> 859 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span> 860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 861 862 <span class="c"># Is this bond in a molecule?</span> 863 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 864 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 865 <span class="s">}</span> 866 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 867 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 868 869 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 870 <span class="s">}</span> 871 872 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span> 873 <span class="c">#</span> <a name="GetRingsWithSize-"></a> 874 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span> 875 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 876 877 <span class="c"># Is this bond in a molecule?</span> 878 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 879 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 880 <span class="s">}</span> 881 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 882 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 883 884 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithSize</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> 885 <span class="s">}</span> 886 887 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> 888 <span class="c">#</span> <a name="GetRingsWithSizeLessThan-"></a> 889 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span> 890 <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> 891 892 <span class="c"># Is this bond in a molecule?</span> 893 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 894 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 895 <span class="s">}</span> 896 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 897 <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> 898 899 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 900 <span class="s">}</span> 901 902 <span class="c"># Get rings with size greater than specfied size as an array of references to arrays containing ring atoms...</span> 903 <span class="c">#</span> <a name="GetRingsWithSizeGreaterThan-"></a> 904 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span> 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 906 907 <span class="c"># Is this bond in a molecule?</span> 908 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 909 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 910 <span class="s">}</span> 911 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 912 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 913 914 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithSizeGreaterThan</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> 915 <span class="s">}</span> 916 917 <span class="c"># Get next object ID...</span> <a name="_GetNewObjectID-"></a> 918 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span> 919 <span class="i">$ObjectID</span>++<span class="sc">;</span> 920 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span> 921 <span class="s">}</span> 922 923 <span class="c"># Return a string containing bond and other properties...</span> <a name="StringifyBond-"></a> 924 <span class="k">sub </span><span class="m">StringifyBond</span> <span class="s">{</span> 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 926 <span class="k">my</span><span class="s">(</span><span class="i">$BondString</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="cm">,</span> <span class="i">$AtomsString</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$AromaticBond</span><span class="cm">,</span> <span class="i">$NumOfRings</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 927 928 <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> 929 <span class="i">$BondOrder</span> = <span class="i">$This</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 930 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span> 931 <span class="i">$BondOrder</span> = <span class="q">"undefined"</span><span class="sc">;</span> 932 <span class="s">}</span> 933 <span class="i">$BondType</span> = <span class="i">$This</span><span class="i">->GetBondType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 934 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span> 935 <span class="i">$BondType</span> = <span class="q">"undefined"</span><span class="sc">;</span> 936 <span class="s">}</span> 937 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span> && <span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 938 <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> 939 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Stereochemistry</span><span class="s">)</span> <span class="s">{</span> 940 <span class="i">$Stereochemistry</span> = <span class="q">"undefined"</span><span class="sc">;</span> 941 <span class="s">}</span> 942 <span class="s">}</span> 943 <span class="i">$RingBond</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 944 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$RingBond</span><span class="s">)</span> <span class="s">{</span> 945 <span class="i">$RingBond</span> = <span class="i">$RingBond</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> 946 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 947 <span class="s">}</span> 948 <span class="k">else</span> <span class="s">{</span> 949 <span class="i">$RingBond</span> = <span class="q">'undefined'</span><span class="sc">;</span> 950 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span> 951 <span class="s">}</span> 952 953 <span class="i">$AromaticBond</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 954 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticBond</span><span class="s">)</span> <span class="s">{</span> 955 <span class="i">$AromaticBond</span> = <span class="i">$AromaticBond</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> 956 <span class="s">}</span> 957 <span class="k">else</span> <span class="s">{</span> 958 <span class="i">$AromaticBond</span> = <span class="q">'undefined'</span><span class="sc">;</span> 959 <span class="s">}</span> 960 961 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 962 <span class="i">$AtomsString</span> = <span class="q">"Atoms: undefined"</span><span class="sc">;</span> 963 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 964 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">@BondAtoms</span><span class="s">)</span><span class="sc">;</span> 965 <span class="i">@BondAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 966 <span class="k">push</span> <span class="i">@BondAtoms</span><span class="cm">,</span> <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 967 <span class="i">$AtomCount</span> = <span class="n">0</span><span class="sc">;</span> 968 <span class="i">$AtomsString</span> = <span class="q">""</span><span class="sc">;</span> 969 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@BondAtoms</span><span class="s">)</span> <span class="s">{</span> 970 <span class="i">$AtomCount</span>++<span class="sc">;</span> 971 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 972 <span class="i">$AtomName</span> = <span class="i">$Atom</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 973 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 974 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 975 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomCount</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 976 <span class="i">$AtomsString</span> .= <span class="q">"FirstAtom:"</span><span class="sc">;</span> 977 <span class="s">}</span> 978 <span class="k">else</span> <span class="s">{</span> 979 <span class="i">$AtomsString</span> .= <span class="q">"; SecondAtom:"</span><span class="sc">;</span> 980 <span class="s">}</span> 981 <span class="i">$AtomsString</span> .= <span class="q">" [ ID: $AtomID; Name: \"$AtomName\"; AtomSymbol: \"$AtomSymbol\"; AtomicNumber: $AtomicNumber ]"</span><span class="sc">;</span> 982 <span class="s">}</span> 983 <span class="s">}</span> 984 <span class="i">$BondString</span> = <span class="q">"Bond: ID: $ID; BondOrder: $BondOrder; BondType: $BondType; RingBond: $RingBond; NumOfBondRings: $NumOfRings; AromaticBond: $AromaticBond;"</span><span class="sc">;</span> 985 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span> && <span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 986 <span class="i">$BondString</span> .= <span class="q">" Stereochemistry: $Stereochemistry;"</span><span class="sc">;</span> 987 <span class="s">}</span> 988 <span class="i">$BondString</span> .= <span class="q">" $AtomsString"</span><span class="sc">;</span> 989 990 <span class="k">return</span> <span class="i">$BondString</span><span class="sc">;</span> 991 <span class="s">}</span> 992 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>