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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/Bond.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,1013 @@ +<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>