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| date | Wed, 20 Jan 2016 09:10:43 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:Bond.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-Bond-"></a> 1 <span class="k">package </span><span class="i">Bond</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: Bond.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span> | |
| 18 5 <span class="c"># $Revision: 1.40 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">Storable</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> | |
| 48 35 | |
| 49 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> | |
| 50 37 | |
| 51 38 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> | |
| 52 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 53 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 54 41 | |
| 55 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> | |
| 56 43 | |
| 57 44 <span class="c"># Setup class variables...</span> | |
| 58 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="s">)</span><span class="sc">;</span> | |
| 59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 60 47 | |
| 61 48 <span class="c"># Overload Perl functions...</span> | |
| 62 49 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyBond'</span><span class="sc">;</span> | |
| 63 50 | |
| 64 51 <span class="c"># Class constructor...</span> | |
| 65 <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 66 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 67 54 | |
| 68 55 <span class="c"># Initialize object...</span> | |
| 69 56 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> | |
| 70 57 <span class="k">bless</span> <span class="i">$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> | |
| 71 58 <span class="i">$This</span><span class="i">->_InitializeBond</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 72 59 | |
| 73 60 <span class="i">$This</span><span class="i">->_InitializeBondProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 74 61 | |
| 75 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 76 63 <span class="s">}</span> | |
| 77 64 | |
| 78 65 <span class="c"># Initialize object data...</span> | |
| 79 66 <span class="c">#</span> | |
| 80 <a name="_InitializeBond-"></a> 67 <span class="k">sub </span><span class="m">_InitializeBond</span> <span class="s">{</span> | |
| 81 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 82 69 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 83 70 | |
| 84 71 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> | |
| 85 72 <span class="c"># are implemented on-demand using ObjectProperty class.</span> | |
| 86 73 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span> | |
| 87 74 | |
| 88 75 <span class="c"># Bond from and to atoms indicate begining and ending bond atoms...</span> | |
| 89 76 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 90 77 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 91 78 | |
| 92 79 <span class="i">$This</span>->{<span class="w">BondOrder</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 93 80 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 94 81 <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 95 82 <span class="s">}</span> | |
| 96 83 | |
| 97 84 <span class="c"># Initialize class ...</span> | |
| 98 <a name="_InitializeClass-"></a> 85 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 99 86 <span class="c">#Class name...</span> | |
| 100 87 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 101 88 | |
| 102 89 <span class="c"># ID to keep track of objects...</span> | |
| 103 90 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span> | |
| 104 91 <span class="s">}</span> | |
| 105 92 | |
| 106 93 <span class="c"># Initialize bond properties...</span> | |
| 107 <a name="_InitializeBondProperties-"></a> 94 <span class="k">sub </span><span class="m">_InitializeBondProperties</span> <span class="s">{</span> | |
| 108 95 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 109 96 | |
| 110 97 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 111 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> | |
| 112 99 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 113 100 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 114 101 <span class="s">}</span> | |
| 115 102 | |
| 116 103 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'Atoms'</span>}<span class="s">)</span> <span class="s">{</span> | |
| 117 104 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Bond object instantiated without specifying atoms list..."</span><span class="sc">;</span> | |
| 118 105 <span class="s">}</span> | |
| 119 106 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'BondOrder'</span>}<span class="s">)</span> <span class="s">{</span> | |
| 120 107 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Bond object instantiated without setting bond order..."</span><span class="sc">;</span> | |
| 121 108 <span class="s">}</span> | |
| 122 109 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 123 110 <span class="s">}</span> | |
| 124 111 | |
| 125 112 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span> | |
| 126 <a name="SetID-"></a> 113 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span> | |
| 127 114 <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> | |
| 128 115 | |
| 129 116 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> | |
| 130 117 | |
| 131 118 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 132 119 <span class="s">}</span> | |
| 133 120 | |
| 134 121 <span class="c"># Setup an explicit SetMolecule method to block setting of ID by AUTOLOAD function...</span> | |
| 135 <a name="SetMolecule-"></a> 122 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> | |
| 136 123 <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> | |
| 137 124 | |
| 138 125 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMolecule: Molecule property can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> | |
| 139 126 | |
| 140 127 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 141 128 <span class="s">}</span> | |
| 142 129 | |
| 143 130 <span class="c"># Assign bond to molecule...</span> | |
| 144 <a name="_SetMolecule-"></a> 131 <span class="k">sub </span><span class="m">_SetMolecule</span> <span class="s">{</span> | |
| 145 132 <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> | |
| 146 133 | |
| 147 134 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> | |
| 148 135 | |
| 149 136 <span class="c"># Weaken the reference to disable increment of reference count; otherwise,</span> | |
| 150 137 <span class="c"># it it becomes a circular reference and destruction of Molecule object doesn't</span> | |
| 151 138 <span class="c"># get initiated which in turn disables destruction of bond object.</span> | |
| 152 139 <span class="c">#</span> | |
| 153 140 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
| 154 141 | |
| 155 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 156 143 <span class="s">}</span> | |
| 157 144 | |
| 158 145 <span class="c"># Set bond atoms...</span> | |
| 159 <a name="SetAtoms-"></a> 146 <span class="k">sub </span><span class="m">SetAtoms</span> <span class="s">{</span> | |
| 160 147 <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> | |
| 161 148 | |
| 162 149 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 163 150 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtoms: No atoms specified..."</span><span class="sc">;</span> | |
| 164 151 <span class="s">}</span> | |
| 165 152 | |
| 166 153 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 167 154 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 168 155 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 169 156 | |
| 170 157 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 171 158 <span class="c"># Initialize using array refernce...</span> | |
| 172 159 <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> | |
| 173 160 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Number of atoms specified in bond object is not equal to 2..."</span><span class="sc">;</span> | |
| 174 161 <span class="s">}</span> | |
| 175 162 <span class="s">(</span><span class="i">$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> | |
| 176 163 <span class="s">}</span> | |
| 177 164 <span class="k">else</span> <span class="s">{</span> | |
| 178 165 <span class="c"># It's a list of values...</span> | |
| 179 166 <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> | |
| 180 167 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Number of atoms specified in bond object is not equal to 2..."</span><span class="sc">;</span> | |
| 181 168 <span class="s">}</span> | |
| 182 169 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@Values</span><span class="sc">;</span> | |
| 183 170 <span class="s">}</span> | |
| 184 171 | |
| 185 172 <span class="i">$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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 186 173 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$AtomID2</span><span class="s">)</span> <span class="s">{</span> | |
| 187 174 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Can't specify same atoms to create a bond..."</span><span class="sc">;</span> | |
| 188 175 <span class="s">}</span> | |
| 189 176 | |
| 190 177 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="i">$Atom1</span><span class="sc">;</span> | |
| 191 178 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="i">$Atom2</span><span class="sc">;</span> | |
| 192 179 | |
| 193 180 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 194 181 <span class="s">}</span> | |
| 195 182 | |
| 196 183 <span class="c"># Get bond atoms as array. In scalar context, return number of atoms involved in</span> | |
| 197 184 <span class="c"># bond...</span> | |
| 198 185 <span class="c">#</span> | |
| 199 <a name="GetAtoms-"></a> 186 <span class="k">sub </span><span class="m">GetAtoms</span> <span class="s">{</span> | |
| 200 187 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 201 188 | |
| 202 189 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondFromAtom</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">BondToAtom</span>}<span class="s">)</span> <span class="co">:</span> <span class="n">2</span><span class="sc">;</span> | |
| 203 190 <span class="s">}</span> | |
| 204 191 | |
| 205 192 <span class="c"># Get atom bonded to specified atom...</span> | |
| 206 <a name="GetBondedAtom-"></a> 193 <span class="k">sub </span><span class="m">GetBondedAtom</span> <span class="s">{</span> | |
| 207 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 208 195 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 209 196 | |
| 210 197 <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">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 211 198 <span class="i">$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">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 212 199 | |
| 213 200 <span class="k">return</span> <span class="s">(</span><span class="i">$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">$Atom1</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="sc">;</span> | |
| 214 201 <span class="s">}</span> | |
| 215 202 | |
| 216 203 <span class="c"># Get common atom between two bonds...</span> | |
| 217 <a name="GetCommonAtom-"></a> 204 <span class="k">sub </span><span class="m">GetCommonAtom</span> <span class="s">{</span> | |
| 218 205 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 219 206 <span class="k">my</span><span class="s">(</span><span class="i">$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">$OtherAtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 220 207 | |
| 221 208 <span class="s">(</span><span class="i">$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> | |
| 222 209 <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> | |
| 223 210 | |
| 224 211 <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">$Other</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 225 212 <span class="i">$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">$OtherAtom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 226 213 | |
| 227 214 <span class="k">return</span> <span class="s">(</span><span class="i">$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">$Atom2</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="sc">;</span> | |
| 228 215 <span class="s">}</span> | |
| 229 216 | |
| 230 217 <span class="c"># Get bond from atom indicating begining atom of a bond...</span> | |
| 231 <a name="GetBondFromAtom-"></a> 218 <span class="k">sub </span><span class="m">GetBondFromAtom</span> <span class="s">{</span> | |
| 232 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 233 220 | |
| 234 221 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">BondFromAtom</span>}<span class="sc">;</span> | |
| 235 222 <span class="s">}</span> | |
| 236 223 | |
| 237 224 <span class="c"># Get begin bond atom...</span> | |
| 238 <a name="GetBondBeginAtom-"></a> 225 <span class="k">sub </span><span class="m">GetBondBeginAtom</span> <span class="s">{</span> | |
| 239 226 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 240 227 | |
| 241 228 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondFromAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 242 229 <span class="s">}</span> | |
| 243 230 | |
| 244 231 <span class="c"># Get bond to atom indicating ending atom of a bond...</span> | |
| 245 <a name="GetBondToAtom-"></a> 232 <span class="k">sub </span><span class="m">GetBondToAtom</span> <span class="s">{</span> | |
| 246 233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 247 234 | |
| 248 235 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">BondToAtom</span>}<span class="sc">;</span> | |
| 249 236 <span class="s">}</span> | |
| 250 237 | |
| 251 238 <span class="c"># Get begin bond atom...</span> | |
| 252 <a name="GetBondEndAtom-"></a> 239 <span class="k">sub </span><span class="m">GetBondEndAtom</span> <span class="s">{</span> | |
| 253 240 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 254 241 | |
| 255 242 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 256 243 <span class="s">}</span> | |
| 257 244 | |
| 258 245 <span class="c"># Switch bond from and to atoms...</span> | |
| 259 <a name="SwitchBondFromAndToAtoms-"></a> 246 <span class="k">sub </span><span class="m">SwitchBondFromAndToAtoms</span> <span class="s">{</span> | |
| 260 247 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 261 248 <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> | |
| 262 249 | |
| 263 250 <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">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 264 251 | |
| 265 252 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="i">$ToAtom</span><span class="sc">;</span> | |
| 266 253 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="i">$FromAtom</span><span class="sc">;</span> | |
| 267 254 | |
| 268 255 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 269 256 <span class="s">}</span> | |
| 270 257 | |
| 271 258 <span class="c"># Set bond order...</span> | |
| 272 259 <span class="c">#</span> | |
| 273 260 <span class="c"># Possible BondOrder are: 0 = None, 1 = Single, 1.5 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple,</span> | |
| 274 261 <span class="c"># 5 = Quintuple, 6 = Sextuple, 7 = Septuple</span> | |
| 275 262 <span class="c">#</span> | |
| 276 263 <span class="c"># Possible BondType for different BondOrders are:</span> | |
| 277 264 <span class="c">#</span> | |
| 278 265 <span class="c"># 0 : None, Ionic, Unspecified</span> | |
| 279 266 <span class="c"># 1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric</span> | |
| 280 267 <span class="c"># 1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic</span> | |
| 281 268 <span class="c"># 2 : Double, Tautomeric, SingleOrDouble, DoubleOrAromatic</span> | |
| 282 269 <span class="c"># 3 : Triple</span> | |
| 283 270 <span class="c"># 4 : Quadruple</span> | |
| 284 271 <span class="c"># 5 : Quintuple</span> | |
| 285 272 <span class="c"># 6 : Sextuple</span> | |
| 286 273 <span class="c"># 7 : Septuple</span> | |
| 287 274 <span class="c">#</span> | |
| 288 275 <span class="c"># Note: BondType Any is valid for all BondOrders.</span> | |
| 289 276 <span class="c">#</span> | |
| 290 277 <span class="c"># Possible BondStereochemistry values for different BondOrders are:</span> | |
| 291 278 <span class="c">#</span> | |
| 292 279 <span class="c"># 0 : None, Unspecified</span> | |
| 293 280 <span class="c"># 1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, None, Unspecified</span> | |
| 294 281 <span class="c"># 2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified</span> | |
| 295 282 <span class="c">#</span> | |
| 296 283 <span class="c"># Notes:</span> | |
| 297 284 <span class="c"># . BondType property is automatically assigned using default BondType values for</span> | |
| 298 285 <span class="c"># specified BondOrder.</span> | |
| 299 286 <span class="c"># . BondType values can also be explicit set.</span> | |
| 300 287 <span class="c"># . To make bonds aromatic in a ring, explicitly set "Aromatic" property for bond/atoms and make sure</span> | |
| 301 288 <span class="c"># appropriate BondOrder values are assigned.</span> | |
| 302 289 <span class="c"># . Dative or coordinate bond types are treated as single bond types with explicit formal charge</span> | |
| 303 290 <span class="c"># of + and - on first and second bond atoms.</span> | |
| 304 291 <span class="c">#</span> | |
| 305 <a name="SetBondOrder-"></a> 292 <span class="k">sub </span><span class="m">SetBondOrder</span> <span class="s">{</span> | |
| 306 293 <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> | |
| 307 294 | |
| 308 295 <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> | |
| 309 296 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondOrder: BondOrder value $BondOrder is not valid. Supported values: 0, 1, 1.5, 2, 3, 4, 5, 6, 7"</span><span class="sc">;</span> | |
| 310 297 <span class="s">}</span> | |
| 311 298 | |
| 312 299 <span class="c"># Set bond order and type...</span> | |
| 313 300 <span class="k">my</span><span class="s">(</span><span class="i">$BondType</span><span class="s">)</span><span class="sc">;</span> | |
| 314 301 | |
| 315 302 <span class="j">BONDORDER:</span> <span class="s">{</span> | |
| 316 303 <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> | |
| 317 304 <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> | |
| 318 305 <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> | |
| 319 306 <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> | |
| 320 307 <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> | |
| 321 308 <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> | |
| 322 309 <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> | |
| 323 310 <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> | |
| 324 311 <span class="i">$BondType</span> = <span class="q">''</span><span class="sc">;</span> | |
| 325 312 <span class="i">$BondOrder</span> = <span class="n">0</span><span class="sc">;</span> | |
| 326 313 <span class="s">}</span> | |
| 327 314 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="i">$BondType</span><span class="sc">;</span> | |
| 328 315 <span class="i">$This</span>->{<span class="w">BondOrder</span>} = <span class="i">$BondOrder</span><span class="sc">;</span> | |
| 329 316 | |
| 330 317 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 331 318 | |
| 332 319 <span class="s">}</span> | |
| 333 320 | |
| 334 321 <span class="c"># Set bond type for a specific bond...</span> | |
| 335 322 <span class="c">#</span> | |
| 336 <a name="SetBondType-"></a> 323 <span class="k">sub </span><span class="m">SetBondType</span> <span class="s">{</span> | |
| 337 324 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 338 325 | |
| 339 326 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 340 327 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondType: BondType value $BondType is not valid. Supported values: None, Ionic, Unspecified, Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Aromatic, Tautomeric, Resonance, DoubleOrAromatic, Double, Triple, Quadruple, Any..."</span><span class="sc">;</span> | |
| 341 328 <span class="s">}</span> | |
| 342 329 | |
| 343 330 <span class="c"># Make sure its a valid BondType value for BondOrder...</span> | |
| 344 331 <span class="k">my</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$ValidBondType</span><span class="s">)</span><span class="sc">;</span> | |
| 345 332 | |
| 346 333 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> | |
| 347 334 <span class="i">$BondOrder</span> = <span class="i">$This</span>->{<span class="w">BondOrder</span>}<span class="sc">;</span> | |
| 348 335 | |
| 349 336 <span class="j">BONDORDER:</span> <span class="s">{</span> | |
| 350 337 <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> | |
| 351 338 <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> | |
| 352 339 <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> | |
| 353 340 <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> | |
| 354 341 <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> | |
| 355 342 <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> | |
| 356 343 <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> | |
| 357 344 <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> | |
| 358 345 <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> | |
| 359 346 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> | |
| 360 347 <span class="s">}</span> | |
| 361 348 | |
| 362 349 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ValidBondType</span><span class="s">)</span> <span class="s">{</span> | |
| 363 350 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetBondType: Assigning invalid BondType value, $BondType, for BondOrder $BondOrder..."</span><span class="sc">;</span> | |
| 364 351 <span class="s">}</span> | |
| 365 352 | |
| 366 353 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="i">$BondType</span><span class="sc">;</span> | |
| 367 354 | |
| 368 355 <span class="c"># Set explicit formal charge for atoms involved in Dative or coordinate bonds...</span> | |
| 369 356 <span class="k">if</span> <span class="s">(</span><span class="i">$BondType</span> =~ <span class="q">/^(Dative|Coordinate)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 370 357 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 371 358 <span class="i">$Atom1</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="q">'1'</span><span class="s">)</span><span class="sc">;</span> | |
| 372 359 <span class="i">$Atom2</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="q">'-1'</span><span class="s">)</span><span class="sc">;</span> | |
| 373 360 <span class="s">}</span> | |
| 374 361 | |
| 375 362 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 376 363 <span class="s">}</span> | |
| 377 364 | |
| 378 365 <span class="c"># Set bond stereochemistry...</span> | |
| 379 366 <span class="c">#</span> | |
| 380 367 <span class="c"># Single bond stereochemistry:</span> | |
| 381 368 <span class="c">#</span> | |
| 382 369 <span class="c"># None, Unspecified: Not a stereo bond or unspecified</span> | |
| 383 370 <span class="c">#</span> | |
| 384 371 <span class="c"># Wedge, Up : Wedge end pointing up</span> | |
| 385 372 <span class="c"># Hash, Down: Wedge end pointing down</span> | |
| 386 373 <span class="c"># Wavy, WedgeOrHash, UpOrDown: Wedge end up or down</span> | |
| 387 374 <span class="c">#</span> | |
| 388 375 <span class="c"># Note: Wedge starts at begin atom of bond making wedge pointed end always at this</span> | |
| 389 376 <span class="c"># atom.</span> | |
| 390 377 <span class="c">#</span> | |
| 391 378 <span class="c"># Upward: Single bond around cis/trans double bonds pointing upward</span> | |
| 392 379 <span class="c"># Downward: Single bond around cis/trans double bonds pointing upward</span> | |
| 393 380 <span class="c">#</span> | |
| 394 381 <span class="c"># Note: Upward/downward bonds start at atoms involved in cis/trans double bond.</span> | |
| 395 382 <span class="c">#</span> | |
| 396 383 <span class="c"># Double bond stereochemistry:</span> | |
| 397 384 <span class="c">#</span> | |
| 398 385 <span class="c"># None, Unspecified: Not a stereo bond or unspecified</span> | |
| 399 386 <span class="c">#</span> | |
| 400 387 <span class="c"># Z, cis: Similar groups on same side of double bond</span> | |
| 401 388 <span class="c"># E, trans: Similar groups on different side of double bond</span> | |
| 402 389 <span class="c">#</span> | |
| 403 390 <span class="c"># CisOrTrans, DoubleCross: cis or trans</span> | |
| 404 391 <span class="c">#</span> | |
| 405 <a name="SetBondStereochemistry-"></a> 392 <span class="k">sub </span><span class="m">SetBondStereochemistry</span> <span class="s">{</span> | |
| 406 393 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondStereochemistry</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 407 394 | |
| 408 395 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 409 396 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondStereochemistry: BondStereochemistry value $BondStereochemistry is not valid. Supported values: None, Unspecified, Wedge, Hash, Up, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, Cis, Trans, Z, E, DoubleCross, CisOrTrans..."</span><span class="sc">;</span> | |
| 410 397 <span class="s">}</span> | |
| 411 398 | |
| 412 399 <span class="c"># Make sure its a valid BondStereochemistry value for BondOrder...</span> | |
| 413 400 <span class="k">my</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$ValidBondType</span><span class="s">)</span><span class="sc">;</span> | |
| 414 401 | |
| 415 402 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> | |
| 416 403 <span class="i">$BondOrder</span> = <span class="i">$This</span>->{<span class="w">BondOrder</span>}<span class="sc">;</span> | |
| 417 404 | |
| 418 405 <span class="j">BONDORDER:</span> <span class="s">{</span> | |
| 419 406 <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> | |
| 420 407 <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> | |
| 421 408 <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> | |
| 422 409 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> | |
| 423 410 <span class="s">}</span> | |
| 424 411 | |
| 425 412 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ValidBondType</span><span class="s">)</span> <span class="s">{</span> | |
| 426 413 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetBondStereochemistry: Assigning invalid BondStereochemistry value, $BondStereochemistry, for BondOrder $BondOrder..."</span><span class="sc">;</span> | |
| 427 414 <span class="s">}</span> | |
| 428 415 | |
| 429 416 <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} = <span class="i">$BondStereochemistry</span><span class="sc">;</span> | |
| 430 417 | |
| 431 418 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 432 419 <span class="s">}</span> | |
| 433 420 | |
| 434 421 <span class="c"># Is it a single bond?</span> | |
| 435 <a name="IsSingle-"></a> 422 <span class="k">sub </span><span class="m">IsSingle</span> <span class="s">{</span> | |
| 436 423 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 437 424 | |
| 438 425 <span class="k">return</span> <span class="s">(</span><span class="i">$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> | |
| 439 426 <span class="s">}</span> | |
| 440 427 | |
| 441 428 <span class="c"># Is it a double bond?</span> | |
| 442 <a name="IsDouble-"></a> 429 <span class="k">sub </span><span class="m">IsDouble</span> <span class="s">{</span> | |
| 443 430 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 444 431 | |
| 445 432 <span class="k">return</span> <span class="s">(</span><span class="i">$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> | |
| 446 433 <span class="s">}</span> | |
| 447 434 | |
| 448 435 <span class="c"># Is it a triple bond?</span> | |
| 449 <a name="IsTriple-"></a> 436 <span class="k">sub </span><span class="m">IsTriple</span> <span class="s">{</span> | |
| 450 437 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 451 438 | |
| 452 439 <span class="k">return</span> <span class="s">(</span><span class="i">$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> | |
| 453 440 <span class="s">}</span> | |
| 454 441 | |
| 455 442 <span class="c"># Is it a quadruple bond?</span> | |
| 456 <a name="IsQuadruple-"></a> 443 <span class="k">sub </span><span class="m">IsQuadruple</span> <span class="s">{</span> | |
| 457 444 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 458 445 | |
| 459 446 <span class="k">return</span> <span class="s">(</span><span class="i">$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> | |
| 460 447 <span class="s">}</span> | |
| 461 448 | |
| 462 449 <span class="c"># Is aromatic property set for the bond?</span> | |
| 463 <a name="IsAromatic-"></a> 450 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span> | |
| 464 451 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 465 452 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span> | |
| 466 453 | |
| 467 454 <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> | |
| 468 455 | |
| 469 456 <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">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">1.5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 470 457 <span class="s">}</span> | |
| 471 458 | |
| 472 459 <span class="c"># Is it a quintuple bond?</span> | |
| 473 <a name="IsQuintuple-"></a> 460 <span class="k">sub </span><span class="m">IsQuintuple</span> <span class="s">{</span> | |
| 474 461 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 475 462 | |
| 476 463 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 477 464 <span class="s">}</span> | |
| 478 465 | |
| 479 466 <span class="c"># Is it a sextuple bond?</span> | |
| 480 <a name="IsSextuple-"></a> 467 <span class="k">sub </span><span class="m">IsSextuple</span> <span class="s">{</span> | |
| 481 468 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 482 469 | |
| 483 470 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">6</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 484 471 <span class="s">}</span> | |
| 485 472 | |
| 486 473 <span class="c"># Is bond type specified?</span> | |
| 487 <a name="IsBondTypeSpecified-"></a> 474 <span class="k">sub </span><span class="m">IsBondTypeSpecified</span> <span class="s">{</span> | |
| 488 475 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 489 476 | |
| 490 477 <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 491 478 <span class="s">}</span> | |
| 492 479 | |
| 493 480 <span class="c"># Is it a dative or coordinate bond?</span> | |
| 494 <a name="IsDative-"></a> 481 <span class="k">sub </span><span class="m">IsDative</span> <span class="s">{</span> | |
| 495 482 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 496 483 | |
| 497 484 <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> | |
| 498 485 <span class="s">}</span> | |
| 499 486 | |
| 500 487 <span class="c"># Is it a dative or coordinate bond?</span> | |
| 501 <a name="IsCoordinate-"></a> 488 <span class="k">sub </span><span class="m">IsCoordinate</span> <span class="s">{</span> | |
| 502 489 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 503 490 | |
| 504 491 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsDative</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 505 492 <span class="s">}</span> | |
| 506 493 | |
| 507 494 <span class="c"># Is it a ionic bond?</span> | |
| 508 <a name="IsIonic-"></a> 495 <span class="k">sub </span><span class="m">IsIonic</span> <span class="s">{</span> | |
| 509 496 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 510 497 | |
| 511 498 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^Ionic$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 512 499 <span class="s">}</span> | |
| 513 500 | |
| 514 501 <span class="c"># Is it a tautomeric bond?</span> | |
| 515 <a name="IsTautomeric-"></a> 502 <span class="k">sub </span><span class="m">IsTautomeric</span> <span class="s">{</span> | |
| 516 503 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 517 504 | |
| 518 505 <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> | |
| 519 506 <span class="s">}</span> | |
| 520 507 | |
| 521 508 <span class="c"># Is bond stereochemistry specified?</span> | |
| 522 <a name="IsBondStereochemistrySpecified-"></a> 509 <span class="k">sub </span><span class="m">IsBondStereochemistrySpecified</span> <span class="s">{</span> | |
| 523 510 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 524 511 | |
| 525 512 <span class="k">return</span> <span class="s">(</span><span class="i">$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> | |
| 526 513 <span class="s">}</span> | |
| 527 514 | |
| 528 515 <span class="c"># Is it a Wedge or Up single bond?</span> | |
| 529 <a name="IsWedge-"></a> 516 <span class="k">sub </span><span class="m">IsWedge</span> <span class="s">{</span> | |
| 530 517 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 531 518 | |
| 532 519 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUp</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 533 520 <span class="s">}</span> | |
| 534 521 | |
| 535 522 <span class="c"># Is it a Wedge or Up single bond?</span> | |
| 536 <a name="IsUp-"></a> 523 <span class="k">sub </span><span class="m">IsUp</span> <span class="s">{</span> | |
| 537 524 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 538 525 | |
| 539 526 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Wedge|Up)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 540 527 <span class="s">}</span> | |
| 541 528 | |
| 542 529 <span class="c"># Is it a Hash or Down single bond?</span> | |
| 543 <a name="IsHash-"></a> 530 <span class="k">sub </span><span class="m">IsHash</span> <span class="s">{</span> | |
| 544 531 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 545 532 | |
| 546 533 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsDown</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 547 534 <span class="s">}</span> | |
| 548 535 | |
| 549 536 <span class="c"># Is it a Hash or Down single bond?</span> | |
| 550 <a name="IsDown-"></a> 537 <span class="k">sub </span><span class="m">IsDown</span> <span class="s">{</span> | |
| 551 538 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 552 539 | |
| 553 540 <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> | |
| 554 541 <span class="s">}</span> | |
| 555 542 | |
| 556 543 <span class="c"># Is it a Wavy, WedgeOrHash or UpOrDown single bond?</span> | |
| 557 <a name="IsWedgeOrHash-"></a> 544 <span class="k">sub </span><span class="m">IsWedgeOrHash</span> <span class="s">{</span> | |
| 558 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 559 546 | |
| 560 547 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUpOrDown</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 561 548 <span class="s">}</span> | |
| 562 549 | |
| 563 550 <span class="c"># Is it a Wavy, WedgeOrHash or UpOrDown single bond?</span> | |
| 564 <a name="IsUpOrDown-"></a> 551 <span class="k">sub </span><span class="m">IsUpOrDown</span> <span class="s">{</span> | |
| 565 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 566 553 | |
| 567 554 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Wavy|WedgeOrHash|UpOrDown)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 568 555 <span class="s">}</span> | |
| 569 556 | |
| 570 557 <span class="c"># Is it a upward single bond?</span> | |
| 571 <a name="IsUpward-"></a> 558 <span class="k">sub </span><span class="m">IsUpward</span> <span class="s">{</span> | |
| 572 559 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 573 560 | |
| 574 561 <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> | |
| 575 562 <span class="s">}</span> | |
| 576 563 | |
| 577 564 <span class="c"># Is it a Downward single bond?</span> | |
| 578 <a name="IsDownward-"></a> 565 <span class="k">sub </span><span class="m">IsDownward</span> <span class="s">{</span> | |
| 579 566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 580 567 | |
| 581 568 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^Downward$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 582 569 <span class="s">}</span> | |
| 583 570 <span class="c"># Is it a cis or Z double bond?</span> | |
| 584 <a name="IsCis-"></a> 571 <span class="k">sub </span><span class="m">IsCis</span> <span class="s">{</span> | |
| 585 572 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 586 573 | |
| 587 574 <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> | |
| 588 575 <span class="s">}</span> | |
| 589 576 | |
| 590 577 <span class="c"># Is it a trans or E double bond?</span> | |
| 591 <a name="IsTrans-"></a> 578 <span class="k">sub </span><span class="m">IsTrans</span> <span class="s">{</span> | |
| 592 579 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 593 580 | |
| 594 581 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Trans|E)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 595 582 <span class="s">}</span> | |
| 596 583 | |
| 597 584 <span class="c"># Is it a cis or trans double bond?</span> | |
| 598 <a name="IsCisOrTrans-"></a> 585 <span class="k">sub </span><span class="m">IsCisOrTrans</span> <span class="s">{</span> | |
| 599 586 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 600 587 | |
| 601 588 <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> | |
| 602 589 <span class="s">}</span> | |
| 603 590 | |
| 604 591 <span class="c"># Delete bond...</span> | |
| 605 <a name="DeleteBond-"></a> 592 <span class="k">sub </span><span class="m">DeleteBond</span> <span class="s">{</span> | |
| 606 593 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 607 594 | |
| 608 595 <span class="c"># Is this atom in a molecule?</span> | |
| 609 596 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 610 597 <span class="c"># Nothing to do...</span> | |
| 611 598 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 612 599 <span class="s">}</span> | |
| 613 600 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 614 601 <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> | |
| 615 602 <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> | |
| 616 603 | |
| 617 604 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 618 605 <span class="s">}</span> | |
| 619 606 | |
| 620 607 <span class="c"># Copy bond and all its associated data...</span> | |
| 621 <a name="Copy-"></a> 608 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span> | |
| 622 609 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 623 610 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 624 611 | |
| 625 612 <span class="i">$Bond</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 626 613 | |
| 627 614 <span class="k">return</span> <span class="i">$Bond</span><span class="sc">;</span> | |
| 628 615 <span class="s">}</span> | |
| 629 616 | |
| 630 617 <span class="c"># Is bond in a ring?</span> | |
| 631 618 <span class="c">#</span> | |
| 632 <a name="IsInRing-"></a> 619 <span class="k">sub </span><span class="m">IsInRing</span> <span class="s">{</span> | |
| 633 620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 634 621 | |
| 635 622 <span class="c"># Is this bond in a molecule?</span> | |
| 636 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 637 624 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 638 625 <span class="s">}</span> | |
| 639 626 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 640 627 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 641 628 | |
| 642 629 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 643 630 <span class="s">}</span> | |
| 644 631 | |
| 645 632 <span class="c"># Is bond not in a ring?</span> | |
| 646 633 <span class="c">#</span> | |
| 647 <a name="IsNotInRing-"></a> 634 <span class="k">sub </span><span class="m">IsNotInRing</span> <span class="s">{</span> | |
| 648 635 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 649 636 | |
| 650 637 <span class="c"># Is this bond in a molecule?</span> | |
| 651 638 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 652 639 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 653 640 <span class="s">}</span> | |
| 654 641 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 655 642 <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> | |
| 656 643 | |
| 657 644 <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> | |
| 658 645 <span class="s">}</span> | |
| 659 646 | |
| 660 647 <span class="c"># Is bond only in one ring?</span> | |
| 661 648 <span class="c">#</span> | |
| 662 <a name="IsOnlyInOneRing-"></a> 649 <span class="k">sub </span><span class="m">IsOnlyInOneRing</span> <span class="s">{</span> | |
| 663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 664 651 | |
| 665 652 <span class="c"># Is this bond in a molecule?</span> | |
| 666 653 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 667 654 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 668 655 <span class="s">}</span> | |
| 669 656 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 670 657 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 671 658 | |
| 672 659 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInOnlyOneRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 673 660 <span class="s">}</span> | |
| 674 661 | |
| 675 662 <span class="c"># Is bond in a ring of specific size?</span> | |
| 676 663 <span class="c">#</span> | |
| 677 <a name="IsInRingOfSize-"></a> 664 <span class="k">sub </span><span class="m">IsInRingOfSize</span> <span class="s">{</span> | |
| 678 665 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 679 666 | |
| 680 667 <span class="c"># Is this bond in a molecule?</span> | |
| 681 668 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 682 669 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 683 670 <span class="s">}</span> | |
| 684 671 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 685 672 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 686 673 | |
| 687 674 <span class="k">return</span> <span class="i">$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> | |
| 688 675 <span class="s">}</span> | |
| 689 676 | |
| 690 677 <span class="c"># Get size of smallest ring containing the bond...</span> | |
| 691 678 <span class="c">#</span> | |
| 692 <a name="GetSizeOfSmallestRing-"></a> 679 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span> | |
| 693 680 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 694 681 | |
| 695 682 <span class="c"># Is this bond in a molecule?</span> | |
| 696 683 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 697 684 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 698 685 <span class="s">}</span> | |
| 699 686 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 700 687 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 701 688 | |
| 702 689 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfSmallestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 703 690 <span class="s">}</span> | |
| 704 691 | |
| 705 692 <span class="c"># Get size of largest ring containing the bond...</span> | |
| 706 693 <span class="c">#</span> | |
| 707 <a name="GetSizeOfLargestRing-"></a> 694 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span> | |
| 708 695 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 709 696 | |
| 710 697 <span class="c"># Is this bond in a molecule?</span> | |
| 711 698 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 712 699 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 713 700 <span class="s">}</span> | |
| 714 701 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 715 702 <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> | |
| 716 703 | |
| 717 704 <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> | |
| 718 705 <span class="s">}</span> | |
| 719 706 | |
| 720 707 <span class="c"># Get number of rings containing the bond...</span> | |
| 721 708 <span class="c">#</span> | |
| 722 <a name="GetNumOfRings-"></a> 709 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span> | |
| 723 710 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 724 711 | |
| 725 712 <span class="c"># Is this bond in a molecule?</span> | |
| 726 713 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 727 714 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 728 715 <span class="s">}</span> | |
| 729 716 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 730 717 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 731 718 | |
| 732 719 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 733 720 <span class="s">}</span> | |
| 734 721 | |
| 735 722 <span class="c"># Get number of rings with odd size containing the bond...</span> | |
| 736 723 <span class="c">#</span> | |
| 737 <a name="GetNumOfRingsWithOddSize-"></a> 724 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span> | |
| 738 725 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 739 726 | |
| 740 727 <span class="c"># Is this bond in a molecule?</span> | |
| 741 728 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 742 729 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 743 730 <span class="s">}</span> | |
| 744 731 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 745 732 <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> | |
| 746 733 | |
| 747 734 <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> | |
| 748 735 <span class="s">}</span> | |
| 749 736 | |
| 750 737 <span class="c"># Get number of rings with even size containing the bond...</span> | |
| 751 738 <span class="c">#</span> | |
| 752 <a name="GetNumOfRingsWithEvenSize-"></a> 739 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span> | |
| 753 740 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 754 741 | |
| 755 742 <span class="c"># Is this bond in a molecule?</span> | |
| 756 743 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 757 744 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 758 745 <span class="s">}</span> | |
| 759 746 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 760 747 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 761 748 | |
| 762 749 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 763 750 <span class="s">}</span> | |
| 764 751 | |
| 765 752 <span class="c"># Get number of rings with specified size containing the bond...</span> | |
| 766 753 <span class="c">#</span> | |
| 767 <a name="GetNumOfRingsWithSize-"></a> 754 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span> | |
| 768 755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 769 756 | |
| 770 757 <span class="c"># Is this bond in a molecule?</span> | |
| 771 758 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 772 759 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 773 760 <span class="s">}</span> | |
| 774 761 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 775 762 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 776 763 | |
| 777 764 <span class="k">return</span> <span class="i">$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> | |
| 778 765 <span class="s">}</span> | |
| 779 766 | |
| 780 767 <span class="c"># Get number of rings with size less than specified containing the bond...</span> | |
| 781 768 <span class="c">#</span> | |
| 782 <a name="GetNumOfRingsWithSizeLessThan-"></a> 769 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 783 770 <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> | |
| 784 771 | |
| 785 772 <span class="c"># Is this bond in a molecule?</span> | |
| 786 773 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 787 774 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 788 775 <span class="s">}</span> | |
| 789 776 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 790 777 <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> | |
| 791 778 | |
| 792 779 <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">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 793 780 <span class="s">}</span> | |
| 794 781 | |
| 795 782 <span class="c"># Get number of rings with size greater than specified size containing the bond...</span> | |
| 796 783 <span class="c">#</span> | |
| 797 <a name="GetNumOfRingsWithSizeGreaterThan-"></a> 784 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 798 785 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 799 786 | |
| 800 787 <span class="c"># Is this bond in a molecule?</span> | |
| 801 788 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 802 789 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 803 790 <span class="s">}</span> | |
| 804 791 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 805 792 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 806 793 | |
| 807 794 <span class="k">return</span> <span class="i">$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> | |
| 808 795 <span class="s">}</span> | |
| 809 796 | |
| 810 797 <span class="c"># Get all rings as an array of references to arrays containing ring atoms...</span> | |
| 811 798 <span class="c">#</span> | |
| 812 <a name="GetRings-"></a> 799 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span> | |
| 813 800 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 814 801 | |
| 815 802 <span class="c"># Is this bond in a molecule?</span> | |
| 816 803 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 817 804 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 818 805 <span class="s">}</span> | |
| 819 806 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 820 807 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 821 808 | |
| 822 809 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 823 810 <span class="s">}</span> | |
| 824 811 | |
| 825 812 <span class="c"># Get smallest ring as an array containing ring atoms...</span> | |
| 826 813 <span class="c">#</span> | |
| 827 <a name="GetSmallestRing-"></a> 814 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span> | |
| 828 815 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 829 816 | |
| 830 817 <span class="c"># Is this bond in a molecule?</span> | |
| 831 818 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 832 819 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 833 820 <span class="s">}</span> | |
| 834 821 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 835 822 <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> | |
| 836 823 | |
| 837 824 <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> | |
| 838 825 <span class="s">}</span> | |
| 839 826 | |
| 840 827 <span class="c"># Get largest ring as an array containing ring atoms...</span> | |
| 841 828 <span class="c">#</span> | |
| 842 <a name="GetLargestRing-"></a> 829 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span> | |
| 843 830 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 844 831 | |
| 845 832 <span class="c"># Is this bond in a molecule?</span> | |
| 846 833 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 847 834 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 848 835 <span class="s">}</span> | |
| 849 836 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 850 837 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 851 838 | |
| 852 839 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetLargestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 853 840 <span class="s">}</span> | |
| 854 841 | |
| 855 842 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> | |
| 856 843 <span class="c">#</span> | |
| 857 <a name="GetRingsWithOddSize-"></a> 844 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span> | |
| 858 845 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 859 846 | |
| 860 847 <span class="c"># Is this bond in a molecule?</span> | |
| 861 848 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 862 849 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 863 850 <span class="s">}</span> | |
| 864 851 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 865 852 <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> | |
| 866 853 | |
| 867 854 <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> | |
| 868 855 <span class="s">}</span> | |
| 869 856 | |
| 870 857 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span> | |
| 871 858 <span class="c">#</span> | |
| 872 <a name="GetRingsWithEvenSize-"></a> 859 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span> | |
| 873 860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 874 861 | |
| 875 862 <span class="c"># Is this bond in a molecule?</span> | |
| 876 863 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 877 864 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 878 865 <span class="s">}</span> | |
| 879 866 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 880 867 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 881 868 | |
| 882 869 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 883 870 <span class="s">}</span> | |
| 884 871 | |
| 885 872 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span> | |
| 886 873 <span class="c">#</span> | |
| 887 <a name="GetRingsWithSize-"></a> 874 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span> | |
| 888 875 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 889 876 | |
| 890 877 <span class="c"># Is this bond in a molecule?</span> | |
| 891 878 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 892 879 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 893 880 <span class="s">}</span> | |
| 894 881 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 895 882 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 896 883 | |
| 897 884 <span class="k">return</span> <span class="i">$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> | |
| 898 885 <span class="s">}</span> | |
| 899 886 | |
| 900 887 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> | |
| 901 888 <span class="c">#</span> | |
| 902 <a name="GetRingsWithSizeLessThan-"></a> 889 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 903 890 <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> | |
| 904 891 | |
| 905 892 <span class="c"># Is this bond in a molecule?</span> | |
| 906 893 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 907 894 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 908 895 <span class="s">}</span> | |
| 909 896 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 910 897 <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> | |
| 911 898 | |
| 912 899 <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">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 913 900 <span class="s">}</span> | |
| 914 901 | |
| 915 902 <span class="c"># Get rings with size greater than specfied size as an array of references to arrays containing ring atoms...</span> | |
| 916 903 <span class="c">#</span> | |
| 917 <a name="GetRingsWithSizeGreaterThan-"></a> 904 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 918 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 919 906 | |
| 920 907 <span class="c"># Is this bond in a molecule?</span> | |
| 921 908 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 922 909 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 923 910 <span class="s">}</span> | |
| 924 911 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 925 912 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
| 926 913 | |
| 927 914 <span class="k">return</span> <span class="i">$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> | |
| 928 915 <span class="s">}</span> | |
| 929 916 | |
| 930 917 <span class="c"># Get next object ID...</span> | |
| 931 <a name="_GetNewObjectID-"></a> 918 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span> | |
| 932 919 <span class="i">$ObjectID</span>++<span class="sc">;</span> | |
| 933 920 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span> | |
| 934 921 <span class="s">}</span> | |
| 935 922 | |
| 936 923 <span class="c"># Return a string containing bond and other properties...</span> | |
| 937 <a name="StringifyBond-"></a> 924 <span class="k">sub </span><span class="m">StringifyBond</span> <span class="s">{</span> | |
| 938 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 939 926 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 940 927 | |
| 941 928 <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> | |
| 942 929 <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> | |
| 943 930 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 944 931 <span class="i">$BondOrder</span> = <span class="q">"undefined"</span><span class="sc">;</span> | |
| 945 932 <span class="s">}</span> | |
| 946 933 <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> | |
| 947 934 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 948 935 <span class="i">$BondType</span> = <span class="q">"undefined"</span><span class="sc">;</span> | |
| 949 936 <span class="s">}</span> | |
| 950 937 <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> | |
| 951 938 <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> | |
| 952 939 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Stereochemistry</span><span class="s">)</span> <span class="s">{</span> | |
| 953 940 <span class="i">$Stereochemistry</span> = <span class="q">"undefined"</span><span class="sc">;</span> | |
| 954 941 <span class="s">}</span> | |
| 955 942 <span class="s">}</span> | |
| 956 943 <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> | |
| 957 944 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$RingBond</span><span class="s">)</span> <span class="s">{</span> | |
| 958 945 <span class="i">$RingBond</span> = <span class="i">$RingBond</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> | |
| 959 946 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 960 947 <span class="s">}</span> | |
| 961 948 <span class="k">else</span> <span class="s">{</span> | |
| 962 949 <span class="i">$RingBond</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 963 950 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 964 951 <span class="s">}</span> | |
| 965 952 | |
| 966 953 <span class="i">$AromaticBond</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 967 954 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticBond</span><span class="s">)</span> <span class="s">{</span> | |
| 968 955 <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> | |
| 969 956 <span class="s">}</span> | |
| 970 957 <span class="k">else</span> <span class="s">{</span> | |
| 971 958 <span class="i">$AromaticBond</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 972 959 <span class="s">}</span> | |
| 973 960 | |
| 974 961 <span class="s">(</span><span class="i">$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> | |
| 975 962 <span class="i">$AtomsString</span> = <span class="q">"Atoms: undefined"</span><span class="sc">;</span> | |
| 976 963 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 977 964 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomicNumber</span><span class="cm">,</span> <span class="i">@BondAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 978 965 <span class="i">@BondAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 979 966 <span class="k">push</span> <span class="i">@BondAtoms</span><span class="cm">,</span> <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 980 967 <span class="i">$AtomCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 981 968 <span class="i">$AtomsString</span> = <span class="q">""</span><span class="sc">;</span> | |
| 982 969 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@BondAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 983 970 <span class="i">$AtomCount</span>++<span class="sc">;</span> | |
| 984 971 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 985 972 <span class="i">$AtomName</span> = <span class="i">$Atom</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 986 973 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 987 974 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 988 975 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomCount</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 989 976 <span class="i">$AtomsString</span> .= <span class="q">"FirstAtom:"</span><span class="sc">;</span> | |
| 990 977 <span class="s">}</span> | |
| 991 978 <span class="k">else</span> <span class="s">{</span> | |
| 992 979 <span class="i">$AtomsString</span> .= <span class="q">"; SecondAtom:"</span><span class="sc">;</span> | |
| 993 980 <span class="s">}</span> | |
| 994 981 <span class="i">$AtomsString</span> .= <span class="q">" [ ID: $AtomID; Name: \"$AtomName\"; AtomSymbol: \"$AtomSymbol\"; AtomicNumber: $AtomicNumber ]"</span><span class="sc">;</span> | |
| 995 982 <span class="s">}</span> | |
| 996 983 <span class="s">}</span> | |
| 997 984 <span class="i">$BondString</span> = <span class="q">"Bond: ID: $ID; BondOrder: $BondOrder; BondType: $BondType; RingBond: $RingBond; NumOfBondRings: $NumOfRings; AromaticBond: $AromaticBond;"</span><span class="sc">;</span> | |
| 998 985 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span> && <span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 999 986 <span class="i">$BondString</span> .= <span class="q">" Stereochemistry: $Stereochemistry;"</span><span class="sc">;</span> | |
| 1000 987 <span class="s">}</span> | |
| 1001 988 <span class="i">$BondString</span> .= <span class="q">" $AtomsString"</span><span class="sc">;</span> | |
| 1002 989 | |
| 1003 990 <span class="k">return</span> <span class="i">$BondString</span><span class="sc">;</span> | |
| 1004 991 <span class="s">}</span> | |
| 1005 992 | |
| 1006 <a name="EOF-"></a></pre> | |
| 1007 <p> </p> | |
| 1008 <br /> | |
| 1009 <center> | |
| 1010 <img src="../../../images/h2o2.png"> | |
| 1011 </center> | |
| 1012 </body> | |
| 1013 </html> |