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comparison docs/modules/html/code/RotatableBondsDescriptors.html @ 1:2abf0d43254d draft
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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:MolecularDescriptors::RotatableBondsDescriptors.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"> | |
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| 8 <br/> | |
| 9 <center> | |
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| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-MolecularDescriptors::RotatableBondsDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::RotatableBondsDescriptors</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: RotatableBondsDescriptors.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> | |
| 18 5 <span class="c"># $Revision: 1.18 $</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">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> | |
| 50 37 | |
| 51 38 <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> | |
| 52 39 | |
| 53 40 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> | |
| 54 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 55 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span> | |
| 56 43 | |
| 57 44 <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> | |
| 58 45 | |
| 59 46 <span class="c"># Setup class variables...</span> | |
| 60 47 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 61 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 62 49 | |
| 63 50 <span class="c"># Overload Perl functions...</span> | |
| 64 51 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyRotatableBondsDescriptors'</span><span class="sc">;</span> | |
| 65 52 | |
| 66 53 <span class="c"># Class constructor...</span> | |
| 67 <a name="new-"></a> 54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 68 55 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 69 56 | |
| 70 57 <span class="c"># Initialize object...</span> | |
| 71 58 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 72 59 <span class="k">bless</span> <span class="i">$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> | |
| 73 60 <span class="i">$This</span><span class="i">->_InitializeRotatableBondsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 74 61 | |
| 75 62 <span class="i">$This</span><span class="i">->_InitializeRotatableBondsDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 76 63 | |
| 77 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 78 65 <span class="s">}</span> | |
| 79 66 | |
| 80 67 <span class="c"># Initialize class ...</span> | |
| 81 <a name="_InitializeClass-"></a> 68 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 82 69 <span class="c">#Class name...</span> | |
| 83 70 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 84 71 | |
| 85 72 <span class="c"># Descriptor names...</span> | |
| 86 73 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'RotatableBonds'</span><span class="s">)</span><span class="sc">;</span> | |
| 87 74 | |
| 88 75 <span class="s">}</span> | |
| 89 76 | |
| 90 77 <span class="c"># Get descriptor names as an array.</span> | |
| 91 78 <span class="c">#</span> | |
| 92 79 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 93 80 <span class="c"># object method.</span> | |
| 94 81 <span class="c">#</span> | |
| 95 <a name="GetDescriptorNames-"></a> 82 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> | |
| 96 83 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
| 97 84 <span class="s">}</span> | |
| 98 85 | |
| 99 86 <span class="c"># Initialize object data...</span> | |
| 100 87 <span class="c">#</span> | |
| 101 <a name="_InitializeRotatableBondsDescriptors-"></a> 88 <span class="k">sub </span><span class="m">_InitializeRotatableBondsDescriptors</span> <span class="s">{</span> | |
| 102 89 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 103 90 | |
| 104 91 <span class="c"># Type of MolecularDescriptor...</span> | |
| 105 92 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'RotatableBonds'</span><span class="sc">;</span> | |
| 106 93 | |
| 107 94 <span class="c"># MayaChemTools rotatable bonds default definition corresponds to modifed</span> | |
| 108 95 <span class="c"># version of rotatable bonds definition used by Veber et al. [ Ref 92 ]</span> | |
| 109 96 <span class="c">#</span> | |
| 110 97 <span class="i">$This</span>->{<span class="w">IgnoreTerminalBonds</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 111 98 <span class="i">$This</span>->{<span class="w">IgnoreBondsToTripleBonds</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 112 99 <span class="i">$This</span>->{<span class="w">IgnoreAmideBonds</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 113 100 <span class="i">$This</span>->{<span class="w">IgnoreThioamideBonds</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 114 101 <span class="i">$This</span>->{<span class="w">IgnoreSulfonamideBonds</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 115 102 | |
| 116 103 <span class="c"># Intialize descriptor names and values...</span> | |
| 117 104 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 118 105 | |
| 119 106 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 120 107 <span class="s">}</span> | |
| 121 108 | |
| 122 109 <span class="c"># Initialize object properties...</span> | |
| 123 110 <span class="c">#</span> | |
| 124 <a name="_InitializeRotatableBondsDescriptorsProperties-"></a> 111 <span class="k">sub </span><span class="m">_InitializeRotatableBondsDescriptorsProperties</span> <span class="s">{</span> | |
| 125 112 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 126 113 | |
| 127 114 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 128 115 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 129 116 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 130 117 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 131 118 <span class="s">}</span> | |
| 132 119 | |
| 133 120 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 134 121 <span class="s">}</span> | |
| 135 122 | |
| 136 123 <span class="c"># Calculate number of rotatable bonds in a molecule...</span> | |
| 137 124 <span class="c">#</span> | |
| 138 125 <span class="c"># A rotatable bond is defined as any single bond which is not in a ring</span> | |
| 139 126 <span class="c"># and involves only non-hydrogen atoms. By default, the following types</span> | |
| 140 127 <span class="c"># of single bonds are not considered rotatable bonds:</span> | |
| 141 128 <span class="c">#</span> | |
| 142 129 <span class="c"># . Terminal bonds</span> | |
| 143 130 <span class="c"># . Bonds attached to triple bonds</span> | |
| 144 131 <span class="c"># . Amide C-N bonds</span> | |
| 145 132 <span class="c"># . Thioamide C-N bond bonds</span> | |
| 146 133 <span class="c"># . Sulfonamide S-N bonds</span> | |
| 147 134 <span class="c">#</span> | |
| 148 135 <span class="c"># MayaChemTools rotatable bonds default definition corresponds to modifed</span> | |
| 149 136 <span class="c"># version of rotatable bonds definition used by Veber et al. [ Ref 92 ]</span> | |
| 150 137 <span class="c">#</span> | |
| 151 <a name="GenerateDescriptors-"></a> 138 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> | |
| 152 139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 153 140 | |
| 154 141 <span class="c"># Initialize descriptor values...</span> | |
| 155 142 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 156 143 | |
| 157 144 <span class="c"># Check availability of molecule...</span> | |
| 158 145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
| 159 146 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> | |
| 160 147 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 161 148 <span class="s">}</span> | |
| 162 149 | |
| 163 150 <span class="c"># Calculate descriptor values...</span> | |
| 164 151 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 165 152 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate RotatableBonds values..."</span><span class="sc">;</span> | |
| 166 153 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 167 154 <span class="s">}</span> | |
| 168 155 | |
| 169 156 <span class="c"># Set final descriptor values...</span> | |
| 170 157 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 171 158 | |
| 172 159 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 173 160 <span class="s">}</span> | |
| 174 161 | |
| 175 162 <span class="c"># Calculate RotatableBonds value...</span> | |
| 176 163 <span class="c">#</span> | |
| 177 <a name="_CalculateDescriptorValues-"></a> 164 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> | |
| 178 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 179 166 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RotatableBonds</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> | |
| 180 167 | |
| 181 168 <span class="i">$RotatableBonds</span> = <span class="n">0</span><span class="sc">;</span> | |
| 182 169 | |
| 183 170 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 184 171 <span class="c"># Is it a non-ring ring bond?</span> | |
| 185 172 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Bond</span><span class="i">->IsSingle</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 186 173 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 187 174 <span class="s">}</span> | |
| 188 175 | |
| 189 176 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 190 177 | |
| 191 178 <span class="c"># Does bond contain any Hydrogen atoms?</span> | |
| 192 179 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Atom2</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 193 180 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 194 181 <span class="s">}</span> | |
| 195 182 | |
| 196 183 <span class="c"># Check for terminal bonds...</span> | |
| 197 184 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreTerminalBonds</span>} && <span class="i">$This</span><span class="i">->_IsTerminalBond</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="s">)</span> <span class="s">{</span> | |
| 198 185 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 199 186 <span class="s">}</span> | |
| 200 187 | |
| 201 188 <span class="c"># Check for bonds attached to triple bonds...</span> | |
| 202 189 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreBondsToTripleBonds</span>} && <span class="i">$This</span><span class="i">->_IsAttachedToTripleBond</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="s">)</span> <span class="s">{</span> | |
| 203 190 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 204 191 <span class="s">}</span> | |
| 205 192 | |
| 206 193 <span class="c"># Check for amide bonds...</span> | |
| 207 194 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreAmideBonds</span>} && <span class="i">$This</span><span class="i">->_IsAmideBond</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="s">)</span> <span class="s">{</span> | |
| 208 195 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 209 196 <span class="s">}</span> | |
| 210 197 | |
| 211 198 <span class="c"># Check for amide bonds...</span> | |
| 212 199 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreThioamideBonds</span>} && <span class="i">$This</span><span class="i">->_IsThioamideBond</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="s">)</span> <span class="s">{</span> | |
| 213 200 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 214 201 <span class="s">}</span> | |
| 215 202 | |
| 216 203 <span class="c"># Check for sulfonamide bonds...</span> | |
| 217 204 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreSulfonamideBonds</span>} && <span class="i">$This</span><span class="i">->_IsSulfonamideBond</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="s">)</span> <span class="s">{</span> | |
| 218 205 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 219 206 <span class="s">}</span> | |
| 220 207 | |
| 221 208 <span class="i">$RotatableBonds</span> += <span class="n">1</span><span class="sc">;</span> | |
| 222 209 <span class="s">}</span> | |
| 223 210 | |
| 224 211 <span class="c"># Track the calculated values...</span> | |
| 225 212 <span class="i">$This</span>->{<span class="w">RotatableBonds</span>} = <span class="i">$RotatableBonds</span><span class="sc">;</span> | |
| 226 213 | |
| 227 214 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 228 215 <span class="s">}</span> | |
| 229 216 | |
| 230 217 <span class="c"># Is it a terminal bond?</span> | |
| 231 218 <span class="c">#</span> | |
| 232 <a name="_IsTerminalBond-"></a> 219 <span class="k">sub </span><span class="m">_IsTerminalBond</span> <span class="s">{</span> | |
| 233 220 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 234 221 | |
| 235 222 <span class="k">return</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> <= <span class="n">1</span> || <span class="i">$Atom2</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> <= <span class="n">1</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 236 223 <span class="s">}</span> | |
| 237 224 | |
| 238 225 <span class="c"># Is it attached to a terminal bond?</span> | |
| 239 226 <span class="c">#</span> | |
| 240 <a name="_IsAttachedToTripleBond-"></a> 227 <span class="k">sub </span><span class="m">_IsAttachedToTripleBond</span> <span class="s">{</span> | |
| 241 228 <span class="k">my</span><span class="s">(</span><span class="i">$This</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="i">@_</span><span class="sc">;</span> | |
| 242 229 | |
| 243 230 <span class="k">return</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'LBO'</span><span class="s">)</span> == <span class="n">3</span> || <span class="i">$Atom2</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'LBO'</span><span class="s">)</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> | |
| 244 231 <span class="s">}</span> | |
| 245 232 | |
| 246 233 <span class="c"># Is it an amide bond?</span> | |
| 247 234 <span class="c">#</span> | |
| 248 235 <span class="c"># Amide: R-C(=O)-N(-R)(-R")</span> | |
| 249 236 <span class="c">#</span> | |
| 250 <a name="_IsAmideBond-"></a> 237 <span class="k">sub </span><span class="m">_IsAmideBond</span> <span class="s">{</span> | |
| 251 238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 252 239 <span class="k">my</span><span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span> | |
| 253 240 | |
| 254 241 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 255 242 | |
| 256 243 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 257 244 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 258 245 <span class="s">}</span> | |
| 259 246 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 260 247 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span> | |
| 261 248 <span class="s">}</span> | |
| 262 249 | |
| 263 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CarbonAtom</span><span class="s">)</span> <span class="s">{</span> | |
| 264 251 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 265 252 <span class="s">}</span> | |
| 266 253 | |
| 267 254 <span class="k">return</span> <span class="i">$CarbonAtom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'C.T3.DB1'</span><span class="cm">,</span> <span class="s">[</span><span class="q">'O'</span><span class="cm">,</span> <span class="q">'N'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">]</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 268 255 <span class="s">}</span> | |
| 269 256 | |
| 270 257 <span class="c"># Is it a thioamide bond?</span> | |
| 271 258 <span class="c">#</span> | |
| 272 259 <span class="c"># Thioamide: R-C(=S)-N(-R)(-R")</span> | |
| 273 260 <span class="c">#</span> | |
| 274 <a name="_IsThioamideBond-"></a> 261 <span class="k">sub </span><span class="m">_IsThioamideBond</span> <span class="s">{</span> | |
| 275 262 <span class="k">my</span><span class="s">(</span><span class="i">$This</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="i">@_</span><span class="sc">;</span> | |
| 276 263 <span class="k">my</span><span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span> | |
| 277 264 | |
| 278 265 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 279 266 | |
| 280 267 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 281 268 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</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> | |
| 282 269 <span class="s">}</span> | |
| 283 270 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 284 271 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span> | |
| 285 272 <span class="s">}</span> | |
| 286 273 | |
| 287 274 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CarbonAtom</span><span class="s">)</span> <span class="s">{</span> | |
| 288 275 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 289 276 <span class="s">}</span> | |
| 290 277 | |
| 291 278 <span class="k">return</span> <span class="i">$CarbonAtom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'C.T3.DB1'</span><span class="cm">,</span> <span class="s">[</span><span class="q">'S'</span><span class="cm">,</span> <span class="q">'N'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">]</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 292 279 <span class="s">}</span> | |
| 293 280 | |
| 294 281 <span class="c"># Is it a sulfonamide bond?</span> | |
| 295 282 <span class="c">#</span> | |
| 296 283 <span class="c"># Sulfonamide: R-S(=O)(=O)-N(-R)(-R")</span> | |
| 297 284 <span class="c">#</span> | |
| 298 <a name="_IsSulfonamideBond-"></a> 285 <span class="k">sub </span><span class="m">_IsSulfonamideBond</span> <span class="s">{</span> | |
| 299 286 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 300 287 <span class="k">my</span><span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span> | |
| 301 288 | |
| 302 289 <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 303 290 | |
| 304 291 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsSulfur</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 305 292 <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 306 293 <span class="s">}</span> | |
| 307 294 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">->IsSulfur</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 308 295 <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span> | |
| 309 296 <span class="s">}</span> | |
| 310 297 | |
| 311 298 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SulfurAtom</span><span class="s">)</span> <span class="s">{</span> | |
| 312 299 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 313 300 <span class="s">}</span> | |
| 314 301 | |
| 315 302 <span class="k">return</span> <span class="i">$SulfurAtom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'S.T4.DB2'</span><span class="cm">,</span> <span class="s">[</span><span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'N'</span><span class="cm">,</span> <span class="q">'!O'</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">'='</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">]</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 316 303 <span class="s">}</span> | |
| 317 304 | |
| 318 305 <span class="c"># Setup final descriptor values...</span> | |
| 319 306 <span class="c">#</span> | |
| 320 <a name="_SetFinalDescriptorValues-"></a> 307 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> | |
| 321 308 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 322 309 | |
| 323 310 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 324 311 | |
| 325 312 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">RotatableBonds</span>}<span class="s">)</span><span class="sc">;</span> | |
| 326 313 | |
| 327 314 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 328 315 <span class="s">}</span> | |
| 329 316 | |
| 330 317 <span class="c"># Return a string containg data for RotatableBondsDescriptors object...</span> | |
| 331 318 <span class="c">#</span> | |
| 332 <a name="StringifyRotatableBondsDescriptors-"></a> 319 <span class="k">sub </span><span class="m">StringifyRotatableBondsDescriptors</span> <span class="s">{</span> | |
| 333 320 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 334 321 <span class="k">my</span><span class="s">(</span><span class="i">$RotatableBondsDescriptorsString</span><span class="s">)</span><span class="sc">;</span> | |
| 335 322 | |
| 336 323 <span class="c"># Type of MolecularDescriptors...</span> | |
| 337 324 <span class="i">$RotatableBondsDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; IgnoreTerminalBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreTerminalBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreBondsToTripleBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreBondsToTripleBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreAmideBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreAmideBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreThioamideBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreThioamideBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreSulfonamideBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreSulfonamideBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> | |
| 338 325 | |
| 339 326 <span class="c"># Setup molecular descriptor information...</span> | |
| 340 327 <span class="i">$RotatableBondsDescriptorsString</span> .= <span class="q">"; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 341 328 | |
| 342 329 <span class="k">return</span> <span class="i">$RotatableBondsDescriptorsString</span><span class="sc">;</span> | |
| 343 330 <span class="s">}</span> | |
| 344 331 | |
| 345 332 <span class="c"># Is it a RotatableBondsDescriptors object?</span> | |
| 346 <a name="_IsRotatableBondsDescriptors-"></a> 333 <span class="k">sub </span><span class="m">_IsRotatableBondsDescriptors</span> <span class="s">{</span> | |
| 347 334 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 348 335 | |
| 349 336 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 350 337 <span class="s">}</span> | |
| 351 338 | |
| 352 <a name="EOF-"></a></pre> | |
| 353 <p> </p> | |
| 354 <br /> | |
| 355 <center> | |
| 356 <img src="../../../images/h2o2.png"> | |
| 357 </center> | |
| 358 </body> | |
| 359 </html> |