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<html> <head> <title>MayaChemTools:Code:MolecularDescriptors::RotatableBondsDescriptors.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-MolecularDescriptors::RotatableBondsDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::RotatableBondsDescriptors</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: RotatableBondsDescriptors.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> 5 <span class="c"># $Revision: 1.18 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> 37 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> 39 40 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span> 43 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> 45 46 <span class="c"># Setup class variables...</span> 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> 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 49 50 <span class="c"># Overload Perl functions...</span> 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> 52 53 <span class="c"># Class constructor...</span> <a name="new-"></a> 54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 55 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 56 57 <span class="c"># Initialize object...</span> 58 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 59 <span class="k">bless</span> <span class="i">$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> 60 <span class="i">$This</span><span class="i">->_InitializeRotatableBondsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 61 62 <span class="i">$This</span><span class="i">->_InitializeRotatableBondsDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 63 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 65 <span class="s">}</span> 66 67 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 68 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 69 <span class="c">#Class name...</span> 70 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 71 72 <span class="c"># Descriptor names...</span> 73 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'RotatableBonds'</span><span class="s">)</span><span class="sc">;</span> 74 75 <span class="s">}</span> 76 77 <span class="c"># Get descriptor names as an array.</span> 78 <span class="c">#</span> 79 <span class="c"># This functionality can be either invoked as a class function or an</span> 80 <span class="c"># object method.</span> 81 <span class="c">#</span> <a name="GetDescriptorNames-"></a> 82 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> 83 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> 84 <span class="s">}</span> 85 86 <span class="c"># Initialize object data...</span> 87 <span class="c">#</span> <a name="_InitializeRotatableBondsDescriptors-"></a> 88 <span class="k">sub </span><span class="m">_InitializeRotatableBondsDescriptors</span> <span class="s">{</span> 89 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 90 91 <span class="c"># Type of MolecularDescriptor...</span> 92 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'RotatableBonds'</span><span class="sc">;</span> 93 94 <span class="c"># MayaChemTools rotatable bonds default definition corresponds to modifed</span> 95 <span class="c"># version of rotatable bonds definition used by Veber et al. [ Ref 92 ]</span> 96 <span class="c">#</span> 97 <span class="i">$This</span>->{<span class="w">IgnoreTerminalBonds</span>} = <span class="n">1</span><span class="sc">;</span> 98 <span class="i">$This</span>->{<span class="w">IgnoreBondsToTripleBonds</span>} = <span class="n">1</span><span class="sc">;</span> 99 <span class="i">$This</span>->{<span class="w">IgnoreAmideBonds</span>} = <span class="n">1</span><span class="sc">;</span> 100 <span class="i">$This</span>->{<span class="w">IgnoreThioamideBonds</span>} = <span class="n">1</span><span class="sc">;</span> 101 <span class="i">$This</span>->{<span class="w">IgnoreSulfonamideBonds</span>} = <span class="n">1</span><span class="sc">;</span> 102 103 <span class="c"># Intialize descriptor names and values...</span> 104 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> 105 106 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 107 <span class="s">}</span> 108 109 <span class="c"># Initialize object properties...</span> 110 <span class="c">#</span> <a name="_InitializeRotatableBondsDescriptorsProperties-"></a> 111 <span class="k">sub </span><span class="m">_InitializeRotatableBondsDescriptorsProperties</span> <span class="s">{</span> 112 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 113 114 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> 115 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 116 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 117 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 118 <span class="s">}</span> 119 120 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 121 <span class="s">}</span> 122 123 <span class="c"># Calculate number of rotatable bonds in a molecule...</span> 124 <span class="c">#</span> 125 <span class="c"># A rotatable bond is defined as any single bond which is not in a ring</span> 126 <span class="c"># and involves only non-hydrogen atoms. By default, the following types</span> 127 <span class="c"># of single bonds are not considered rotatable bonds:</span> 128 <span class="c">#</span> 129 <span class="c"># . Terminal bonds</span> 130 <span class="c"># . Bonds attached to triple bonds</span> 131 <span class="c"># . Amide C-N bonds</span> 132 <span class="c"># . Thioamide C-N bond bonds</span> 133 <span class="c"># . Sulfonamide S-N bonds</span> 134 <span class="c">#</span> 135 <span class="c"># MayaChemTools rotatable bonds default definition corresponds to modifed</span> 136 <span class="c"># version of rotatable bonds definition used by Veber et al. [ Ref 92 ]</span> 137 <span class="c">#</span> <a name="GenerateDescriptors-"></a> 138 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> 139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 140 141 <span class="c"># Initialize descriptor values...</span> 142 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 143 144 <span class="c"># Check availability of molecule...</span> 145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 146 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> 147 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 148 <span class="s">}</span> 149 150 <span class="c"># Calculate descriptor values...</span> 151 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 152 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate RotatableBonds values..."</span><span class="sc">;</span> 153 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 154 <span class="s">}</span> 155 156 <span class="c"># Set final descriptor values...</span> 157 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 158 159 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 160 <span class="s">}</span> 161 162 <span class="c"># Calculate RotatableBonds value...</span> 163 <span class="c">#</span> <a name="_CalculateDescriptorValues-"></a> 164 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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> 167 168 <span class="i">$RotatableBonds</span> = <span class="n">0</span><span class="sc">;</span> 169 170 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 171 <span class="c"># Is it a non-ring ring bond?</span> 172 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Bond</span><span class="i">->IsSingle</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 173 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 174 <span class="s">}</span> 175 176 <span class="s">(</span><span class="i">$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> 177 178 <span class="c"># Does bond contain any Hydrogen atoms?</span> 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> 180 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 181 <span class="s">}</span> 182 183 <span class="c"># Check for terminal bonds...</span> 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> 185 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 186 <span class="s">}</span> 187 188 <span class="c"># Check for bonds attached to triple bonds...</span> 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> 190 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 191 <span class="s">}</span> 192 193 <span class="c"># Check for amide bonds...</span> 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> 195 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 196 <span class="s">}</span> 197 198 <span class="c"># Check for amide bonds...</span> 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> 200 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 201 <span class="s">}</span> 202 203 <span class="c"># Check for sulfonamide bonds...</span> 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> 205 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 206 <span class="s">}</span> 207 208 <span class="i">$RotatableBonds</span> += <span class="n">1</span><span class="sc">;</span> 209 <span class="s">}</span> 210 211 <span class="c"># Track the calculated values...</span> 212 <span class="i">$This</span>->{<span class="w">RotatableBonds</span>} = <span class="i">$RotatableBonds</span><span class="sc">;</span> 213 214 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 215 <span class="s">}</span> 216 217 <span class="c"># Is it a terminal bond?</span> 218 <span class="c">#</span> <a name="_IsTerminalBond-"></a> 219 <span class="k">sub </span><span class="m">_IsTerminalBond</span> <span class="s">{</span> 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">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 221 222 <span class="k">return</span> <span class="s">(</span><span class="i">$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">$Atom2</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> <= <span class="n">1</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 223 <span class="s">}</span> 224 225 <span class="c"># Is it attached to a terminal bond?</span> 226 <span class="c">#</span> <a name="_IsAttachedToTripleBond-"></a> 227 <span class="k">sub </span><span class="m">_IsAttachedToTripleBond</span> <span class="s">{</span> 228 <span class="k">my</span><span class="s">(</span><span class="i">$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> 229 230 <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> 231 <span class="s">}</span> 232 233 <span class="c"># Is it an amide bond?</span> 234 <span class="c">#</span> 235 <span class="c"># Amide: R-C(=O)-N(-R)(-R")</span> 236 <span class="c">#</span> <a name="_IsAmideBond-"></a> 237 <span class="k">sub </span><span class="m">_IsAmideBond</span> <span class="s">{</span> 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">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 239 <span class="k">my</span><span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span> 240 241 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> 242 243 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 244 <span class="s">(</span><span class="i">$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">$Atom2</span><span class="s">)</span><span class="sc">;</span> 245 <span class="s">}</span> 246 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 247 <span class="s">(</span><span class="i">$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">$Atom1</span><span class="s">)</span><span class="sc">;</span> 248 <span class="s">}</span> 249 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CarbonAtom</span><span class="s">)</span> <span class="s">{</span> 251 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 252 <span class="s">}</span> 253 254 <span class="k">return</span> <span class="i">$CarbonAtom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'C.T3.DB1'</span><span class="cm">,</span> <span class="s">[</span><span class="q">'O'</span><span class="cm">,</span> <span class="q">'N'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">]</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 255 <span class="s">}</span> 256 257 <span class="c"># Is it a thioamide bond?</span> 258 <span class="c">#</span> 259 <span class="c"># Thioamide: R-C(=S)-N(-R)(-R")</span> 260 <span class="c">#</span> <a name="_IsThioamideBond-"></a> 261 <span class="k">sub </span><span class="m">_IsThioamideBond</span> <span class="s">{</span> 262 <span class="k">my</span><span class="s">(</span><span class="i">$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> 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> 264 265 <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> 266 267 <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> 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> 269 <span class="s">}</span> 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> 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> 272 <span class="s">}</span> 273 274 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CarbonAtom</span><span class="s">)</span> <span class="s">{</span> 275 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 276 <span class="s">}</span> 277 278 <span class="k">return</span> <span class="i">$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> 279 <span class="s">}</span> 280 281 <span class="c"># Is it a sulfonamide bond?</span> 282 <span class="c">#</span> 283 <span class="c"># Sulfonamide: R-S(=O)(=O)-N(-R)(-R")</span> 284 <span class="c">#</span> <a name="_IsSulfonamideBond-"></a> 285 <span class="k">sub </span><span class="m">_IsSulfonamideBond</span> <span class="s">{</span> 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">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 287 <span class="k">my</span><span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span> 288 289 <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> 290 291 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsSulfur</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 292 <span class="s">(</span><span class="i">$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">$Atom2</span><span class="s">)</span><span class="sc">;</span> 293 <span class="s">}</span> 294 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">->IsSulfur</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 295 <span class="s">(</span><span class="i">$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">$Atom1</span><span class="s">)</span><span class="sc">;</span> 296 <span class="s">}</span> 297 298 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SulfurAtom</span><span class="s">)</span> <span class="s">{</span> 299 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 300 <span class="s">}</span> 301 302 <span class="k">return</span> <span class="i">$SulfurAtom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'S.T4.DB2'</span><span class="cm">,</span> <span class="s">[</span><span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'N'</span><span class="cm">,</span> <span class="q">'!O'</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">'='</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">]</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 303 <span class="s">}</span> 304 305 <span class="c"># Setup final descriptor values...</span> 306 <span class="c">#</span> <a name="_SetFinalDescriptorValues-"></a> 307 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> 308 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 309 310 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 311 312 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">RotatableBonds</span>}<span class="s">)</span><span class="sc">;</span> 313 314 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 315 <span class="s">}</span> 316 317 <span class="c"># Return a string containg data for RotatableBondsDescriptors object...</span> 318 <span class="c">#</span> <a name="StringifyRotatableBondsDescriptors-"></a> 319 <span class="k">sub </span><span class="m">StringifyRotatableBondsDescriptors</span> <span class="s">{</span> 320 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 321 <span class="k">my</span><span class="s">(</span><span class="i">$RotatableBondsDescriptorsString</span><span class="s">)</span><span class="sc">;</span> 322 323 <span class="c"># Type of MolecularDescriptors...</span> 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> 325 326 <span class="c"># Setup molecular descriptor information...</span> 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> 328 329 <span class="k">return</span> <span class="i">$RotatableBondsDescriptorsString</span><span class="sc">;</span> 330 <span class="s">}</span> 331 332 <span class="c"># Is it a RotatableBondsDescriptors object?</span> <a name="_IsRotatableBondsDescriptors-"></a> 333 <span class="k">sub </span><span class="m">_IsRotatableBondsDescriptors</span> <span class="s">{</span> 334 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 335 336 <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> 337 <span class="s">}</span> 338 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>