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| date | Thu, 15 Dec 2016 14:18:03 -0500 |
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<html> <head> <title>MayaChemTools:Code:MolecularDescriptors::TPSADescriptors.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::TPSADescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::TPSADescriptors</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: TPSADescriptors.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">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> 38 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> 39 40 <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> 41 42 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> 43 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 44 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span> 45 46 <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> 47 48 <span class="c"># Setup class variables...</span> 49 <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> 50 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 51 52 <span class="c"># Overload Perl functions...</span> 53 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTPSADescriptors'</span><span class="sc">;</span> 54 55 <span class="c"># Class constructor...</span> <a name="new-"></a> 56 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 57 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 58 59 <span class="c"># Initialize object...</span> 60 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 61 <span class="k">bless</span> <span class="i">$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> 62 <span class="i">$This</span><span class="i">->_InitializeTPSADescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 63 64 <span class="i">$This</span><span class="i">->_InitializeTPSADescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 65 66 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 67 <span class="s">}</span> 68 69 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 70 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 71 <span class="c">#Class name...</span> 72 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 73 74 <span class="c"># Descriptor names...</span> 75 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'TPSA'</span><span class="s">)</span><span class="sc">;</span> 76 77 <span class="s">}</span> 78 79 <span class="c"># Get descriptor names as an array.</span> 80 <span class="c">#</span> 81 <span class="c"># This functionality can be either invoked as a class function or an</span> 82 <span class="c"># object method.</span> 83 <span class="c">#</span> <a name="GetDescriptorNames-"></a> 84 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> 85 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> 86 <span class="s">}</span> 87 88 <span class="c"># Initialize object data...</span> 89 <span class="c">#</span> <a name="_InitializeTPSADescriptors-"></a> 90 <span class="k">sub </span><span class="m">_InitializeTPSADescriptors</span> <span class="s">{</span> 91 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 92 93 <span class="c"># Type of MolecularDescriptor...</span> 94 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TPSA'</span><span class="sc">;</span> 95 96 <span class="c"># By default, TPSA atom contributions from Phosphorus and Sulfur atoms</span> 97 <span class="c"># are not included during TPSA calculations. [ Ref 91 ]</span> 98 <span class="c">#</span> 99 <span class="i">$This</span>->{<span class="w">IgnorePhosphorus</span>} = <span class="n">1</span><span class="sc">;</span> 100 <span class="i">$This</span>->{<span class="w">IgnoreSulfur</span>} = <span class="n">1</span><span class="sc">;</span> 101 102 <span class="c"># TPSA atom types assigned to appropriate atoms...</span> 103 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 104 105 <span class="c"># Intialize descriptor names and values...</span> 106 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> 107 108 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 109 <span class="s">}</span> 110 111 <span class="c"># Initialize object properties...</span> 112 <span class="c">#</span> <a name="_InitializeTPSADescriptorsProperties-"></a> 113 <span class="k">sub </span><span class="m">_InitializeTPSADescriptorsProperties</span> <span class="s">{</span> 114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 115 116 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> 117 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 118 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 119 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 120 <span class="s">}</span> 121 122 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 123 <span class="s">}</span> 124 125 <span class="c"># Calculate Topological Polar Surface Area (TPSA) value [ Ref 90-91 ] for molecule...</span> 126 <span class="c">#</span> 127 <span class="c"># Methodology:</span> 128 <span class="c"># . Assign TPSA atom types [ Ref 90-91 ] to Nitrogen and Oxygen</span> 129 <span class="c"># atoms with optional assignment to Phosphorus and Sulfur atoms.</span> 130 <span class="c"># . Calculate TPSA value adding contribution of appropriate atom types.</span> 131 <span class="c">#</span> <a name="GenerateDescriptors-"></a> 132 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> 133 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 134 135 <span class="c"># Initialize descriptor values...</span> 136 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 137 138 <span class="c"># Check availability of molecule...</span> 139 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 140 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> 141 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 142 <span class="s">}</span> 143 144 <span class="c"># Cache appropriate molecule data...</span> 145 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 146 147 <span class="c"># Assign TPSA atom types...</span> 148 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 149 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't assign valid TPSA atom types to appropriate atoms..."</span><span class="sc">;</span> 150 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 151 <span class="s">}</span> 152 153 <span class="c"># Calculate descriptor values...</span> 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 155 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate TPSA values corresponding to assigned TPSA atom types..."</span><span class="sc">;</span> 156 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 157 <span class="s">}</span> 158 159 <span class="c"># Set final descriptor values...</span> 160 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 161 162 <span class="c"># Clear cached molecule data...</span> 163 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 164 165 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 166 <span class="s">}</span> 167 168 <span class="c"># Assign TPSA atom types..</span> 169 <span class="c">#</span> <a name="_AssignAtomTypes-"></a> 170 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span> 171 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 172 <span class="k">my</span><span class="s">(</span><span class="i">$TPSAAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 173 174 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 175 176 <span class="c"># Assign atom types...</span> 177 <span class="i">$TPSAAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">IgnorePhosphorus</span>}<span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">IgnoreSulfur</span>}<span class="s">)</span><span class="sc">;</span> 178 <span class="i">$TPSAAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 179 180 <span class="c"># Make sure TPSA atom types assignment is successful...</span> 181 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TPSAAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 182 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 183 <span class="s">}</span> 184 185 <span class="c"># Collect assigned atom types...</span> 186 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 187 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 188 <span class="i">$This</span>->{<span class="w">AtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$TPSAAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 189 <span class="s">}</span> 190 191 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 192 <span class="s">}</span> 193 194 <span class="c"># Calculate TPSA value...</span> 195 <span class="c">#</span> <a name="_CalculateDescriptorValues-"></a> 196 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> 197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 198 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$TPSA</span><span class="cm">,</span> <span class="i">$TPSAContribution</span><span class="cm">,</span> <span class="i">$TPSADataRef</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="s">)</span><span class="sc">;</span> 199 200 <span class="i">$TPSA</span> = <span class="n">0</span><span class="sc">;</span> 201 202 <span class="c"># Get TPSA atom types data...</span> 203 <span class="i">$TPSADataRef</span> = <span class="i">AtomTypes::TPSAAtomTypes::GetTPSAAtomTypesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 204 205 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 206 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 207 <span class="i">$AtomType</span> = <span class="i">$This</span>->{<span class="w">AtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> 208 209 <span class="c"># Ignore inappropriate atoms...</span> 210 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> 211 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 212 <span class="s">}</span> 213 214 <span class="i">$TPSAContribution</span> = <span class="n">0.0</span><span class="sc">;</span> 215 216 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^(N|O)$/i</span><span class="s">)</span> <span class="s">{</span> 217 <span class="c"># TPSA contributions for Nitrogen and Oxygen atoms not explicity defined using atom</span> 218 <span class="c"># environments in Table 1 [ Ref 90 ]</span> 219 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^N$/i</span><span class="s">)</span> <span class="s">{</span> 220 <span class="c"># N = 30.5 - X*8.2 + H*1.5 or 0.0 for negative value</span> 221 <span class="i">$TPSAContribution</span> = <span class="n">30.5</span> - <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> * <span class="n">8.2</span> + <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span> * <span class="n">1.5</span><span class="sc">;</span> 222 <span class="s">}</span> 223 <span class="k">elsif</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^O$/i</span><span class="s">)</span> <span class="s">{</span> 224 <span class="c"># O = 28.5 - X*8.6 + H*1.5 or 0.0 for negative value</span> 225 <span class="i">$TPSAContribution</span> = <span class="n">28.5</span> - <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> * <span class="n">8.6</span> + <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span> * <span class="n">1.5</span><span class="sc">;</span> 226 <span class="s">}</span> 227 <span class="k">if</span> <span class="s">(</span><span class="i">$TPSAContribution</span> < <span class="n">0.0</span><span class="s">)</span> <span class="s">{</span> 228 <span class="i">$TPSAContribution</span> = <span class="n">0.0</span><span class="sc">;</span> 229 <span class="s">}</span> 230 <span class="s">}</span> 231 <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$TPSADataRef</span>->{<span class="w">DataCol3</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span> 232 <span class="c"># Data for TPSA contribution is in column number 3...</span> 233 <span class="i">$TPSAContribution</span> = <span class="i">$TPSADataRef</span>->{<span class="w">DataCol3</span>}{<span class="i">$AtomType</span>}<span class="sc">;</span> 234 <span class="s">}</span> 235 <span class="k">else</span> <span class="s">{</span> 236 <span class="c"># No TPSA data for assigned atom type...</span> 237 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 238 <span class="s">}</span> 239 <span class="i">$TPSA</span> += <span class="i">$TPSAContribution</span><span class="sc">;</span> 240 <span class="s">}</span> 241 242 <span class="c"># Track the calculated values...</span> 243 <span class="i">$This</span>->{<span class="w">TPSA</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$TPSA</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> 244 245 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 246 <span class="s">}</span> 247 248 <span class="c"># Setup final descriptor values...</span> 249 <span class="c">#</span> <a name="_SetFinalDescriptorValues-"></a> 250 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> 251 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 252 253 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 254 255 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">TPSA</span>}<span class="s">)</span><span class="sc">;</span> 256 257 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 258 <span class="s">}</span> 259 260 <span class="c"># Cache appropriate molecule data...</span> 261 <span class="c">#</span> <a name="_SetupMoleculeDataCache-"></a> 262 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> 263 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 264 265 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 266 267 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 268 <span class="s">}</span> 269 270 <span class="c"># Clear cached molecule data...</span> 271 <span class="c">#</span> <a name="_ClearMoleculeDataCache-"></a> 272 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> 273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 274 275 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 276 277 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 278 <span class="s">}</span> 279 280 <span class="c"># Return a string containg data for TPSADescriptors object...</span> 281 <span class="c">#</span> <a name="StringifyTPSADescriptors-"></a> 282 <span class="k">sub </span><span class="m">StringifyTPSADescriptors</span> <span class="s">{</span> 283 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 284 <span class="k">my</span><span class="s">(</span><span class="i">$TPSADescriptorsString</span><span class="s">)</span><span class="sc">;</span> 285 286 <span class="c"># Type of MolecularDescriptors...</span> 287 <span class="i">$TPSADescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; IgnorePhosphorus: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnorePhosphorus</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreSulfur: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreSulfur</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> 288 289 <span class="c"># Setup molecular descriptor information...</span> 290 <span class="i">$TPSADescriptorsString</span> .= <span class="q">"; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 291 292 <span class="k">return</span> <span class="i">$TPSADescriptorsString</span><span class="sc">;</span> 293 <span class="s">}</span> 294 295 <span class="c"># Is it a TPSADescriptors object?</span> <a name="_IsTPSADescriptors-"></a> 296 <span class="k">sub </span><span class="m">_IsTPSADescriptors</span> <span class="s">{</span> 297 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 298 299 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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> 300 <span class="s">}</span> 301 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>