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comparison mayachemtools/docs/modules/html/code/SLogPAndSMRDescriptors.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:MolecularDescriptors::SLogPAndSMRDescriptors.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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| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
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| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-MolecularDescriptors::SLogPAndSMRDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::SLogPAndSMRDescriptors</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: SLogPAndSMRDescriptors.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">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span> | |
| 52 39 | |
| 53 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> | |
| 54 41 | |
| 55 42 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> | |
| 56 43 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 57 44 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span> | |
| 58 45 | |
| 59 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> | |
| 60 47 | |
| 61 48 <span class="c"># Setup class variables...</span> | |
| 62 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> | |
| 63 50 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 64 51 | |
| 65 52 <span class="c"># Overload Perl functions...</span> | |
| 66 53 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifySLogPAndSMRDescriptors'</span><span class="sc">;</span> | |
| 67 54 | |
| 68 55 <span class="c"># Class constructor...</span> | |
| 69 <a name="new-"></a> 56 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 70 57 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 71 58 | |
| 72 59 <span class="c"># Initialize object...</span> | |
| 73 60 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 74 61 <span class="k">bless</span> <span class="i">$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> | |
| 75 62 <span class="i">$This</span><span class="i">->_InitializeSLogPAndSMRDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 76 63 | |
| 77 64 <span class="i">$This</span><span class="i">->_InitializeSLogPAndSMRDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 78 65 | |
| 79 66 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 80 67 <span class="s">}</span> | |
| 81 68 | |
| 82 69 <span class="c"># Initialize class ...</span> | |
| 83 <a name="_InitializeClass-"></a> 70 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 84 71 <span class="c">#Class name...</span> | |
| 85 72 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 86 73 | |
| 87 74 <span class="c"># Descriptor names...</span> | |
| 88 75 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'SLogP'</span><span class="cm">,</span> <span class="q">'SMR'</span><span class="s">)</span><span class="sc">;</span> | |
| 89 76 <span class="s">}</span> | |
| 90 77 | |
| 91 78 <span class="c"># Get descriptor names as an array.</span> | |
| 92 79 <span class="c">#</span> | |
| 93 80 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 94 81 <span class="c"># object method.</span> | |
| 95 82 <span class="c">#</span> | |
| 96 <a name="GetDescriptorNames-"></a> 83 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> | |
| 97 84 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
| 98 85 <span class="s">}</span> | |
| 99 86 | |
| 100 87 <span class="c"># Initialize object data...</span> | |
| 101 88 <span class="c">#</span> | |
| 102 <a name="_InitializeSLogPAndSMRDescriptors-"></a> 89 <span class="k">sub </span><span class="m">_InitializeSLogPAndSMRDescriptors</span> <span class="s">{</span> | |
| 103 90 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 104 91 | |
| 105 92 <span class="c"># Type of MolecularDescriptor...</span> | |
| 106 93 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'SLogPAndSMR'</span><span class="sc">;</span> | |
| 107 94 | |
| 108 95 <span class="c"># SLogPAndSMR atom types assigned to hydrogen and non-hydrogen atoms...</span> | |
| 109 96 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 110 97 | |
| 111 98 <span class="c"># Intialize descriptor names and values...</span> | |
| 112 99 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 113 100 | |
| 114 101 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 115 102 <span class="s">}</span> | |
| 116 103 | |
| 117 104 <span class="c"># Initialize object properties...</span> | |
| 118 105 <span class="c">#</span> | |
| 119 <a name="_InitializeSLogPAndSMRDescriptorsProperties-"></a> 106 <span class="k">sub </span><span class="m">_InitializeSLogPAndSMRDescriptorsProperties</span> <span class="s">{</span> | |
| 120 107 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 121 108 | |
| 122 109 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 123 110 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 124 111 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 125 112 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 126 113 <span class="s">}</span> | |
| 127 114 | |
| 128 115 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 129 116 <span class="s">}</span> | |
| 130 117 | |
| 131 118 | |
| 132 119 <span class="c"># Calculate SLogPAndSMR value [ Ref 89 ] for a molecule...</span> | |
| 133 120 <span class="c">#</span> | |
| 134 121 <span class="c"># Methodology:</span> | |
| 135 122 <span class="c"># . Assign SLogP atom types to all atoms.</span> | |
| 136 123 <span class="c"># . Calculate SLogP and SMR value by adding contribution of each atom type.</span> | |
| 137 124 <span class="c">#</span> | |
| 138 125 <span class="c"># Caveats:</span> | |
| 139 126 <span class="c"># . All hydrogens must be added to molecule before calling GenerateDescriptors.</span> | |
| 140 127 <span class="c">#</span> | |
| 141 <a name="GenerateDescriptors-"></a> 128 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> | |
| 142 129 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 143 130 | |
| 144 131 <span class="c"># Initialize descriptor values...</span> | |
| 145 132 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 146 133 | |
| 147 134 <span class="c"># Check availability of molecule...</span> | |
| 148 135 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
| 149 136 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> | |
| 150 137 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 151 138 <span class="s">}</span> | |
| 152 139 | |
| 153 140 <span class="c"># Cache appropriate molecule data...</span> | |
| 154 141 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 155 142 | |
| 156 143 <span class="c"># Assign SLogP atom types...</span> | |
| 157 144 <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> | |
| 158 145 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't assign valid SLogPAndSMR atom types to all atoms..."</span><span class="sc">;</span> | |
| 159 146 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 160 147 <span class="s">}</span> | |
| 161 148 | |
| 162 149 <span class="c"># Calculate descriptor values...</span> | |
| 163 150 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 164 151 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular description generation didn't succeed: Couldn't calculate SLogPAndSMR values corresponding to assigned SLogP atom types..."</span><span class="sc">;</span> | |
| 165 152 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 166 153 <span class="s">}</span> | |
| 167 154 | |
| 168 155 <span class="c"># Set final descriptor values...</span> | |
| 169 156 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 170 157 | |
| 171 158 <span class="c"># Clear cached molecule data...</span> | |
| 172 159 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 173 160 | |
| 174 161 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 175 162 <span class="s">}</span> | |
| 176 163 | |
| 177 164 <span class="c"># Assign SLogPAndSMR atom types..</span> | |
| 178 165 <span class="c">#</span> | |
| 179 <a name="_AssignAtomTypes-"></a> 166 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span> | |
| 180 167 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 181 168 <span class="k">my</span><span class="s">(</span><span class="i">$SLogPAtomTypes</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> | |
| 182 169 | |
| 183 170 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 184 171 | |
| 185 172 <span class="c"># Assign atom types...</span> | |
| 186 173 <span class="i">$SLogPAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SLogPAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> | |
| 187 174 <span class="i">$SLogPAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 188 175 | |
| 189 176 <span class="c"># Make sure SLogP atom types assignment is successful...</span> | |
| 190 177 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SLogPAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 191 178 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 192 179 <span class="s">}</span> | |
| 193 180 | |
| 194 181 <span class="c"># Collect assigned atom types...</span> | |
| 195 182 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 196 183 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 197 184 <span class="i">$This</span>->{<span class="w">AtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$SLogPAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 198 185 <span class="s">}</span> | |
| 199 186 | |
| 200 187 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 201 188 <span class="s">}</span> | |
| 202 189 | |
| 203 190 <span class="c"># Calculate SLogP and SMR values...</span> | |
| 204 191 <span class="c">#</span> | |
| 205 <a name="_CalculateDescriptorValues-"></a> 192 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> | |
| 206 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 207 194 <span class="k">my</span><span class="s">(</span><span class="i">$SLogP</span><span class="cm">,</span> <span class="i">$SMR</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$SLogPAndSMRDataRef</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="s">)</span><span class="sc">;</span> | |
| 208 195 | |
| 209 196 <span class="i">$SLogP</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$SMR</span> = <span class="n">0</span><span class="sc">;</span> | |
| 210 197 | |
| 211 198 <span class="c"># Get SLogP and SMR atom types data...</span> | |
| 212 199 <span class="i">$SLogPAndSMRDataRef</span> = <span class="i">AtomTypes::SLogPAtomTypes::GetSLogPAtomTypesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 213 200 | |
| 214 201 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypes</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 215 202 <span class="i">$AtomType</span> = <span class="i">$This</span>->{<span class="w">AtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 216 203 | |
| 217 204 <span class="c"># Makes sure data for SLogp and SMR contribution exists for atom type...</span> | |
| 218 205 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SLogPAndSMRDataRef</span>->{<span class="w">DataCol4</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> && <span class="k">exists</span><span class="s">(</span><span class="i">$SLogPAndSMRDataRef</span>->{<span class="w">DataCol5</span>}{<span class="i">$AtomType</span>}<span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 219 206 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 220 207 <span class="s">}</span> | |
| 221 208 | |
| 222 209 <span class="c"># Data for SLogP contribution is in column number 4...</span> | |
| 223 210 <span class="i">$SLogP</span> += <span class="i">$SLogPAndSMRDataRef</span>->{<span class="w">DataCol4</span>}{<span class="i">$AtomType</span>}<span class="sc">;</span> | |
| 224 211 | |
| 225 212 <span class="c"># Data for SMR contribution is in column number 5...</span> | |
| 226 213 <span class="i">$SMR</span> += <span class="i">$SLogPAndSMRDataRef</span>->{<span class="w">DataCol5</span>}{<span class="i">$AtomType</span>}<span class="sc">;</span> | |
| 227 214 <span class="s">}</span> | |
| 228 215 | |
| 229 216 <span class="c"># Track the calculated values...</span> | |
| 230 217 <span class="i">$This</span>->{<span class="w">SLogP</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$SLogP</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> | |
| 231 218 <span class="i">$This</span>->{<span class="w">SMR</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$SMR</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> | |
| 232 219 | |
| 233 220 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 234 221 <span class="s">}</span> | |
| 235 222 | |
| 236 223 <span class="c"># Setup final descriptor values...</span> | |
| 237 224 <span class="c">#</span> | |
| 238 <a name="_SetFinalDescriptorValues-"></a> 225 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> | |
| 239 226 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 240 227 | |
| 241 228 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 242 229 | |
| 243 230 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">SLogP</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">SMR</span>}<span class="s">)</span><span class="sc">;</span> | |
| 244 231 | |
| 245 232 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 246 233 <span class="s">}</span> | |
| 247 234 | |
| 248 235 <span class="c"># Cache appropriate molecule data...</span> | |
| 249 236 <span class="c">#</span> | |
| 250 <a name="_SetupMoleculeDataCache-"></a> 237 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> | |
| 251 238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 252 239 | |
| 253 240 <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> | |
| 254 241 | |
| 255 242 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 256 243 <span class="s">}</span> | |
| 257 244 | |
| 258 245 <span class="c"># Clear cached molecule data...</span> | |
| 259 246 <span class="c">#</span> | |
| 260 <a name="_ClearMoleculeDataCache-"></a> 247 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> | |
| 261 248 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 262 249 | |
| 263 250 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 264 251 | |
| 265 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 266 253 <span class="s">}</span> | |
| 267 254 | |
| 268 255 <span class="c"># Return a string containg data for SLogPAndSMRDescriptors object...</span> | |
| 269 256 <span class="c">#</span> | |
| 270 <a name="StringifySLogPAndSMRDescriptors-"></a> 257 <span class="k">sub </span><span class="m">StringifySLogPAndSMRDescriptors</span> <span class="s">{</span> | |
| 271 258 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 272 259 <span class="k">my</span><span class="s">(</span><span class="i">$SLogPAndSMRDescriptorsString</span><span class="s">)</span><span class="sc">;</span> | |
| 273 260 | |
| 274 261 <span class="i">$SLogPAndSMRDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 275 262 | |
| 276 263 <span class="k">return</span> <span class="i">$SLogPAndSMRDescriptorsString</span><span class="sc">;</span> | |
| 277 264 <span class="s">}</span> | |
| 278 265 | |
| 279 266 <span class="c"># Is it a SLogPAndSMRDescriptors object?</span> | |
| 280 <a name="_IsSLogPAndSMRDescriptors-"></a> 267 <span class="k">sub </span><span class="m">_IsSLogPAndSMRDescriptors</span> <span class="s">{</span> | |
| 281 268 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 282 269 | |
| 283 270 <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> | |
| 284 271 <span class="s">}</span> | |
| 285 272 | |
| 286 <a name="EOF-"></a></pre> | |
| 287 <p> </p> | |
| 288 <br /> | |
| 289 <center> | |
| 290 <img src="../../../images/h2o2.png"> | |
| 291 </center> | |
| 292 </body> | |
| 293 </html> |