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comparison mayachemtools/docs/modules/html/code/EStateIndiciesFingerprints.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:Fingerprints::EStateIndiciesFingerprints.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-Fingerprints::EStateIndiciesFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::EStateIndiciesFingerprints</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: EStateIndiciesFingerprints.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> | |
| 18 5 <span class="c"># $Revision: 1.19 $</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">Text::ParseWords</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">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> | |
| 52 39 <span class="k">use</span> <span class="w">AtomicDescriptors::EStateValuesDescriptors</span><span class="sc">;</span> | |
| 53 40 | |
| 54 41 <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> | |
| 55 42 | |
| 56 43 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> | |
| 57 44 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 58 45 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 59 46 | |
| 60 47 <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> | |
| 61 48 | |
| 62 49 <span class="c"># Setup class variables...</span> | |
| 63 50 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 64 51 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 65 52 | |
| 66 53 <span class="c"># Overload Perl functions...</span> | |
| 67 54 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyEStateIndiciesFingerprints'</span><span class="sc">;</span> | |
| 68 55 | |
| 69 56 <span class="c"># Class constructor...</span> | |
| 70 <a name="new-"></a> 57 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 71 58 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 72 59 | |
| 73 60 <span class="c"># Initialize object...</span> | |
| 74 61 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 75 62 <span class="k">bless</span> <span class="i">$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> | |
| 76 63 <span class="i">$This</span><span class="i">->_InitializeEStateIndiciesFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 77 64 | |
| 78 65 <span class="i">$This</span><span class="i">->_InitializeEStateIndiciesFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 79 66 | |
| 80 67 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 81 68 <span class="s">}</span> | |
| 82 69 | |
| 83 70 <span class="c"># Initialize object data...</span> | |
| 84 71 <span class="c">#</span> | |
| 85 <a name="_InitializeEStateIndiciesFingerprints-"></a> 72 <span class="k">sub </span><span class="m">_InitializeEStateIndiciesFingerprints</span> <span class="s">{</span> | |
| 86 73 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 87 74 | |
| 88 75 <span class="c"># EStateIndicies is a vector containing sum of E-state values for E-state atom types</span> | |
| 89 76 <span class="c">#</span> | |
| 90 77 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'EStateIndicies'</span><span class="sc">;</span> | |
| 91 78 | |
| 92 79 <span class="c"># EStateAtomTypesSetToUse for EStateIndicies:</span> | |
| 93 80 <span class="c">#</span> | |
| 94 81 <span class="c"># ArbitrarySize - Corrresponds to only E-state atom types detected in molecule</span> | |
| 95 82 <span class="c"># FixedSize - Corresponds to fixed number of E-state atom types previously defined [ Ref 77 ]</span> | |
| 96 83 <span class="c">#</span> | |
| 97 84 <span class="c"># The default EStateAtomTypesSetToUse value for EStateIndicies fingerprints type: ArbitrarySize.</span> | |
| 98 85 <span class="c"># Possible values: ArbitrarySize or FixedSize.</span> | |
| 99 86 <span class="c">#</span> | |
| 100 87 <span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 101 88 | |
| 102 89 <span class="c"># Assigned E-state atom types...</span> | |
| 103 90 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 104 91 | |
| 105 92 <span class="c"># Vector values precision for real values during E-state indicies...</span> | |
| 106 93 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="n">3</span><span class="sc">;</span> | |
| 107 94 | |
| 108 95 <span class="c"># Calculated E-state values and indicies for generating E-state indicies fingerprints...</span> | |
| 109 96 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 110 97 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateIndicies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 111 98 <span class="s">}</span> | |
| 112 99 | |
| 113 100 <span class="c"># Initialize class ...</span> | |
| 114 <a name="_InitializeClass-"></a> 101 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 115 102 <span class="c">#Class name...</span> | |
| 116 103 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 117 104 | |
| 118 105 <span class="s">}</span> | |
| 119 106 | |
| 120 107 <span class="c"># Initialize object properties....</span> | |
| 121 <a name="_InitializeEStateIndiciesFingerprintsProperties-"></a> 108 <span class="k">sub </span><span class="m">_InitializeEStateIndiciesFingerprintsProperties</span> <span class="s">{</span> | |
| 122 109 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 123 110 | |
| 124 111 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 125 112 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 126 113 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 127 114 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 128 115 <span class="s">}</span> | |
| 129 116 | |
| 130 117 <span class="c"># Make sure molecule object was specified...</span> | |
| 131 118 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
| 132 119 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> | |
| 133 120 <span class="s">}</span> | |
| 134 121 | |
| 135 122 <span class="i">$This</span><span class="i">->_InitializeEstateIndicies</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 136 123 | |
| 137 124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 138 125 <span class="s">}</span> | |
| 139 126 | |
| 140 127 <span class="c"># Initialize E-state indicies...</span> | |
| 141 128 <span class="c">#</span> | |
| 142 <a name="_InitializeEstateIndicies-"></a> 129 <span class="k">sub </span><span class="m">_InitializeEstateIndicies</span> <span class="s">{</span> | |
| 143 130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 144 131 | |
| 145 132 <span class="c"># Set default EStateAtomTypesSetToUse...</span> | |
| 146 133 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>}<span class="s">)</span> <span class="s">{</span> | |
| 147 134 <span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span> | |
| 148 135 <span class="s">}</span> | |
| 149 136 | |
| 150 137 <span class="c"># Vector type...</span> | |
| 151 138 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
| 152 139 | |
| 153 140 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 154 141 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</span><span class="sc">;</span> | |
| 155 142 <span class="s">}</span> | |
| 156 143 <span class="k">else</span> <span class="s">{</span> | |
| 157 144 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> | |
| 158 145 <span class="s">}</span> | |
| 159 146 | |
| 160 147 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 161 148 | |
| 162 149 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 163 150 <span class="s">}</span> | |
| 164 151 | |
| 165 152 <span class="c"># Disable set size method...</span> | |
| 166 153 <span class="c">#</span> | |
| 167 <a name="SetSize-"></a> 154 <span class="k">sub </span><span class="m">SetSize</span> <span class="s">{</span> | |
| 168 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 169 156 | |
| 170 157 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetSize: Can't change size: It's not allowed..."</span><span class="sc">;</span> | |
| 171 158 <span class="s">}</span> | |
| 172 159 | |
| 173 160 <span class="c"># Set E-state atom types set to use...</span> | |
| 174 161 <span class="c">#</span> | |
| 175 <a name="SetEStateAtomTypesSetToUse-"></a> 162 <span class="k">sub </span><span class="m">SetEStateAtomTypesSetToUse</span> <span class="s">{</span> | |
| 176 163 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 177 164 | |
| 178 165 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>}<span class="s">)</span> <span class="s">{</span> | |
| 179 166 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetEStateAtomTypesSetToUse: Can't change size: It's already set..."</span><span class="sc">;</span> | |
| 180 167 <span class="s">}</span> | |
| 181 168 | |
| 182 169 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)/i</span><span class="s">)</span> <span class="s">{</span> | |
| 183 170 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetEStateAtomTypesSetToUse: Unknown EStateAtomTypesSetToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span> | |
| 184 171 <span class="s">}</span> | |
| 185 172 | |
| 186 173 <span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 187 174 | |
| 188 175 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 189 176 <span class="s">}</span> | |
| 190 177 | |
| 191 178 <span class="c"># Set vector values precision for real values for E-state indicies...</span> | |
| 192 179 <span class="c">#</span> | |
| 193 <a name="SetValuesPrecision-"></a> 180 <span class="k">sub </span><span class="m">SetValuesPrecision</span> <span class="s">{</span> | |
| 194 181 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 195 182 | |
| 196 183 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 197 184 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValuesPrecision: ValuesPrecision value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 198 185 <span class="s">}</span> | |
| 199 186 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 200 187 | |
| 201 188 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 202 189 <span class="s">}</span> | |
| 203 190 | |
| 204 191 <span class="c"># Generate fingerprints description...</span> | |
| 205 192 <span class="c">#</span> | |
| 206 <a name="GetDescription-"></a> 193 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> | |
| 207 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 208 195 | |
| 209 196 <span class="c"># Is description explicity set?</span> | |
| 210 197 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> | |
| 211 198 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> | |
| 212 199 <span class="s">}</span> | |
| 213 200 | |
| 214 201 <span class="c"># Generate fingerprints description...</span> | |
| 215 202 | |
| 216 203 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{EStateAtomTypesSetToUse}"</span><span class="sc">;</span> | |
| 217 204 <span class="s">}</span> | |
| 218 205 | |
| 219 206 <span class="c"># Generate electrotopological state indicies (E-state) [ Ref 75-78 ] fingerprints for</span> | |
| 220 207 <span class="c"># non-hydrogen atoms in a molecule...</span> | |
| 221 208 <span class="c">#</span> | |
| 222 209 <span class="c"># EStateIndicies fingerprints constitute a vector containing sum of E-state values</span> | |
| 223 210 <span class="c"># for E-state atom types. Two types of E-state atom types set size are allowed:</span> | |
| 224 211 <span class="c">#</span> | |
| 225 212 <span class="c"># ArbitrarySize - Corrresponds to only E-state atom types detected in molecule</span> | |
| 226 213 <span class="c"># FixedSize - Corresponds to fixed number of E-state atom types previously defined</span> | |
| 227 214 <span class="c">#</span> | |
| 228 215 <span class="c"># Module AtomTypes::EStateAtomTypes.pm is used to assign E-state atom types to</span> | |
| 229 216 <span class="c"># non-hydrogen atoms in the molecule which is able to assign atom types to any valid</span> | |
| 230 217 <span class="c"># atom group. However, for FixedSize value of EStateAtomTypesSetToUse, only a fixed</span> | |
| 231 218 <span class="c"># set of E-state atom types corresponding to specific atom groups [ Appendix III in</span> | |
| 232 219 <span class="c"># Ref 77 ] are used for fingerprints.</span> | |
| 233 220 <span class="c">#</span> | |
| 234 221 <span class="c"># The fixed size E-state atom type set size used during generation of fingerprints corresponding</span> | |
| 235 222 <span class="c"># FixedSize value of EStateAtomTypesSetToUse contains 87 E-state non-hydrogen atom types</span> | |
| 236 223 <span class="c"># in EStateAtomTypes.csv data file distributed with MayaChemTools.</span> | |
| 237 224 <span class="c">#</span> | |
| 238 225 <span class="c"># Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of</span> | |
| 239 226 <span class="c"># E-state indicies fingerprints:</span> | |
| 240 227 <span class="c">#</span> | |
| 241 228 <span class="c"># Type EStateAtomTypesSetToUse</span> | |
| 242 229 <span class="c">#</span> | |
| 243 230 <span class="c"># EStateIndicies ArbitrarySize [ default fingerprints ]</span> | |
| 244 231 <span class="c"># EStateIndicies FixedSize</span> | |
| 245 232 <span class="c">#</span> | |
| 246 233 <span class="c"># The default is generate EStateIndicies type fingeprints corresponding to ArbitrarySize as</span> | |
| 247 234 <span class="c"># EStateAtomTypesSetToUse value.</span> | |
| 248 235 <span class="c">#</span> | |
| 249 236 <span class="c">#</span> | |
| 250 <a name="GenerateFingerprints-"></a> 237 <span class="k">sub </span><span class="m">GenerateFingerprints</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="c"># Cache appropriate molecule data...</span> | |
| 254 241 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 255 242 | |
| 256 243 <span class="c"># Assign E-state atom types...</span> | |
| 257 244 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignEStateAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 258 245 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{Type} fingerprints generation didn't succeed: Couldn't assign valid E-state atom types to all atoms..."</span><span class="sc">;</span> | |
| 259 246 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 260 247 <span class="s">}</span> | |
| 261 248 | |
| 262 249 <span class="c"># Calculate E-state indicies...</span> | |
| 263 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateEStateIndicies</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 264 251 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{Type} fingerprints generation didn't succeed: Couldn't calculate E-state values for all atoms..."</span><span class="sc">;</span> | |
| 265 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 266 253 <span class="s">}</span> | |
| 267 254 | |
| 268 255 <span class="c"># Set final fingerprints...</span> | |
| 269 256 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 270 257 | |
| 271 258 <span class="c"># Clear cached molecule data...</span> | |
| 272 259 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 273 260 | |
| 274 261 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 275 262 <span class="s">}</span> | |
| 276 263 | |
| 277 264 <span class="c"># Assign E-state atom types...</span> | |
| 278 265 <span class="c">#</span> | |
| 279 <a name="_AssignEStateAtomTypes-"></a> 266 <span class="k">sub </span><span class="m">_AssignEStateAtomTypes</span> <span class="s">{</span> | |
| 280 267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 281 268 <span class="k">my</span><span class="s">(</span><span class="i">$EStateAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="s">)</span><span class="sc">;</span> | |
| 282 269 | |
| 283 270 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 284 271 | |
| 285 272 <span class="c"># Assign E-state atom types...</span> | |
| 286 273 <span class="i">$EStateAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 287 274 <span class="i">$EStateAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 288 275 | |
| 289 276 <span class="c"># Make sure atom types assignment is successful...</span> | |
| 290 277 <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 291 278 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 292 279 <span class="s">}</span> | |
| 293 280 | |
| 294 281 <span class="c"># Collect assigned atom types...</span> | |
| 295 282 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 296 283 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 297 284 | |
| 298 285 <span class="i">$AtomType</span> = <span class="i">$EStateAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 299 286 <span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomType</span><span class="sc">;</span> | |
| 300 287 <span class="s">}</span> | |
| 301 288 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 302 289 <span class="s">}</span> | |
| 303 290 | |
| 304 291 <span class="c"># Calculate E-state indicies by summing up E-state values for specific</span> | |
| 305 292 <span class="c"># E-state atom types...</span> | |
| 306 293 <span class="c">#</span> | |
| 307 <a name="_CalculateEStateIndicies-"></a> 294 <span class="k">sub </span><span class="m">_CalculateEStateIndicies</span> <span class="s">{</span> | |
| 308 295 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 309 296 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span> | |
| 310 297 | |
| 311 298 <span class="c"># Calculate E-state values to generate E-state indicies...</span> | |
| 312 299 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateEStateValuesDescriptors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 313 300 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 314 301 <span class="s">}</span> | |
| 315 302 | |
| 316 303 <span class="c"># Calculate E-state indicies...</span> | |
| 317 304 <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> | |
| 318 305 <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> | |
| 319 306 | |
| 320 307 <span class="i">$AtomType</span> = <span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 321 308 <span class="i">$EStateValue</span> = <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 322 309 | |
| 323 310 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 324 311 <span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 325 312 <span class="s">}</span> | |
| 326 313 | |
| 327 314 <span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>} += <span class="i">$EStateValue</span><span class="sc">;</span> | |
| 328 315 <span class="s">}</span> | |
| 329 316 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 330 317 <span class="s">}</span> | |
| 331 318 | |
| 332 319 <span class="c"># Calculate E-state values for E-state indicies...</span> | |
| 333 320 <span class="c">#</span> | |
| 334 <a name="_CalculateEStateValuesDescriptors-"></a> 321 <span class="k">sub </span><span class="m">_CalculateEStateValuesDescriptors</span> <span class="s">{</span> | |
| 335 322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 336 323 <span class="k">my</span><span class="s">(</span><span class="i">$EStateValuesDescriptors</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span> | |
| 337 324 | |
| 338 325 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 339 326 | |
| 340 327 <span class="c"># Calculate and assign E-state values...</span> | |
| 341 328 <span class="i">$EStateValuesDescriptors</span> = <span class="i">new</span> <span class="i">AtomicDescriptors::EStateValuesDescriptors</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
| 342 329 <span class="i">$EStateValuesDescriptors</span><span class="i">->GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 343 330 | |
| 344 331 <span class="c"># Make sure E-state values calculation is successful...</span> | |
| 345 332 <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateValuesDescriptors</span><span class="i">->IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 346 333 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 347 334 <span class="s">}</span> | |
| 348 335 | |
| 349 336 <span class="c"># Collect assigned E-state values...</span> | |
| 350 337 <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> | |
| 351 338 <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> | |
| 352 339 <span class="i">$EStateValue</span> = <span class="i">$EStateValuesDescriptors</span><span class="i">->GetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 353 340 <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$EStateValue</span><span class="sc">;</span> | |
| 354 341 <span class="s">}</span> | |
| 355 342 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 356 343 <span class="s">}</span> | |
| 357 344 | |
| 358 345 <span class="c"># Set final final fingerpritns for E-state indicies...</span> | |
| 359 346 <span class="c">#</span> | |
| 360 <a name="_SetFinalFingerprints-"></a> 347 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> | |
| 361 348 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 362 349 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="cm">,</span> <span class="i">$EStateAtomTypesDataRef</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span> | |
| 363 350 | |
| 364 351 <span class="c"># Mark successful generation of fingerprints...</span> | |
| 365 352 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 366 353 | |
| 367 354 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 368 355 <span class="i">@IDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 369 356 | |
| 370 357 <span class="i">$ValuesPrecision</span> = <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>}<span class="sc">;</span> | |
| 371 358 | |
| 372 359 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 373 360 <span class="c"># Use fixed size E-state atom types set for non-hydrogen atoms...</span> | |
| 374 361 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">AtomTypes::EStateAtomTypes::GetAllPossibleEStateNonHydrogenAtomTypes</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> | |
| 375 362 <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="q">"S${AtomType}"</span><span class="sc">;</span> | |
| 376 363 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> ? <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 377 364 <span class="s">}</span> | |
| 378 365 <span class="s">}</span> | |
| 379 366 <span class="k">else</span> <span class="s">{</span> | |
| 380 367 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateIndicies</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 381 368 <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="q">"S${AtomType}"</span><span class="sc">;</span> | |
| 382 369 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="s">)</span><span class="sc">;</span> | |
| 383 370 <span class="s">}</span> | |
| 384 371 <span class="s">}</span> | |
| 385 372 | |
| 386 373 <span class="c"># Add IDs and values to fingerprint vector...</span> | |
| 387 374 <span class="k">if</span> <span class="s">(</span><span class="i">@IDs</span><span class="s">)</span> <span class="s">{</span> | |
| 388 375 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span> | |
| 389 376 <span class="s">}</span> | |
| 390 377 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> | |
| 391 378 | |
| 392 379 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 393 380 <span class="s">}</span> | |
| 394 381 | |
| 395 382 <span class="c"># Cache appropriate molecule data...</span> | |
| 396 383 <span class="c">#</span> | |
| 397 <a name="_SetupMoleculeDataCache-"></a> 384 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> | |
| 398 385 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 399 386 | |
| 400 387 <span class="c"># Get all non-hydrogen atoms...</span> | |
| 401 388 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> | |
| 402 389 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span> | |
| 403 390 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="q">"IsHydrogen"</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> | |
| 404 391 | |
| 405 392 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 406 393 <span class="s">}</span> | |
| 407 394 | |
| 408 395 <span class="c"># Clear cached molecule data...</span> | |
| 409 396 <span class="c">#</span> | |
| 410 <a name="_ClearMoleculeDataCache-"></a> 397 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> | |
| 411 398 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 412 399 | |
| 413 400 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 414 401 | |
| 415 402 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 416 403 <span class="s">}</span> | |
| 417 404 | |
| 418 405 <span class="c"># Return a string containg data for EStateIndiciesFingerprints object...</span> | |
| 419 <a name="StringifyEStateIndiciesFingerprints-"></a> 406 <span class="k">sub </span><span class="m">StringifyEStateIndiciesFingerprints</span> <span class="s">{</span> | |
| 420 407 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 421 408 <span class="k">my</span><span class="s">(</span><span class="i">$EStateIndiciesFingerprintsString</span><span class="s">)</span><span class="sc">;</span> | |
| 422 409 | |
| 423 410 <span class="c"># Type of Keys...</span> | |
| 424 411 <span class="i">$EStateIndiciesFingerprintsString</span> = <span class="q">"Type: $This->{Type}; EStateAtomTypesSetToUse: $This->{EStateAtomTypesSetToUse}"</span><span class="sc">;</span> | |
| 425 412 | |
| 426 413 <span class="c"># Fingerprint vector...</span> | |
| 427 414 <span class="i">$EStateIndiciesFingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> | |
| 428 415 | |
| 429 416 <span class="k">return</span> <span class="i">$EStateIndiciesFingerprintsString</span><span class="sc">;</span> | |
| 430 417 <span class="s">}</span> | |
| 431 418 | |
| 432 <a name="EOF-"></a></pre> | |
| 433 <p> </p> | |
| 434 <br /> | |
| 435 <center> | |
| 436 <img src="../../../images/h2o2.png"> | |
| 437 </center> | |
| 438 </body> | |
| 439 </html> |