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comparison mayachemtools/docs/modules/html/code/MolecularDescriptorsGenerator.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::MolecularDescriptorsGenerator.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-MolecularDescriptors::MolecularDescriptorsGenerator-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularDescriptorsGenerator</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: MolecularDescriptorsGenerator.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> | |
| 18 5 <span class="c"># $Revision: 1.13 $</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">ObjectProperty</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</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 | |
| 52 39 <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> | |
| 53 40 | |
| 54 41 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> | |
| 55 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 56 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetAvailableDescriptorClassNames GetAvailableClassAndDescriptorNames GetAvailableDescriptorNames GetAvailableDescriptorNamesForDescriptorClass GetAvailableClassNameForDescriptorName GetRuleOf5DescriptorNames GetRuleOf3DescriptorNames IsDescriptorClassNameAvailable IsDescriptorNameAvailable)</span><span class="sc">;</span> | |
| 57 44 | |
| 58 45 <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> | |
| 59 46 | |
| 60 47 <span class="c"># Setup class variables...</span> | |
| 61 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">%DescriptorsDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 62 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 63 50 | |
| 64 51 <span class="c"># Overload Perl functions...</span> | |
| 65 52 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecularDescriptorsGenerator'</span><span class="sc">;</span> | |
| 66 53 | |
| 67 54 <span class="c"># Class constructor...</span> | |
| 68 <a name="new-"></a> 55 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 69 56 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 70 57 | |
| 71 58 <span class="c"># Initialize object...</span> | |
| 72 59 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> | |
| 73 60 <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">$Class</span><span class="sc">;</span> | |
| 74 61 <span class="i">$This</span><span class="i">->_InitializeMolecularDescriptorsGenerator</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 75 62 | |
| 76 63 <span class="i">$This</span><span class="i">->_InitializeMolecularDescriptorsGeneratorProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 77 64 | |
| 78 65 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 79 66 <span class="s">}</span> | |
| 80 67 | |
| 81 68 <span class="c"># Initialize class ...</span> | |
| 82 <a name="_InitializeClass-"></a> 69 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 83 70 <span class="c">#Class name...</span> | |
| 84 71 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 85 72 | |
| 86 73 <span class="c"># Load available molecular descriptor classes...</span> | |
| 87 74 <span class="i">_LoadMolecularDescriptorsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 88 75 | |
| 89 76 <span class="s">}</span> | |
| 90 77 | |
| 91 78 <span class="c"># Initialize object data...</span> | |
| 92 79 <span class="c">#</span> | |
| 93 <a name="_InitializeMolecularDescriptorsGenerator-"></a> 80 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptorsGenerator</span> <span class="s">{</span> | |
| 94 81 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 95 82 | |
| 96 83 <span class="c"># Type of desciptors to generate...</span> | |
| 97 84 <span class="c">#</span> | |
| 98 85 <span class="c"># The current release of MayaChemTools supports generation of four sets of</span> | |
| 99 86 <span class="c"># descriptors: All available descriptors, rule of 5 or 3 descriptors or a specified</span> | |
| 100 87 <span class="c"># set of descriptors.</span> | |
| 101 88 <span class="c">#</span> | |
| 102 89 <span class="c"># Possible values: All, RuleOf5, RuleOf3 or Specify</span> | |
| 103 90 <span class="c">#</span> | |
| 104 91 <span class="c"># RuleOf5 [ Ref 91 ] descriptor names: MolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors,</span> | |
| 105 92 <span class="c"># SLogP. RuleOf5 states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10,</span> | |
| 106 93 <span class="c"># and logP <= 5.</span> | |
| 107 94 <span class="c">#</span> | |
| 108 95 <span class="c"># RuleOf3 [ Ref 92 ] descriptor names: MolecularWeight, RotatableBonds, HydrogenBondDonors,</span> | |
| 109 96 <span class="c"># HydrogenBondAcceptors, SLogP, TPSA. RuleOf3 states: MolecularWeight <= 300, RotatableBonds <= 3,</span> | |
| 110 97 <span class="c"># HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</span> | |
| 111 98 <span class="c">#</span> | |
| 112 99 <span class="c"># For Specify value of Mode, a set of descritor names must be specified using</span> | |
| 113 100 <span class="c"># DescriptorNames parameter.</span> | |
| 114 101 <span class="c">#</span> | |
| 115 102 <span class="c"># Default: All</span> | |
| 116 103 <span class="c">#</span> | |
| 117 104 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 118 105 | |
| 119 106 <span class="c"># Descriptor names used to generate descriptor values during a specified descriptor</span> | |
| 120 107 <span class="c"># generation mode...</span> | |
| 121 108 <span class="c">#</span> | |
| 122 109 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 123 110 | |
| 124 111 <span class="c"># Descriptor calculation control parameters for specified descriptor class names...</span> | |
| 125 112 <span class="c">#</span> | |
| 126 113 <span class="c"># These parameters are passed on to appropriate descriptor classes during</span> | |
| 127 114 <span class="c"># instantiations of descriptor class objects.</span> | |
| 128 115 <span class="c">#</span> | |
| 129 116 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 130 117 | |
| 131 118 <span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 132 119 | |
| 133 120 <span class="c"># Descriptor class names and objects corresponding to specified descriptor names...</span> | |
| 134 121 <span class="c">#</span> | |
| 135 122 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 136 123 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 137 124 | |
| 138 125 <span class="c"># Descriptor values generated for specified descriptor names...</span> | |
| 139 126 <span class="c">#</span> | |
| 140 127 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 141 128 | |
| 142 129 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 143 130 <span class="s">}</span> | |
| 144 131 | |
| 145 132 <span class="c"># Initialize object properties...</span> | |
| 146 133 <span class="c">#</span> | |
| 147 <a name="_InitializeMolecularDescriptorsGeneratorProperties-"></a> 134 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptorsGeneratorProperties</span> <span class="s">{</span> | |
| 148 135 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 149 136 | |
| 150 137 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 151 138 <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> | |
| 152 139 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 153 140 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 154 141 <span class="s">}</span> | |
| 155 142 | |
| 156 143 <span class="c"># Set default value for Mode...</span> | |
| 157 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Mode</span>}<span class="s">)</span> <span class="s">{</span> | |
| 158 145 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="q">'All'</span><span class="sc">;</span> | |
| 159 146 <span class="s">}</span> | |
| 160 147 | |
| 161 148 <span class="i">$This</span><span class="i">->_CheckAndInitializeDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 162 149 | |
| 163 150 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 164 151 <span class="s">}</span> | |
| 165 152 | |
| 166 153 <span class="c"># Set descriptors generation mode......</span> | |
| 167 154 <span class="c">#</span> | |
| 168 <a name="SetMode-"></a> 155 <span class="k">sub </span><span class="m">SetMode</span> <span class="s">{</span> | |
| 169 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 170 157 | |
| 171 158 <span class="c"># All - all available descriptors</span> | |
| 172 159 <span class="c"># Specify - Specified set of descriptors</span> | |
| 173 160 | |
| 174 161 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(All|RuleOf5|RuleOf3|Specify)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 175 162 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMode: Mode value, $Value, is not valid; Supported values: All, RuleOf5, RuleOf3 or Specify..."</span><span class="sc">;</span> | |
| 176 163 <span class="s">}</span> | |
| 177 164 | |
| 178 165 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 179 166 | |
| 180 167 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 181 168 <span class="s">}</span> | |
| 182 169 | |
| 183 170 <span class="c"># Set descriptor names to use for generating descriptor values using an array</span> | |
| 184 171 <span class="c"># or reference to an array...</span> | |
| 185 172 <span class="c">#</span> | |
| 186 <a name="SetDescriptorNames-"></a> 173 <span class="k">sub </span><span class="m">SetDescriptorNames</span> <span class="s">{</span> | |
| 187 174 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 188 175 | |
| 189 176 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 190 177 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDescriptorNames: Descriptor names cann't be specified during \"All\" value of descsriptors generation \"Mode\"..."</span><span class="sc">;</span> | |
| 191 178 <span class="s">}</span> | |
| 192 179 | |
| 193 180 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 194 181 <span class="k">return</span><span class="sc">;</span> | |
| 195 182 <span class="s">}</span> | |
| 196 183 | |
| 197 184 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="s">)</span><span class="sc">;</span> | |
| 198 185 | |
| 199 186 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 200 187 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 201 188 | |
| 202 189 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 203 190 | |
| 204 191 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 205 192 <span class="c"># Initialize using array refernce...</span> | |
| 206 193 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
| 207 194 <span class="s">}</span> | |
| 208 195 <span class="k">else</span> <span class="s">{</span> | |
| 209 196 <span class="c"># It's a list of values...</span> | |
| 210 197 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
| 211 198 <span class="s">}</span> | |
| 212 199 | |
| 213 200 <span class="c"># Make sure specified descriptor names are valid...</span> | |
| 214 201 <span class="i">$This</span><span class="i">->_ValidateDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 215 202 | |
| 216 203 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 217 204 <span class="s">}</span> | |
| 218 205 | |
| 219 206 <span class="c"># Get descriptor names as an array...</span> | |
| 220 207 <span class="c">#</span> | |
| 221 <a name="GetDescriptorNames-"></a> 208 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> | |
| 222 209 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 223 210 | |
| 224 211 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span> | |
| 225 212 <span class="s">}</span> | |
| 226 213 | |
| 227 214 <span class="c"># Get all descriptor values as an array...</span> | |
| 228 215 <span class="c">#</span> | |
| 229 <a name="GetDescriptorValues-"></a> 216 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span> | |
| 230 217 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 231 218 | |
| 232 219 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>}<span class="s">)</span> <span class="s">{</span> | |
| 233 220 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="sc">;</span> | |
| 234 221 <span class="s">}</span> | |
| 235 222 <span class="k">else</span> <span class="s">{</span> | |
| 236 223 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorValues</span><span class="s">)</span><span class="sc">;</span> | |
| 237 224 | |
| 238 225 <span class="i">@DescriptorValues</span> = <span class="s">(</span><span class="q">'None'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span> | |
| 239 226 | |
| 240 227 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorValues</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorValues</span><span class="sc">;</span> | |
| 241 228 <span class="s">}</span> | |
| 242 229 <span class="s">}</span> | |
| 243 230 | |
| 244 231 <span class="c"># Get descriptor value for a specified descriptor name...</span> | |
| 245 232 <span class="c">#</span> | |
| 246 <a name="GetDescriptorValueByName-"></a> 233 <span class="k">sub </span><span class="m">GetDescriptorValueByName</span> <span class="s">{</span> | |
| 247 234 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 248 235 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 249 236 | |
| 250 237 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 251 238 | |
| 252 239 <span class="k">return</span> <span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} ? <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> | |
| 253 240 | |
| 254 241 <span class="s">}</span> | |
| 255 242 | |
| 256 243 <span class="c"># Get calculated molecular descriptor names sand values as a hash with names</span> | |
| 257 244 <span class="c"># and values as key/value pairs...</span> | |
| 258 245 <span class="c">#</span> | |
| 259 <a name="GetDescriptorNamesAndValues-"></a> 246 <span class="k">sub </span><span class="m">GetDescriptorNamesAndValues</span> <span class="s">{</span> | |
| 260 247 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 261 248 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 262 249 | |
| 263 250 <span class="i">%NamesAndValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 264 251 <span class="i">@NamesAndValues</span>{ <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} } = <span class="i">$This</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 265 252 | |
| 266 253 <span class="k">return</span> <span class="i">%NamesAndValues</span><span class="sc">;</span> | |
| 267 254 <span class="s">}</span> | |
| 268 255 | |
| 269 256 <span class="c"># Set up descriptor calculation control parameters for a specified descriptor class name...</span> | |
| 270 257 <span class="c">#</span> | |
| 271 258 <span class="c"># The specified parameter names and values are simply passed on to specified descriptor</span> | |
| 272 259 <span class="c"># class during instantiation of descriptor class object without any performing any validation</span> | |
| 273 260 <span class="c"># of parameter names and associated values. It's up to the appropriate descriptor class methods</span> | |
| 274 261 <span class="c"># to validate these parameters and values.</span> | |
| 275 262 <span class="c">#</span> | |
| 276 263 <span class="c"># In addition to specified parameter names and values, the parameter hash must also contain</span> | |
| 277 264 <span class="c"># descriptor class name as key and value pair with DescriptorClassName as key with class</span> | |
| 278 265 <span class="c"># name as value.</span> | |
| 279 266 <span class="c">#</span> | |
| 280 <a name="SetDescriptorClassParameters-"></a> 267 <span class="k">sub </span><span class="m">SetDescriptorClassParameters</span> <span class="s">{</span> | |
| 281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 282 269 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 283 270 | |
| 284 271 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 285 272 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_SetDescriptorNameParameters: Can't set descriptor class name paramaters: DescriptorClassName is not specified..."</span><span class="sc">;</span> | |
| 286 273 <span class="s">}</span> | |
| 287 274 | |
| 288 275 <span class="i">$DescriptorClassName</span> = <span class="i">$NamesAndValues</span>{<span class="w">DescriptorClassName</span>}<span class="sc">;</span> | |
| 289 276 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsDescriptorClassNameAvailable</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 290 277 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_SetDescriptorClassParameters: Can't set descriptor class name paramaters: Specified descriptor class name, $DescriptorClassName, is not available..."</span><span class="sc">;</span> | |
| 291 278 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 292 279 <span class="s">}</span> | |
| 293 280 | |
| 294 281 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 295 282 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetDescriptorClassParameters: Class name parameters for $DescriptorClassName have already been specified: Replacing previous values..."</span><span class="sc">;</span> | |
| 296 283 <span class="s">}</span> | |
| 297 284 | |
| 298 285 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 299 286 <span class="j">NAME:</span> <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 300 287 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^DescriptorClassName$/</span><span class="s">)</span> <span class="s">{</span> | |
| 301 288 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 302 289 <span class="s">}</span> | |
| 303 290 <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 304 291 <span class="s">}</span> | |
| 305 292 | |
| 306 293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 307 294 <span class="s">}</span> | |
| 308 295 | |
| 309 296 <span class="c"># Get descriptor name parameters as a reference to hash of hashes with hash</span> | |
| 310 297 <span class="c"># keys corresponding to class name and class parameter name with hash value</span> | |
| 311 298 <span class="c"># as class parameter value...</span> | |
| 312 299 <span class="c">#</span> | |
| 313 <a name="GetDescriptorClassParameters-"></a> 300 <span class="k">sub </span><span class="m">GetDescriptorClassParameters</span> <span class="s">{</span> | |
| 314 301 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 315 302 | |
| 316 303 <span class="k">return</span> \<span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}}<span class="sc">;</span> | |
| 317 304 <span class="s">}</span> | |
| 318 305 | |
| 319 306 <span class="c"># Get available descriptor class names as an array.</span> | |
| 320 307 <span class="c">#</span> | |
| 321 308 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 322 309 <span class="c"># object method.</span> | |
| 323 310 <span class="c">#</span> | |
| 324 <a name="GetAvailableDescriptorClassNames-"></a> 311 <span class="k">sub </span><span class="m">GetAvailableDescriptorClassNames</span> <span class="s">{</span> | |
| 325 312 | |
| 326 313 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="sc">;</span> | |
| 327 314 <span class="s">}</span> | |
| 328 315 | |
| 329 316 <span class="c"># Get available descriptors class and descriptors names as a hash containing key/value</span> | |
| 330 317 <span class="c"># pairs corresponding to class name and an array of descriptor names available for the</span> | |
| 331 318 <span class="c"># class.</span> | |
| 332 319 <span class="c">#</span> | |
| 333 320 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 334 321 <span class="c"># object method.</span> | |
| 335 322 <span class="c">#</span> | |
| 336 <a name="GetAvailableClassAndDescriptorNames-"></a> 323 <span class="k">sub </span><span class="m">GetAvailableClassAndDescriptorNames</span> <span class="s">{</span> | |
| 337 324 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">%ClassAndDescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 338 325 | |
| 339 326 <span class="i">%ClassAndDescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 340 327 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 341 328 <span class="i">@</span>{<span class="i">$ClassAndDescriptorNames</span>{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 342 329 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ClassAndDescriptorNames</span>{<span class="i">$DescriptorClassName</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}}<span class="sc">;</span> | |
| 343 330 <span class="s">}</span> | |
| 344 331 | |
| 345 332 <span class="k">return</span> <span class="i">%ClassAndDescriptorNames</span><span class="sc">;</span> | |
| 346 333 <span class="s">}</span> | |
| 347 334 | |
| 348 335 <span class="c"># Get available descriptor names as an array.</span> | |
| 349 336 <span class="c">#</span> | |
| 350 337 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 351 338 <span class="c"># object method.</span> | |
| 352 339 <span class="c">#</span> | |
| 353 <a name="GetAvailableDescriptorNames-"></a> 340 <span class="k">sub </span><span class="m">GetAvailableDescriptorNames</span> <span class="s">{</span> | |
| 354 341 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 355 342 | |
| 356 343 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 357 344 <span class="k">push</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="k">map</span> <span class="s">{</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$_</span>}} <span class="s">}</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="sc">;</span> | |
| 358 345 | |
| 359 346 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
| 360 347 <span class="s">}</span> | |
| 361 348 | |
| 362 349 <span class="c"># Is it a valid descriptors class name?</span> | |
| 363 350 <span class="c">#</span> | |
| 364 351 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 365 352 <span class="c"># object method.</span> | |
| 366 353 <span class="c">#</span> | |
| 367 <a name="IsDescriptorClassNameAvailable-"></a> 354 <span class="k">sub </span><span class="m">IsDescriptorClassNameAvailable</span> <span class="s">{</span> | |
| 368 355 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 369 356 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 370 357 | |
| 371 358 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 372 359 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 373 360 <span class="s">}</span> | |
| 374 361 <span class="k">else</span> <span class="s">{</span> | |
| 375 362 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 376 363 <span class="s">}</span> | |
| 377 364 | |
| 378 365 <span class="k">return</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 379 366 <span class="s">}</span> | |
| 380 367 | |
| 381 368 <span class="c"># Is it a valid descriptor name?</span> | |
| 382 369 <span class="c">#</span> | |
| 383 370 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 384 371 <span class="c"># object method.</span> | |
| 385 372 <span class="c">#</span> | |
| 386 <a name="IsDescriptorNameAvailable-"></a> 373 <span class="k">sub </span><span class="m">IsDescriptorNameAvailable</span> <span class="s">{</span> | |
| 387 374 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 388 375 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> | |
| 389 376 | |
| 390 377 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 391 378 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 392 379 <span class="s">}</span> | |
| 393 380 <span class="k">else</span> <span class="s">{</span> | |
| 394 381 <span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 395 382 <span class="s">}</span> | |
| 396 383 | |
| 397 384 <span class="k">return</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 398 385 <span class="s">}</span> | |
| 399 386 | |
| 400 387 <span class="c"># Get available descriptors names for a descriptor class as an array.</span> | |
| 401 388 <span class="c">#</span> | |
| 402 389 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 403 390 <span class="c"># object method.</span> | |
| 404 391 <span class="c">#</span> | |
| 405 <a name="GetAvailableDescriptorNamesForDescriptorClass-"></a> 392 <span class="k">sub </span><span class="m">GetAvailableDescriptorNamesForDescriptorClass</span> <span class="s">{</span> | |
| 406 393 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 407 394 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 408 395 | |
| 409 396 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 410 397 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 411 398 <span class="s">}</span> | |
| 412 399 <span class="k">else</span> <span class="s">{</span> | |
| 413 400 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 414 401 <span class="s">}</span> | |
| 415 402 | |
| 416 403 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 417 404 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 418 405 <span class="k">push</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}}<span class="sc">;</span> | |
| 419 406 <span class="s">}</span> | |
| 420 407 | |
| 421 408 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
| 422 409 <span class="s">}</span> | |
| 423 410 | |
| 424 411 <span class="c"># Get available descriptors class name for a descriptor name.</span> | |
| 425 412 <span class="c">#</span> | |
| 426 413 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 427 414 <span class="c"># object method.</span> | |
| 428 415 <span class="c">#</span> | |
| 429 <a name="GetAvailableClassNameForDescriptorName-"></a> 416 <span class="k">sub </span><span class="m">GetAvailableClassNameForDescriptorName</span> <span class="s">{</span> | |
| 430 417 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 431 418 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> | |
| 432 419 | |
| 433 420 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 434 421 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 435 422 <span class="s">}</span> | |
| 436 423 <span class="k">else</span> <span class="s">{</span> | |
| 437 424 <span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 438 425 <span class="s">}</span> | |
| 439 426 | |
| 440 427 <span class="i">$DescriptorClassName</span> = <span class="q">''</span><span class="sc">;</span> | |
| 441 428 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 442 429 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span> | |
| 443 430 <span class="s">}</span> | |
| 444 431 | |
| 445 432 <span class="k">return</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span> | |
| 446 433 <span class="s">}</span> | |
| 447 434 | |
| 448 435 <span class="c"># Get RuleOf5 descriptor names as an array.</span> | |
| 449 436 <span class="c">#</span> | |
| 450 437 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 451 438 <span class="c"># object method.</span> | |
| 452 439 <span class="c">#</span> | |
| 453 <a name="GetRuleOf5DescriptorNames-"></a> 440 <span class="k">sub </span><span class="m">GetRuleOf5DescriptorNames</span> <span class="s">{</span> | |
| 454 441 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 455 442 | |
| 456 443 <span class="i">@DescriptorNames</span> = <span class="q">qw(MolecularWeight HydrogenBondDonors HydrogenBondAcceptors SLogP)</span><span class="sc">;</span> | |
| 457 444 | |
| 458 445 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
| 459 446 <span class="s">}</span> | |
| 460 447 | |
| 461 448 <span class="c"># Get RuleOf3 descriptor names as an array.</span> | |
| 462 449 <span class="c">#</span> | |
| 463 450 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 464 451 <span class="c"># object method.</span> | |
| 465 452 <span class="c">#</span> | |
| 466 <a name="GetRuleOf3DescriptorNames-"></a> 453 <span class="k">sub </span><span class="m">GetRuleOf3DescriptorNames</span> <span class="s">{</span> | |
| 467 454 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 468 455 | |
| 469 456 <span class="i">@DescriptorNames</span> = <span class="q">qw(MolecularWeight RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span> | |
| 470 457 | |
| 471 458 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
| 472 459 <span class="s">}</span> | |
| 473 460 | |
| 474 461 | |
| 475 462 <span class="c"># Set molecule object...</span> | |
| 476 463 <span class="c">#</span> | |
| 477 <a name="SetMolecule-"></a> 464 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> | |
| 478 465 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 479 466 | |
| 480 467 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> | |
| 481 468 | |
| 482 469 <span class="c"># Weaken the reference to disable increment of reference count...</span> | |
| 483 470 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
| 484 471 | |
| 485 472 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 486 473 <span class="s">}</span> | |
| 487 474 | |
| 488 475 <span class="c"># Generate specified molecular descriptors...</span> | |
| 489 476 <span class="c">#</span> | |
| 490 477 <span class="c"># After instantiating descriptor class objects at first invocation and initialializing</span> | |
| 491 478 <span class="c"># descriptor values during subsequent invocations, GenerateDescriptors method</span> | |
| 492 479 <span class="c"># provided by each descriptor class is used to calculate descriptor values for</span> | |
| 493 480 <span class="c"># specified descriptors.</span> | |
| 494 481 <span class="c">#</span> | |
| 495 <a name="GenerateDescriptors-"></a> 482 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> | |
| 496 483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 497 484 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="s">)</span><span class="sc">;</span> | |
| 498 485 | |
| 499 486 <span class="c"># Initialize descriptor values...</span> | |
| 500 487 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 501 488 | |
| 502 489 <span class="c"># Instantiate decriptor classed corresponding to specified descriptors...</span> | |
| 503 490 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>}<span class="s">)</span> <span class="s">{</span> | |
| 504 491 <span class="i">$This</span><span class="i">->_InstantiateDescriptorClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 505 492 <span class="s">}</span> | |
| 506 493 | |
| 507 494 <span class="c"># Check availability of molecule...</span> | |
| 508 495 <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> | |
| 509 496 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> | |
| 510 497 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 511 498 <span class="s">}</span> | |
| 512 499 | |
| 513 500 <span class="c"># Calculate descriptor values...</span> | |
| 514 501 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 515 502 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
| 516 503 | |
| 517 504 <span class="i">$DescriptorClassObject</span><span class="i">->SetMolecule</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
| 518 505 <span class="i">$DescriptorClassObject</span><span class="i">->GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 519 506 | |
| 520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$DescriptorClassObject</span><span class="i">->IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 521 508 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 522 509 <span class="s">}</span> | |
| 523 510 <span class="s">}</span> | |
| 524 511 | |
| 525 512 <span class="c"># Set final descriptor values...</span> | |
| 526 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 527 514 | |
| 528 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 529 516 <span class="s">}</span> | |
| 530 517 | |
| 531 518 <span class="c"># Initialize descriptor values...</span> | |
| 532 519 <span class="c">#</span> | |
| 533 <a name="_InitializeDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span> | |
| 534 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 535 522 | |
| 536 523 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 537 524 | |
| 538 525 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 539 526 | |
| 540 527 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 541 528 <span class="s">}</span> | |
| 542 529 | |
| 543 530 <span class="c"># Setup final descriptor values...</span> | |
| 544 531 <span class="c">#</span> | |
| 545 <a name="_SetFinalDescriptorValues-"></a> 532 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> | |
| 546 533 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 547 534 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="s">)</span><span class="sc">;</span> | |
| 548 535 | |
| 549 536 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 550 537 | |
| 551 538 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 552 539 | |
| 553 540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 554 541 <span class="c"># Set descriptor values for all available descriptors...</span> | |
| 555 542 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 556 543 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
| 557 544 | |
| 558 545 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 559 546 <span class="s">}</span> | |
| 560 547 <span class="s">}</span> | |
| 561 548 <span class="k">else</span> <span class="s">{</span> | |
| 562 549 <span class="c"># Set descriptor values for a subset of available descriptors...</span> | |
| 563 550 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 564 551 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span> | |
| 565 552 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
| 566 553 | |
| 567 554 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="i">->GetDescriptorValueByName</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> | |
| 568 555 <span class="s">}</span> | |
| 569 556 <span class="s">}</span> | |
| 570 557 | |
| 571 558 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 572 559 <span class="s">}</span> | |
| 573 560 | |
| 574 561 <span class="c"># Is descriptors generation successful?</span> | |
| 575 562 <span class="c">#</span> | |
| 576 563 <span class="c"># Notes:</span> | |
| 577 564 <span class="c"># . After successful generation of descriptor values by each descriptor class</span> | |
| 578 565 <span class="c"># corresponding to specified descriptor names, DescriptorsCalculated to 1;</span> | |
| 579 566 <span class="c"># otherwise, it's set to 0.</span> | |
| 580 567 <span class="c">#</span> | |
| 581 <a name="IsDescriptorsGenerationSuccessful-"></a> 568 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span> | |
| 582 569 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 583 570 | |
| 584 571 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 585 572 <span class="s">}</span> | |
| 586 573 | |
| 587 574 <span class="c"># Check and set default descriptor names for generating descriptor values...</span> | |
| 588 575 <span class="c">#</span> | |
| 589 <a name="_CheckAndInitializeDescriptorNames-"></a> 576 <span class="k">sub </span><span class="m">_CheckAndInitializeDescriptorNames</span> <span class="s">{</span> | |
| 590 577 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 591 578 | |
| 592 579 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^(All|RuleOf5|RuleOf3)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 593 580 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 594 581 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: Descriptor names can't be specified during \"All, RuleOf5 or RuleOf3\" values of descsriptors generation \"Mode\"..."</span><span class="sc">;</span> | |
| 595 582 <span class="s">}</span> | |
| 596 583 <span class="s">}</span> | |
| 597 584 | |
| 598 585 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 599 586 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetAvailableDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 600 587 <span class="s">}</span> | |
| 601 588 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 602 589 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetRuleOf5DescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 603 590 <span class="s">}</span> | |
| 604 591 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 605 592 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetRuleOf3DescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 606 593 <span class="s">}</span> | |
| 607 594 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 608 595 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 609 596 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: DescriptorNames must be specified during Specify value for Mode..."</span><span class="sc">;</span> | |
| 610 597 <span class="s">}</span> | |
| 611 598 <span class="s">}</span> | |
| 612 599 <span class="k">else</span> <span class="s">{</span> | |
| 613 600 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: Mode value, $This->{Mode}, is not valid..."</span><span class="sc">;</span> | |
| 614 601 <span class="s">}</span> | |
| 615 602 <span class="s">}</span> | |
| 616 603 | |
| 617 604 <span class="c"># Instantiate descriptor classes corresponding to specified descriptor names...</span> | |
| 618 605 <span class="c">#</span> | |
| 619 <a name="_InstantiateDescriptorClasses-"></a> 606 <span class="k">sub </span><span class="m">_InstantiateDescriptorClasses</span> <span class="s">{</span> | |
| 620 607 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 621 608 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="cm">,</span> <span class="i">$DescriptorClassPath</span><span class="s">)</span><span class="sc">;</span> | |
| 622 609 | |
| 623 610 <span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 624 611 | |
| 625 612 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 626 613 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 627 614 | |
| 628 615 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 629 616 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span> | |
| 630 617 | |
| 631 618 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 632 619 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 633 620 <span class="s">}</span> | |
| 634 621 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span> | |
| 635 622 | |
| 636 623 <span class="i">$DescriptorClassPath</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
| 637 624 | |
| 638 625 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 639 626 <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="i">->new</span><span class="s">(</span><span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}}<span class="s">)</span><span class="sc">;</span> | |
| 640 627 <span class="s">}</span> | |
| 641 628 <span class="k">else</span> <span class="s">{</span> | |
| 642 629 <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="i">->new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 643 630 <span class="s">}</span> | |
| 644 631 <span class="s">}</span> | |
| 645 632 | |
| 646 633 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 647 634 <span class="s">}</span> | |
| 648 635 | |
| 649 636 <span class="c"># Return a string containg data for MolecularDescriptorsGenerator object...</span> | |
| 650 637 <span class="c">#</span> | |
| 651 <a name="StringifyMolecularDescriptorsGenerator-"></a> 638 <span class="k">sub </span><span class="m">StringifyMolecularDescriptorsGenerator</span> <span class="s">{</span> | |
| 652 639 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 653 640 <span class="k">my</span><span class="s">(</span><span class="i">$TheString</span><span class="cm">,</span> <span class="i">$NamesAndValuesString</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 654 641 | |
| 655 642 <span class="c"># Type of MolecularDescriptors...</span> | |
| 656 643 <span class="i">$TheString</span> = <span class="q">"MolecularDescriptorsGenerator: Mode - $This->{Mode}; SpecifiedDescriptorNames - < @{$This->{DescriptorNames}} >; AvailableMolecularDescriptorClassNames - < @{$DescriptorsDataMap{ClassNames}} >"</span><span class="sc">;</span> | |
| 657 644 | |
| 658 645 <span class="i">@NamesAndValuesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 659 646 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 660 647 | |
| 661 648 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 662 649 <span class="i">$Value</span> = <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>}<span class="sc">;</span> | |
| 663 650 <span class="i">$Value</span> = <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> || <span class="i">$Value</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> ? <span class="q">'None'</span> <span class="co">:</span> <span class="i">$Value</span><span class="sc">;</span> | |
| 664 651 <span class="k">push</span> <span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="q">"$Name - $Value"</span><span class="sc">;</span> | |
| 665 652 <span class="s">}</span> | |
| 666 653 <span class="k">if</span> <span class="s">(</span><span class="i">@NamesAndValuesInfo</span><span class="s">)</span> <span class="s">{</span> | |
| 667 654 <span class="i">$TheString</span> .= <span class="q">"Names - Values: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 668 655 <span class="s">}</span> | |
| 669 656 <span class="k">else</span> <span class="s">{</span> | |
| 670 657 <span class="i">$TheString</span> .= <span class="q">"Names - Values: < None>"</span><span class="sc">;</span> | |
| 671 658 <span class="s">}</span> | |
| 672 659 | |
| 673 660 <span class="k">return</span> <span class="i">$TheString</span><span class="sc">;</span> | |
| 674 661 <span class="s">}</span> | |
| 675 662 | |
| 676 663 <span class="c"># Is it a MolecularDescriptorsGenerator object?</span> | |
| 677 <a name="_IsMolecularDescriptorsGenerator-"></a> 664 <span class="k">sub </span><span class="m">_IsMolecularDescriptorsGenerator</span> <span class="s">{</span> | |
| 678 665 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 679 666 | |
| 680 667 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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> | |
| 681 668 <span class="s">}</span> | |
| 682 669 | |
| 683 670 <span class="c"># Validate descriptor names for generating descriptor values...</span> | |
| 684 671 <span class="c">#</span> | |
| 685 <a name="_ValidateDescriptorNames-"></a> 672 <span class="k">sub </span><span class="m">_ValidateDescriptorNames</span> <span class="s">{</span> | |
| 686 673 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 687 674 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> | |
| 688 675 | |
| 689 676 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 690 677 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 691 678 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_SetAndValidateDescriptorNames: Specified descriptor name, $DescriptorName, is not valid..."</span><span class="sc">;</span> | |
| 692 679 <span class="s">}</span> | |
| 693 680 <span class="s">}</span> | |
| 694 681 | |
| 695 682 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 696 683 <span class="s">}</span> | |
| 697 684 | |
| 698 685 <span class="c">#</span> | |
| 699 686 <span class="c"># Load available molecular descriptors data...</span> | |
| 700 687 <span class="c">#</span> | |
| 701 688 <span class="c"># All available molecular descriptors classes are automatically detected in</span> | |
| 702 689 <span class="c"># MolecularDescriptors directory under <MayaChemTools>/lib directory and</span> | |
| 703 690 <span class="c"># information about available descriptor names is retrieved from each descriptor</span> | |
| 704 691 <span class="c"># class using function GetDescriptorNames. The following %DescriptorsDataMap</span> | |
| 705 692 <span class="c"># is setup containing all available molecular descriptors data:</span> | |
| 706 693 <span class="c">#</span> | |
| 707 694 <span class="c"># @{$DescriptorsDataMap{ClassNames}}</span> | |
| 708 695 <span class="c"># %{$DescriptorsDataMap{ClassNameToPath}}</span> | |
| 709 696 <span class="c"># %{$DescriptorsDataMap{ClassToDescriptorNames}}</span> | |
| 710 697 <span class="c"># %{$DescriptorsDataMap{DescriptorToClassName}}</span> | |
| 711 698 <span class="c">#</span> | |
| 712 699 <span class="c"># GenerateDescriptors method is invoked fo each specified descriptor class</span> | |
| 713 700 <span class="c"># object to calculate descriptor values for specified descriptors. After successful</span> | |
| 714 701 <span class="c"># calculation of descriptors, GetDescriptorValues or GetDescriptorValueByName</span> | |
| 715 702 <span class="c"># methods provided by descriptor objects are used to retrieve calculated</span> | |
| 716 703 <span class="c"># descriptor values.</span> | |
| 717 704 <span class="c">#</span> | |
| 718 <a name="_LoadMolecularDescriptorsData-"></a> 705 <span class="k">sub </span><span class="m">_LoadMolecularDescriptorsData</span> <span class="s">{</span> | |
| 719 706 | |
| 720 707 <span class="i">%DescriptorsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 721 708 | |
| 722 709 <span class="i">_RetrieveAndLoadDescriptorClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 723 710 <span class="i">_SetupDescriptorsDataMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 724 711 <span class="s">}</span> | |
| 725 712 | |
| 726 713 <span class="c">#</span> | |
| 727 714 <span class="c"># Retrieve available molecular descriptors classes from MolecularDescriptors directory under</span> | |
| 728 715 <span class="c"># <MayaChemTools>/lib directory...</span> | |
| 729 716 <span class="c">#</span> | |
| 730 <a name="_RetrieveAndLoadDescriptorClasses-"></a> 717 <span class="k">sub </span><span class="m">_RetrieveAndLoadDescriptorClasses</span> <span class="s">{</span> | |
| 731 718 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorsDirName</span><span class="cm">,</span> <span class="i">$MayaChemToolsLibDir</span><span class="cm">,</span> <span class="i">$DescriptorsDirPath</span><span class="cm">,</span> <span class="i">$IncludeDirName</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassPath</span><span class="cm">,</span> <span class="i">$DescriptorsClassFileName</span><span class="cm">,</span> <span class="i">@FileNames</span><span class="cm">,</span> <span class="i">@DescriptorsClassFileNames</span><span class="s">)</span><span class="sc">;</span> | |
| 732 719 | |
| 733 720 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 734 721 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToPath</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 735 722 | |
| 736 723 <span class="i">$DescriptorsDirName</span> = <span class="q">"MolecularDescriptors"</span><span class="sc">;</span> | |
| 737 724 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">FileUtil::GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 738 725 | |
| 739 726 <span class="i">$DescriptorsDirPath</span> = <span class="q">"$MayaChemToolsLibDir/$DescriptorsDirName"</span><span class="sc">;</span> | |
| 740 727 | |
| 741 728 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="q">"$DescriptorsDirPath"</span><span class="s">)</span> <span class="s">{</span> | |
| 742 729 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, is missing: Possible installation problems..."</span><span class="sc">;</span> | |
| 743 730 <span class="s">}</span> | |
| 744 731 | |
| 745 732 <span class="i">@FileNames</span> = <span class="s">(</span><span class="q">"$DescriptorsDirPath/*"</span><span class="s">)</span><span class="sc">;</span> | |
| 746 733 <span class="i">$IncludeDirName</span> = <span class="n">0</span><span class="sc">;</span> | |
| 747 734 <span class="i">@DescriptorsClassFileNames</span> = <span class="i">FileUtil::ExpandFileNames</span><span class="s">(</span>\<span class="i">@FileNames</span><span class="cm">,</span> <span class="q">"pm"</span><span class="cm">,</span> <span class="i">$IncludeDirName</span><span class="s">)</span><span class="sc">;</span> | |
| 748 735 | |
| 749 736 <span class="k">if</span> <span class="s">(</span>!<span class="i">@DescriptorsClassFileNames</span><span class="s">)</span> <span class="s">{</span> | |
| 750 737 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, doesn't contain any molecular descriptor class: Possible installation problems..."</span><span class="sc">;</span> | |
| 751 738 <span class="s">}</span> | |
| 752 739 | |
| 753 740 <span class="j">FILENAME:</span> <span class="k">for</span> <span class="i">$DescriptorsClassFileName</span> <span class="s">(</span><span class="k">sort</span> <span class="i">@DescriptorsClassFileNames</span><span class="s">)</span> <span class="s">{</span> | |
| 754 741 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorsClassFileName</span> !~ <span class="q">/\.pm/</span><span class="s">)</span> <span class="s">{</span> | |
| 755 742 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, contains invalid class file name $DescriptorsClassFileName: Possible installation problems..."</span><span class="sc">;</span> | |
| 756 743 <span class="s">}</span> | |
| 757 744 | |
| 758 745 <span class="c"># Ignore base class and descriptors generator class...</span> | |
| 759 746 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorsClassFileName</span> =~ <span class="q">/^(MolecularDescriptorsGenerator\.pm|MolecularDescriptors\.pm)$/</span><span class="s">)</span> <span class="s">{</span> | |
| 760 747 <span class="k">next</span> <span class="j">FILENAME</span><span class="sc">;</span> | |
| 761 748 <span class="s">}</span> | |
| 762 749 | |
| 763 750 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$DescriptorsClassFileName</span><span class="sc">;</span> | |
| 764 751 <span class="i">$DescriptorClassPath</span> = <span class="q">"${DescriptorsDirName}::${DescriptorClassName}"</span><span class="sc">;</span> | |
| 765 752 | |
| 766 753 <span class="c"># Load descriptors class...</span> | |
| 767 754 <span class="k">eval</span> <span class="q">"use $DescriptorClassPath"</span><span class="sc">;</span> | |
| 768 755 | |
| 769 756 <span class="k">if</span> <span class="s">(</span><span class="i">$@</span><span class="s">)</span> <span class="s">{</span> | |
| 770 757 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: use $DescriptorClassPath failed: $@ ..."</span><span class="sc">;</span> | |
| 771 758 <span class="s">}</span> | |
| 772 759 | |
| 773 760 <span class="k">push</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span> | |
| 774 761 | |
| 775 762 <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="sc">;</span> | |
| 776 763 <span class="s">}</span> | |
| 777 764 <span class="s">}</span> | |
| 778 765 | |
| 779 766 <span class="c">#</span> | |
| 780 767 <span class="c"># Setup descriptors data map using loaded descriptor classes...</span> | |
| 781 768 <span class="c">#</span> | |
| 782 <a name="_SetupDescriptorsDataMap-"></a> 769 <span class="k">sub </span><span class="m">_SetupDescriptorsDataMap</span> <span class="s">{</span> | |
| 783 770 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="cm">,</span> <span class="i">$DescriptorClassPath</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 784 771 | |
| 785 772 <span class="c"># Class to decriptor names map...</span> | |
| 786 773 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 787 774 | |
| 788 775 <span class="c"># Descriptor to class name map...</span> | |
| 789 776 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 790 777 | |
| 791 778 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 792 779 <span class="i">$DescriptorClassPath</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
| 793 780 | |
| 794 781 <span class="i">@DescriptorNames</span> = <span class="i">$DescriptorClassPath</span><span class="i">->GetDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 795 782 | |
| 796 783 <span class="k">if</span> <span class="s">(</span>!<span class="i">@DescriptorNames</span><span class="s">)</span> <span class="s">{</span> | |
| 797 784 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName doesn't provide any descriptor names..."</span><span class="sc">;</span> | |
| 798 785 <span class="s">}</span> | |
| 799 786 | |
| 800 787 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>} <span class="s">)</span> <span class="s">{</span> | |
| 801 788 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName has already been processed..."</span><span class="sc">;</span> | |
| 802 789 <span class="s">}</span> | |
| 803 790 | |
| 804 791 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 805 792 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
| 806 793 | |
| 807 794 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span> <span class="s">{</span> | |
| 808 795 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 809 796 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor name, $DescriptorName, in class name, $DescriptorClassName, has already been provided by class name $DescriptorsDataMap{DescriptorToClassName}{$DescriptorName}..."</span><span class="sc">;</span> | |
| 810 797 <span class="s">}</span> | |
| 811 798 | |
| 812 799 <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>} = <span class="i">$DescriptorClassName</span><span class="sc">;</span> | |
| 813 800 <span class="s">}</span> | |
| 814 801 <span class="s">}</span> | |
| 815 802 <span class="s">}</span> | |
| 816 803 | |
| 817 <a name="EOF-"></a></pre> | |
| 818 <p> </p> | |
| 819 <br /> | |
| 820 <center> | |
| 821 <img src="../../../images/h2o2.png"> | |
| 822 </center> | |
| 823 </body> | |
| 824 </html> |