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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/MolecularDescriptorsGenerator.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,824 @@ +<html> +<head> +<title>MayaChemTools:Code:MolecularDescriptors::MolecularDescriptorsGenerator.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> +<a name="package-MolecularDescriptors::MolecularDescriptorsGenerator-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularDescriptorsGenerator</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: MolecularDescriptorsGenerator.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> + 5 <span class="c"># $Revision: 1.13 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> + 38 + 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> + 40 + 41 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> + 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> + 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> + 44 + 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> + 46 + 47 <span class="c"># Setup class variables...</span> + 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> + 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 50 + 51 <span class="c"># Overload Perl functions...</span> + 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> + 53 + 54 <span class="c"># Class constructor...</span> +<a name="new-"></a> 55 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> + 56 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 57 + 58 <span class="c"># Initialize object...</span> + 59 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> + 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">$Class</span><span class="sc">;</span> + 61 <span class="i">$This</span><span class="i">->_InitializeMolecularDescriptorsGenerator</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 62 + 63 <span class="i">$This</span><span class="i">->_InitializeMolecularDescriptorsGeneratorProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 64 + 65 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 66 <span class="s">}</span> + 67 + 68 <span class="c"># Initialize class ...</span> +<a name="_InitializeClass-"></a> 69 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> + 70 <span class="c">#Class name...</span> + 71 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> + 72 + 73 <span class="c"># Load available molecular descriptor classes...</span> + 74 <span class="i">_LoadMolecularDescriptorsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 75 + 76 <span class="s">}</span> + 77 + 78 <span class="c"># Initialize object data...</span> + 79 <span class="c">#</span> +<a name="_InitializeMolecularDescriptorsGenerator-"></a> 80 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptorsGenerator</span> <span class="s">{</span> + 81 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 82 + 83 <span class="c"># Type of desciptors to generate...</span> + 84 <span class="c">#</span> + 85 <span class="c"># The current release of MayaChemTools supports generation of four sets of</span> + 86 <span class="c"># descriptors: All available descriptors, rule of 5 or 3 descriptors or a specified</span> + 87 <span class="c"># set of descriptors.</span> + 88 <span class="c">#</span> + 89 <span class="c"># Possible values: All, RuleOf5, RuleOf3 or Specify</span> + 90 <span class="c">#</span> + 91 <span class="c"># RuleOf5 [ Ref 91 ] descriptor names: MolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors,</span> + 92 <span class="c"># SLogP. RuleOf5 states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10,</span> + 93 <span class="c"># and logP <= 5.</span> + 94 <span class="c">#</span> + 95 <span class="c"># RuleOf3 [ Ref 92 ] descriptor names: MolecularWeight, RotatableBonds, HydrogenBondDonors,</span> + 96 <span class="c"># HydrogenBondAcceptors, SLogP, TPSA. RuleOf3 states: MolecularWeight <= 300, RotatableBonds <= 3,</span> + 97 <span class="c"># HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</span> + 98 <span class="c">#</span> + 99 <span class="c"># For Specify value of Mode, a set of descritor names must be specified using</span> + 100 <span class="c"># DescriptorNames parameter.</span> + 101 <span class="c">#</span> + 102 <span class="c"># Default: All</span> + 103 <span class="c">#</span> + 104 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="q">''</span><span class="sc">;</span> + 105 + 106 <span class="c"># Descriptor names used to generate descriptor values during a specified descriptor</span> + 107 <span class="c"># generation mode...</span> + 108 <span class="c">#</span> + 109 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 110 + 111 <span class="c"># Descriptor calculation control parameters for specified descriptor class names...</span> + 112 <span class="c">#</span> + 113 <span class="c"># These parameters are passed on to appropriate descriptor classes during</span> + 114 <span class="c"># instantiations of descriptor class objects.</span> + 115 <span class="c">#</span> + 116 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 117 + 118 <span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>} = <span class="n">0</span><span class="sc">;</span> + 119 + 120 <span class="c"># Descriptor class names and objects corresponding to specified descriptor names...</span> + 121 <span class="c">#</span> + 122 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 123 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 124 + 125 <span class="c"># Descriptor values generated for specified descriptor names...</span> + 126 <span class="c">#</span> + 127 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 128 + 129 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 130 <span class="s">}</span> + 131 + 132 <span class="c"># Initialize object properties...</span> + 133 <span class="c">#</span> +<a name="_InitializeMolecularDescriptorsGeneratorProperties-"></a> 134 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptorsGeneratorProperties</span> <span class="s">{</span> + 135 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 136 + 137 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 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> + 139 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> + 140 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 141 <span class="s">}</span> + 142 + 143 <span class="c"># Set default value for Mode...</span> + 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Mode</span>}<span class="s">)</span> <span class="s">{</span> + 145 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="q">'All'</span><span class="sc">;</span> + 146 <span class="s">}</span> + 147 + 148 <span class="i">$This</span><span class="i">->_CheckAndInitializeDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 149 + 150 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 151 <span class="s">}</span> + 152 + 153 <span class="c"># Set descriptors generation mode......</span> + 154 <span class="c">#</span> +<a name="SetMode-"></a> 155 <span class="k">sub </span><span class="m">SetMode</span> <span class="s">{</span> + 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 157 + 158 <span class="c"># All - all available descriptors</span> + 159 <span class="c"># Specify - Specified set of descriptors</span> + 160 + 161 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(All|RuleOf5|RuleOf3|Specify)$/i</span><span class="s">)</span> <span class="s">{</span> + 162 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMode: Mode value, $Value, is not valid; Supported values: All, RuleOf5, RuleOf3 or Specify..."</span><span class="sc">;</span> + 163 <span class="s">}</span> + 164 + 165 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="i">$Value</span><span class="sc">;</span> + 166 + 167 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 168 <span class="s">}</span> + 169 + 170 <span class="c"># Set descriptor names to use for generating descriptor values using an array</span> + 171 <span class="c"># or reference to an array...</span> + 172 <span class="c">#</span> +<a name="SetDescriptorNames-"></a> 173 <span class="k">sub </span><span class="m">SetDescriptorNames</span> <span class="s">{</span> + 174 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 175 + 176 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> + 177 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDescriptorNames: Descriptor names cann't be specified during \"All\" value of descsriptors generation \"Mode\"..."</span><span class="sc">;</span> + 178 <span class="s">}</span> + 179 + 180 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> + 181 <span class="k">return</span><span class="sc">;</span> + 182 <span class="s">}</span> + 183 + 184 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="s">)</span><span class="sc">;</span> + 185 + 186 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> + 187 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> + 188 + 189 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 190 + 191 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> + 192 <span class="c"># Initialize using array refernce...</span> + 193 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> + 194 <span class="s">}</span> + 195 <span class="k">else</span> <span class="s">{</span> + 196 <span class="c"># It's a list of values...</span> + 197 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> + 198 <span class="s">}</span> + 199 + 200 <span class="c"># Make sure specified descriptor names are valid...</span> + 201 <span class="i">$This</span><span class="i">->_ValidateDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 202 + 203 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 204 <span class="s">}</span> + 205 + 206 <span class="c"># Get descriptor names as an array...</span> + 207 <span class="c">#</span> +<a name="GetDescriptorNames-"></a> 208 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> + 209 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 210 + 211 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span> + 212 <span class="s">}</span> + 213 + 214 <span class="c"># Get all descriptor values as an array...</span> + 215 <span class="c">#</span> +<a name="GetDescriptorValues-"></a> 216 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span> + 217 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 218 + 219 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>}<span class="s">)</span> <span class="s">{</span> + 220 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="sc">;</span> + 221 <span class="s">}</span> + 222 <span class="k">else</span> <span class="s">{</span> + 223 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorValues</span><span class="s">)</span><span class="sc">;</span> + 224 + 225 <span class="i">@DescriptorValues</span> = <span class="s">(</span><span class="q">'None'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span> + 226 + 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> + 228 <span class="s">}</span> + 229 <span class="s">}</span> + 230 + 231 <span class="c"># Get descriptor value for a specified descriptor name...</span> + 232 <span class="c">#</span> +<a name="GetDescriptorValueByName-"></a> 233 <span class="k">sub </span><span class="m">GetDescriptorValueByName</span> <span class="s">{</span> + 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> + 235 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 236 + 237 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 238 + 239 <span class="k">return</span> <span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} ? <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> + 240 + 241 <span class="s">}</span> + 242 + 243 <span class="c"># Get calculated molecular descriptor names sand values as a hash with names</span> + 244 <span class="c"># and values as key/value pairs...</span> + 245 <span class="c">#</span> +<a name="GetDescriptorNamesAndValues-"></a> 246 <span class="k">sub </span><span class="m">GetDescriptorNamesAndValues</span> <span class="s">{</span> + 247 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 248 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 249 + 250 <span class="i">%NamesAndValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 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> + 252 + 253 <span class="k">return</span> <span class="i">%NamesAndValues</span><span class="sc">;</span> + 254 <span class="s">}</span> + 255 + 256 <span class="c"># Set up descriptor calculation control parameters for a specified descriptor class name...</span> + 257 <span class="c">#</span> + 258 <span class="c"># The specified parameter names and values are simply passed on to specified descriptor</span> + 259 <span class="c"># class during instantiation of descriptor class object without any performing any validation</span> + 260 <span class="c"># of parameter names and associated values. It's up to the appropriate descriptor class methods</span> + 261 <span class="c"># to validate these parameters and values.</span> + 262 <span class="c">#</span> + 263 <span class="c"># In addition to specified parameter names and values, the parameter hash must also contain</span> + 264 <span class="c"># descriptor class name as key and value pair with DescriptorClassName as key with class</span> + 265 <span class="c"># name as value.</span> + 266 <span class="c">#</span> +<a name="SetDescriptorClassParameters-"></a> 267 <span class="k">sub </span><span class="m">SetDescriptorClassParameters</span> <span class="s">{</span> + 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 269 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 270 + 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> + 272 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_SetDescriptorNameParameters: Can't set descriptor class name paramaters: DescriptorClassName is not specified..."</span><span class="sc">;</span> + 273 <span class="s">}</span> + 274 + 275 <span class="i">$DescriptorClassName</span> = <span class="i">$NamesAndValues</span>{<span class="w">DescriptorClassName</span>}<span class="sc">;</span> + 276 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsDescriptorClassNameAvailable</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 277 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_SetDescriptorClassParameters: Can't set descriptor class name paramaters: Specified descriptor class name, $DescriptorClassName, is not available..."</span><span class="sc">;</span> + 278 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 279 <span class="s">}</span> + 280 + 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> + 282 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetDescriptorClassParameters: Class name parameters for $DescriptorClassName have already been specified: Replacing previous values..."</span><span class="sc">;</span> + 283 <span class="s">}</span> + 284 + 285 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 286 <span class="j">NAME:</span> <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> + 287 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^DescriptorClassName$/</span><span class="s">)</span> <span class="s">{</span> + 288 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> + 289 <span class="s">}</span> + 290 <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span> + 291 <span class="s">}</span> + 292 + 293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 294 <span class="s">}</span> + 295 + 296 <span class="c"># Get descriptor name parameters as a reference to hash of hashes with hash</span> + 297 <span class="c"># keys corresponding to class name and class parameter name with hash value</span> + 298 <span class="c"># as class parameter value...</span> + 299 <span class="c">#</span> +<a name="GetDescriptorClassParameters-"></a> 300 <span class="k">sub </span><span class="m">GetDescriptorClassParameters</span> <span class="s">{</span> + 301 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 302 + 303 <span class="k">return</span> \<span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}}<span class="sc">;</span> + 304 <span class="s">}</span> + 305 + 306 <span class="c"># Get available descriptor class names as an array.</span> + 307 <span class="c">#</span> + 308 <span class="c"># This functionality can be either invoked as a class function or an</span> + 309 <span class="c"># object method.</span> + 310 <span class="c">#</span> +<a name="GetAvailableDescriptorClassNames-"></a> 311 <span class="k">sub </span><span class="m">GetAvailableDescriptorClassNames</span> <span class="s">{</span> + 312 + 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> + 314 <span class="s">}</span> + 315 + 316 <span class="c"># Get available descriptors class and descriptors names as a hash containing key/value</span> + 317 <span class="c"># pairs corresponding to class name and an array of descriptor names available for the</span> + 318 <span class="c"># class.</span> + 319 <span class="c">#</span> + 320 <span class="c"># This functionality can be either invoked as a class function or an</span> + 321 <span class="c"># object method.</span> + 322 <span class="c">#</span> +<a name="GetAvailableClassAndDescriptorNames-"></a> 323 <span class="k">sub </span><span class="m">GetAvailableClassAndDescriptorNames</span> <span class="s">{</span> + 324 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">%ClassAndDescriptorNames</span><span class="s">)</span><span class="sc">;</span> + 325 + 326 <span class="i">%ClassAndDescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 327 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="s">)</span> <span class="s">{</span> + 328 <span class="i">@</span>{<span class="i">$ClassAndDescriptorNames</span>{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 329 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">$DescriptorClassName</span>}}<span class="sc">;</span> + 330 <span class="s">}</span> + 331 + 332 <span class="k">return</span> <span class="i">%ClassAndDescriptorNames</span><span class="sc">;</span> + 333 <span class="s">}</span> + 334 + 335 <span class="c"># Get available descriptor names as an array.</span> + 336 <span class="c">#</span> + 337 <span class="c"># This functionality can be either invoked as a class function or an</span> + 338 <span class="c"># object method.</span> + 339 <span class="c">#</span> +<a name="GetAvailableDescriptorNames-"></a> 340 <span class="k">sub </span><span class="m">GetAvailableDescriptorNames</span> <span class="s">{</span> + 341 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> + 342 + 343 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 344 <span class="k">push</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="k">map</span> <span class="s">{</span> <span class="i">@</span>{<span class="i">$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> + 345 + 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> + 347 <span class="s">}</span> + 348 + 349 <span class="c"># Is it a valid descriptors class name?</span> + 350 <span class="c">#</span> + 351 <span class="c"># This functionality can be either invoked as a class function or an</span> + 352 <span class="c"># object method.</span> + 353 <span class="c">#</span> +<a name="IsDescriptorClassNameAvailable-"></a> 354 <span class="k">sub </span><span class="m">IsDescriptorClassNameAvailable</span> <span class="s">{</span> + 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> + 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> + 357 + 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">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 359 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> + 360 <span class="s">}</span> + 361 <span class="k">else</span> <span class="s">{</span> + 362 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> + 363 <span class="s">}</span> + 364 + 365 <span class="k">return</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 366 <span class="s">}</span> + 367 + 368 <span class="c"># Is it a valid descriptor name?</span> + 369 <span class="c">#</span> + 370 <span class="c"># This functionality can be either invoked as a class function or an</span> + 371 <span class="c"># object method.</span> + 372 <span class="c">#</span> +<a name="IsDescriptorNameAvailable-"></a> 373 <span class="k">sub </span><span class="m">IsDescriptorNameAvailable</span> <span class="s">{</span> + 374 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 375 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> + 376 + 377 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 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> + 379 <span class="s">}</span> + 380 <span class="k">else</span> <span class="s">{</span> + 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> + 382 <span class="s">}</span> + 383 + 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> + 385 <span class="s">}</span> + 386 + 387 <span class="c"># Get available descriptors names for a descriptor class as an array.</span> + 388 <span class="c">#</span> + 389 <span class="c"># This functionality can be either invoked as a class function or an</span> + 390 <span class="c"># object method.</span> + 391 <span class="c">#</span> +<a name="GetAvailableDescriptorNamesForDescriptorClass-"></a> 392 <span class="k">sub </span><span class="m">GetAvailableDescriptorNamesForDescriptorClass</span> <span class="s">{</span> + 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> + 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> + 395 + 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">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 397 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> + 398 <span class="s">}</span> + 399 <span class="k">else</span> <span class="s">{</span> + 400 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> + 401 <span class="s">}</span> + 402 + 403 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 404 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> + 405 <span class="k">push</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}}<span class="sc">;</span> + 406 <span class="s">}</span> + 407 + 408 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> + 409 <span class="s">}</span> + 410 + 411 <span class="c"># Get available descriptors class name for a descriptor name.</span> + 412 <span class="c">#</span> + 413 <span class="c"># This functionality can be either invoked as a class function or an</span> + 414 <span class="c"># object method.</span> + 415 <span class="c">#</span> +<a name="GetAvailableClassNameForDescriptorName-"></a> 416 <span class="k">sub </span><span class="m">GetAvailableClassNameForDescriptorName</span> <span class="s">{</span> + 417 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 418 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 419 + 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">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 421 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> + 422 <span class="s">}</span> + 423 <span class="k">else</span> <span class="s">{</span> + 424 <span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> + 425 <span class="s">}</span> + 426 + 427 <span class="i">$DescriptorClassName</span> = <span class="q">''</span><span class="sc">;</span> + 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> + 429 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span> + 430 <span class="s">}</span> + 431 + 432 <span class="k">return</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span> + 433 <span class="s">}</span> + 434 + 435 <span class="c"># Get RuleOf5 descriptor names as an array.</span> + 436 <span class="c">#</span> + 437 <span class="c"># This functionality can be either invoked as a class function or an</span> + 438 <span class="c"># object method.</span> + 439 <span class="c">#</span> +<a name="GetRuleOf5DescriptorNames-"></a> 440 <span class="k">sub </span><span class="m">GetRuleOf5DescriptorNames</span> <span class="s">{</span> + 441 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> + 442 + 443 <span class="i">@DescriptorNames</span> = <span class="q">qw(MolecularWeight HydrogenBondDonors HydrogenBondAcceptors SLogP)</span><span class="sc">;</span> + 444 + 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> + 446 <span class="s">}</span> + 447 + 448 <span class="c"># Get RuleOf3 descriptor names as an array.</span> + 449 <span class="c">#</span> + 450 <span class="c"># This functionality can be either invoked as a class function or an</span> + 451 <span class="c"># object method.</span> + 452 <span class="c">#</span> +<a name="GetRuleOf3DescriptorNames-"></a> 453 <span class="k">sub </span><span class="m">GetRuleOf3DescriptorNames</span> <span class="s">{</span> + 454 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> + 455 + 456 <span class="i">@DescriptorNames</span> = <span class="q">qw(MolecularWeight RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span> + 457 + 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> + 459 <span class="s">}</span> + 460 + 461 + 462 <span class="c"># Set molecule object...</span> + 463 <span class="c">#</span> +<a name="SetMolecule-"></a> 464 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> + 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> + 466 + 467 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> + 468 + 469 <span class="c"># Weaken the reference to disable increment of reference count...</span> + 470 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> + 471 + 472 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 473 <span class="s">}</span> + 474 + 475 <span class="c"># Generate specified molecular descriptors...</span> + 476 <span class="c">#</span> + 477 <span class="c"># After instantiating descriptor class objects at first invocation and initialializing</span> + 478 <span class="c"># descriptor values during subsequent invocations, GenerateDescriptors method</span> + 479 <span class="c"># provided by each descriptor class is used to calculate descriptor values for</span> + 480 <span class="c"># specified descriptors.</span> + 481 <span class="c">#</span> +<a name="GenerateDescriptors-"></a> 482 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> + 483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 484 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="s">)</span><span class="sc">;</span> + 485 + 486 <span class="c"># Initialize descriptor values...</span> + 487 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 488 + 489 <span class="c"># Instantiate decriptor classed corresponding to specified descriptors...</span> + 490 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>}<span class="s">)</span> <span class="s">{</span> + 491 <span class="i">$This</span><span class="i">->_InstantiateDescriptorClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 492 <span class="s">}</span> + 493 + 494 <span class="c"># Check availability of molecule...</span> + 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> + 496 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> + 497 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 498 <span class="s">}</span> + 499 + 500 <span class="c"># Calculate descriptor values...</span> + 501 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="s">)</span> <span class="s">{</span> + 502 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> + 503 + 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> + 505 <span class="i">$DescriptorClassObject</span><span class="i">->GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 506 + 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$DescriptorClassObject</span><span class="i">->IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 508 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 509 <span class="s">}</span> + 510 <span class="s">}</span> + 511 + 512 <span class="c"># Set final descriptor values...</span> + 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 514 + 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 516 <span class="s">}</span> + 517 + 518 <span class="c"># Initialize descriptor values...</span> + 519 <span class="c">#</span> +<a name="_InitializeDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span> + 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 522 + 523 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">0</span><span class="sc">;</span> + 524 + 525 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 526 + 527 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 528 <span class="s">}</span> + 529 + 530 <span class="c"># Setup final descriptor values...</span> + 531 <span class="c">#</span> +<a name="_SetFinalDescriptorValues-"></a> 532 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> + 533 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 534 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 535 + 536 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> + 537 + 538 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 539 + 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> + 541 <span class="c"># Set descriptor values for all available descriptors...</span> + 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> + 543 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> + 544 + 545 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 546 <span class="s">}</span> + 547 <span class="s">}</span> + 548 <span class="k">else</span> <span class="s">{</span> + 549 <span class="c"># Set descriptor values for a subset of available descriptors...</span> + 550 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> + 551 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span> + 552 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> + 553 + 554 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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> + 555 <span class="s">}</span> + 556 <span class="s">}</span> + 557 + 558 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 559 <span class="s">}</span> + 560 + 561 <span class="c"># Is descriptors generation successful?</span> + 562 <span class="c">#</span> + 563 <span class="c"># Notes:</span> + 564 <span class="c"># . After successful generation of descriptor values by each descriptor class</span> + 565 <span class="c"># corresponding to specified descriptor names, DescriptorsCalculated to 1;</span> + 566 <span class="c"># otherwise, it's set to 0.</span> + 567 <span class="c">#</span> +<a name="IsDescriptorsGenerationSuccessful-"></a> 568 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span> + 569 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 570 + 571 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 572 <span class="s">}</span> + 573 + 574 <span class="c"># Check and set default descriptor names for generating descriptor values...</span> + 575 <span class="c">#</span> +<a name="_CheckAndInitializeDescriptorNames-"></a> 576 <span class="k">sub </span><span class="m">_CheckAndInitializeDescriptorNames</span> <span class="s">{</span> + 577 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 578 + 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> + 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> + 581 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: Descriptor names can't be specified during \"All, RuleOf5 or RuleOf3\" values of descsriptors generation \"Mode\"..."</span><span class="sc">;</span> + 582 <span class="s">}</span> + 583 <span class="s">}</span> + 584 + 585 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> + 586 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetAvailableDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 587 <span class="s">}</span> + 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> + 589 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetRuleOf5DescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 590 <span class="s">}</span> + 591 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span> + 592 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetRuleOf3DescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 593 <span class="s">}</span> + 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> + 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> + 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> + 597 <span class="s">}</span> + 598 <span class="s">}</span> + 599 <span class="k">else</span> <span class="s">{</span> + 600 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: Mode value, $This->{Mode}, is not valid..."</span><span class="sc">;</span> + 601 <span class="s">}</span> + 602 <span class="s">}</span> + 603 + 604 <span class="c"># Instantiate descriptor classes corresponding to specified descriptor names...</span> + 605 <span class="c">#</span> +<a name="_InstantiateDescriptorClasses-"></a> 606 <span class="k">sub </span><span class="m">_InstantiateDescriptorClasses</span> <span class="s">{</span> + 607 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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">$DescriptorClassPath</span><span class="s">)</span><span class="sc">;</span> + 609 + 610 <span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>} = <span class="n">1</span><span class="sc">;</span> + 611 + 612 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 613 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 614 + 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> + 616 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span> + 617 + 618 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> + 619 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> + 620 <span class="s">}</span> + 621 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span> + 622 + 623 <span class="i">$DescriptorClassPath</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> + 624 + 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> + 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">$DescriptorClassName</span>}}<span class="s">)</span><span class="sc">;</span> + 627 <span class="s">}</span> + 628 <span class="k">else</span> <span class="s">{</span> + 629 <span class="i">$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> + 630 <span class="s">}</span> + 631 <span class="s">}</span> + 632 + 633 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 634 <span class="s">}</span> + 635 + 636 <span class="c"># Return a string containg data for MolecularDescriptorsGenerator object...</span> + 637 <span class="c">#</span> +<a name="StringifyMolecularDescriptorsGenerator-"></a> 638 <span class="k">sub </span><span class="m">StringifyMolecularDescriptorsGenerator</span> <span class="s">{</span> + 639 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 641 + 642 <span class="c"># Type of MolecularDescriptors...</span> + 643 <span class="i">$TheString</span> = <span class="q">"MolecularDescriptorsGenerator: Mode - $This->{Mode}; SpecifiedDescriptorNames - < @{$This->{DescriptorNames}} >; AvailableMolecularDescriptorClassNames - < @{$DescriptorsDataMap{ClassNames}} >"</span><span class="sc">;</span> + 644 + 645 <span class="i">@NamesAndValuesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 646 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 647 + 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> + 649 <span class="i">$Value</span> = <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>}<span class="sc">;</span> + 650 <span class="i">$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> + 651 <span class="k">push</span> <span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="q">"$Name - $Value"</span><span class="sc">;</span> + 652 <span class="s">}</span> + 653 <span class="k">if</span> <span class="s">(</span><span class="i">@NamesAndValuesInfo</span><span class="s">)</span> <span class="s">{</span> + 654 <span class="i">$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> + 655 <span class="s">}</span> + 656 <span class="k">else</span> <span class="s">{</span> + 657 <span class="i">$TheString</span> .= <span class="q">"Names - Values: < None>"</span><span class="sc">;</span> + 658 <span class="s">}</span> + 659 + 660 <span class="k">return</span> <span class="i">$TheString</span><span class="sc">;</span> + 661 <span class="s">}</span> + 662 + 663 <span class="c"># Is it a MolecularDescriptorsGenerator object?</span> +<a name="_IsMolecularDescriptorsGenerator-"></a> 664 <span class="k">sub </span><span class="m">_IsMolecularDescriptorsGenerator</span> <span class="s">{</span> + 665 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 666 + 667 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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> + 668 <span class="s">}</span> + 669 + 670 <span class="c"># Validate descriptor names for generating descriptor values...</span> + 671 <span class="c">#</span> +<a name="_ValidateDescriptorNames-"></a> 672 <span class="k">sub </span><span class="m">_ValidateDescriptorNames</span> <span class="s">{</span> + 673 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 674 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> + 675 + 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> + 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> + 678 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_SetAndValidateDescriptorNames: Specified descriptor name, $DescriptorName, is not valid..."</span><span class="sc">;</span> + 679 <span class="s">}</span> + 680 <span class="s">}</span> + 681 + 682 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 683 <span class="s">}</span> + 684 + 685 <span class="c">#</span> + 686 <span class="c"># Load available molecular descriptors data...</span> + 687 <span class="c">#</span> + 688 <span class="c"># All available molecular descriptors classes are automatically detected in</span> + 689 <span class="c"># MolecularDescriptors directory under <MayaChemTools>/lib directory and</span> + 690 <span class="c"># information about available descriptor names is retrieved from each descriptor</span> + 691 <span class="c"># class using function GetDescriptorNames. The following %DescriptorsDataMap</span> + 692 <span class="c"># is setup containing all available molecular descriptors data:</span> + 693 <span class="c">#</span> + 694 <span class="c"># @{$DescriptorsDataMap{ClassNames}}</span> + 695 <span class="c"># %{$DescriptorsDataMap{ClassNameToPath}}</span> + 696 <span class="c"># %{$DescriptorsDataMap{ClassToDescriptorNames}}</span> + 697 <span class="c"># %{$DescriptorsDataMap{DescriptorToClassName}}</span> + 698 <span class="c">#</span> + 699 <span class="c"># GenerateDescriptors method is invoked fo each specified descriptor class</span> + 700 <span class="c"># object to calculate descriptor values for specified descriptors. After successful</span> + 701 <span class="c"># calculation of descriptors, GetDescriptorValues or GetDescriptorValueByName</span> + 702 <span class="c"># methods provided by descriptor objects are used to retrieve calculated</span> + 703 <span class="c"># descriptor values.</span> + 704 <span class="c">#</span> +<a name="_LoadMolecularDescriptorsData-"></a> 705 <span class="k">sub </span><span class="m">_LoadMolecularDescriptorsData</span> <span class="s">{</span> + 706 + 707 <span class="i">%DescriptorsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 708 + 709 <span class="i">_RetrieveAndLoadDescriptorClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 710 <span class="i">_SetupDescriptorsDataMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 711 <span class="s">}</span> + 712 + 713 <span class="c">#</span> + 714 <span class="c"># Retrieve available molecular descriptors classes from MolecularDescriptors directory under</span> + 715 <span class="c"># <MayaChemTools>/lib directory...</span> + 716 <span class="c">#</span> +<a name="_RetrieveAndLoadDescriptorClasses-"></a> 717 <span class="k">sub </span><span class="m">_RetrieveAndLoadDescriptorClasses</span> <span class="s">{</span> + 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">$DescriptorsClassFileName</span><span class="cm">,</span> <span class="i">@FileNames</span><span class="cm">,</span> <span class="i">@DescriptorsClassFileNames</span><span class="s">)</span><span class="sc">;</span> + 719 + 720 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 721 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToPath</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 722 + 723 <span class="i">$DescriptorsDirName</span> = <span class="q">"MolecularDescriptors"</span><span class="sc">;</span> + 724 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">FileUtil::GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 725 + 726 <span class="i">$DescriptorsDirPath</span> = <span class="q">"$MayaChemToolsLibDir/$DescriptorsDirName"</span><span class="sc">;</span> + 727 + 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> + 729 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, is missing: Possible installation problems..."</span><span class="sc">;</span> + 730 <span class="s">}</span> + 731 + 732 <span class="i">@FileNames</span> = <span class="s">(</span><span class="q">"$DescriptorsDirPath/*"</span><span class="s">)</span><span class="sc">;</span> + 733 <span class="i">$IncludeDirName</span> = <span class="n">0</span><span class="sc">;</span> + 734 <span class="i">@DescriptorsClassFileNames</span> = <span class="i">FileUtil::ExpandFileNames</span><span class="s">(</span>\<span class="i">@FileNames</span><span class="cm">,</span> <span class="q">"pm"</span><span class="cm">,</span> <span class="i">$IncludeDirName</span><span class="s">)</span><span class="sc">;</span> + 735 + 736 <span class="k">if</span> <span class="s">(</span>!<span class="i">@DescriptorsClassFileNames</span><span class="s">)</span> <span class="s">{</span> + 737 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, doesn't contain any molecular descriptor class: Possible installation problems..."</span><span class="sc">;</span> + 738 <span class="s">}</span> + 739 + 740 <span class="j">FILENAME:</span> <span class="k">for</span> <span class="i">$DescriptorsClassFileName</span> <span class="s">(</span><span class="k">sort</span> <span class="i">@DescriptorsClassFileNames</span><span class="s">)</span> <span class="s">{</span> + 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> + 742 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, contains invalid class file name $DescriptorsClassFileName: Possible installation problems..."</span><span class="sc">;</span> + 743 <span class="s">}</span> + 744 + 745 <span class="c"># Ignore base class and descriptors generator class...</span> + 746 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorsClassFileName</span> =~ <span class="q">/^(MolecularDescriptorsGenerator\.pm|MolecularDescriptors\.pm)$/</span><span class="s">)</span> <span class="s">{</span> + 747 <span class="k">next</span> <span class="j">FILENAME</span><span class="sc">;</span> + 748 <span class="s">}</span> + 749 + 750 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$DescriptorsClassFileName</span><span class="sc">;</span> + 751 <span class="i">$DescriptorClassPath</span> = <span class="q">"${DescriptorsDirName}::${DescriptorClassName}"</span><span class="sc">;</span> + 752 + 753 <span class="c"># Load descriptors class...</span> + 754 <span class="k">eval</span> <span class="q">"use $DescriptorClassPath"</span><span class="sc">;</span> + 755 + 756 <span class="k">if</span> <span class="s">(</span><span class="i">$@</span><span class="s">)</span> <span class="s">{</span> + 757 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: use $DescriptorClassPath failed: $@ ..."</span><span class="sc">;</span> + 758 <span class="s">}</span> + 759 + 760 <span class="k">push</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span> + 761 + 762 <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="sc">;</span> + 763 <span class="s">}</span> + 764 <span class="s">}</span> + 765 + 766 <span class="c">#</span> + 767 <span class="c"># Setup descriptors data map using loaded descriptor classes...</span> + 768 <span class="c">#</span> +<a name="_SetupDescriptorsDataMap-"></a> 769 <span class="k">sub </span><span class="m">_SetupDescriptorsDataMap</span> <span class="s">{</span> + 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">$DescriptorClassPath</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> + 771 + 772 <span class="c"># Class to decriptor names map...</span> + 773 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 774 + 775 <span class="c"># Descriptor to class name map...</span> + 776 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 777 + 778 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="s">)</span> <span class="s">{</span> + 779 <span class="i">$DescriptorClassPath</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> + 780 + 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> + 782 + 783 <span class="k">if</span> <span class="s">(</span>!<span class="i">@DescriptorNames</span><span class="s">)</span> <span class="s">{</span> + 784 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName doesn't provide any descriptor names..."</span><span class="sc">;</span> + 785 <span class="s">}</span> + 786 + 787 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>} <span class="s">)</span> <span class="s">{</span> + 788 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName has already been processed..."</span><span class="sc">;</span> + 789 <span class="s">}</span> + 790 + 791 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 792 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="i">@DescriptorNames</span><span class="sc">;</span> + 793 + 794 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span> <span class="s">{</span> + 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> + 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> + 797 <span class="s">}</span> + 798 + 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> + 800 <span class="s">}</span> + 801 <span class="s">}</span> + 802 <span class="s">}</span> + 803 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>