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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 &lt;msud@san.rr.com&gt;</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 &lt;http://www.gnu.org/licenses/&gt; 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">=&gt;</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">&#39;&quot;&quot;&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;StringifyMolecularDescriptorsGenerator&#39;</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">-&gt;_InitializeMolecularDescriptorsGenerator</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
75 62
76 63 <span class="i">$This</span><span class="i">-&gt;_InitializeMolecularDescriptorsGeneratorProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
77 64
78 65 <span class="k">return</span> <span class="i">$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 &lt;= 500, HydrogenBondDonors &lt;= 5, HydrogenBondAcceptors &lt;= 10,</span>
106 93 <span class="c"># and logP &lt;= 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 &lt;= 300, RotatableBonds &lt;= 3,</span>
110 97 <span class="c"># HydrogenBondDonors &lt;= 3, HydrogenBondAcceptors &lt;= 3, logP &lt;= 3, and TPSA &lt;= 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">$This</span>-&gt;{<span class="w">Mode</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
118 105
119 106 <span class="c"># Descriptor names used to generate descriptor values during a specified descriptor</span>
120 107 <span class="c"># generation mode...</span>
121 108 <span class="c">#</span>
122 109 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<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">$This</span>-&gt;{<span class="w">DescriptorClassParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
130 117
131 118 <span class="i">$This</span>-&gt;{<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">$This</span>-&gt;{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
136 123 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<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">$This</span>-&gt;{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
141 128
142 129 <span class="k">return</span> <span class="i">$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">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
153 140 <span class="i">$This</span><span class="i">-&gt;$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>-&gt;{<span class="w">Mode</span>}<span class="s">)</span> <span class="s">{</span>
158 145 <span class="i">$This</span>-&gt;{<span class="w">Mode</span>} = <span class="q">&#39;All&#39;</span><span class="sc">;</span>
159 146 <span class="s">}</span>
160 147
161 148 <span class="i">$This</span><span class="i">-&gt;_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">&quot;Error: ${ClassName}-&gt;SetMode: Mode value, $Value, is not valid; Supported values: All, RuleOf5, RuleOf3 or Specify...&quot;</span><span class="sc">;</span>
176 163 <span class="s">}</span>
177 164
178 165 <span class="i">$This</span>-&gt;{<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>-&gt;{<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">&quot;Error: ${ClassName}-&gt;SetDescriptorNames: Descriptor names cann&#39;t be specified during \&quot;All\&quot; value of descsriptors generation \&quot;Mode\&quot;...&quot;</span><span class="sc">;</span>
191 178 <span class="s">}</span>
192 179
193 180 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
194 181 <span class="k">return</span><span class="sc">;</span>
195 182 <span class="s">}</span>
196 183
197 184 <span class="k">my</span><span class="s">(</span><span class="i">$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>-&gt;{<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>-&gt;{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
207 194 <span class="s">}</span>
208 195 <span class="k">else</span> <span class="s">{</span>
209 196 <span class="c"># It&#39;s a list of values...</span>
210 197 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<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">$This</span><span class="i">-&gt;_ValidateDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
215 202
216 203 <span class="k">return</span> <span class="i">$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>-&gt;{<span class="w">DescriptorNames</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">DescriptorNames</span>}}<span class="sc">;</span>
225 212 <span class="s">}</span>
226 213
227 214 <span class="c"># Get all descriptor values as an array...</span>
228 215 <span class="c">#</span>
229 <a name="GetDescriptorValues-"></a> 216 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span>
230 217 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>}<span class="s">)</span> <span class="s">{</span>
233 220 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}}<span class="sc">;</span>
234 221 <span class="s">}</span>
235 222 <span class="k">else</span> <span class="s">{</span>
236 223 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorValues</span><span class="s">)</span><span class="sc">;</span>
237 224
238 225 <span class="i">@DescriptorValues</span> = <span class="s">(</span><span class="q">&#39;None&#39;</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<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">$This</span><span class="i">-&gt;GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
251 238
252 239 <span class="k">return</span> <span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} ? <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} <span class="co">:</span> <span class="q">&#39;None&#39;</span><span class="sc">;</span>
253 240
254 241 <span class="s">}</span>
255 242
256 243 <span class="c"># Get calculated molecular descriptor names sand values as a hash with names</span>
257 244 <span class="c"># and values as key/value pairs...</span>
258 245 <span class="c">#</span>
259 <a name="GetDescriptorNamesAndValues-"></a> 246 <span class="k">sub </span><span class="m">GetDescriptorNamesAndValues</span> <span class="s">{</span>
260 247 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">DescriptorNames</span>}} } = <span class="i">$This</span><span class="i">-&gt;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&#39;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">&quot;Error: ${ClassName}-&gt;_SetDescriptorNameParameters: Can&#39;t set descriptor class name paramaters: DescriptorClassName is not specified...&quot;</span><span class="sc">;</span>
286 273 <span class="s">}</span>
287 274
288 275 <span class="i">$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">&quot;Warning: ${ClassName}-&gt;_SetDescriptorClassParameters: Can&#39;t set descriptor class name paramaters: Specified descriptor class name, $DescriptorClassName, is not available...&quot;</span><span class="sc">;</span>
291 278 <span class="k">return</span> <span class="i">$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">$This</span>-&gt;{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span>
295 282 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetDescriptorClassParameters: Class name parameters for $DescriptorClassName have already been specified: Replacing previous values...&quot;</span><span class="sc">;</span>
296 283 <span class="s">}</span>
297 284
298 285 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<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>-&gt;{<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>-&gt;{<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> &amp;&amp; <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">$DescriptorName</span><span class="s">)</span><span class="sc">;</span>
389 376
390 377 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$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> &amp;&amp; <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> &amp;&amp; <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">&#39;&#39;</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">$This</span>-&gt;{<span class="w">Molecule</span>} = <span class="i">$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">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
484 471
485 472 <span class="k">return</span> <span class="i">$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">-&gt;_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">$This</span>-&gt;{<span class="w">DescriptorClassesInstantiated</span>}<span class="s">)</span> <span class="s">{</span>
504 491 <span class="i">$This</span><span class="i">-&gt;_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>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
509 496 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Molecule data is not available: Molecule object hasn&#39;t been set...&quot;</span><span class="sc">;</span>
510 497 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
511 498 <span class="s">}</span>
512 499
513 500 <span class="c"># Calculate descriptor values...</span>
514 501 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">DescriptorClassNames</span>}}<span class="s">)</span> <span class="s">{</span>
515 502 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>-&gt;{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span>
516 503
517 504 <span class="i">$DescriptorClassObject</span><span class="i">-&gt;SetMolecule</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
518 505 <span class="i">$DescriptorClassObject</span><span class="i">-&gt;GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
519 506
520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$DescriptorClassObject</span><span class="i">-&gt;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">$This</span><span class="i">-&gt;_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
527 514
528 515 <span class="k">return</span> <span class="i">$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>-&gt;{<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">$This</span>-&gt;{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
539 526
540 527 <span class="k">return</span> <span class="i">$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">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
550 537
551 538 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<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">$This</span>-&gt;{<span class="w">Mode</span>} =~ <span class="q">/^All$/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>-&gt;{<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>-&gt;{<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>-&gt;{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="i">-&gt;GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
559 546 <span class="s">}</span>
560 547 <span class="s">}</span>
561 548 <span class="k">else</span> <span class="s">{</span>
562 549 <span class="c"># Set descriptor values for a subset of available descriptors...</span>
563 550 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span>
564 551 <span class="i">$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>-&gt;{<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>-&gt;{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="i">-&gt;GetDescriptorValueByName</span><span class="s">(</span><span class="i">$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">$This</span><span class="sc">;</span>
572 559 <span class="s">}</span>
573 560
574 561 <span class="c"># Is descriptors generation successful?</span>
575 562 <span class="c">#</span>
576 563 <span class="c"># Notes:</span>
577 564 <span class="c"># . After successful generation of descriptor values by each descriptor class</span>
578 565 <span class="c"># corresponding to specified descriptor names, DescriptorsCalculated to 1;</span>
579 566 <span class="c"># otherwise, it&#39;s set to 0.</span>
580 567 <span class="c">#</span>
581 <a name="IsDescriptorsGenerationSuccessful-"></a> 568 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span>
582 569 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
585 572 <span class="s">}</span>
586 573
587 574 <span class="c"># Check and set default descriptor names for generating descriptor values...</span>
588 575 <span class="c">#</span>
589 <a name="_CheckAndInitializeDescriptorNames-"></a> 576 <span class="k">sub </span><span class="m">_CheckAndInitializeDescriptorNames</span> <span class="s">{</span>
590 577 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">Mode</span>} =~ <span class="q">/^(All|RuleOf5|RuleOf3)$/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>-&gt;{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span>
594 581 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_CheckAndInitializeDescriptorNames: Descriptor names can&#39;t be specified during \&quot;All, RuleOf5 or RuleOf3\&quot; values of descsriptors generation \&quot;Mode\&quot;...&quot;</span><span class="sc">;</span>
595 582 <span class="s">}</span>
596 583 <span class="s">}</span>
597 584
598 585 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<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>-&gt;{<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">$This</span>-&gt;{<span class="w">Mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span>
602 589 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">DescriptorNames</span>}} = <span class="i">GetRuleOf5DescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
603 590 <span class="s">}</span>
604 591 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<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>-&gt;{<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">$This</span>-&gt;{<span class="w">Mode</span>} =~ <span class="q">/^Specify$/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>-&gt;{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span>
609 596 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_CheckAndInitializeDescriptorNames: DescriptorNames must be specified during Specify value for Mode...&quot;</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">&quot;Error: ${ClassName}-&gt;_CheckAndInitializeDescriptorNames: Mode value, $This-&gt;{Mode}, is not valid...&quot;</span><span class="sc">;</span>
614 601 <span class="s">}</span>
615 602 <span class="s">}</span>
616 603
617 604 <span class="c"># Instantiate descriptor classes corresponding to specified descriptor names...</span>
618 605 <span class="c">#</span>
619 <a name="_InstantiateDescriptorClasses-"></a> 606 <span class="k">sub </span><span class="m">_InstantiateDescriptorClasses</span> <span class="s">{</span>
620 607 <span class="k">my</span><span class="s">(</span><span class="i">$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>-&gt;{<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">$This</span>-&gt;{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
626 613 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<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>-&gt;{<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>-&gt;{<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>-&gt;{<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">$This</span>-&gt;{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span>
639 626 <span class="i">$This</span>-&gt;{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="i">-&gt;new</span><span class="s">(</span><span class="i">%</span>{<span class="i">$This</span>-&gt;{<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>-&gt;{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="i">-&gt;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">&quot;MolecularDescriptorsGenerator: Mode - $This-&gt;{Mode}; SpecifiedDescriptorNames - &lt; @{$This-&gt;{DescriptorNames}} &gt;; AvailableMolecularDescriptorClassNames - &lt; @{$DescriptorsDataMap{ClassNames}} &gt;&quot;</span><span class="sc">;</span>
657 644
658 645 <span class="i">@NamesAndValuesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
659 646 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">-&gt;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>-&gt;{<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$/i</span><span class="s">)</span> ? <span class="q">&#39;None&#39;</span> <span class="co">:</span> <span class="i">$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">&quot;$Name - $Value&quot;</span><span class="sc">;</span>
665 652 <span class="s">}</span>
666 653 <span class="k">if</span> <span class="s">(</span><span class="i">@NamesAndValuesInfo</span><span class="s">)</span> <span class="s">{</span>
667 654 <span class="i">$TheString</span> .= <span class="q">&quot;Names - Values: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</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">$TheString</span> .= <span class="q">&quot;Names - Values: &lt; None&gt;&quot;</span><span class="sc">;</span>
671 658 <span class="s">}</span>
672 659
673 660 <span class="k">return</span> <span class="i">$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> &amp;&amp; <span class="i">$Object</span><span class="i">-&gt;isa</span><span class="s">(</span><span class="i">$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>-&gt;{<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">&quot;Error: ${ClassName}-&gt;_SetAndValidateDescriptorNames: Specified descriptor name, $DescriptorName, is not valid...&quot;</span><span class="sc">;</span>
692 679 <span class="s">}</span>
693 680 <span class="s">}</span>
694 681
695 682 <span class="k">return</span> <span class="i">$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 &lt;MayaChemTools&gt;/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"># &lt;MayaChemTools&gt;/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">&quot;MolecularDescriptors&quot;</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">&quot;$MayaChemToolsLibDir/$DescriptorsDirName&quot;</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">&quot;$DescriptorsDirPath&quot;</span><span class="s">)</span> <span class="s">{</span>
742 729 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, is missing: Possible installation problems...&quot;</span><span class="sc">;</span>
743 730 <span class="s">}</span>
744 731
745 732 <span class="i">@FileNames</span> = <span class="s">(</span><span class="q">&quot;$DescriptorsDirPath/*&quot;</span><span class="s">)</span><span class="sc">;</span>
746 733 <span class="i">$IncludeDirName</span> = <span class="n">0</span><span class="sc">;</span>
747 734 <span class="i">@DescriptorsClassFileNames</span> = <span class="i">FileUtil::ExpandFileNames</span><span class="s">(</span>\<span class="i">@FileNames</span><span class="cm">,</span> <span class="q">&quot;pm&quot;</span><span class="cm">,</span> <span class="i">$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">&quot;Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, doesn&#39;t contain any molecular descriptor class: Possible installation problems...&quot;</span><span class="sc">;</span>
751 738 <span class="s">}</span>
752 739
753 740 <span class="j">FILENAME:</span> <span class="k">for</span> <span class="i">$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">&quot;Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, contains invalid class file name $DescriptorsClassFileName: Possible installation problems...&quot;</span><span class="sc">;</span>
756 743 <span class="s">}</span>
757 744
758 745 <span class="c"># Ignore base class and descriptors generator class...</span>
759 746 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;${DescriptorsDirName}::${DescriptorClassName}&quot;</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">&quot;use $DescriptorClassPath&quot;</span><span class="sc">;</span>
768 755
769 756 <span class="k">if</span> <span class="s">(</span><span class="i">$@</span><span class="s">)</span> <span class="s">{</span>
770 757 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: use $DescriptorClassPath failed: $@ ...&quot;</span><span class="sc">;</span>
771 758 <span class="s">}</span>
772 759
773 760 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">-&gt;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">&quot;Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName doesn&#39;t provide any descriptor names...&quot;</span><span class="sc">;</span>
798 785 <span class="s">}</span>
799 786
800 787 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$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">&quot;Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName has already been processed...&quot;</span><span class="sc">;</span>
802 789 <span class="s">}</span>
803 790
804 791 <span class="i">@</span>{<span class="i">$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">&quot;Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor name, $DescriptorName, in class name, $DescriptorClassName, has already been provided by class name $DescriptorsDataMap{DescriptorToClassName}{$DescriptorName}...&quot;</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>&nbsp;</p>
819 <br />
820 <center>
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