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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:MolecularDescriptors::MolecularDescriptorsGenerator.pm</title> | |
4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
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13 <pre> | |
14 <a name="package-MolecularDescriptors::MolecularDescriptorsGenerator-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularDescriptorsGenerator</span><span class="sc">;</span> | |
15 2 <span class="c">#</span> | |
16 3 <span class="c"># $RCSfile: MolecularDescriptorsGenerator.pm,v $</span> | |
17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> | |
18 5 <span class="c"># $Revision: 1.13 $</span> | |
19 6 <span class="c">#</span> | |
20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
21 8 <span class="c">#</span> | |
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
23 10 <span class="c">#</span> | |
24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
25 12 <span class="c">#</span> | |
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
29 16 <span class="c"># later version.</span> | |
30 17 <span class="c">#</span> | |
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
34 21 <span class="c"># details.</span> | |
35 22 <span class="c">#</span> | |
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
40 27 <span class="c">#</span> | |
41 28 | |
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
46 33 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> | |
47 34 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
48 35 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
49 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
50 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> | |
51 38 | |
52 39 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> | |
53 40 | |
54 41 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> | |
55 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
56 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetAvailableDescriptorClassNames GetAvailableClassAndDescriptorNames GetAvailableDescriptorNames GetAvailableDescriptorNamesForDescriptorClass GetAvailableClassNameForDescriptorName GetRuleOf5DescriptorNames GetRuleOf3DescriptorNames IsDescriptorClassNameAvailable IsDescriptorNameAvailable)</span><span class="sc">;</span> | |
57 44 | |
58 45 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
59 46 | |
60 47 <span class="c"># Setup class variables...</span> | |
61 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">%DescriptorsDataMap</span><span class="s">)</span><span class="sc">;</span> | |
62 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
63 50 | |
64 51 <span class="c"># Overload Perl functions...</span> | |
65 52 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecularDescriptorsGenerator'</span><span class="sc">;</span> | |
66 53 | |
67 54 <span class="c"># Class constructor...</span> | |
68 <a name="new-"></a> 55 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
69 56 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
70 57 | |
71 58 <span class="c"># Initialize object...</span> | |
72 59 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> | |
73 60 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> | |
74 61 <span class="i">$This</span><span class="i">->_InitializeMolecularDescriptorsGenerator</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
75 62 | |
76 63 <span class="i">$This</span><span class="i">->_InitializeMolecularDescriptorsGeneratorProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
77 64 | |
78 65 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
79 66 <span class="s">}</span> | |
80 67 | |
81 68 <span class="c"># Initialize class ...</span> | |
82 <a name="_InitializeClass-"></a> 69 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
83 70 <span class="c">#Class name...</span> | |
84 71 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
85 72 | |
86 73 <span class="c"># Load available molecular descriptor classes...</span> | |
87 74 <span class="i">_LoadMolecularDescriptorsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
88 75 | |
89 76 <span class="s">}</span> | |
90 77 | |
91 78 <span class="c"># Initialize object data...</span> | |
92 79 <span class="c">#</span> | |
93 <a name="_InitializeMolecularDescriptorsGenerator-"></a> 80 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptorsGenerator</span> <span class="s">{</span> | |
94 81 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
95 82 | |
96 83 <span class="c"># Type of desciptors to generate...</span> | |
97 84 <span class="c">#</span> | |
98 85 <span class="c"># The current release of MayaChemTools supports generation of four sets of</span> | |
99 86 <span class="c"># descriptors: All available descriptors, rule of 5 or 3 descriptors or a specified</span> | |
100 87 <span class="c"># set of descriptors.</span> | |
101 88 <span class="c">#</span> | |
102 89 <span class="c"># Possible values: All, RuleOf5, RuleOf3 or Specify</span> | |
103 90 <span class="c">#</span> | |
104 91 <span class="c"># RuleOf5 [ Ref 91 ] descriptor names: MolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors,</span> | |
105 92 <span class="c"># SLogP. RuleOf5 states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10,</span> | |
106 93 <span class="c"># and logP <= 5.</span> | |
107 94 <span class="c">#</span> | |
108 95 <span class="c"># RuleOf3 [ Ref 92 ] descriptor names: MolecularWeight, RotatableBonds, HydrogenBondDonors,</span> | |
109 96 <span class="c"># HydrogenBondAcceptors, SLogP, TPSA. RuleOf3 states: MolecularWeight <= 300, RotatableBonds <= 3,</span> | |
110 97 <span class="c"># HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</span> | |
111 98 <span class="c">#</span> | |
112 99 <span class="c"># For Specify value of Mode, a set of descritor names must be specified using</span> | |
113 100 <span class="c"># DescriptorNames parameter.</span> | |
114 101 <span class="c">#</span> | |
115 102 <span class="c"># Default: All</span> | |
116 103 <span class="c">#</span> | |
117 104 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="q">''</span><span class="sc">;</span> | |
118 105 | |
119 106 <span class="c"># Descriptor names used to generate descriptor values during a specified descriptor</span> | |
120 107 <span class="c"># generation mode...</span> | |
121 108 <span class="c">#</span> | |
122 109 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
123 110 | |
124 111 <span class="c"># Descriptor calculation control parameters for specified descriptor class names...</span> | |
125 112 <span class="c">#</span> | |
126 113 <span class="c"># These parameters are passed on to appropriate descriptor classes during</span> | |
127 114 <span class="c"># instantiations of descriptor class objects.</span> | |
128 115 <span class="c">#</span> | |
129 116 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
130 117 | |
131 118 <span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>} = <span class="n">0</span><span class="sc">;</span> | |
132 119 | |
133 120 <span class="c"># Descriptor class names and objects corresponding to specified descriptor names...</span> | |
134 121 <span class="c">#</span> | |
135 122 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
136 123 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
137 124 | |
138 125 <span class="c"># Descriptor values generated for specified descriptor names...</span> | |
139 126 <span class="c">#</span> | |
140 127 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
141 128 | |
142 129 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
143 130 <span class="s">}</span> | |
144 131 | |
145 132 <span class="c"># Initialize object properties...</span> | |
146 133 <span class="c">#</span> | |
147 <a name="_InitializeMolecularDescriptorsGeneratorProperties-"></a> 134 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptorsGeneratorProperties</span> <span class="s">{</span> | |
148 135 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
149 136 | |
150 137 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
151 138 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
152 139 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
153 140 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
154 141 <span class="s">}</span> | |
155 142 | |
156 143 <span class="c"># Set default value for Mode...</span> | |
157 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Mode</span>}<span class="s">)</span> <span class="s">{</span> | |
158 145 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="q">'All'</span><span class="sc">;</span> | |
159 146 <span class="s">}</span> | |
160 147 | |
161 148 <span class="i">$This</span><span class="i">->_CheckAndInitializeDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
162 149 | |
163 150 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
164 151 <span class="s">}</span> | |
165 152 | |
166 153 <span class="c"># Set descriptors generation mode......</span> | |
167 154 <span class="c">#</span> | |
168 <a name="SetMode-"></a> 155 <span class="k">sub </span><span class="m">SetMode</span> <span class="s">{</span> | |
169 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
170 157 | |
171 158 <span class="c"># All - all available descriptors</span> | |
172 159 <span class="c"># Specify - Specified set of descriptors</span> | |
173 160 | |
174 161 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(All|RuleOf5|RuleOf3|Specify)$/i</span><span class="s">)</span> <span class="s">{</span> | |
175 162 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMode: Mode value, $Value, is not valid; Supported values: All, RuleOf5, RuleOf3 or Specify..."</span><span class="sc">;</span> | |
176 163 <span class="s">}</span> | |
177 164 | |
178 165 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
179 166 | |
180 167 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
181 168 <span class="s">}</span> | |
182 169 | |
183 170 <span class="c"># Set descriptor names to use for generating descriptor values using an array</span> | |
184 171 <span class="c"># or reference to an array...</span> | |
185 172 <span class="c">#</span> | |
186 <a name="SetDescriptorNames-"></a> 173 <span class="k">sub </span><span class="m">SetDescriptorNames</span> <span class="s">{</span> | |
187 174 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
188 175 | |
189 176 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> | |
190 177 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDescriptorNames: Descriptor names cann't be specified during \"All\" value of descsriptors generation \"Mode\"..."</span><span class="sc">;</span> | |
191 178 <span class="s">}</span> | |
192 179 | |
193 180 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
194 181 <span class="k">return</span><span class="sc">;</span> | |
195 182 <span class="s">}</span> | |
196 183 | |
197 184 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="s">)</span><span class="sc">;</span> | |
198 185 | |
199 186 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
200 187 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
201 188 | |
202 189 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
203 190 | |
204 191 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
205 192 <span class="c"># Initialize using array refernce...</span> | |
206 193 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
207 194 <span class="s">}</span> | |
208 195 <span class="k">else</span> <span class="s">{</span> | |
209 196 <span class="c"># It's a list of values...</span> | |
210 197 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
211 198 <span class="s">}</span> | |
212 199 | |
213 200 <span class="c"># Make sure specified descriptor names are valid...</span> | |
214 201 <span class="i">$This</span><span class="i">->_ValidateDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
215 202 | |
216 203 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
217 204 <span class="s">}</span> | |
218 205 | |
219 206 <span class="c"># Get descriptor names as an array...</span> | |
220 207 <span class="c">#</span> | |
221 <a name="GetDescriptorNames-"></a> 208 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> | |
222 209 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
223 210 | |
224 211 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span> | |
225 212 <span class="s">}</span> | |
226 213 | |
227 214 <span class="c"># Get all descriptor values as an array...</span> | |
228 215 <span class="c">#</span> | |
229 <a name="GetDescriptorValues-"></a> 216 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span> | |
230 217 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
231 218 | |
232 219 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>}<span class="s">)</span> <span class="s">{</span> | |
233 220 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="sc">;</span> | |
234 221 <span class="s">}</span> | |
235 222 <span class="k">else</span> <span class="s">{</span> | |
236 223 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorValues</span><span class="s">)</span><span class="sc">;</span> | |
237 224 | |
238 225 <span class="i">@DescriptorValues</span> = <span class="s">(</span><span class="q">'None'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span> | |
239 226 | |
240 227 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorValues</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorValues</span><span class="sc">;</span> | |
241 228 <span class="s">}</span> | |
242 229 <span class="s">}</span> | |
243 230 | |
244 231 <span class="c"># Get descriptor value for a specified descriptor name...</span> | |
245 232 <span class="c">#</span> | |
246 <a name="GetDescriptorValueByName-"></a> 233 <span class="k">sub </span><span class="m">GetDescriptorValueByName</span> <span class="s">{</span> | |
247 234 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
248 235 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
249 236 | |
250 237 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
251 238 | |
252 239 <span class="k">return</span> <span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} ? <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> | |
253 240 | |
254 241 <span class="s">}</span> | |
255 242 | |
256 243 <span class="c"># Get calculated molecular descriptor names sand values as a hash with names</span> | |
257 244 <span class="c"># and values as key/value pairs...</span> | |
258 245 <span class="c">#</span> | |
259 <a name="GetDescriptorNamesAndValues-"></a> 246 <span class="k">sub </span><span class="m">GetDescriptorNamesAndValues</span> <span class="s">{</span> | |
260 247 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
261 248 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
262 249 | |
263 250 <span class="i">%NamesAndValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
264 251 <span class="i">@NamesAndValues</span>{ <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} } = <span class="i">$This</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
265 252 | |
266 253 <span class="k">return</span> <span class="i">%NamesAndValues</span><span class="sc">;</span> | |
267 254 <span class="s">}</span> | |
268 255 | |
269 256 <span class="c"># Set up descriptor calculation control parameters for a specified descriptor class name...</span> | |
270 257 <span class="c">#</span> | |
271 258 <span class="c"># The specified parameter names and values are simply passed on to specified descriptor</span> | |
272 259 <span class="c"># class during instantiation of descriptor class object without any performing any validation</span> | |
273 260 <span class="c"># of parameter names and associated values. It's up to the appropriate descriptor class methods</span> | |
274 261 <span class="c"># to validate these parameters and values.</span> | |
275 262 <span class="c">#</span> | |
276 263 <span class="c"># In addition to specified parameter names and values, the parameter hash must also contain</span> | |
277 264 <span class="c"># descriptor class name as key and value pair with DescriptorClassName as key with class</span> | |
278 265 <span class="c"># name as value.</span> | |
279 266 <span class="c">#</span> | |
280 <a name="SetDescriptorClassParameters-"></a> 267 <span class="k">sub </span><span class="m">SetDescriptorClassParameters</span> <span class="s">{</span> | |
281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
282 269 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
283 270 | |
284 271 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
285 272 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_SetDescriptorNameParameters: Can't set descriptor class name paramaters: DescriptorClassName is not specified..."</span><span class="sc">;</span> | |
286 273 <span class="s">}</span> | |
287 274 | |
288 275 <span class="i">$DescriptorClassName</span> = <span class="i">$NamesAndValues</span>{<span class="w">DescriptorClassName</span>}<span class="sc">;</span> | |
289 276 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsDescriptorClassNameAvailable</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
290 277 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_SetDescriptorClassParameters: Can't set descriptor class name paramaters: Specified descriptor class name, $DescriptorClassName, is not available..."</span><span class="sc">;</span> | |
291 278 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
292 279 <span class="s">}</span> | |
293 280 | |
294 281 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
295 282 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetDescriptorClassParameters: Class name parameters for $DescriptorClassName have already been specified: Replacing previous values..."</span><span class="sc">;</span> | |
296 283 <span class="s">}</span> | |
297 284 | |
298 285 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
299 286 <span class="j">NAME:</span> <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
300 287 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^DescriptorClassName$/</span><span class="s">)</span> <span class="s">{</span> | |
301 288 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> | |
302 289 <span class="s">}</span> | |
303 290 <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
304 291 <span class="s">}</span> | |
305 292 | |
306 293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
307 294 <span class="s">}</span> | |
308 295 | |
309 296 <span class="c"># Get descriptor name parameters as a reference to hash of hashes with hash</span> | |
310 297 <span class="c"># keys corresponding to class name and class parameter name with hash value</span> | |
311 298 <span class="c"># as class parameter value...</span> | |
312 299 <span class="c">#</span> | |
313 <a name="GetDescriptorClassParameters-"></a> 300 <span class="k">sub </span><span class="m">GetDescriptorClassParameters</span> <span class="s">{</span> | |
314 301 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
315 302 | |
316 303 <span class="k">return</span> \<span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}}<span class="sc">;</span> | |
317 304 <span class="s">}</span> | |
318 305 | |
319 306 <span class="c"># Get available descriptor class names as an array.</span> | |
320 307 <span class="c">#</span> | |
321 308 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
322 309 <span class="c"># object method.</span> | |
323 310 <span class="c">#</span> | |
324 <a name="GetAvailableDescriptorClassNames-"></a> 311 <span class="k">sub </span><span class="m">GetAvailableDescriptorClassNames</span> <span class="s">{</span> | |
325 312 | |
326 313 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="sc">;</span> | |
327 314 <span class="s">}</span> | |
328 315 | |
329 316 <span class="c"># Get available descriptors class and descriptors names as a hash containing key/value</span> | |
330 317 <span class="c"># pairs corresponding to class name and an array of descriptor names available for the</span> | |
331 318 <span class="c"># class.</span> | |
332 319 <span class="c">#</span> | |
333 320 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
334 321 <span class="c"># object method.</span> | |
335 322 <span class="c">#</span> | |
336 <a name="GetAvailableClassAndDescriptorNames-"></a> 323 <span class="k">sub </span><span class="m">GetAvailableClassAndDescriptorNames</span> <span class="s">{</span> | |
337 324 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">%ClassAndDescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
338 325 | |
339 326 <span class="i">%ClassAndDescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
340 327 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
341 328 <span class="i">@</span>{<span class="i">$ClassAndDescriptorNames</span>{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
342 329 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ClassAndDescriptorNames</span>{<span class="i">$DescriptorClassName</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}}<span class="sc">;</span> | |
343 330 <span class="s">}</span> | |
344 331 | |
345 332 <span class="k">return</span> <span class="i">%ClassAndDescriptorNames</span><span class="sc">;</span> | |
346 333 <span class="s">}</span> | |
347 334 | |
348 335 <span class="c"># Get available descriptor names as an array.</span> | |
349 336 <span class="c">#</span> | |
350 337 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
351 338 <span class="c"># object method.</span> | |
352 339 <span class="c">#</span> | |
353 <a name="GetAvailableDescriptorNames-"></a> 340 <span class="k">sub </span><span class="m">GetAvailableDescriptorNames</span> <span class="s">{</span> | |
354 341 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
355 342 | |
356 343 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
357 344 <span class="k">push</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="k">map</span> <span class="s">{</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$_</span>}} <span class="s">}</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="sc">;</span> | |
358 345 | |
359 346 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
360 347 <span class="s">}</span> | |
361 348 | |
362 349 <span class="c"># Is it a valid descriptors class name?</span> | |
363 350 <span class="c">#</span> | |
364 351 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
365 352 <span class="c"># object method.</span> | |
366 353 <span class="c">#</span> | |
367 <a name="IsDescriptorClassNameAvailable-"></a> 354 <span class="k">sub </span><span class="m">IsDescriptorClassNameAvailable</span> <span class="s">{</span> | |
368 355 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
369 356 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="s">)</span><span class="sc">;</span> | |
370 357 | |
371 358 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
372 359 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
373 360 <span class="s">}</span> | |
374 361 <span class="k">else</span> <span class="s">{</span> | |
375 362 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> | |
376 363 <span class="s">}</span> | |
377 364 | |
378 365 <span class="k">return</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
379 366 <span class="s">}</span> | |
380 367 | |
381 368 <span class="c"># Is it a valid descriptor name?</span> | |
382 369 <span class="c">#</span> | |
383 370 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
384 371 <span class="c"># object method.</span> | |
385 372 <span class="c">#</span> | |
386 <a name="IsDescriptorNameAvailable-"></a> 373 <span class="k">sub </span><span class="m">IsDescriptorNameAvailable</span> <span class="s">{</span> | |
387 374 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
388 375 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> | |
389 376 | |
390 377 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
391 378 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
392 379 <span class="s">}</span> | |
393 380 <span class="k">else</span> <span class="s">{</span> | |
394 381 <span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> | |
395 382 <span class="s">}</span> | |
396 383 | |
397 384 <span class="k">return</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
398 385 <span class="s">}</span> | |
399 386 | |
400 387 <span class="c"># Get available descriptors names for a descriptor class as an array.</span> | |
401 388 <span class="c">#</span> | |
402 389 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
403 390 <span class="c"># object method.</span> | |
404 391 <span class="c">#</span> | |
405 <a name="GetAvailableDescriptorNamesForDescriptorClass-"></a> 392 <span class="k">sub </span><span class="m">GetAvailableDescriptorNamesForDescriptorClass</span> <span class="s">{</span> | |
406 393 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
407 394 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
408 395 | |
409 396 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
410 397 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
411 398 <span class="s">}</span> | |
412 399 <span class="k">else</span> <span class="s">{</span> | |
413 400 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> | |
414 401 <span class="s">}</span> | |
415 402 | |
416 403 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
417 404 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
418 405 <span class="k">push</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}}<span class="sc">;</span> | |
419 406 <span class="s">}</span> | |
420 407 | |
421 408 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
422 409 <span class="s">}</span> | |
423 410 | |
424 411 <span class="c"># Get available descriptors class name for a descriptor name.</span> | |
425 412 <span class="c">#</span> | |
426 413 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
427 414 <span class="c"># object method.</span> | |
428 415 <span class="c">#</span> | |
429 <a name="GetAvailableClassNameForDescriptorName-"></a> 416 <span class="k">sub </span><span class="m">GetAvailableClassNameForDescriptorName</span> <span class="s">{</span> | |
430 417 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
431 418 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> | |
432 419 | |
433 420 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
434 421 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
435 422 <span class="s">}</span> | |
436 423 <span class="k">else</span> <span class="s">{</span> | |
437 424 <span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> | |
438 425 <span class="s">}</span> | |
439 426 | |
440 427 <span class="i">$DescriptorClassName</span> = <span class="q">''</span><span class="sc">;</span> | |
441 428 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> <span class="s">{</span> | |
442 429 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span> | |
443 430 <span class="s">}</span> | |
444 431 | |
445 432 <span class="k">return</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span> | |
446 433 <span class="s">}</span> | |
447 434 | |
448 435 <span class="c"># Get RuleOf5 descriptor names as an array.</span> | |
449 436 <span class="c">#</span> | |
450 437 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
451 438 <span class="c"># object method.</span> | |
452 439 <span class="c">#</span> | |
453 <a name="GetRuleOf5DescriptorNames-"></a> 440 <span class="k">sub </span><span class="m">GetRuleOf5DescriptorNames</span> <span class="s">{</span> | |
454 441 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
455 442 | |
456 443 <span class="i">@DescriptorNames</span> = <span class="q">qw(MolecularWeight HydrogenBondDonors HydrogenBondAcceptors SLogP)</span><span class="sc">;</span> | |
457 444 | |
458 445 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
459 446 <span class="s">}</span> | |
460 447 | |
461 448 <span class="c"># Get RuleOf3 descriptor names as an array.</span> | |
462 449 <span class="c">#</span> | |
463 450 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
464 451 <span class="c"># object method.</span> | |
465 452 <span class="c">#</span> | |
466 <a name="GetRuleOf3DescriptorNames-"></a> 453 <span class="k">sub </span><span class="m">GetRuleOf3DescriptorNames</span> <span class="s">{</span> | |
467 454 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
468 455 | |
469 456 <span class="i">@DescriptorNames</span> = <span class="q">qw(MolecularWeight RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span> | |
470 457 | |
471 458 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
472 459 <span class="s">}</span> | |
473 460 | |
474 461 | |
475 462 <span class="c"># Set molecule object...</span> | |
476 463 <span class="c">#</span> | |
477 <a name="SetMolecule-"></a> 464 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> | |
478 465 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
479 466 | |
480 467 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> | |
481 468 | |
482 469 <span class="c"># Weaken the reference to disable increment of reference count...</span> | |
483 470 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
484 471 | |
485 472 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
486 473 <span class="s">}</span> | |
487 474 | |
488 475 <span class="c"># Generate specified molecular descriptors...</span> | |
489 476 <span class="c">#</span> | |
490 477 <span class="c"># After instantiating descriptor class objects at first invocation and initialializing</span> | |
491 478 <span class="c"># descriptor values during subsequent invocations, GenerateDescriptors method</span> | |
492 479 <span class="c"># provided by each descriptor class is used to calculate descriptor values for</span> | |
493 480 <span class="c"># specified descriptors.</span> | |
494 481 <span class="c">#</span> | |
495 <a name="GenerateDescriptors-"></a> 482 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> | |
496 483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
497 484 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="s">)</span><span class="sc">;</span> | |
498 485 | |
499 486 <span class="c"># Initialize descriptor values...</span> | |
500 487 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
501 488 | |
502 489 <span class="c"># Instantiate decriptor classed corresponding to specified descriptors...</span> | |
503 490 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>}<span class="s">)</span> <span class="s">{</span> | |
504 491 <span class="i">$This</span><span class="i">->_InstantiateDescriptorClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
505 492 <span class="s">}</span> | |
506 493 | |
507 494 <span class="c"># Check availability of molecule...</span> | |
508 495 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
509 496 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> | |
510 497 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
511 498 <span class="s">}</span> | |
512 499 | |
513 500 <span class="c"># Calculate descriptor values...</span> | |
514 501 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
515 502 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
516 503 | |
517 504 <span class="i">$DescriptorClassObject</span><span class="i">->SetMolecule</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
518 505 <span class="i">$DescriptorClassObject</span><span class="i">->GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
519 506 | |
520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$DescriptorClassObject</span><span class="i">->IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
521 508 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
522 509 <span class="s">}</span> | |
523 510 <span class="s">}</span> | |
524 511 | |
525 512 <span class="c"># Set final descriptor values...</span> | |
526 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
527 514 | |
528 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
529 516 <span class="s">}</span> | |
530 517 | |
531 518 <span class="c"># Initialize descriptor values...</span> | |
532 519 <span class="c">#</span> | |
533 <a name="_InitializeDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span> | |
534 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
535 522 | |
536 523 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">0</span><span class="sc">;</span> | |
537 524 | |
538 525 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
539 526 | |
540 527 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
541 528 <span class="s">}</span> | |
542 529 | |
543 530 <span class="c"># Setup final descriptor values...</span> | |
544 531 <span class="c">#</span> | |
545 <a name="_SetFinalDescriptorValues-"></a> 532 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> | |
546 533 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
547 534 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="s">)</span><span class="sc">;</span> | |
548 535 | |
549 536 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
550 537 | |
551 538 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
552 539 | |
553 540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> | |
554 541 <span class="c"># Set descriptor values for all available descriptors...</span> | |
555 542 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
556 543 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
557 544 | |
558 545 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
559 546 <span class="s">}</span> | |
560 547 <span class="s">}</span> | |
561 548 <span class="k">else</span> <span class="s">{</span> | |
562 549 <span class="c"># Set descriptor values for a subset of available descriptors...</span> | |
563 550 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
564 551 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span> | |
565 552 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
566 553 | |
567 554 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="i">->GetDescriptorValueByName</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> | |
568 555 <span class="s">}</span> | |
569 556 <span class="s">}</span> | |
570 557 | |
571 558 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
572 559 <span class="s">}</span> | |
573 560 | |
574 561 <span class="c"># Is descriptors generation successful?</span> | |
575 562 <span class="c">#</span> | |
576 563 <span class="c"># Notes:</span> | |
577 564 <span class="c"># . After successful generation of descriptor values by each descriptor class</span> | |
578 565 <span class="c"># corresponding to specified descriptor names, DescriptorsCalculated to 1;</span> | |
579 566 <span class="c"># otherwise, it's set to 0.</span> | |
580 567 <span class="c">#</span> | |
581 <a name="IsDescriptorsGenerationSuccessful-"></a> 568 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span> | |
582 569 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
583 570 | |
584 571 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
585 572 <span class="s">}</span> | |
586 573 | |
587 574 <span class="c"># Check and set default descriptor names for generating descriptor values...</span> | |
588 575 <span class="c">#</span> | |
589 <a name="_CheckAndInitializeDescriptorNames-"></a> 576 <span class="k">sub </span><span class="m">_CheckAndInitializeDescriptorNames</span> <span class="s">{</span> | |
590 577 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
591 578 | |
592 579 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^(All|RuleOf5|RuleOf3)$/i</span><span class="s">)</span> <span class="s">{</span> | |
593 580 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
594 581 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: Descriptor names can't be specified during \"All, RuleOf5 or RuleOf3\" values of descsriptors generation \"Mode\"..."</span><span class="sc">;</span> | |
595 582 <span class="s">}</span> | |
596 583 <span class="s">}</span> | |
597 584 | |
598 585 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> | |
599 586 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetAvailableDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
600 587 <span class="s">}</span> | |
601 588 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span> | |
602 589 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetRuleOf5DescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
603 590 <span class="s">}</span> | |
604 591 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span> | |
605 592 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetRuleOf3DescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
606 593 <span class="s">}</span> | |
607 594 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> | |
608 595 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
609 596 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: DescriptorNames must be specified during Specify value for Mode..."</span><span class="sc">;</span> | |
610 597 <span class="s">}</span> | |
611 598 <span class="s">}</span> | |
612 599 <span class="k">else</span> <span class="s">{</span> | |
613 600 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: Mode value, $This->{Mode}, is not valid..."</span><span class="sc">;</span> | |
614 601 <span class="s">}</span> | |
615 602 <span class="s">}</span> | |
616 603 | |
617 604 <span class="c"># Instantiate descriptor classes corresponding to specified descriptor names...</span> | |
618 605 <span class="c">#</span> | |
619 <a name="_InstantiateDescriptorClasses-"></a> 606 <span class="k">sub </span><span class="m">_InstantiateDescriptorClasses</span> <span class="s">{</span> | |
620 607 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
621 608 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="cm">,</span> <span class="i">$DescriptorClassPath</span><span class="s">)</span><span class="sc">;</span> | |
622 609 | |
623 610 <span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>} = <span class="n">1</span><span class="sc">;</span> | |
624 611 | |
625 612 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
626 613 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
627 614 | |
628 615 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
629 616 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span> | |
630 617 | |
631 618 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
632 619 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> | |
633 620 <span class="s">}</span> | |
634 621 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span> | |
635 622 | |
636 623 <span class="i">$DescriptorClassPath</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
637 624 | |
638 625 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span> | |
639 626 <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="i">->new</span><span class="s">(</span><span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}}<span class="s">)</span><span class="sc">;</span> | |
640 627 <span class="s">}</span> | |
641 628 <span class="k">else</span> <span class="s">{</span> | |
642 629 <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="i">->new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
643 630 <span class="s">}</span> | |
644 631 <span class="s">}</span> | |
645 632 | |
646 633 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
647 634 <span class="s">}</span> | |
648 635 | |
649 636 <span class="c"># Return a string containg data for MolecularDescriptorsGenerator object...</span> | |
650 637 <span class="c">#</span> | |
651 <a name="StringifyMolecularDescriptorsGenerator-"></a> 638 <span class="k">sub </span><span class="m">StringifyMolecularDescriptorsGenerator</span> <span class="s">{</span> | |
652 639 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
653 640 <span class="k">my</span><span class="s">(</span><span class="i">$TheString</span><span class="cm">,</span> <span class="i">$NamesAndValuesString</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
654 641 | |
655 642 <span class="c"># Type of MolecularDescriptors...</span> | |
656 643 <span class="i">$TheString</span> = <span class="q">"MolecularDescriptorsGenerator: Mode - $This->{Mode}; SpecifiedDescriptorNames - < @{$This->{DescriptorNames}} >; AvailableMolecularDescriptorClassNames - < @{$DescriptorsDataMap{ClassNames}} >"</span><span class="sc">;</span> | |
657 644 | |
658 645 <span class="i">@NamesAndValuesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
659 646 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
660 647 | |
661 648 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
662 649 <span class="i">$Value</span> = <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>}<span class="sc">;</span> | |
663 650 <span class="i">$Value</span> = <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> || <span class="i">$Value</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> ? <span class="q">'None'</span> <span class="co">:</span> <span class="i">$Value</span><span class="sc">;</span> | |
664 651 <span class="k">push</span> <span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="q">"$Name - $Value"</span><span class="sc">;</span> | |
665 652 <span class="s">}</span> | |
666 653 <span class="k">if</span> <span class="s">(</span><span class="i">@NamesAndValuesInfo</span><span class="s">)</span> <span class="s">{</span> | |
667 654 <span class="i">$TheString</span> .= <span class="q">"Names - Values: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
668 655 <span class="s">}</span> | |
669 656 <span class="k">else</span> <span class="s">{</span> | |
670 657 <span class="i">$TheString</span> .= <span class="q">"Names - Values: < None>"</span><span class="sc">;</span> | |
671 658 <span class="s">}</span> | |
672 659 | |
673 660 <span class="k">return</span> <span class="i">$TheString</span><span class="sc">;</span> | |
674 661 <span class="s">}</span> | |
675 662 | |
676 663 <span class="c"># Is it a MolecularDescriptorsGenerator object?</span> | |
677 <a name="_IsMolecularDescriptorsGenerator-"></a> 664 <span class="k">sub </span><span class="m">_IsMolecularDescriptorsGenerator</span> <span class="s">{</span> | |
678 665 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
679 666 | |
680 667 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
681 668 <span class="s">}</span> | |
682 669 | |
683 670 <span class="c"># Validate descriptor names for generating descriptor values...</span> | |
684 671 <span class="c">#</span> | |
685 <a name="_ValidateDescriptorNames-"></a> 672 <span class="k">sub </span><span class="m">_ValidateDescriptorNames</span> <span class="s">{</span> | |
686 673 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
687 674 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span> | |
688 675 | |
689 676 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
690 677 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> <span class="s">{</span> | |
691 678 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_SetAndValidateDescriptorNames: Specified descriptor name, $DescriptorName, is not valid..."</span><span class="sc">;</span> | |
692 679 <span class="s">}</span> | |
693 680 <span class="s">}</span> | |
694 681 | |
695 682 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
696 683 <span class="s">}</span> | |
697 684 | |
698 685 <span class="c">#</span> | |
699 686 <span class="c"># Load available molecular descriptors data...</span> | |
700 687 <span class="c">#</span> | |
701 688 <span class="c"># All available molecular descriptors classes are automatically detected in</span> | |
702 689 <span class="c"># MolecularDescriptors directory under <MayaChemTools>/lib directory and</span> | |
703 690 <span class="c"># information about available descriptor names is retrieved from each descriptor</span> | |
704 691 <span class="c"># class using function GetDescriptorNames. The following %DescriptorsDataMap</span> | |
705 692 <span class="c"># is setup containing all available molecular descriptors data:</span> | |
706 693 <span class="c">#</span> | |
707 694 <span class="c"># @{$DescriptorsDataMap{ClassNames}}</span> | |
708 695 <span class="c"># %{$DescriptorsDataMap{ClassNameToPath}}</span> | |
709 696 <span class="c"># %{$DescriptorsDataMap{ClassToDescriptorNames}}</span> | |
710 697 <span class="c"># %{$DescriptorsDataMap{DescriptorToClassName}}</span> | |
711 698 <span class="c">#</span> | |
712 699 <span class="c"># GenerateDescriptors method is invoked fo each specified descriptor class</span> | |
713 700 <span class="c"># object to calculate descriptor values for specified descriptors. After successful</span> | |
714 701 <span class="c"># calculation of descriptors, GetDescriptorValues or GetDescriptorValueByName</span> | |
715 702 <span class="c"># methods provided by descriptor objects are used to retrieve calculated</span> | |
716 703 <span class="c"># descriptor values.</span> | |
717 704 <span class="c">#</span> | |
718 <a name="_LoadMolecularDescriptorsData-"></a> 705 <span class="k">sub </span><span class="m">_LoadMolecularDescriptorsData</span> <span class="s">{</span> | |
719 706 | |
720 707 <span class="i">%DescriptorsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
721 708 | |
722 709 <span class="i">_RetrieveAndLoadDescriptorClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
723 710 <span class="i">_SetupDescriptorsDataMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
724 711 <span class="s">}</span> | |
725 712 | |
726 713 <span class="c">#</span> | |
727 714 <span class="c"># Retrieve available molecular descriptors classes from MolecularDescriptors directory under</span> | |
728 715 <span class="c"># <MayaChemTools>/lib directory...</span> | |
729 716 <span class="c">#</span> | |
730 <a name="_RetrieveAndLoadDescriptorClasses-"></a> 717 <span class="k">sub </span><span class="m">_RetrieveAndLoadDescriptorClasses</span> <span class="s">{</span> | |
731 718 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorsDirName</span><span class="cm">,</span> <span class="i">$MayaChemToolsLibDir</span><span class="cm">,</span> <span class="i">$DescriptorsDirPath</span><span class="cm">,</span> <span class="i">$IncludeDirName</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassPath</span><span class="cm">,</span> <span class="i">$DescriptorsClassFileName</span><span class="cm">,</span> <span class="i">@FileNames</span><span class="cm">,</span> <span class="i">@DescriptorsClassFileNames</span><span class="s">)</span><span class="sc">;</span> | |
732 719 | |
733 720 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
734 721 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToPath</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
735 722 | |
736 723 <span class="i">$DescriptorsDirName</span> = <span class="q">"MolecularDescriptors"</span><span class="sc">;</span> | |
737 724 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">FileUtil::GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
738 725 | |
739 726 <span class="i">$DescriptorsDirPath</span> = <span class="q">"$MayaChemToolsLibDir/$DescriptorsDirName"</span><span class="sc">;</span> | |
740 727 | |
741 728 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="q">"$DescriptorsDirPath"</span><span class="s">)</span> <span class="s">{</span> | |
742 729 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, is missing: Possible installation problems..."</span><span class="sc">;</span> | |
743 730 <span class="s">}</span> | |
744 731 | |
745 732 <span class="i">@FileNames</span> = <span class="s">(</span><span class="q">"$DescriptorsDirPath/*"</span><span class="s">)</span><span class="sc">;</span> | |
746 733 <span class="i">$IncludeDirName</span> = <span class="n">0</span><span class="sc">;</span> | |
747 734 <span class="i">@DescriptorsClassFileNames</span> = <span class="i">FileUtil::ExpandFileNames</span><span class="s">(</span>\<span class="i">@FileNames</span><span class="cm">,</span> <span class="q">"pm"</span><span class="cm">,</span> <span class="i">$IncludeDirName</span><span class="s">)</span><span class="sc">;</span> | |
748 735 | |
749 736 <span class="k">if</span> <span class="s">(</span>!<span class="i">@DescriptorsClassFileNames</span><span class="s">)</span> <span class="s">{</span> | |
750 737 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, doesn't contain any molecular descriptor class: Possible installation problems..."</span><span class="sc">;</span> | |
751 738 <span class="s">}</span> | |
752 739 | |
753 740 <span class="j">FILENAME:</span> <span class="k">for</span> <span class="i">$DescriptorsClassFileName</span> <span class="s">(</span><span class="k">sort</span> <span class="i">@DescriptorsClassFileNames</span><span class="s">)</span> <span class="s">{</span> | |
754 741 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorsClassFileName</span> !~ <span class="q">/\.pm/</span><span class="s">)</span> <span class="s">{</span> | |
755 742 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, contains invalid class file name $DescriptorsClassFileName: Possible installation problems..."</span><span class="sc">;</span> | |
756 743 <span class="s">}</span> | |
757 744 | |
758 745 <span class="c"># Ignore base class and descriptors generator class...</span> | |
759 746 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorsClassFileName</span> =~ <span class="q">/^(MolecularDescriptorsGenerator\.pm|MolecularDescriptors\.pm)$/</span><span class="s">)</span> <span class="s">{</span> | |
760 747 <span class="k">next</span> <span class="j">FILENAME</span><span class="sc">;</span> | |
761 748 <span class="s">}</span> | |
762 749 | |
763 750 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$DescriptorsClassFileName</span><span class="sc">;</span> | |
764 751 <span class="i">$DescriptorClassPath</span> = <span class="q">"${DescriptorsDirName}::${DescriptorClassName}"</span><span class="sc">;</span> | |
765 752 | |
766 753 <span class="c"># Load descriptors class...</span> | |
767 754 <span class="k">eval</span> <span class="q">"use $DescriptorClassPath"</span><span class="sc">;</span> | |
768 755 | |
769 756 <span class="k">if</span> <span class="s">(</span><span class="i">$@</span><span class="s">)</span> <span class="s">{</span> | |
770 757 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: use $DescriptorClassPath failed: $@ ..."</span><span class="sc">;</span> | |
771 758 <span class="s">}</span> | |
772 759 | |
773 760 <span class="k">push</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span> | |
774 761 | |
775 762 <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="sc">;</span> | |
776 763 <span class="s">}</span> | |
777 764 <span class="s">}</span> | |
778 765 | |
779 766 <span class="c">#</span> | |
780 767 <span class="c"># Setup descriptors data map using loaded descriptor classes...</span> | |
781 768 <span class="c">#</span> | |
782 <a name="_SetupDescriptorsDataMap-"></a> 769 <span class="k">sub </span><span class="m">_SetupDescriptorsDataMap</span> <span class="s">{</span> | |
783 770 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="cm">,</span> <span class="i">$DescriptorClassPath</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
784 771 | |
785 772 <span class="c"># Class to decriptor names map...</span> | |
786 773 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
787 774 | |
788 775 <span class="c"># Descriptor to class name map...</span> | |
789 776 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
790 777 | |
791 778 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="s">)</span> <span class="s">{</span> | |
792 779 <span class="i">$DescriptorClassPath</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span> | |
793 780 | |
794 781 <span class="i">@DescriptorNames</span> = <span class="i">$DescriptorClassPath</span><span class="i">->GetDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
795 782 | |
796 783 <span class="k">if</span> <span class="s">(</span>!<span class="i">@DescriptorNames</span><span class="s">)</span> <span class="s">{</span> | |
797 784 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName doesn't provide any descriptor names..."</span><span class="sc">;</span> | |
798 785 <span class="s">}</span> | |
799 786 | |
800 787 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>} <span class="s">)</span> <span class="s">{</span> | |
801 788 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName has already been processed..."</span><span class="sc">;</span> | |
802 789 <span class="s">}</span> | |
803 790 | |
804 791 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
805 792 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
806 793 | |
807 794 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span> <span class="s">{</span> | |
808 795 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> <span class="s">{</span> | |
809 796 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor name, $DescriptorName, in class name, $DescriptorClassName, has already been provided by class name $DescriptorsDataMap{DescriptorToClassName}{$DescriptorName}..."</span><span class="sc">;</span> | |
810 797 <span class="s">}</span> | |
811 798 | |
812 799 <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>} = <span class="i">$DescriptorClassName</span><span class="sc">;</span> | |
813 800 <span class="s">}</span> | |
814 801 <span class="s">}</span> | |
815 802 <span class="s">}</span> | |
816 803 | |
817 <a name="EOF-"></a></pre> | |
818 <p> </p> | |
819 <br /> | |
820 <center> | |
821 <img src="../../../images/h2o2.png"> | |
822 </center> | |
823 </body> | |
824 </html> |