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3 <title>MayaChemTools:Code:MolecularDescriptors::RingsCountDescriptors.pm</title>
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14 <a name="package-MolecularDescriptors::RingsCountDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::RingsCountDescriptors</span><span class="sc">;</span>
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: RingsCountDescriptors.pm,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span>
18 5 <span class="c"># $Revision: 1.10 $</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">Molecule</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span>
48 35
49 36 <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>
50 37
51 38 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span>
52 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
53 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span>
54 41
55 42 <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>
56 43
57 44 <span class="c"># Setup class variables...</span>
58 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
60 47
61 48 <span class="c"># Overload Perl functions...</span>
62 49 <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;StringifyRingsCountDescriptors&#39;</span><span class="sc">;</span>
63 50
64 51 <span class="c"># Class constructor...</span>
65 <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
66 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
67 54
68 55 <span class="c"># Initialize object...</span>
69 56 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
70 57 <span class="k">bless</span> <span class="i">$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>
71 58 <span class="i">$This</span><span class="i">-&gt;_InitializeRingsCountDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
72 59
73 60 <span class="i">$This</span><span class="i">-&gt;_InitializeRingsCountDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
74 61
75 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
76 63 <span class="s">}</span>
77 64
78 65 <span class="c"># Initialize class ...</span>
79 <a name="_InitializeClass-"></a> 66 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
80 67 <span class="c">#Class name...</span>
81 68 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
82 69
83 70 <span class="c"># Descriptor names...</span>
84 71 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">&#39;Rings&#39;</span><span class="cm">,</span> <span class="q">&#39;AromaticRings&#39;</span><span class="s">)</span><span class="sc">;</span>
85 72
86 73 <span class="s">}</span>
87 74
88 75 <span class="c"># Get descriptor names as an array.</span>
89 76 <span class="c">#</span>
90 77 <span class="c"># This functionality can be either invoked as a class function or an</span>
91 78 <span class="c"># object method.</span>
92 79 <span class="c">#</span>
93 <a name="GetDescriptorNames-"></a> 80 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
94 81 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
95 82 <span class="s">}</span>
96 83
97 84 <span class="c"># Initialize object data...</span>
98 85 <span class="c">#</span>
99 <a name="_InitializeRingsCountDescriptors-"></a> 86 <span class="k">sub </span><span class="m">_InitializeRingsCountDescriptors</span> <span class="s">{</span>
100 87 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
101 88
102 89 <span class="c"># Type of MolecularDescriptor...</span>
103 90 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;RingsCount&#39;</span><span class="sc">;</span>
104 91
105 92 <span class="c"># Intialize descriptor names and values...</span>
106 93 <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
107 94
108 95 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
109 96 <span class="s">}</span>
110 97
111 98 <span class="c"># Initialize object properties...</span>
112 99 <span class="c">#</span>
113 <a name="_InitializeRingsCountDescriptorsProperties-"></a> 100 <span class="k">sub </span><span class="m">_InitializeRingsCountDescriptorsProperties</span> <span class="s">{</span>
114 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
115 102
116 103 <span class="k">my</span><span class="s">(</span><span class="i">$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>
117 104 <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>
118 105 <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
119 106 <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
120 107 <span class="s">}</span>
121 108
122 109 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
123 110 <span class="s">}</span>
124 111
125 112 <span class="c"># Generate molecular weight and exact mass values...</span>
126 113 <span class="c">#</span>
127 <a name="GenerateDescriptors-"></a> 114 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
128 115 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
129 116
130 117 <span class="c"># Initialize descriptor values...</span>
131 118 <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
132 119
133 120 <span class="c"># Check availability of molecule...</span>
134 121 <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>
135 122 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Molecule data is not available: Molecule object hasn&#39;t been set...&quot;</span><span class="sc">;</span>
136 123 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
137 124 <span class="s">}</span>
138 125
139 126 <span class="c"># Calculate descriptor values...</span>
140 127 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
141 128 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed...&quot;</span><span class="sc">;</span>
142 129 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
143 130 <span class="s">}</span>
144 131
145 132 <span class="c"># Set final descriptor values...</span>
146 133 <span class="i">$This</span><span class="i">-&gt;_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
147 134
148 135 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
149 136 <span class="s">}</span>
150 137
151 138 <span class="c"># Calculate molecular weight and exact mass values..</span>
152 139 <span class="c">#</span>
153 <a name="_CalculateDescriptorValues-"></a> 140 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
154 141 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
155 142 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$ExactMass</span><span class="s">)</span><span class="sc">;</span>
156 143
157 144 <span class="i">$This</span>-&gt;{<span class="w">Rings</span>} = <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
158 145 <span class="i">$This</span>-&gt;{<span class="w">AromaticRings</span>} = <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetNumOfAromaticRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
159 146
160 147 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
161 148 <span class="s">}</span>
162 149
163 150 <span class="c"># Setup final descriptor values...</span>
164 151 <span class="c">#</span>
165 <a name="_SetFinalDescriptorValues-"></a> 152 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
166 153 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
167 154
168 155 <span class="i">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
169 156
170 157 <span class="i">$This</span><span class="i">-&gt;SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Rings</span>}<span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">AromaticRings</span>}<span class="s">)</span><span class="sc">;</span>
171 158
172 159 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
173 160 <span class="s">}</span>
174 161
175 162 <span class="c"># Return a string containg data for RingsCountDescriptors object...</span>
176 163 <span class="c">#</span>
177 <a name="StringifyRingsCountDescriptors-"></a> 164 <span class="k">sub </span><span class="m">StringifyRingsCountDescriptors</span> <span class="s">{</span>
178 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
179 166 <span class="k">my</span><span class="s">(</span><span class="i">$TheString</span><span class="s">)</span><span class="sc">;</span>
180 167
181 168 <span class="i">$TheString</span> = <span class="q">&quot;MolecularDescriptorType: $This-&gt;{Type}; &quot;</span> . <span class="i">$This</span><span class="i">-&gt;_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
182 169
183 170 <span class="k">return</span> <span class="i">$TheString</span><span class="sc">;</span>
184 171 <span class="s">}</span>
185 172
186 173 <span class="c"># Is it a RingsCountDescriptors object?</span>
187 <a name="_IsRingsCountDescriptors-"></a> 174 <span class="k">sub </span><span class="m">_IsRingsCountDescriptors</span> <span class="s">{</span>
188 175 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
189 176
190 177 <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>
191 178 <span class="s">}</span>
192 179
193 <a name="EOF-"></a></pre>
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