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14 <a name="package-MolecularDescriptors::Fsp3CarbonsDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::Fsp3CarbonsDescriptors</span><span class="sc">;</span>
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: Fsp3CarbonsDescriptors.pm,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:49:19 $</span>
18 5 <span class="c"># $Revision: 1.12 $</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">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
48 35 <span class="k">use</span> <span class="w">Atom</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(MolecularDescriptors::MolecularDescriptors 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(GetDescriptorNames)</span><span class="sc">;</span>
57 44
58 45 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=&gt;</span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
59 46
60 47 <span class="c"># Setup class variables...</span>
61 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
62 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
63 50
64 51 <span class="c"># Overload Perl functions...</span>
65 52 <span class="k">use</span> <span class="w">overload</span> <span class="q">&#39;&quot;&quot;&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;StringifyFsp3CarbonsDescriptors&#39;</span><span class="sc">;</span>
66 53
67 54 <span class="c"># Class constructor...</span>
68 <a name="new-"></a> 55 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
69 56 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
70 57
71 58 <span class="c"># Initialize object...</span>
72 59 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73 60 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span>
74 61 <span class="i">$This</span><span class="i">-&gt;_InitializeFsp3CarbonsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
75 62
76 63 <span class="i">$This</span><span class="i">-&gt;_InitializeFsp3CarbonsDescriptorsProperties</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"># Descriptor names...</span>
87 74 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">&#39;Fsp3Carbons&#39;</span><span class="cm">,</span> <span class="q">&#39;Sp3Carbons&#39;</span><span class="s">)</span><span class="sc">;</span>
88 75
89 76 <span class="s">}</span>
90 77
91 78 <span class="c"># Get descriptor names as an array.</span>
92 79 <span class="c">#</span>
93 80 <span class="c"># This functionality can be either invoked as a class function or an</span>
94 81 <span class="c"># object method.</span>
95 82 <span class="c">#</span>
96 <a name="GetDescriptorNames-"></a> 83 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
97 84 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
98 85 <span class="s">}</span>
99 86
100 87 <span class="c"># Initialize object data...</span>
101 88 <span class="c">#</span>
102 <a name="_InitializeFsp3CarbonsDescriptors-"></a> 89 <span class="k">sub </span><span class="m">_InitializeFsp3CarbonsDescriptors</span> <span class="s">{</span>
103 90 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
104 91
105 92 <span class="c"># Type of MolecularDescriptor...</span>
106 93 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;Fsp3Carbons&#39;</span><span class="sc">;</span>
107 94
108 95 <span class="c"># Intialize descriptor names and values...</span>
109 96 <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
110 97
111 98 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
112 99 <span class="s">}</span>
113 100
114 101 <span class="c"># Initialize object properties...</span>
115 102 <span class="c">#</span>
116 <a name="_InitializeFsp3CarbonsDescriptorsProperties-"></a> 103 <span class="k">sub </span><span class="m">_InitializeFsp3CarbonsDescriptorsProperties</span> <span class="s">{</span>
117 104 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
118 105
119 106 <span class="k">my</span><span class="s">(</span><span class="i">$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>
120 107 <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>
121 108 <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
122 109 <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
123 110 <span class="s">}</span>
124 111
125 112 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
126 113 <span class="s">}</span>
127 114
128 115 <span class="c"># Calculate fraction of SP3 carbons (Fsp3Carbons) [ Ref 115-116, Ref 119 ] in a molecule...</span>
129 116 <span class="c">#</span>
130 117 <span class="c"># It is defined as follows:</span>
131 118 <span class="c">#</span>
132 119 <span class="c"># Fsp3 = Number of SP3 carbons/Total number of carbons</span>
133 120 <span class="c">#</span>
134 <a name="GenerateDescriptors-"></a> 121 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
135 122 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
136 123
137 124 <span class="c"># Initialize descriptor values...</span>
138 125 <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
139 126
140 127 <span class="c"># Check availability of molecule...</span>
141 128 <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>
142 129 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Molecule data is not available: Molecule object hasn&#39;t been set...&quot;</span><span class="sc">;</span>
143 130 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
144 131 <span class="s">}</span>
145 132
146 133 <span class="c"># Calculate descriptor values...</span>
147 134 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
148 135 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Couldn&#39;t calculate Fsp3Carbons values corresponding to assigned Fsp3Carbons atom types...&quot;</span><span class="sc">;</span>
149 136 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
150 137 <span class="s">}</span>
151 138
152 139 <span class="c"># Set final descriptor values...</span>
153 140 <span class="i">$This</span><span class="i">-&gt;_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
154 141
155 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
156 143 <span class="s">}</span>
157 144
158 145 <span class="c"># Calculate Fsp3Carbons value...</span>
159 146 <span class="c">#</span>
160 <a name="_CalculateDescriptorValues-"></a> 147 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
161 148 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
162 149 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$TotalCarbons</span><span class="cm">,</span> <span class="i">$NumOfSp3Carbons</span><span class="cm">,</span> <span class="i">$Fsp3Carbons</span><span class="s">)</span><span class="sc">;</span>
163 150
164 151 <span class="i">$TotalCarbons</span> = <span class="n">0</span><span class="sc">;</span>
165 152 <span class="i">$NumOfSp3Carbons</span> = <span class="n">0</span><span class="sc">;</span>
166 153
167 154 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
168 155 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">-&gt;IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
169 156 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
170 157 <span class="s">}</span>
171 158 <span class="i">$TotalCarbons</span> += <span class="n">1</span><span class="sc">;</span>
172 159
173 160 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">&#39;C.T4.TSB4&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
174 161 <span class="i">$NumOfSp3Carbons</span> += <span class="n">1</span><span class="sc">;</span>
175 162 <span class="s">}</span>
176 163 <span class="s">}</span>
177 164
178 165 <span class="i">$Fsp3Carbons</span> = <span class="i">$NumOfSp3Carbons</span> ? <span class="i">$NumOfSp3Carbons</span>/<span class="i">$TotalCarbons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
179 166
180 167 <span class="c"># Track values...</span>
181 168 <span class="i">$This</span>-&gt;{<span class="w">Fsp3Carbons</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$Fsp3Carbons</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span>
182 169 <span class="i">$This</span>-&gt;{<span class="w">Sp3Carbons</span>} = <span class="i">$NumOfSp3Carbons</span><span class="sc">;</span>
183 170
184 171 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
185 172 <span class="s">}</span>
186 173
187 174 <span class="c"># Setup final descriptor values...</span>
188 175 <span class="c">#</span>
189 <a name="_SetFinalDescriptorValues-"></a> 176 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
190 177 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
191 178
192 179 <span class="i">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
193 180
194 181 <span class="i">$This</span><span class="i">-&gt;SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Fsp3Carbons</span>}<span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">Sp3Carbons</span>}<span class="s">)</span><span class="sc">;</span>
195 182
196 183 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
197 184 <span class="s">}</span>
198 185
199 186 <span class="c"># Return a string containg data for Fsp3CarbonsDescriptors object...</span>
200 187 <span class="c">#</span>
201 <a name="StringifyFsp3CarbonsDescriptors-"></a> 188 <span class="k">sub </span><span class="m">StringifyFsp3CarbonsDescriptors</span> <span class="s">{</span>
202 189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
203 190 <span class="k">my</span><span class="s">(</span><span class="i">$Fsp3CarbonsDescriptorsString</span><span class="s">)</span><span class="sc">;</span>
204 191
205 192 <span class="i">$Fsp3CarbonsDescriptorsString</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>
206 193
207 194 <span class="k">return</span> <span class="i">$Fsp3CarbonsDescriptorsString</span><span class="sc">;</span>
208 195 <span class="s">}</span>
209 196
210 197 <span class="c"># Is it a Fsp3CarbonsDescriptors object?</span>
211 <a name="_IsFsp3CarbonsDescriptors-"></a> 198 <span class="k">sub </span><span class="m">_IsFsp3CarbonsDescriptors</span> <span class="s">{</span>
212 199 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
213 200
214 201 <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>
215 202 <span class="s">}</span>
216 203
217 <a name="EOF-"></a></pre>
218 <p>&nbsp;</p>
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