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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:MolecularDescriptors::Fsp3CarbonsDescriptors.pm</title> | |
4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
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13 <pre> | |
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 <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">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">=></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">'""'</span> <span class="cm">=></span> <span class="q">'StringifyFsp3CarbonsDescriptors'</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">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
73 60 <span class="k">bless</span> <span class="i">$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">$This</span><span class="i">->_InitializeFsp3CarbonsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
75 62 | |
76 63 <span class="i">$This</span><span class="i">->_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">'Fsp3Carbons'</span><span class="cm">,</span> <span class="q">'Sp3Carbons'</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>->{<span class="w">Type</span>} = <span class="q">'Fsp3Carbons'</span><span class="sc">;</span> | |
107 94 | |
108 95 <span class="c"># Intialize descriptor names and values...</span> | |
109 96 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
110 97 | |
111 98 <span class="k">return</span> <span class="i">$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">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
122 109 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
123 110 <span class="s">}</span> | |
124 111 | |
125 112 <span class="k">return</span> <span class="i">$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">->_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>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
142 129 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> | |
143 130 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
144 131 <span class="s">}</span> | |
145 132 | |
146 133 <span class="c"># Calculate descriptor values...</span> | |
147 134 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_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">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate Fsp3Carbons values corresponding to assigned Fsp3Carbons atom types..."</span><span class="sc">;</span> | |
149 136 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
150 137 <span class="s">}</span> | |
151 138 | |
152 139 <span class="c"># Set final descriptor values...</span> | |
153 140 <span class="i">$This</span><span class="i">->_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">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
168 155 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->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">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'C.T4.TSB4'</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>->{<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>->{<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>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
193 180 | |
194 181 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Fsp3Carbons</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">Sp3Carbons</span>}<span class="s">)</span><span class="sc">;</span> | |
195 182 | |
196 183 <span class="k">return</span> <span class="i">$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">"MolecularDescriptorType: $This->{Type}; "</span> . <span class="i">$This</span><span class="i">->_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">$Object</span><span class="s">)</span> && <span class="i">$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> | |
215 202 <span class="s">}</span> | |
216 203 | |
217 <a name="EOF-"></a></pre> | |
218 <p> </p> | |
219 <br /> | |
220 <center> | |
221 <img src="../../../images/h2o2.png"> | |
222 </center> | |
223 </body> | |
224 </html> |