Mercurial > repos > deepakjadmin > mayatool3_test3
comparison mayachemtools/docs/modules/html/code/TPSADescriptors.html @ 0:73ae111cf86f draft
Uploaded
author | deepakjadmin |
---|---|
date | Wed, 20 Jan 2016 11:55:01 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:73ae111cf86f |
---|---|
1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:MolecularDescriptors::TPSADescriptors.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"> | |
6 </head> | |
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
8 <br/> | |
9 <center> | |
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
11 </center> | |
12 <br/> | |
13 <pre> | |
14 <a name="package-MolecularDescriptors::TPSADescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::TPSADescriptors</span><span class="sc">;</span> | |
15 2 <span class="c">#</span> | |
16 3 <span class="c"># $RCSfile: TPSADescriptors.pm,v $</span> | |
17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> | |
18 5 <span class="c"># $Revision: 1.18 $</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 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> | |
52 39 | |
53 40 <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> | |
54 41 | |
55 42 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> | |
56 43 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
57 44 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span> | |
58 45 | |
59 46 <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> | |
60 47 | |
61 48 <span class="c"># Setup class variables...</span> | |
62 49 <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> | |
63 50 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
64 51 | |
65 52 <span class="c"># Overload Perl functions...</span> | |
66 53 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTPSADescriptors'</span><span class="sc">;</span> | |
67 54 | |
68 55 <span class="c"># Class constructor...</span> | |
69 <a name="new-"></a> 56 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
70 57 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
71 58 | |
72 59 <span class="c"># Initialize object...</span> | |
73 60 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
74 61 <span class="k">bless</span> <span class="i">$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> | |
75 62 <span class="i">$This</span><span class="i">->_InitializeTPSADescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
76 63 | |
77 64 <span class="i">$This</span><span class="i">->_InitializeTPSADescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
78 65 | |
79 66 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
80 67 <span class="s">}</span> | |
81 68 | |
82 69 <span class="c"># Initialize class ...</span> | |
83 <a name="_InitializeClass-"></a> 70 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
84 71 <span class="c">#Class name...</span> | |
85 72 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
86 73 | |
87 74 <span class="c"># Descriptor names...</span> | |
88 75 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'TPSA'</span><span class="s">)</span><span class="sc">;</span> | |
89 76 | |
90 77 <span class="s">}</span> | |
91 78 | |
92 79 <span class="c"># Get descriptor names as an array.</span> | |
93 80 <span class="c">#</span> | |
94 81 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
95 82 <span class="c"># object method.</span> | |
96 83 <span class="c">#</span> | |
97 <a name="GetDescriptorNames-"></a> 84 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> | |
98 85 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
99 86 <span class="s">}</span> | |
100 87 | |
101 88 <span class="c"># Initialize object data...</span> | |
102 89 <span class="c">#</span> | |
103 <a name="_InitializeTPSADescriptors-"></a> 90 <span class="k">sub </span><span class="m">_InitializeTPSADescriptors</span> <span class="s">{</span> | |
104 91 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
105 92 | |
106 93 <span class="c"># Type of MolecularDescriptor...</span> | |
107 94 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TPSA'</span><span class="sc">;</span> | |
108 95 | |
109 96 <span class="c"># By default, TPSA atom contributions from Phosphorus and Sulfur atoms</span> | |
110 97 <span class="c"># are not included during TPSA calculations. [ Ref 91 ]</span> | |
111 98 <span class="c">#</span> | |
112 99 <span class="i">$This</span>->{<span class="w">IgnorePhosphorus</span>} = <span class="n">1</span><span class="sc">;</span> | |
113 100 <span class="i">$This</span>->{<span class="w">IgnoreSulfur</span>} = <span class="n">1</span><span class="sc">;</span> | |
114 101 | |
115 102 <span class="c"># TPSA atom types assigned to appropriate atoms...</span> | |
116 103 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
117 104 | |
118 105 <span class="c"># Intialize descriptor names and values...</span> | |
119 106 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
120 107 | |
121 108 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
122 109 <span class="s">}</span> | |
123 110 | |
124 111 <span class="c"># Initialize object properties...</span> | |
125 112 <span class="c">#</span> | |
126 <a name="_InitializeTPSADescriptorsProperties-"></a> 113 <span class="k">sub </span><span class="m">_InitializeTPSADescriptorsProperties</span> <span class="s">{</span> | |
127 114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
128 115 | |
129 116 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
130 117 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
131 118 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
132 119 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
133 120 <span class="s">}</span> | |
134 121 | |
135 122 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
136 123 <span class="s">}</span> | |
137 124 | |
138 125 <span class="c"># Calculate Topological Polar Surface Area (TPSA) value [ Ref 90-91 ] for molecule...</span> | |
139 126 <span class="c">#</span> | |
140 127 <span class="c"># Methodology:</span> | |
141 128 <span class="c"># . Assign TPSA atom types [ Ref 90-91 ] to Nitrogen and Oxygen</span> | |
142 129 <span class="c"># atoms with optional assignment to Phosphorus and Sulfur atoms.</span> | |
143 130 <span class="c"># . Calculate TPSA value adding contribution of appropriate atom types.</span> | |
144 131 <span class="c">#</span> | |
145 <a name="GenerateDescriptors-"></a> 132 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> | |
146 133 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
147 134 | |
148 135 <span class="c"># Initialize descriptor values...</span> | |
149 136 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
150 137 | |
151 138 <span class="c"># Check availability of molecule...</span> | |
152 139 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
153 140 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> | |
154 141 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
155 142 <span class="s">}</span> | |
156 143 | |
157 144 <span class="c"># Cache appropriate molecule data...</span> | |
158 145 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
159 146 | |
160 147 <span class="c"># Assign TPSA atom types...</span> | |
161 148 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
162 149 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't assign valid TPSA atom types to appropriate atoms..."</span><span class="sc">;</span> | |
163 150 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
164 151 <span class="s">}</span> | |
165 152 | |
166 153 <span class="c"># Calculate descriptor values...</span> | |
167 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
168 155 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate TPSA values corresponding to assigned TPSA atom types..."</span><span class="sc">;</span> | |
169 156 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
170 157 <span class="s">}</span> | |
171 158 | |
172 159 <span class="c"># Set final descriptor values...</span> | |
173 160 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
174 161 | |
175 162 <span class="c"># Clear cached molecule data...</span> | |
176 163 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
177 164 | |
178 165 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
179 166 <span class="s">}</span> | |
180 167 | |
181 168 <span class="c"># Assign TPSA atom types..</span> | |
182 169 <span class="c">#</span> | |
183 <a name="_AssignAtomTypes-"></a> 170 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span> | |
184 171 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
185 172 <span class="k">my</span><span class="s">(</span><span class="i">$TPSAAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
186 173 | |
187 174 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
188 175 | |
189 176 <span class="c"># Assign atom types...</span> | |
190 177 <span class="i">$TPSAAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">IgnorePhosphorus</span>}<span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">IgnoreSulfur</span>}<span class="s">)</span><span class="sc">;</span> | |
191 178 <span class="i">$TPSAAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
192 179 | |
193 180 <span class="c"># Make sure TPSA atom types assignment is successful...</span> | |
194 181 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TPSAAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
195 182 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
196 183 <span class="s">}</span> | |
197 184 | |
198 185 <span class="c"># Collect assigned atom types...</span> | |
199 186 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
200 187 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
201 188 <span class="i">$This</span>->{<span class="w">AtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$TPSAAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
202 189 <span class="s">}</span> | |
203 190 | |
204 191 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
205 192 <span class="s">}</span> | |
206 193 | |
207 194 <span class="c"># Calculate TPSA value...</span> | |
208 195 <span class="c">#</span> | |
209 <a name="_CalculateDescriptorValues-"></a> 196 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> | |
210 197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
211 198 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$TPSA</span><span class="cm">,</span> <span class="i">$TPSAContribution</span><span class="cm">,</span> <span class="i">$TPSADataRef</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="s">)</span><span class="sc">;</span> | |
212 199 | |
213 200 <span class="i">$TPSA</span> = <span class="n">0</span><span class="sc">;</span> | |
214 201 | |
215 202 <span class="c"># Get TPSA atom types data...</span> | |
216 203 <span class="i">$TPSADataRef</span> = <span class="i">AtomTypes::TPSAAtomTypes::GetTPSAAtomTypesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
217 204 | |
218 205 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
219 206 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
220 207 <span class="i">$AtomType</span> = <span class="i">$This</span>->{<span class="w">AtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
221 208 | |
222 209 <span class="c"># Ignore inappropriate atoms...</span> | |
223 210 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> | |
224 211 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
225 212 <span class="s">}</span> | |
226 213 | |
227 214 <span class="i">$TPSAContribution</span> = <span class="n">0.0</span><span class="sc">;</span> | |
228 215 | |
229 216 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^(N|O)$/i</span><span class="s">)</span> <span class="s">{</span> | |
230 217 <span class="c"># TPSA contributions for Nitrogen and Oxygen atoms not explicity defined using atom</span> | |
231 218 <span class="c"># environments in Table 1 [ Ref 90 ]</span> | |
232 219 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^N$/i</span><span class="s">)</span> <span class="s">{</span> | |
233 220 <span class="c"># N = 30.5 - X*8.2 + H*1.5 or 0.0 for negative value</span> | |
234 221 <span class="i">$TPSAContribution</span> = <span class="n">30.5</span> - <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> * <span class="n">8.2</span> + <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span> * <span class="n">1.5</span><span class="sc">;</span> | |
235 222 <span class="s">}</span> | |
236 223 <span class="k">elsif</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^O$/i</span><span class="s">)</span> <span class="s">{</span> | |
237 224 <span class="c"># O = 28.5 - X*8.6 + H*1.5 or 0.0 for negative value</span> | |
238 225 <span class="i">$TPSAContribution</span> = <span class="n">28.5</span> - <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> * <span class="n">8.6</span> + <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span> * <span class="n">1.5</span><span class="sc">;</span> | |
239 226 <span class="s">}</span> | |
240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$TPSAContribution</span> < <span class="n">0.0</span><span class="s">)</span> <span class="s">{</span> | |
241 228 <span class="i">$TPSAContribution</span> = <span class="n">0.0</span><span class="sc">;</span> | |
242 229 <span class="s">}</span> | |
243 230 <span class="s">}</span> | |
244 231 <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$TPSADataRef</span>->{<span class="w">DataCol3</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span> | |
245 232 <span class="c"># Data for TPSA contribution is in column number 3...</span> | |
246 233 <span class="i">$TPSAContribution</span> = <span class="i">$TPSADataRef</span>->{<span class="w">DataCol3</span>}{<span class="i">$AtomType</span>}<span class="sc">;</span> | |
247 234 <span class="s">}</span> | |
248 235 <span class="k">else</span> <span class="s">{</span> | |
249 236 <span class="c"># No TPSA data for assigned atom type...</span> | |
250 237 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
251 238 <span class="s">}</span> | |
252 239 <span class="i">$TPSA</span> += <span class="i">$TPSAContribution</span><span class="sc">;</span> | |
253 240 <span class="s">}</span> | |
254 241 | |
255 242 <span class="c"># Track the calculated values...</span> | |
256 243 <span class="i">$This</span>->{<span class="w">TPSA</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$TPSA</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> | |
257 244 | |
258 245 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
259 246 <span class="s">}</span> | |
260 247 | |
261 248 <span class="c"># Setup final descriptor values...</span> | |
262 249 <span class="c">#</span> | |
263 <a name="_SetFinalDescriptorValues-"></a> 250 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> | |
264 251 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
265 252 | |
266 253 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
267 254 | |
268 255 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">TPSA</span>}<span class="s">)</span><span class="sc">;</span> | |
269 256 | |
270 257 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
271 258 <span class="s">}</span> | |
272 259 | |
273 260 <span class="c"># Cache appropriate molecule data...</span> | |
274 261 <span class="c">#</span> | |
275 <a name="_SetupMoleculeDataCache-"></a> 262 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> | |
276 263 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
277 264 | |
278 265 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
279 266 | |
280 267 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
281 268 <span class="s">}</span> | |
282 269 | |
283 270 <span class="c"># Clear cached molecule data...</span> | |
284 271 <span class="c">#</span> | |
285 <a name="_ClearMoleculeDataCache-"></a> 272 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> | |
286 273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
287 274 | |
288 275 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
289 276 | |
290 277 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
291 278 <span class="s">}</span> | |
292 279 | |
293 280 <span class="c"># Return a string containg data for TPSADescriptors object...</span> | |
294 281 <span class="c">#</span> | |
295 <a name="StringifyTPSADescriptors-"></a> 282 <span class="k">sub </span><span class="m">StringifyTPSADescriptors</span> <span class="s">{</span> | |
296 283 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
297 284 <span class="k">my</span><span class="s">(</span><span class="i">$TPSADescriptorsString</span><span class="s">)</span><span class="sc">;</span> | |
298 285 | |
299 286 <span class="c"># Type of MolecularDescriptors...</span> | |
300 287 <span class="i">$TPSADescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; IgnorePhosphorus: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnorePhosphorus</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreSulfur: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreSulfur</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> | |
301 288 | |
302 289 <span class="c"># Setup molecular descriptor information...</span> | |
303 290 <span class="i">$TPSADescriptorsString</span> .= <span class="q">"; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
304 291 | |
305 292 <span class="k">return</span> <span class="i">$TPSADescriptorsString</span><span class="sc">;</span> | |
306 293 <span class="s">}</span> | |
307 294 | |
308 295 <span class="c"># Is it a TPSADescriptors object?</span> | |
309 <a name="_IsTPSADescriptors-"></a> 296 <span class="k">sub </span><span class="m">_IsTPSADescriptors</span> <span class="s">{</span> | |
310 297 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
311 298 | |
312 299 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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> | |
313 300 <span class="s">}</span> | |
314 301 | |
315 <a name="EOF-"></a></pre> | |
316 <p> </p> | |
317 <br /> | |
318 <center> | |
319 <img src="../../../images/h2o2.png"> | |
320 </center> | |
321 </body> | |
322 </html> |