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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 &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 <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">=&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>
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">&#39;&quot;&quot;&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;StringifyTPSADescriptors&#39;</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">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
74 61 <span class="k">bless</span> <span class="i">$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">$This</span><span class="i">-&gt;_InitializeTPSADescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
76 63
77 64 <span class="i">$This</span><span class="i">-&gt;_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">&#39;TPSA&#39;</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>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;TPSA&#39;</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">$This</span>-&gt;{<span class="w">IgnorePhosphorus</span>} = <span class="n">1</span><span class="sc">;</span>
113 100 <span class="i">$This</span>-&gt;{<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">$This</span>-&gt;{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
117 104
118 105 <span class="c"># Intialize descriptor names and values...</span>
119 106 <span class="i">$This</span><span class="i">-&gt;_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">&quot;Set${Name}&quot;</span><span class="sc">;</span>
132 119 <span class="i">$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>
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">$This</span><span class="i">-&gt;_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
150 137
151 138 <span class="c"># Check availability of molecule...</span>
152 139 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
153 140 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Molecule data is not available: Molecule object hasn&#39;t been set...&quot;</span><span class="sc">;</span>
154 141 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
155 142 <span class="s">}</span>
156 143
157 144 <span class="c"># Cache appropriate molecule data...</span>
158 145 <span class="i">$This</span><span class="i">-&gt;_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">-&gt;_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">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Couldn&#39;t assign valid TPSA atom types to appropriate atoms...&quot;</span><span class="sc">;</span>
163 150 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
164 151 <span class="s">}</span>
165 152
166 153 <span class="c"># Calculate descriptor values...</span>
167 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_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">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Couldn&#39;t calculate TPSA values corresponding to assigned TPSA atom types...&quot;</span><span class="sc">;</span>
169 156 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
170 157 <span class="s">}</span>
171 158
172 159 <span class="c"># Set final descriptor values...</span>
173 160 <span class="i">$This</span><span class="i">-&gt;_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">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
177 164
178 165 <span class="k">return</span> <span class="i">$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">$This</span>-&gt;{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
188 175
189 176 <span class="c"># Assign atom types...</span>
190 177 <span class="i">$TPSAAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnorePhosphorus&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">IgnorePhosphorus</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreSulfur&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">IgnoreSulfur</span>}<span class="s">)</span><span class="sc">;</span>
191 178 <span class="i">$TPSAAtomTypes</span><span class="i">-&gt;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">$TPSAAtomTypes</span><span class="i">-&gt;IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
195 182 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
196 183 <span class="s">}</span>
197 184
198 185 <span class="c"># Collect assigned atom types...</span>
199 186 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
200 187 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
201 188 <span class="i">$This</span>-&gt;{<span class="w">AtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$TPSAAtomTypes</span><span class="i">-&gt;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">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
219 206 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
220 207 <span class="i">$AtomType</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTypes</span>}{<span class="i">$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">$Atom</span><span class="i">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;X&#39;</span><span class="s">)</span> * <span class="n">8.2</span> + <span class="i">$Atom</span><span class="i">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;H&#39;</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">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;X&#39;</span><span class="s">)</span> * <span class="n">8.6</span> + <span class="i">$Atom</span><span class="i">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;H&#39;</span><span class="s">)</span> * <span class="n">1.5</span><span class="sc">;</span>
239 226 <span class="s">}</span>
240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$TPSAContribution</span> &lt; <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>-&gt;{<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">$TPSADataRef</span>-&gt;{<span class="w">DataCol3</span>}{<span class="i">$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">$This</span>-&gt;{<span class="w">TPSA</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
267 254
268 255 <span class="i">$This</span><span class="i">-&gt;SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">TPSA</span>}<span class="s">)</span><span class="sc">;</span>
269 256
270 257 <span class="k">return</span> <span class="i">$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>-&gt;{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
279 266
280 267 <span class="k">return</span> <span class="i">$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>-&gt;{<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">&quot;MolecularDescriptorType: $This-&gt;{Type}; IgnorePhosphorus: &quot;</span> . <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnorePhosphorus</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="s">)</span> . <span class="q">&quot;; IgnoreSulfur: &quot;</span> . <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreSulfur</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="s">)</span><span class="sc">;</span>
301 288
302 289 <span class="c"># Setup molecular descriptor information...</span>
303 290 <span class="i">$TPSADescriptorsString</span> .= <span class="q">&quot;; &quot;</span> . <span class="i">$This</span><span class="i">-&gt;_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
304 291
305 292 <span class="k">return</span> <span class="i">$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> &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>
313 300 <span class="s">}</span>
314 301
315 <a name="EOF-"></a></pre>
316 <p>&nbsp;</p>
317 <br />
318 <center>
319 <img src="../../../images/h2o2.png">
320 </center>
321 </body>
322 </html>