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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:AtomicDescriptors::AtomicDescriptors.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"> | |
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9 <center> | |
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13 <pre> | |
14 <a name="package-AtomicDescriptors::AtomicDescriptors-"></a> 1 <span class="k">package </span><span class="i">AtomicDescriptors::AtomicDescriptors</span><span class="sc">;</span> | |
15 2 <span class="c">#</span> | |
16 3 <span class="c"># $RCSfile: AtomicDescriptors.pm,v $</span> | |
17 4 <span class="c"># $Date: 2015/02/28 20:47:48 $</span> | |
18 5 <span class="c"># $Revision: 1.17 $</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">ObjectProperty</span><span class="sc">;</span> | |
47 34 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
48 35 | |
49 36 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> | |
50 37 | |
51 38 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> | |
52 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
53 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
54 41 | |
55 42 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
56 43 | |
57 44 <span class="c"># Setup class variables...</span> | |
58 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
60 47 | |
61 48 <span class="c"># Class constructor...</span> | |
62 <a name="new-"></a> 49 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
63 50 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%PropertyNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
64 51 | |
65 52 <span class="c"># Initialize object...</span> | |
66 53 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> | |
67 54 <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">$Class</span><span class="sc">;</span> | |
68 55 <span class="i">$This</span><span class="i">->_InitializeAtomicDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
69 56 | |
70 57 <span class="i">$This</span><span class="i">->_InitializeAtomicDescriptorsProperties</span><span class="s">(</span><span class="i">%PropertyNamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
71 58 | |
72 59 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
73 60 <span class="s">}</span> | |
74 61 | |
75 62 <span class="c"># Initialize object data...</span> | |
76 63 <span class="c">#</span> | |
77 <a name="_InitializeAtomicDescriptors-"></a> 64 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptors</span> <span class="s">{</span> | |
78 65 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
79 66 | |
80 67 <span class="c"># Molecule object...</span> | |
81 68 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="q">''</span><span class="sc">;</span> | |
82 69 | |
83 70 <span class="c"># Type of atomic descriptors...</span> | |
84 71 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span> | |
85 72 | |
86 73 <span class="c"># By default, atomic decriptor values are also calculated for hydrogens...</span> | |
87 74 <span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} = <span class="n">0</span><span class="sc">;</span> | |
88 75 | |
89 76 <span class="c"># Calculated atomic descriptor values hash. Instead of assigning the calculated values to Atom</span> | |
90 77 <span class="c"># objects, these values are stored in the current object in a hash with atom ID and atomic descriptor</span> | |
91 78 <span class="c"># values as key/value pairs.</span> | |
92 79 <span class="c">#</span> | |
93 80 <span class="c"># Unlike molecular descriptors, no descriptor names are assigned to individual atomic descriptor</span> | |
94 81 <span class="c"># values.</span> | |
95 82 <span class="c">#</span> | |
96 83 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
97 84 <span class="s">}</span> | |
98 85 | |
99 86 <span class="c"># Initialize class ...</span> | |
100 <a name="_InitializeClass-"></a> 87 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
101 88 <span class="c">#Class name...</span> | |
102 89 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
103 90 <span class="s">}</span> | |
104 91 | |
105 92 <span class="c"># Initialize object properties....</span> | |
106 <a name="_InitializeAtomicDescriptorsProperties-"></a> 93 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptorsProperties</span> <span class="s">{</span> | |
107 94 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%PropertiesNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
108 95 | |
109 96 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
110 97 <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">%PropertiesNamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
111 98 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
112 99 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
113 100 <span class="s">}</span> | |
114 101 | |
115 102 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
116 103 <span class="s">}</span> | |
117 104 | |
118 105 <span class="c"># Initialize descriptor values for all atoms in a molecule...</span> | |
119 106 <span class="c">#</span> | |
120 <a name="_InitializeDescriptorValues-"></a> 107 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span> | |
121 108 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
122 109 | |
123 110 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
124 111 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
125 112 <span class="s">}</span> | |
126 113 | |
127 114 <span class="c"># Assign 'None' to all atomic descriptor values...</span> | |
128 115 <span class="c">#</span> | |
129 116 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
130 117 | |
131 118 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
132 119 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
133 120 <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="q">'None'</span><span class="sc">;</span> | |
134 121 <span class="s">}</span> | |
135 122 | |
136 123 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
137 124 <span class="s">}</span> | |
138 125 | |
139 126 <span class="c"># Set molecule object and make sure it's not already set...</span> | |
140 127 <span class="c">#</span> | |
141 <a name="SetMolecule-"></a> 128 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> | |
142 129 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
143 130 | |
144 131 <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> | |
145 132 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecule: Can't change molecule object: It's already set..."</span><span class="sc">;</span> | |
146 133 <span class="s">}</span> | |
147 134 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> | |
148 135 | |
149 136 <span class="c"># Weaken the reference to disable increment of reference count...</span> | |
150 137 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
151 138 | |
152 139 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
153 140 <span class="s">}</span> | |
154 141 | |
155 142 <span class="c"># Set type and make sure it's not already set...</span> | |
156 143 <span class="c">#</span> | |
157 <a name="SetType-"></a> 144 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> | |
158 145 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
159 146 | |
160 147 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> | |
161 148 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change AtomicDescriptors type: It's already set..."</span><span class="sc">;</span> | |
162 149 <span class="s">}</span> | |
163 150 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span> | |
164 151 | |
165 152 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
166 153 <span class="s">}</span> | |
167 154 | |
168 155 <span class="c"># Set specific atomic descriptor value...</span> | |
169 156 <span class="c">#</span> | |
170 <a name="SetDescriptorValue-"></a> 157 <span class="k">sub </span><span class="m">SetDescriptorValue</span> <span class="s">{</span> | |
171 158 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomicDescriptor</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
172 159 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
173 160 | |
174 161 <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> | |
175 162 <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomicDescriptor</span><span class="sc">;</span> | |
176 163 | |
177 164 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
178 165 <span class="s">}</span> | |
179 166 | |
180 167 <span class="c"># Get specific atomic descriptor value...</span> | |
181 168 <span class="c">#</span> | |
182 <a name="GetDescriptorValue-"></a> 169 <span class="k">sub </span><span class="m">GetDescriptorValue</span> <span class="s">{</span> | |
183 170 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
184 171 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
185 172 | |
186 173 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
187 174 | |
188 175 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} ? <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> | |
189 176 <span class="s">}</span> | |
190 177 | |
191 178 <span class="c"># Get calculated atomic descriptor values as a hash with atom ID and atomic descriptor</span> | |
192 179 <span class="c"># values as key/value pairs...</span> | |
193 180 <span class="c">#</span> | |
194 <a name="GetDescriptorValues-"></a> 181 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span> | |
195 182 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
196 183 | |
197 184 <span class="k">return</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="sc">;</span> | |
198 185 <span class="s">}</span> | |
199 186 | |
200 187 <span class="c"># Are all atomic descriptor values successfully calculated?</span> | |
201 188 <span class="c">#</span> | |
202 189 <span class="c"># Notes:</span> | |
203 190 <span class="c"># . Dynamic checking of calculated descriptor values for atoms eliminates the need</span> | |
204 191 <span class="c"># to check and synchronize valid descriptor values during SetDescriptorValue.</span> | |
205 192 <span class="c">#</span> | |
206 <a name="IsDescriptorsGenerationSuccessful-"></a> 193 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span> | |
207 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
208 195 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> | |
209 196 | |
210 197 <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> | |
211 198 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} && <span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
212 199 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
213 200 <span class="s">}</span> | |
214 201 <span class="i">$DescriptorValue</span> = <span class="i">$This</span><span class="i">->GetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
215 202 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> | |
216 203 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
217 204 <span class="s">}</span> | |
218 205 <span class="s">}</span> | |
219 206 | |
220 207 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
221 208 <span class="s">}</span> | |
222 209 | |
223 <a name="EOF-"></a></pre> | |
224 <p> </p> | |
225 <br /> | |
226 <center> | |
227 <img src="../../../images/h2o2.png"> | |
228 </center> | |
229 </body> | |
230 </html> |