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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 &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">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">=&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>
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">-&gt;_InitializeAtomicDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
69 56
70 57 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomicDescriptorsProperties</span><span class="s">(</span><span class="i">%PropertyNamesAndValues</span><span class="s">)</span><span class="sc">;</span>
71 58
72 59 <span class="k">return</span> <span class="i">$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>-&gt;{<span class="w">Molecule</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
82 69
83 70 <span class="c"># Type of atomic descriptors...</span>
84 71 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
85 72
86 73 <span class="c"># By default, atomic decriptor values are also calculated for hydrogens...</span>
87 74 <span class="i">$This</span>-&gt;{<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">$This</span>-&gt;{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
97 84 <span class="s">}</span>
98 85
99 86 <span class="c"># Initialize class ...</span>
100 <a name="_InitializeClass-"></a> 87 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
101 88 <span class="c">#Class name...</span>
102 89 <span class="i">$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">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
112 99 <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
113 100 <span class="s">}</span>
114 101
115 102 <span class="k">return</span> <span class="i">$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>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
124 111 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
125 112 <span class="s">}</span>
126 113
127 114 <span class="c"># Assign &#39;None&#39; to all atomic descriptor values...</span>
128 115 <span class="c">#</span>
129 116 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
132 119 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
133 120 <span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="q">&#39;None&#39;</span><span class="sc">;</span>
134 121 <span class="s">}</span>
135 122
136 123 <span class="k">return</span> <span class="i">$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&#39;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>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
145 132 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMolecule: Can&#39;t change molecule object: It&#39;s already set...&quot;</span><span class="sc">;</span>
146 133 <span class="s">}</span>
147 134 <span class="i">$This</span>-&gt;{<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>-&gt;{<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">$This</span><span class="sc">;</span>
153 140 <span class="s">}</span>
154 141
155 142 <span class="c"># Set type and make sure it&#39;s not already set...</span>
156 143 <span class="c">#</span>
157 <a name="SetType-"></a> 144 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span>
158 145 <span class="k">my</span><span class="s">(</span><span class="i">$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>-&gt;{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span>
161 148 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetType: Can&#39;t change AtomicDescriptors type: It&#39;s already set...&quot;</span><span class="sc">;</span>
162 149 <span class="s">}</span>
163 150 <span class="i">$This</span>-&gt;{<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">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
175 162 <span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}{<span class="i">$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">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
187 174
188 175 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} ? <span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} <span class="co">:</span> <span class="q">&#39;None&#39;</span><span class="sc">;</span>
189 176 <span class="s">}</span>
190 177
191 178 <span class="c"># Get calculated atomic descriptor values as a hash with atom ID and atomic descriptor</span>
192 179 <span class="c"># values as key/value pairs...</span>
193 180 <span class="c">#</span>
194 <a name="GetDescriptorValues-"></a> 181 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span>
195 182 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">DescriptorValues</span>}}<span class="sc">;</span>
198 185 <span class="s">}</span>
199 186
200 187 <span class="c"># Are all atomic descriptor values successfully calculated?</span>
201 188 <span class="c">#</span>
202 189 <span class="c"># Notes:</span>
203 190 <span class="c"># . Dynamic checking of calculated descriptor values for atoms eliminates the need</span>
204 191 <span class="c"># to check and synchronize valid descriptor values during SetDescriptorValue.</span>
205 192 <span class="c">#</span>
206 <a name="IsDescriptorsGenerationSuccessful-"></a> 193 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span>
207 194 <span class="k">my</span><span class="s">(</span><span class="i">$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>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
211 198 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreHydrogens</span>} &amp;&amp; <span class="i">$Atom</span><span class="i">-&gt;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">-&gt;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>&nbsp;</p>
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