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3 <title>MayaChemTools:Code:MolecularDescriptors::HydrogenBondsDescriptors.pm</title>
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14 <a name="package-MolecularDescriptors::HydrogenBondsDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::HydrogenBondsDescriptors</span><span class="sc">;</span>
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: HydrogenBondsDescriptors.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">Atom</span><span class="sc">;</span>
48 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
49 36 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span>
50 37
51 38 <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>
52 39
53 40 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span>
54 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
55 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span>
56 43
57 44 <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>
58 45
59 46 <span class="c"># Setup class variables...</span>
60 47 <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>
61 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
62 49
63 50 <span class="c"># Overload Perl functions...</span>
64 51 <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;StringifyHydrogenBondsDescriptors&#39;</span><span class="sc">;</span>
65 52
66 53 <span class="c"># Class constructor...</span>
67 <a name="new-"></a> 54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
68 55 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
69 56
70 57 <span class="c"># Initialize object...</span>
71 58 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
72 59 <span class="k">bless</span> <span class="i">$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>
73 60 <span class="i">$This</span><span class="i">-&gt;_InitializeHydrogenBondsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
74 61
75 62 <span class="i">$This</span><span class="i">-&gt;_InitializeHydrogenBondsDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
76 63
77 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
78 65 <span class="s">}</span>
79 66
80 67 <span class="c"># Initialize class ...</span>
81 <a name="_InitializeClass-"></a> 68 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
82 69 <span class="c">#Class name...</span>
83 70 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
84 71
85 72 <span class="c"># Descriptor names...</span>
86 73 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">&#39;HydrogenBondDonors&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrogenBondAcceptors&#39;</span><span class="s">)</span><span class="sc">;</span>
87 74
88 75 <span class="s">}</span>
89 76
90 77 <span class="c"># Get descriptor names as an array.</span>
91 78 <span class="c">#</span>
92 79 <span class="c"># This functionality can be either invoked as a class function or an</span>
93 80 <span class="c"># object method.</span>
94 81 <span class="c">#</span>
95 <a name="GetDescriptorNames-"></a> 82 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
96 83 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
97 84 <span class="s">}</span>
98 85
99 86 <span class="c"># Initialize object data...</span>
100 87 <span class="c">#</span>
101 <a name="_InitializeHydrogenBondsDescriptors-"></a> 88 <span class="k">sub </span><span class="m">_InitializeHydrogenBondsDescriptors</span> <span class="s">{</span>
102 89 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
103 90
104 91 <span class="c"># Type of MolecularDescriptor...</span>
105 92 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;HydrogenBonds&#39;</span><span class="sc">;</span>
106 93
107 94 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span>
108 95 <span class="c"># hydrogen bond donor and acceptor atoms with these names:</span>
109 96 <span class="c">#</span>
110 97 <span class="c"># HBondsType1 or HydrogenBondsType1</span>
111 98 <span class="c"># HBondsType2 or HydrogenBondsType2</span>
112 99 <span class="c">#</span>
113 100 <span class="c"># The names of these hydrogen bond types are rather arbirary. However, their</span>
114 101 <span class="c"># definitions have specific meaning and are as follows:</span>
115 102 <span class="c">#</span>
116 103 <span class="c"># HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</span>
117 104 <span class="c"># . Donor: NH, NH2, OH - Any N and O with available H</span>
118 105 <span class="c"># . Acceptor: N[!H], O - Any N without available H and any O</span>
119 106 <span class="c">#</span>
120 107 <span class="c"># HydrogenBondsType2 [ Ref 91 ]:</span>
121 108 <span class="c"># . Donor: NH, NH2, OH - N and O with availabe H</span>
122 109 <span class="c"># . Acceptor: N, O - Add N and O</span>
123 110 <span class="c">#</span>
124 111 <span class="c"># Note:</span>
125 112 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span>
126 113 <span class="c">#</span>
127 114 <span class="i">$This</span>-&gt;{<span class="w">HydrogenBondsType</span>} = <span class="q">&#39;HBondsType2&#39;</span><span class="sc">;</span>
128 115
129 116 <span class="c"># Intialize descriptor names and values...</span>
130 117 <span class="i">$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>
131 118
132 119 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
133 120 <span class="s">}</span>
134 121
135 122 <span class="c"># Initialize object properties...</span>
136 123 <span class="c">#</span>
137 <a name="_InitializeHydrogenBondsDescriptorsProperties-"></a> 124 <span class="k">sub </span><span class="m">_InitializeHydrogenBondsDescriptorsProperties</span> <span class="s">{</span>
138 125 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
139 126
140 127 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
141 128 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
142 129 <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
143 130 <span class="i">$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>
144 131 <span class="s">}</span>
145 132
146 133 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
147 134 <span class="s">}</span>
148 135
149 136 <span class="c"># Set hydrogen bonds type...</span>
150 137 <span class="c">#</span>
151 <a name="SetHydrogenBondsType-"></a> 138 <span class="k">sub </span><span class="m">SetHydrogenBondsType</span> <span class="s">{</span>
152 139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
153 140
154 141 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> !~ <span class="q">/^(HBondsType1|HBondsType2|HydrogenBondsType1|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span>
155 142 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetHydrogenBondsType: Specified hydrogen bonds type, $HydrogenBondsType, is not supported. Valid values: HBondsType1, HBondsType2, HydrogenBondsType1, HydrogenBondsType2 ...\n &quot;</span><span class="sc">;</span>
156 143 <span class="s">}</span>
157 144
158 145 <span class="i">$This</span>-&gt;{<span class="w">HydrogenBondsType</span>} = <span class="i">$HydrogenBondsType</span><span class="sc">;</span>
159 146
160 147 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
161 148 <span class="s">}</span>
162 149
163 150 <span class="c"># Calculate number of hydrogen bond donors and acceptors in a molecule...</span>
164 151 <span class="c">#</span>
165 <a name="GenerateDescriptors-"></a> 152 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
166 153 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
167 154
168 155 <span class="c"># Initialize descriptor values...</span>
169 156 <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
170 157
171 158 <span class="c"># Check availability of molecule...</span>
172 159 <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>
173 160 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Molecule data is not available: Molecule object hasn&#39;t been set...&quot;</span><span class="sc">;</span>
174 161 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
175 162 <span class="s">}</span>
176 163
177 164 <span class="c"># Calculate descriptor values...</span>
178 165 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
179 166 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;CalculateDescriptorValues: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Couldn&#39;t calculate number of hydrogen bond donor and accepror values...&quot;</span><span class="sc">;</span>
180 167 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
181 168 <span class="s">}</span>
182 169
183 170 <span class="c"># Set final descriptor values...</span>
184 171 <span class="i">$This</span><span class="i">-&gt;_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
185 172
186 173 <span class="s">}</span>
187 174
188 175 <span class="c"># Calculate number of hydrogen bond donors and acceptors...</span>
189 176 <span class="c">#</span>
190 <a name="_CalculateDescriptorValues-"></a> 177 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
191 178 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
192 179 <span class="k">my</span><span class="s">(</span><span class="i">$HydrogenBondDonors</span><span class="cm">,</span> <span class="i">$HydrogenBondAcceptors</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
193 180
194 181 <span class="i">$HydrogenBondDonors</span> = <span class="n">0</span><span class="sc">;</span>
195 182 <span class="i">$HydrogenBondAcceptors</span> = <span class="n">0</span><span class="sc">;</span>
196 183
197 184 <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>
198 185 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;IsHydrogenBondDonor</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">HydrogenBondsType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
199 186 <span class="i">$HydrogenBondDonors</span>++<span class="sc">;</span>
200 187 <span class="s">}</span>
201 188 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;IsHydrogenBondAcceptor</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">HydrogenBondsType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
202 189 <span class="i">$HydrogenBondAcceptors</span>++<span class="sc">;</span>
203 190 <span class="s">}</span>
204 191 <span class="s">}</span>
205 192
206 193 <span class="c"># Track the calculated values...</span>
207 194 <span class="i">$This</span>-&gt;{<span class="w">HydrogenBondDonors</span>} = <span class="i">$HydrogenBondDonors</span><span class="sc">;</span>
208 195 <span class="i">$This</span>-&gt;{<span class="w">HydrogenBondAcceptors</span>} = <span class="i">$HydrogenBondAcceptors</span><span class="sc">;</span>
209 196
210 197 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
211 198 <span class="s">}</span>
212 199
213 200 <span class="c"># Setup final descriptor values...</span>
214 201 <span class="c">#</span>
215 <a name="_SetFinalDescriptorValues-"></a> 202 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
216 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
217 204
218 205 <span class="i">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
219 206
220 207 <span class="i">$This</span><span class="i">-&gt;SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">HydrogenBondDonors</span>}<span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">HydrogenBondAcceptors</span>}<span class="s">)</span><span class="sc">;</span>
221 208
222 209 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
223 210 <span class="s">}</span>
224 211
225 212 <span class="c"># Return a string containg data for HydrogenBondsDescriptors object...</span>
226 213 <span class="c">#</span>
227 <a name="StringifyHydrogenBondsDescriptors-"></a> 214 <span class="k">sub </span><span class="m">StringifyHydrogenBondsDescriptors</span> <span class="s">{</span>
228 215 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
229 216 <span class="k">my</span><span class="s">(</span><span class="i">$HydrogenBondsDescriptorsString</span><span class="s">)</span><span class="sc">;</span>
230 217
231 218 <span class="i">$HydrogenBondsDescriptorsString</span> = <span class="q">&quot;MolecularDescriptorType: $This-&gt;{Type}; HydrogenBondsType: $This-&gt;{HydrogenBondsType}; &quot;</span> . <span class="i">$This</span><span class="i">-&gt;_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
232 219
233 220 <span class="k">return</span> <span class="i">$HydrogenBondsDescriptorsString</span><span class="sc">;</span>
234 221 <span class="s">}</span>
235 222
236 223 <span class="c"># Is it a HydrogenBondsDescriptors object?</span>
237 <a name="_IsHydrogenBondsDescriptors-"></a> 224 <span class="k">sub </span><span class="m">_IsHydrogenBondsDescriptors</span> <span class="s">{</span>
238 225 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
239 226
240 227 <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>
241 228 <span class="s">}</span>
242 229
243 <a name="EOF-"></a></pre>
244 <p>&nbsp;</p>
245 <br />
246 <center>
247 <img src="../../../images/h2o2.png">
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