comparison mayachemtools/docs/modules/html/code/TopologicalPharmacophoreAtomPairsFingerprints.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:Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints.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-Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span>
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: TopologicalPharmacophoreAtomPairsFingerprints.pm,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
18 5 <span class="c"># $Revision: 1.34 $</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">Fingerprints::Fingerprints</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">Molecule</span><span class="sc">;</span>
49 36 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</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(Fingerprints::Fingerprints 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()</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="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;StringifyTopologicalPharmacophoreAtomPairsFingerprints&#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">$This</span><span class="i">-&gt;_InitializeTopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
74 61
75 62 <span class="i">$This</span><span class="i">-&gt;_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties</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">$This</span><span class="sc">;</span>
78 65 <span class="s">}</span>
79 66
80 67 <span class="c"># Initialize object data...</span>
81 68 <span class="c">#</span>
82 <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprints-"></a> 69 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span>
83 70 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
84 71
85 72 <span class="c"># Type of fingerprint...</span>
86 73 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;TopologicalPharmacophoreAtomPairs&#39;</span><span class="sc">;</span>
87 74
88 75 <span class="c"># Type of vector...</span>
89 76 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsVector&#39;</span><span class="sc">;</span>
90 77
91 78 <span class="c"># AtomPairsSetSizeToUse...</span>
92 79 <span class="c">#</span>
93 80 <span class="c"># ArbitrarySize - Corrresponds to atom pairs with non-zero count</span>
94 81 <span class="c"># FixedSize - Corresponds to all atom pairs with zero and non-zero count</span>
95 82 <span class="c">#</span>
96 83 <span class="c"># Possible values: ArbitrarySize or FixedSize. Default: ArbitrarySize</span>
97 84 <span class="c">#</span>
98 85 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
99 86
100 87 <span class="c"># Type of FingerprintsVector...</span>
101 88 <span class="c">#</span>
102 89 <span class="c"># OrderedNumericalValues - For ArbitrarySize value of AtomPairsSetSizeToUse</span>
103 90 <span class="c"># NumericalValues - For FixedSize value of AtomPairsSetSizeToUse</span>
104 91 <span class="c">#</span>
105 92 <span class="c"># Possible values: OrderedNumericalValues or NumericalValues. Default: NumericalValues</span>
106 93 <span class="c">#</span>
107 94 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
108 95
109 96 <span class="c"># Vector values precision for real values which might be generated after</span>
110 97 <span class="c"># normalization and fuzzification...</span>
111 98 <span class="i">$This</span>-&gt;{<span class="w">ValuesPrecision</span>} = <span class="n">2</span><span class="sc">;</span>
112 99
113 100 <span class="c"># Minimum and maximum bond distance between pharmacophore atom paris...</span>
114 101 <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span>
115 102 <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span>
116 103
117 104 <span class="c"># Initialize atom types and weight information...</span>
118 105 <span class="i">$This</span><span class="i">-&gt;_InitializePharmacophoreAtomTypesAndWeightInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
119 106
120 107 <span class="c"># Normalization methodology to use for scaling the occurance count of pharmacophore atom</span>
121 108 <span class="c"># pairs at various distances.</span>
122 109 <span class="c">#</span>
123 110 <span class="c"># Possible values: None, ByHeavyAtomsCount, ByAtomTypesCount. Default: None</span>
124 111 <span class="c">#</span>
125 112 <span class="i">$This</span>-&gt;{<span class="w">NormalizationMethodology</span>} = <span class="q">&#39;None&#39;</span><span class="sc">;</span>
126 113
127 114 <span class="c"># Initialize fuzzification parameters...</span>
128 115 <span class="c">#</span>
129 116 <span class="i">$This</span><span class="i">-&gt;_InitializeFuzzificationInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
130 117
131 118 <span class="c"># Pharmacophore types assigned to each heavy atom...</span>
132 119 <span class="c">#</span>
133 120 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
134 121
135 122 <span class="c"># Assigned Atom types count of each type in the molecule...</span>
136 123 <span class="c">#</span>
137 124 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
138 125
139 126 <span class="c"># All pharmacophore atom pairs between minimum and maximum distance...</span>
140 127 <span class="c">#</span>
141 128 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
142 129 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
143 130 <span class="s">}</span>
144 131
145 132 <span class="c"># Inialize pharmacophore atom types and weight information...</span>
146 133 <span class="c">#</span>
147 <a name="_InitializePharmacophoreAtomTypesAndWeightInformation-"></a> 134 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomTypesAndWeightInformation</span> <span class="s">{</span>
148 135 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
149 136
150 137 <span class="c"># Default pharmacophore atom types to use for atom pairs fingerprint generation</span>
151 138 <span class="c"># are: HBD, HBA, PI, NI, H</span>
152 139 <span class="c">#</span>
153 140 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
154 141 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}} = <span class="k">sort</span> <span class="s">(</span><span class="q">&#39;HBD&#39;</span><span class="cm">,</span> <span class="q">&#39;HBA&#39;</span><span class="cm">,</span> <span class="q">&#39;PI&#39;</span><span class="cm">,</span> <span class="q">&#39;NI&#39;</span><span class="cm">,</span> <span class="q">&#39;H&#39;</span><span class="s">)</span><span class="sc">;</span>
155 142
156 143 <span class="c"># Weight of the various pharmacophore atom types to use for their contribution to atom</span>
157 144 <span class="c"># pair interaction. It allows to increase the importance of specific pharmacophore atom</span>
158 145 <span class="c"># types in the generted fingerprints.</span>
159 146 <span class="c">#</span>
160 147 <span class="c"># A value of 0 eliminates the contribution by a particular pharmacophore atom</span>
161 148 <span class="c"># type and 2 doubles its contribution.</span>
162 149 <span class="c">#</span>
163 150 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span>
164 151
165 152 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
166 153
167 154 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesWeight</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
168 155 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span> <span class="s">{</span>
169 156 <span class="i">$This</span>-&gt;{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>} = <span class="n">1</span><span class="sc">;</span>
170 157 <span class="s">}</span>
171 158 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
172 159 <span class="s">}</span>
173 160
174 161 <span class="c"># Initialize fuzzification information...</span>
175 162 <span class="c">#</span>
176 <a name="_InitializeFuzzificationInformation-"></a> 163 <span class="k">sub </span><span class="m">_InitializeFuzzificationInformation</span> <span class="s">{</span>
177 164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
178 165
179 166 <span class="c"># To fuzz or not to fuzz atom pairs count. Default: No fuzzication</span>
180 167 <span class="c">#</span>
181 168 <span class="i">$This</span>-&gt;{<span class="w">FuzzifyAtomPairsCount</span>} = <span class="n">0</span><span class="sc">;</span>
182 169
183 170 <span class="c"># When to fuzz atom pair count...</span>
184 171 <span class="c">#</span>
185 172 <span class="c"># Possible values: BeforeNormalization or AfterNormalization. Default: AfterNormalization</span>
186 173 <span class="c">#</span>
187 174 <span class="i">$This</span>-&gt;{<span class="w">FuzzificationMode</span>} = <span class="q">&#39;AfterNormalization&#39;</span><span class="sc">;</span>
188 175
189 176 <span class="c"># How to fuzz atom pair count...</span>
190 177 <span class="c">#</span>
191 178 <span class="c"># Possible values: FuzzyBinning or FuzzyBinSmoothing. Default: FuzzyBinning</span>
192 179 <span class="c">#</span>
193 180 <span class="i">$This</span>-&gt;{<span class="w">FuzzificationMethodology</span>} = <span class="q">&#39;FuzzyBinning&#39;</span><span class="sc">;</span>
194 181
195 182 <span class="c"># By how much to fuzz atom pairs count...</span>
196 183 <span class="c">#</span>
197 184 <span class="i">$This</span>-&gt;{<span class="w">FuzzFactor</span>} = <span class="n">0.15</span><span class="sc">;</span>
198 185
199 186 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
200 187 <span class="s">}</span>
201 188
202 189 <span class="c"># Initialize class ...</span>
203 <a name="_InitializeClass-"></a> 190 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
204 191 <span class="c">#Class name...</span>
205 192 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
206 193 <span class="s">}</span>
207 194
208 195 <span class="c"># Initialize object properties....</span>
209 <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties-"></a> 196 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties</span> <span class="s">{</span>
210 197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
211 198
212 199 <span class="k">my</span><span class="s">(</span><span class="i">$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>
213 200 <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>
214 201 <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
215 202 <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
216 203 <span class="s">}</span>
217 204
218 205 <span class="c"># Make sure molecule object was specified...</span>
219 206 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
220 207 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying molecule...&quot;</span><span class="sc">;</span>
221 208 <span class="s">}</span>
222 209
223 210 <span class="i">$This</span><span class="i">-&gt;_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
224 211
225 212 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
226 213 <span class="s">}</span>
227 214
228 215 <span class="c"># Initialize fingerprints vector...</span>
229 216 <span class="c">#</span>
230 <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector-"></a> 217 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector</span> <span class="s">{</span>
231 218 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
232 219
233 220 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">AtomPairsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span>
234 221 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">&#39;ArbitrarySize&#39;</span><span class="sc">;</span>
235 222 <span class="s">}</span>
236 223
237 224 <span class="c"># Vector type and type of values...</span>
238 225 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsVector&#39;</span><span class="sc">;</span>
239 226
240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span>
241 228 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;OrderedNumericalValues&#39;</span><span class="sc">;</span>
242 229 <span class="s">}</span>
243 230 <span class="k">else</span> <span class="s">{</span>
244 231 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;NumericalValues&#39;</span><span class="sc">;</span>
245 232 <span class="s">}</span>
246 233
247 234 <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
248 235 <span class="s">}</span>
249 236
250 237 <span class="c"># Set atom parits set size to use...</span>
251 238 <span class="c">#</span>
252 <a name="SetAtomPairsSetSizeToUse-"></a> 239 <span class="k">sub </span><span class="m">SetAtomPairsSetSizeToUse</span> <span class="s">{</span>
253 240 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
254 241
255 242 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomPairsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span>
256 243 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomPairsSetSizeToUse: Can&#39;t change size: It&#39;s already set...&quot;</span><span class="sc">;</span>
257 244 <span class="s">}</span>
258 245
259 246 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span>
260 247 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomPairsSetSizeToUse: Unknown AtomPairsSetSizeToUse value: $Value; Supported values: ArbitrarySize or FixedSize&quot;</span><span class="sc">;</span>
261 248 <span class="s">}</span>
262 249
263 250 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="i">$Value</span><span class="sc">;</span>
264 251
265 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
266 253 <span class="s">}</span>
267 254
268 255 <span class="c"># Disable change of AvailableAtomTypes...</span>
269 256 <span class="c">#</span>
270 <a name="SetAvailableAtomTypes-"></a> 257 <span class="k">sub </span><span class="m">SetAvailableAtomTypes</span> <span class="s">{</span>
271 258 <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>
272 259
273 260 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetAvailableAtomTypes: AvailableAtomTypes value can&#39;t be set...&quot;</span><span class="sc">;</span>
274 261
275 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
276 263 <span class="s">}</span>
277 264
278 265 <span class="c"># Set atom types to use for atom pairs...</span>
279 266 <span class="c">#</span>
280 <a name="SetAtomTypesToUse-"></a> 267 <span class="k">sub </span><span class="m">SetAtomTypesToUse</span> <span class="s">{</span>
281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
282 269 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$SpecifiedAtomType</span><span class="cm">,</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@AtomTypesToUse</span><span class="s">)</span><span class="sc">;</span>
283 270
284 271 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
285 272 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetAtomTypesToUse: No values specified...&quot;</span><span class="sc">;</span>
286 273 <span class="k">return</span><span class="sc">;</span>
287 274 <span class="s">}</span>
288 275
289 276 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
290 277 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
291 278
292 279 <span class="i">@SpecifiedAtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
293 280 <span class="i">@AtomTypesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
294 281
295 282 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
296 283 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
297 284 <span class="s">}</span>
298 285 <span class="k">else</span> <span class="s">{</span>
299 286 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
300 287 <span class="s">}</span>
301 288
302 289 <span class="c"># Make sure specified AtomTypes are valid...</span>
303 290 <span class="k">for</span> <span class="i">$SpecifiedAtomType</span> <span class="s">(</span><span class="i">@SpecifiedAtomTypes</span><span class="s">)</span> <span class="s">{</span>
304 291 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
305 292 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomTypesToUse: Specified atom type, $SpecifiedAtomType, is not supported...\n &quot;</span><span class="sc">;</span>
306 293 <span class="s">}</span>
307 294 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomType</span><span class="sc">;</span>
308 295 <span class="k">push</span> <span class="i">@AtomTypesToUse</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span>
309 296 <span class="s">}</span>
310 297
311 298 <span class="c"># Set atom types to use...</span>
312 299 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
313 300 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="k">sort</span> <span class="i">@AtomTypesToUse</span><span class="sc">;</span>
314 301
315 302 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
316 303 <span class="s">}</span>
317 304
318 305 <span class="c"># Set vector values precision for real values which might be generated after</span>
319 306 <span class="c"># normalization and fuzzification...</span>
320 307 <span class="c">#</span>
321 <a name="SetValuesPrecision-"></a> 308 <span class="k">sub </span><span class="m">SetValuesPrecision</span> <span class="s">{</span>
322 309 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
323 310
324 311 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
325 312 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetValuesPrecision: ValuesPrecision value, $Value, is not valid: It must be a positive integer...&quot;</span><span class="sc">;</span>
326 313 <span class="s">}</span>
327 314 <span class="i">$This</span>-&gt;{<span class="w">ValuesPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span>
328 315
329 316 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
330 317 <span class="s">}</span>
331 318
332 319 <span class="c"># Set minimum distance for pharmacophore atom pairs...</span>
333 320 <span class="c">#</span>
334 <a name="SetMinDistance-"></a> 321 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span>
335 322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
336 323
337 324 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
338 325 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMinDistance: MinDistance value, $Value, is not valid: It must be an integer...&quot;</span><span class="sc">;</span>
339 326 <span class="s">}</span>
340 327 <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
341 328
342 329 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
343 330 <span class="s">}</span>
344 331
345 332 <span class="c"># Set maximum distance for pharmacophore atom pairs...</span>
346 333 <span class="c">#</span>
347 <a name="SetMaxDistance-"></a> 334 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span>
348 335 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
349 336
350 337 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
351 338 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer...&quot;</span><span class="sc">;</span>
352 339 <span class="s">}</span>
353 340 <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
354 341
355 342 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
356 343 <span class="s">}</span>
357 344
358 345 <span class="c"># Set normalization methodology to use for scaling the occurance count of pharmacophore atom</span>
359 346 <span class="c"># pairs over distance range beween minimum and maximum distance.</span>
360 347 <span class="c">#</span>
361 <a name="SetNormalizationMethodology-"></a> 348 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span>
362 349 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
363 350
364 351 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|ByAtomTypesCount|None)$/i</span><span class="s">)</span> <span class="s">{</span>
365 352 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByAtomTypesCount...&quot;</span><span class="sc">;</span>
366 353 <span class="s">}</span>
367 354
368 355 <span class="i">$This</span>-&gt;{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span>
369 356
370 357 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
371 358 <span class="s">}</span>
372 359
373 360 <span class="c"># Set weight of the various pharmacophore atom types to use for their contribution to atom</span>
374 361 <span class="c"># pair interaction using atom types label and value hash.</span>
375 362 <span class="c">#</span>
376 363 <span class="c"># It allows to increase the importance of specific pharmacophore atom</span>
377 364 <span class="c"># types in the generted fingerprints.</span>
378 365 <span class="c">#</span>
379 366 <span class="c"># A value of 0 eliminates the contribution by a particular pharmacophore atom</span>
380 367 <span class="c"># type and 2 doubles its contribution.</span>
381 368 <span class="c">#</span>
382 <a name="SetAtomTypesWeight-"></a> 369 <span class="k">sub </span><span class="m">SetAtomTypesWeight</span> <span class="s">{</span>
383 370 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%AtomTypesWeight</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
384 371 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span><span class="sc">;</span>
385 372
386 373 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%AtomTypesWeight</span><span class="s">)</span> <span class="s">{</span>
387 374 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span>
388 375 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomTypesWeight: AtomTypeWeight for $AtomType couldn&#39;t be set: Unknown atom type...&quot;</span><span class="sc">;</span>
389 376 <span class="s">}</span>
390 377 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Weight</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$Weight</span> &gt;= <span class="n">0</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
391 378 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomTypesWeight: Specified weight value, $Weight, for AtomType, $AtomType, muts be &gt;= 0...&quot;</span><span class="sc">;</span>
392 379 <span class="s">}</span>
393 380 <span class="i">$This</span>-&gt;{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>} = <span class="i">$Weight</span><span class="sc">;</span>
394 381 <span class="s">}</span>
395 382 <span class="s">}</span>
396 383
397 384 <span class="c"># Set fuzzification methodology to use for fuzzifying atom pairs count...</span>
398 385 <span class="c">#</span>
399 <a name="SetFuzzificationMethodology-"></a> 386 <span class="k">sub </span><span class="m">SetFuzzificationMethodology</span> <span class="s">{</span>
400 387 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
401 388
402 389 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(FuzzyBinning|FuzzyBinSmoothing)$/i</span><span class="s">)</span> <span class="s">{</span>
403 390 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFuzzificationMethodology: FuzzificationMethodology value, $Value, is not valid. Supported values: FuzzyBinning or FuzzyBinSmoothing...&quot;</span><span class="sc">;</span>
404 391 <span class="s">}</span>
405 392
406 393 <span class="i">$This</span>-&gt;{<span class="w">FuzzificationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span>
407 394
408 395 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
409 396 <span class="s">}</span>
410 397
411 398 <span class="c"># Set fuzzification mode for fuzzifying atom pairs count...</span>
412 399 <span class="c">#</span>
413 <a name="SetFuzzificationMode-"></a> 400 <span class="k">sub </span><span class="m">SetFuzzificationMode</span> <span class="s">{</span>
414 401 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
415 402
416 403 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(BeforeNormalization|AfterNormalization)$/i</span><span class="s">)</span> <span class="s">{</span>
417 404 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFuzzificationMode: FuzzificationMode value, $Value, is not valid. Supported values: BeforeNormalization or AfterNormalization...&quot;</span><span class="sc">;</span>
418 405 <span class="s">}</span>
419 406
420 407 <span class="i">$This</span>-&gt;{<span class="w">FuzzificationMode</span>} = <span class="i">$Value</span><span class="sc">;</span>
421 408
422 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
423 410 <span class="s">}</span>
424 411
425 412 <span class="c"># Set fuzz factor values used for fuzzifying atom pairs count...</span>
426 413 <span class="c">#</span>
427 <a name="SetFuzzFactor-"></a> 414 <span class="k">sub </span><span class="m">SetFuzzFactor</span> <span class="s">{</span>
428 415 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
429 416
430 417 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinning$/i</span><span class="s">)</span> <span class="s">{</span>
431 418 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$Value</span> &gt;=<span class="n">0</span> &amp;&amp; <span class="i">$Value</span> &lt;= <span class="n">1.0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
432 419 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFuzzFactor: Specified fuzz factor value, $Value, must be &gt;= 0 and &lt;= 1...&quot;</span><span class="sc">;</span>
433 420 <span class="s">}</span>
434 421 <span class="s">}</span>
435 422 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinSmoothing$/i</span><span class="s">)</span> <span class="s">{</span>
436 423 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$Value</span> &gt;=<span class="n">0</span> &amp;&amp; <span class="i">$Value</span> &lt;= <span class="n">0.5</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
437 424 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFuzzFactor: Specified fuzz factor value, $Value, must be &gt;= 0 and &lt;= 0.5...&quot;</span><span class="sc">;</span>
438 425 <span class="s">}</span>
439 426 <span class="s">}</span>
440 427 <span class="k">else</span> <span class="s">{</span>
441 428 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFuzzFactor: Fuzz factor value can&#39;t be changed: Uknown FuzzificationMethodology: $This-&gt;{FuzzificationMethodology}...&quot;</span><span class="sc">;</span>
442 429 <span class="s">}</span>
443 430
444 431 <span class="i">$This</span>-&gt;{<span class="w">FuzzFactor</span>} = <span class="i">$Value</span><span class="sc">;</span>
445 432
446 433 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
447 434 <span class="s">}</span>
448 435
449 436 <span class="c"># Generate fingerprints description...</span>
450 437 <span class="c">#</span>
451 <a name="GetDescription-"></a> 438 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
452 439 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
453 440
454 441 <span class="c"># Is description explicity set?</span>
455 442 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
456 443 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="sc">;</span>
457 444 <span class="s">}</span>
458 445
459 446 <span class="c"># Generate fingerprints description...</span>
460 447
461 448 <span class="k">return</span> <span class="q">&quot;$This-&gt;{Type}:$This-&gt;{AtomPairsSetSizeToUse}:MinDistance$This-&gt;{MinDistance}:MaxDistance$This-&gt;{MaxDistance}&quot;</span><span class="sc">;</span>
462 449 <span class="s">}</span>
463 450
464 451 <span class="c"># Generate topological pharmacophore atom pairs [ Ref 60-62, Ref 65, Ref 68 ] fingerprints...</span>
465 452 <span class="c">#</span>
466 453 <span class="c"># Methodology:</span>
467 454 <span class="c"># . Generate a distance matrix.</span>
468 455 <span class="c"># . Assign pharmacophore atom types to all the atoms.</span>
469 456 <span class="c"># . Initialize pharmacophore atom pairs basis set for all unique pairs between</span>
470 457 <span class="c"># minimum and maximum distance.</span>
471 458 <span class="c"># . Using distance matrix and pharmacophore atom types, count occurance of</span>
472 459 <span class="c"># unique atom pairs between specified distance range - It corresponds to the</span>
473 460 <span class="c"># correlation-vector for the atom pairs.</span>
474 461 <span class="c"># . Weigh contribution of each atom type to atom pair interaction by its specified</span>
475 462 <span class="c"># weight during occurance count.</span>
476 463 <span class="c"># . Assign count to appropriate distance bin for a specific atom pair</span>
477 464 <span class="c">#</span>
478 465 <span class="c"># . Normalize occurance count of pharmacophore atom pairs by heavy atom count</span>
479 466 <span class="c"># or sum of AtomTypeCounts of each pharmacophore atom type in the atom pair</span>
480 467 <span class="c"># at a specific distance.</span>
481 468 <span class="c">#</span>
482 469 <span class="c"># . Fuzzify occurance count of pharmacophore atom pairs using FuzzyBinning or</span>
483 470 <span class="c"># FuzzySmothing methodology.</span>
484 471 <span class="c">#</span>
485 472 <span class="c"># Notes:</span>
486 473 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span>
487 474 <span class="c">#</span>
488 <a name="GenerateFingerprints-"></a> 475 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
489 476 <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>
490 477
491 478 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
492 479 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;GenerateTopologicalPharmacophoreAtomPairsFingerprints: No fingerpritns generated: MinDistance, $This-&gt;{MinDistance}, must be &lt;= MaxDistance, $This-&gt;{MaxDistance}...&quot;</span><span class="sc">;</span>
493 480 <span class="s">}</span>
494 481
495 482 <span class="c"># Cache appropriate molecule data...</span>
496 483 <span class="i">$This</span><span class="i">-&gt;_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
497 484
498 485 <span class="c"># Generate distance matrix...</span>
499 486 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_SetupDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
500 487 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateFingerprints: Fingerprints generation didn&#39;t succeed: Couldn&#39;t generate distance matrix...&quot;</span><span class="sc">;</span>
501 488 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
502 489 <span class="s">}</span>
503 490
504 491 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span>
505 492 <span class="i">$This</span><span class="i">-&gt;_AssignPharmacophoreAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
506 493
507 494 <span class="c"># Initialize values of all possible pharmacohore atom pairs...</span>
508 495 <span class="i">$This</span><span class="i">-&gt;_InitializePharmacophoreAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
509 496
510 497 <span class="c"># Count atom pairs...</span>
511 498 <span class="i">$This</span><span class="i">-&gt;_CountPharmacohoreAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
512 499
513 500 <span class="c"># Fuzzify atom pairs count...</span>
514 501 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">FuzzificationMode</span>} =~ <span class="q">/^BeforeNormalization$/i</span><span class="s">)</span> <span class="s">{</span>
515 502 <span class="i">$This</span><span class="i">-&gt;_FuzzifyPharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
516 503 <span class="s">}</span>
517 504
518 505 <span class="c"># Normalize atom pairs count...</span>
519 506 <span class="i">$This</span><span class="i">-&gt;_NormalizePharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
520 507
521 508 <span class="c"># Fuzzify atom pairs count...</span>
522 509 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">FuzzificationMode</span>} =~ <span class="q">/^AfterNormalization$/i</span><span class="s">)</span> <span class="s">{</span>
523 510 <span class="i">$This</span><span class="i">-&gt;_FuzzifyPharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
524 511 <span class="s">}</span>
525 512
526 513 <span class="c"># Set final fingerprints...</span>
527 514 <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
528 515
529 516 <span class="c"># Clear cached molecule data...</span>
530 517 <span class="i">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
531 518
532 519 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
533 520 <span class="s">}</span>
534 521
535 522 <span class="c"># Setup distance matrix...</span>
536 523 <span class="c">#</span>
537 <a name="_SetupDistanceMatrix-"></a> 524 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span>
538 525 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
539 526
540 527 <span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
541 528
542 529 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span>
543 530 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
544 531 <span class="s">}</span>
545 532
546 533 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
547 534 <span class="s">}</span>
548 535
549 536 <span class="c"># Assign pharmacohore atom types to all heavy atoms and count each atom</span>
550 537 <span class="c"># types assigned...</span>
551 538 <span class="c">#</span>
552 <a name="_AssignPharmacophoreAtomTypes-"></a> 539 <span class="k">sub </span><span class="m">_AssignPharmacophoreAtomTypes</span> <span class="s">{</span>
553 540 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
554 541 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$AssignedAtomType</span><span class="cm">,</span> <span class="i">$FunctionalClassAtomTypes</span><span class="s">)</span><span class="sc">;</span>
555 542
556 543 <span class="c"># Assign topological pharmacophore atom types...</span>
557 544 <span class="i">$FunctionalClassAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="cm">,</span> <span class="q">&#39;FunctionalClassesToUse&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}<span class="s">)</span><span class="sc">;</span>
558 545 <span class="i">$FunctionalClassAtomTypes</span><span class="i">-&gt;AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
559 546
560 547 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
561 548
562 549 <span class="c"># Initialize assigned atom types count...</span>
563 550 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
564 551 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
565 552 <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType</span>} = <span class="n">0</span><span class="sc">;</span>
566 553 <span class="s">}</span>
567 554
568 555 <span class="i">$This</span>-&gt;{<span class="w">HeavyAtomCount</span>} = <span class="n">0</span><span class="sc">;</span>
569 556
570 557 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
571 558 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
572 559 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
573 560 <span class="s">}</span>
574 561 <span class="i">$This</span>-&gt;{<span class="w">HeavyAtomCount</span>} += <span class="n">1</span><span class="sc">;</span>
575 562
576 563 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
577 564
578 565 <span class="c"># Collect all possible pharmacophore atom types which could be assigned to atom...</span>
579 566 <span class="k">my</span><span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span><span class="sc">;</span>
580 567
581 568 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
582 569 <span class="i">$AssignedAtomType</span> = <span class="i">$FunctionalClassAtomTypes</span><span class="i">-&gt;GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
583 570 <span class="k">if</span> <span class="s">(</span><span class="i">$AssignedAtomType</span> &amp;&amp; <span class="i">$AssignedAtomType</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
584 571 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AssignedAtomType</span><span class="sc">;</span>
585 572 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span> <span class="s">{</span>
586 573 <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType</span>} += <span class="n">1</span><span class="sc">;</span>
587 574 <span class="s">}</span>
588 575 <span class="s">}</span>
589 576
590 577 <span class="c"># Assign phramacophore types to atom...</span>
591 578 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
592 579 <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = \<span class="i">@AtomTypes</span><span class="sc">;</span>
593 580 <span class="s">}</span>
594 581 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
595 582 <span class="s">}</span>
596 583
597 584 <span class="c"># Initialize values of all possible pharmacohore atom pairs...</span>
598 585 <span class="c">#</span>
599 586 <span class="c"># Let:</span>
600 587 <span class="c"># Dmin = Minimum distance correspoding to number of bonds between two atoms</span>
601 588 <span class="c"># Dmax = Maximum distance correspoding to number of bonds between two atoms</span>
602 589 <span class="c"># D = Distance correspoding to number of bonds between two atoms</span>
603 590 <span class="c">#</span>
604 591 <span class="c"># P = Number of pharmacophore atom types to consider</span>
605 592 <span class="c"># PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn</span>
606 593 <span class="c">#</span>
607 594 <span class="c"># PPT = Total number of possible pharmacophore atom pairs at all distances between Dmin and Dmax</span>
608 595 <span class="c">#</span>
609 596 <span class="c"># Then:</span>
610 597 <span class="c">#</span>
611 598 <span class="c"># PPD = (P * (P - 1))/2 + P</span>
612 599 <span class="c">#</span>
613 600 <span class="c"># PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)</span>
614 601 <span class="c"># = ((Dmax - Dmin) + 1) * PPD</span>
615 602 <span class="c">#</span>
616 603 <span class="c">#</span>
617 604 <span class="c"># So for default values of Dmin = 1, Dmax = 10 and P = 5,</span>
618 605 <span class="c">#</span>
619 606 <span class="c"># PPD = (5 * (5 - 1))/2 + 5 = 15</span>
620 607 <span class="c"># PPT = ((10 - 1) + 1) * 15 = 150</span>
621 608 <span class="c">#</span>
622 609 <span class="c"># the pharmacophore atom pairs bais set includes 150 values.</span>
623 610 <span class="c">#</span>
624 <a name="_InitializePharmacophoreAtomPairs-"></a> 611 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomPairs</span> <span class="s">{</span>
625 612 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
626 613 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span>
627 614
628 615 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
629 616
630 617 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} .. <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
631 618 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
632 619
633 620 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
634 621 <span class="i">$AtomType1</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span>
635 622 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
636 623
637 624 <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
638 625 <span class="i">$AtomType2</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span>
639 626 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">0</span><span class="sc">;</span>
640 627 <span class="s">}</span>
641 628 <span class="s">}</span>
642 629 <span class="s">}</span>
643 630 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
644 631 <span class="s">}</span>
645 632
646 633 <span class="c"># Count pharmacophore atom pairs between mininum and maximum distance at each</span>
647 634 <span class="c"># distance using distance matrix and pharmacophore atom types assiged to each heavy</span>
648 635 <span class="c"># atom.</span>
649 636 <span class="c">#</span>
650 637 <span class="c"># Let:</span>
651 638 <span class="c"># Px = Pharmacophore atom type x</span>
652 639 <span class="c"># Py = Pharmacophore atom type y</span>
653 640 <span class="c"># Dn = Distance between Px and Py in specified distance range</span>
654 641 <span class="c">#</span>
655 642 <span class="c"># Then:</span>
656 643 <span class="c"># Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn</span>
657 644 <span class="c">#</span>
658 645 <span class="c"># For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on</span>
659 646 <span class="c">#</span>
660 647 <span class="c"># Notes:</span>
661 648 <span class="c"># . The row and column indices of distance matrix correspond to atom indices.</span>
662 649 <span class="c"># . Distance value of BigNumber implies the atom is not connected to any other atom.</span>
663 650 <span class="c"># . Due to symmetric nature of distance matrix, only upper or lower triangular matrix</span>
664 651 <span class="c"># needs to be processed during identification and count of pharmacophore atom pairs.</span>
665 652 <span class="c">#</span>
666 <a name="_CountPharmacohoreAtomPairs-"></a> 653 <span class="k">sub </span><span class="m">_CountPharmacohoreAtomPairs</span> <span class="s">{</span>
667 654 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
668 655 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$CountIncrement</span><span class="s">)</span><span class="sc">;</span>
669 656
670 657 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>}<span class="sc">;</span>
671 658 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DistanceMatrix</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
672 659 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span>
673 660
674 661 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
675 662 <span class="i">$AtomID1</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span>
676 663 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span> &amp;&amp; <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
677 664 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span>
678 665 <span class="s">}</span>
679 666
680 667 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="i">$RowIndex</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
681 668 <span class="i">$AtomID2</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span>
682 669 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span> &amp;&amp; <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
683 670 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
684 671 <span class="s">}</span>
685 672
686 673 <span class="i">$Distance</span> = <span class="i">$DistanceMatrix</span><span class="i">-&gt;GetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
687 674 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> &lt; <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} || <span class="i">$Distance</span> &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
688 675 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
689 676 <span class="s">}</span>
690 677
691 678 <span class="j">ATOMTYPE1:</span> <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}}<span class="s">)</span> <span class="s">{</span>
692 679 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType1</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
693 680 <span class="k">next</span> <span class="j">ATOMTYPE1</span><span class="sc">;</span>
694 681 <span class="s">}</span>
695 682 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}}<span class="s">)</span> <span class="s">{</span>
696 683 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
697 684 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span>
698 685 <span class="s">}</span>
699 686 <span class="i">$CountIncrement</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType1</span>} * <span class="i">$This</span>-&gt;{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
700 687 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType1</span> <span class="k">le</span> <span class="i">$AtomType2</span><span class="s">)</span> <span class="s">{</span>
701 688 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="i">$CountIncrement</span><span class="sc">;</span>
702 689 <span class="s">}</span>
703 690 <span class="k">else</span> <span class="s">{</span>
704 691 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType2</span>}{<span class="i">$AtomType1</span>} += <span class="i">$CountIncrement</span><span class="sc">;</span>
705 692 <span class="s">}</span>
706 693 <span class="s">}</span>
707 694 <span class="s">}</span>
708 695 <span class="s">}</span>
709 696 <span class="s">}</span>
710 697 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
711 698 <span class="s">}</span>
712 699
713 700 <span class="c"># Normalize the occurance count of pharmacophore atom pairs over the specified distance</span>
714 701 <span class="c"># range...</span>
715 702 <span class="c">#</span>
716 <a name="_NormalizePharmacohoreAtomPairsCount-"></a> 703 <span class="k">sub </span><span class="m">_NormalizePharmacohoreAtomPairsCount</span> <span class="s">{</span>
717 704 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
718 705
719 706 <span class="j">METHODOLOGY:</span> <span class="s">{</span>
720 707 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
721 708 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span>
722 709 <span class="s">}</span>
723 710 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByHeavyAtomsCount$/i</span><span class="s">)</span> <span class="s">{</span>
724 711 <span class="i">$This</span><span class="i">-&gt;_NormalizeAtomPairsCountByHeavyAtomsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
725 712 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span>
726 713 <span class="s">}</span>
727 714 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByAtomTypesCount$/i</span><span class="s">)</span> <span class="s">{</span>
728 715 <span class="i">$This</span><span class="i">-&gt;_NormalizeAtomPairsCountByAtomTypesCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
729 716 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span>
730 717 <span class="s">}</span>
731 718 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_NormalizePharmacohoreAtomPairsCount: Unknown NormalizationMethodology: $This-&gt;{NormalizationMethodology}...&quot;</span><span class="sc">;</span>
732 719 <span class="s">}</span>
733 720 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
734 721 <span class="s">}</span>
735 722
736 723
737 724 <span class="c"># Normalize the occurance count of pharmacophore atom pairs at various distances by</span>
738 725 <span class="c"># heavy atom count...</span>
739 726 <span class="c">#</span>
740 <a name="_NormalizeAtomPairsCountByHeavyAtomsCount-"></a> 727 <span class="k">sub </span><span class="m">_NormalizeAtomPairsCountByHeavyAtomsCount</span> <span class="s">{</span>
741 728 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
742 729 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span>
743 730
744 731 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">HeavyAtomCount</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
745 732 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
746 733 <span class="s">}</span>
747 734
748 735 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}} <span class="s">)</span> <span class="s">{</span>
749 736 <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span>
750 737 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span>
751 738 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
752 739 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span>
753 740 <span class="s">}</span>
754 741 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} /= <span class="i">$This</span>-&gt;{<span class="w">HeavyAtomCount</span>}<span class="sc">;</span>
755 742 <span class="s">}</span>
756 743 <span class="s">}</span>
757 744 <span class="s">}</span>
758 745 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
759 746 <span class="s">}</span>
760 747
761 748 <span class="c"># Normalize the occurance count of pharmacophore atom pairs at various distances by</span>
762 749 <span class="c"># dividing it using sum of the count of each pharmacophore atom type present in the</span>
763 750 <span class="c"># molecule for the corresponding atom pair.</span>
764 751 <span class="c">#</span>
765 <a name="_NormalizeAtomPairsCountByAtomTypesCount-"></a> 752 <span class="k">sub </span><span class="m">_NormalizeAtomPairsCountByAtomTypesCount</span> <span class="s">{</span>
766 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
767 754 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType1Count</span><span class="cm">,</span> <span class="i">$AtomType2Count</span><span class="cm">,</span> <span class="i">$NormalizationFactor</span><span class="s">)</span><span class="sc">;</span>
768 755
769 756 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}} <span class="s">)</span> <span class="s">{</span>
770 757 <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span>
771 758 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span>
772 759 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
773 760 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span>
774 761 <span class="s">}</span>
775 762 <span class="i">$NormalizationFactor</span> = <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType1</span>} + <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
776 763 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} /= <span class="i">$NormalizationFactor</span><span class="sc">;</span>
777 764 <span class="s">}</span>
778 765 <span class="s">}</span>
779 766 <span class="s">}</span>
780 767 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
781 768 <span class="s">}</span>
782 769
783 770 <span class="c"># Fuzzify pharmacophore atom pairs count...</span>
784 771 <span class="c">#</span>
785 772 <span class="c"># Let:</span>
786 773 <span class="c"># Px = Pharmacophore atom type x</span>
787 774 <span class="c"># Py = Pharmacophore atom type y</span>
788 775 <span class="c">#</span>
789 776 <span class="c"># PPxy = Pharmacophore atom pair between atom type Px and Py</span>
790 777 <span class="c">#</span>
791 778 <span class="c"># PPxyDn = Pharmacophore atom pairs count between atom type Px and Py at distance Dn</span>
792 779 <span class="c"># PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py at distance Dn - 1</span>
793 780 <span class="c"># PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py at distance Dn + 1</span>
794 781 <span class="c">#</span>
795 782 <span class="c"># FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing</span>
796 783 <span class="c">#</span>
797 784 <span class="c"># Then:</span>
798 785 <span class="c">#</span>
799 786 <span class="c"># For FuzzyBinning:</span>
800 787 <span class="c">#</span>
801 788 <span class="c"># PPxyDn = PPxyDn (Unchanged)</span>
802 789 <span class="c">#</span>
803 790 <span class="c"># PPxyDn-1 = PPxyDn-1 + PPxyDn * FF</span>
804 791 <span class="c"># PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</span>
805 792 <span class="c">#</span>
806 793 <span class="c"># For FuzzyBinSmoothing:</span>
807 794 <span class="c">#</span>
808 795 <span class="c"># PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin &lt; Dn &lt; Dmax</span>
809 796 <span class="c"># PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax</span>
810 797 <span class="c">#</span>
811 798 <span class="c"># PPxyDn-1 = PPxyDn-1 + PPxyDn * FF</span>
812 799 <span class="c"># PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</span>
813 800 <span class="c">#</span>
814 801 <span class="c"># In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurance counts.</span>
815 802 <span class="c"># A value of 1 during FuzzyBinning corresponds to maximum fuzzification of occurance counts;</span>
816 803 <span class="c"># however, a value of 1 during FuzzyBinSmoothing ends up completely distributing the value over</span>
817 804 <span class="c"># the previous and next distance bins.</span>
818 805 <span class="c">#</span>
819 806 <span class="c"># So for default value of FuzzFactor (FF) 0.15, the occurance count of pharmacohore atom pairs</span>
820 807 <span class="c"># at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1</span>
821 808 <span class="c"># are incremened by PPxyDn * 0.15.</span>
822 809 <span class="c">#</span>
823 810 <span class="c"># And during FuzzyBinSmoothing the occurance counts at Distance Dn is scaled back using multiplicate</span>
824 811 <span class="c"># factor of (1 - 2*0.15) and the occurance counts at distances Dn -1 and Dn + 1 are incremened by</span>
825 812 <span class="c"># PPxyDn * 0.15. In otherwords, occurance bin count is smoothed out by distributing it over the</span>
826 813 <span class="c"># previous and next distance value.</span>
827 814 <span class="c">#</span>
828 <a name="_FuzzifyPharmacohoreAtomPairsCount-"></a> 815 <span class="k">sub </span><span class="m">_FuzzifyPharmacohoreAtomPairsCount</span> <span class="s">{</span>
829 816 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
830 817 <span class="k">my</span><span class="s">(</span><span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$CurrentDistance</span><span class="cm">,</span> <span class="i">$CurrentCount</span><span class="cm">,</span> <span class="i">$NextDistance</span><span class="cm">,</span> <span class="i">$NextCount</span><span class="cm">,</span> <span class="i">$PreviousDistance</span><span class="cm">,</span> <span class="i">$ModifyCurrentCount</span><span class="cm">,</span> <span class="i">$ChangeInCountValue</span><span class="s">)</span><span class="sc">;</span>
831 818
832 819 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">FuzzifyAtomPairsCount</span>} &amp;&amp; <span class="i">$This</span>-&gt;{<span class="w">FuzzFactor</span>} &gt; <span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
833 820 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
834 821 <span class="s">}</span>
835 822
836 823 <span class="i">$ModifyCurrentCount</span> = <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinSmoothing$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
837 824
838 825 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
839 826 <span class="i">$AtomType1</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span>
840 827 <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
841 828 <span class="i">$AtomType2</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span>
842 829
843 830 <span class="i">$CurrentCount</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NextCount</span> = <span class="n">0</span><span class="sc">;</span>
844 831
845 832 <span class="i">$NextDistance</span> = <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>}<span class="sc">;</span>
846 833 <span class="i">$NextCount</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$NextDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
847 834
848 835 <span class="j">DISTANCE:</span> <span class="k">for</span> <span class="i">$CurrentDistance</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} .. <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
849 836 <span class="i">$NextDistance</span> = <span class="i">$CurrentDistance</span> + <span class="n">1</span><span class="sc">;</span>
850 837 <span class="i">$PreviousDistance</span> = <span class="i">$CurrentDistance</span> - <span class="n">1</span><span class="sc">;</span>
851 838
852 839 <span class="i">$CurrentCount</span> = <span class="i">$NextCount</span><span class="sc">;</span>
853 840 <span class="i">$NextCount</span> = <span class="s">(</span><span class="i">$CurrentDistance</span> &lt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> ? <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$NextDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
854 841
855 842 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentCount</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
856 843 <span class="c"># No contribution to fuzzy binning from this distance...</span>
857 844 <span class="k">next</span> <span class="j">DISTANCE</span><span class="sc">;</span>
858 845 <span class="s">}</span>
859 846
860 847 <span class="i">$ChangeInCountValue</span> = <span class="i">$CurrentCount</span> * <span class="i">$This</span>-&gt;{<span class="w">FuzzFactor</span>}<span class="sc">;</span>
861 848
862 849 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentDistance</span> &gt; <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>}<span class="s">)</span> <span class="s">{</span>
863 850 <span class="c"># Increment count at previous distance...</span>
864 851 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$PreviousDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="i">$ChangeInCountValue</span><span class="sc">;</span>
865 852 <span class="s">}</span>
866 853
867 854 <span class="k">if</span> <span class="s">(</span><span class="i">$ModifyCurrentCount</span><span class="s">)</span> <span class="s">{</span>
868 855 <span class="c"># Decrement count at current distance for FuzzyBinSmoothing...</span>
869 856 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentDistance</span> &gt; <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} &amp;&amp; <span class="i">$CurrentDistance</span> &lt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
870 857 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$CurrentDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} -= <span class="n">2</span> * <span class="i">$ChangeInCountValue</span><span class="sc">;</span>
871 858 <span class="s">}</span>
872 859 <span class="k">else</span> <span class="s">{</span>
873 860 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$CurrentDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} -= <span class="i">$ChangeInCountValue</span><span class="sc">;</span>
874 861 <span class="s">}</span>
875 862 <span class="s">}</span>
876 863
877 864 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentDistance</span> &lt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
878 865 <span class="c"># Increment count at next distance...</span>
879 866 <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$NextDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="i">$ChangeInCountValue</span><span class="sc">;</span>
880 867 <span class="s">}</span>
881 868 <span class="s">}</span>
882 869 <span class="s">}</span>
883 870 <span class="s">}</span>
884 871 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
885 872 <span class="s">}</span>
886 873
887 874 <span class="c"># Set final fingerpritns vector...</span>
888 875 <span class="c">#</span>
889 <a name="_SetFinalFingerprints-"></a> 876 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
890 877 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
891 878 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$RoundOffValues</span><span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="cm">,</span> <span class="i">$UseArbitrarySetSize</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
892 879
893 880 <span class="c"># Mark successful generation of fingerprints...</span>
894 881 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
895 882
896 883 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
897 884 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
898 885
899 886 <span class="c"># Do values need to be rounded off?</span>
900 887 <span class="i">$RoundOffValues</span> = <span class="s">(</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> || <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">FuzzifyAtomPairsCount</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>
901 888 <span class="i">$ValuesPrecision</span> = <span class="i">$This</span>-&gt;{<span class="w">ValuesPrecision</span>}<span class="sc">;</span>
902 889
903 890 <span class="c"># Is it an ArbitraySize atom pairs set size?</span>
904 891 <span class="i">$UseArbitrarySetSize</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
905 892
906 893 <span class="c"># Collect all atom paris count values...</span>
907 894 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} .. <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
908 895 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
909 896 <span class="i">$AtomType1</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span>
910 897 <span class="j">INDEX2:</span> <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
911 898 <span class="i">$AtomType2</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span>
912 899
913 900 <span class="c"># Atom pair count...</span>
914 901 <span class="i">$Value</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
915 902 <span class="k">if</span> <span class="s">(</span><span class="i">$RoundOffValues</span><span class="s">)</span> <span class="s">{</span>
916 903 <span class="i">$Value</span> = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$Value</span><span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">ValuesPrecision</span>}<span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
917 904 <span class="s">}</span>
918 905
919 906 <span class="c"># Ignore or not to ignore...</span>
920 907 <span class="k">if</span> <span class="s">(</span><span class="i">$UseArbitrarySetSize</span> &amp;&amp; <span class="i">$Value</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
921 908 <span class="k">next</span> <span class="j">INDEX2</span><span class="sc">;</span>
922 909 <span class="s">}</span>
923 910
924 911 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}}<span class="cm">,</span> <span class="q">&quot;${AtomType1}-D${Distance}-${AtomType2}&quot;</span><span class="sc">;</span>
925 912 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span>
926 913 <span class="s">}</span>
927 914 <span class="s">}</span>
928 915 <span class="s">}</span>
929 916
930 917 <span class="c"># Add AtomPairsIDs and count values to fingerprint vector...</span>
931 918 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}}<span class="s">)</span><span class="sc">;</span>
932 919 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
933 920
934 921 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
935 922 <span class="s">}</span>
936 923
937 924 <span class="c"># Get pharmacophore atom pair IDs corresponding to atom pairs count values in</span>
938 925 <span class="c"># fingerprint vector as an array or reference to an array...</span>
939 926 <span class="c">#</span>
940 927 <span class="c"># AtomPairIDs list is generated during finalization of fingerprints and the fingerprint</span>
941 928 <span class="c"># vector containing count values matches the atom pairs array.</span>
942 929 <span class="c">#</span>
943 930 <span class="c">#</span>
944 <a name="GetAtomPairIDs-"></a> 931 <span class="k">sub </span><span class="m">GetAtomPairIDs</span> <span class="s">{</span>
945 932 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
946 933
947 934 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}}<span class="sc">;</span>
948 935 <span class="s">}</span>
949 936
950 937 <span class="c"># Cache appropriate molecule data...</span>
951 938 <span class="c">#</span>
952 <a name="_SetupMoleculeDataCache-"></a> 939 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
953 940 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
954 941
955 942 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span>
956 943 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span>
957 944 <span class="c">#</span>
958 945 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
959 946
960 947 <span class="c"># Get all atom IDs...</span>
961 948 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
962 949 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
963 950 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="sc">;</span>
964 951
965 952 <span class="c"># Set AtomIndex to AtomID hash...</span>
966 953 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
967 954 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span>
968 955
969 956 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
970 957 <span class="s">}</span>
971 958
972 959 <span class="c"># Clear cached molecule data...</span>
973 960 <span class="c">#</span>
974 <a name="_ClearMoleculeDataCache-"></a> 961 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
975 962 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
976 963
977 964 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
978 965
979 966 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
980 967 <span class="s">}</span>
981 968
982 969
983 970 <span class="c"># Return a string containg data for TopologicalPharmacophoreAtomPairsFingerprints object...</span>
984 <a name="StringifyTopologicalPharmacophoreAtomPairsFingerprints-"></a> 971 <span class="k">sub </span><span class="m">StringifyTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span>
985 972 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
986 973 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span>
987 974
988 975 <span class="c"># Type of fingerprint...</span>
989 976 <span class="i">$FingerprintsString</span> = <span class="q">&quot;Fingerprint type: $This-&gt;{Type}; AtomPairsSetSizeToUse: $This-&gt;{AtomPairsSetSizeToUse}&quot;</span><span class="sc">;</span>
990 977
991 978 <span class="c"># Min and max distance...</span>
992 979 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; MinDistance: $This-&gt;{MinDistance}; MaxDistance: $This-&gt;{MaxDistance}&quot;</span><span class="sc">;</span>
993 980
994 981 <span class="c"># Pharmacophore type labels and description...</span>
995 982 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span>
996 983
997 984 <span class="i">@AtomTypesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
998 985 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
999 986
1000 987 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1001 988 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesOrder</span><span class="s">)</span> <span class="s">{</span>
1002 989 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="q">&quot;$AtomType: $AvailableAtomTypes{$AtomType}&quot;</span><span class="sc">;</span>
1003 990 <span class="s">}</span>
1004 991
1005 992 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AtomTypesToUse: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
1006 993 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AtomTypesOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
1007 994 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AvailableAtomTypes: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypes</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
1008 995
1009 996 <span class="c"># Normalization method...</span>
1010 997 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; NormalizationMethodology: $This-&gt;{NormalizationMethodology}&quot;</span><span class="sc">;</span>
1011 998
1012 999 <span class="c"># Weights...</span>
1013 1000 <span class="k">my</span><span class="s">(</span><span class="i">$FirstLabel</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span><span class="sc">;</span>
1014 1001
1015 1002 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AtomTypesWeight &lt;Labels: Weight&gt;: &lt;&quot;</span><span class="sc">;</span>
1016 1003 <span class="i">$FirstLabel</span> = <span class="n">1</span><span class="sc">;</span>
1017 1004 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
1018 1005 <span class="i">$Weight</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTypesWeight</span>}{<span class="i">$Label</span>}<span class="sc">;</span>
1019 1006 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstLabel</span><span class="s">)</span> <span class="s">{</span>
1020 1007 <span class="i">$FirstLabel</span> = <span class="n">0</span><span class="sc">;</span>
1021 1008 <span class="i">$FingerprintsString</span> .= <span class="q">&quot; ${Label}: ${Weight}&quot;</span><span class="sc">;</span>
1022 1009 <span class="s">}</span>
1023 1010 <span class="k">else</span> <span class="s">{</span>
1024 1011 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; ${Label}: ${Weight}&quot;</span><span class="sc">;</span>
1025 1012 <span class="s">}</span>
1026 1013 <span class="s">}</span>
1027 1014 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
1028 1015
1029 1016 <span class="c"># Fuzzification of count...</span>
1030 1017 <span class="k">my</span><span class="s">(</span><span class="i">$FuzzifyFlag</span><span class="s">)</span><span class="sc">;</span>
1031 1018 <span class="i">$FuzzifyFlag</span> = <span class="i">$This</span>-&gt;{<span class="w">FuzzifyAtomPairsCount</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="sc">;</span>
1032 1019 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FuzzifyAtomPairsCount: $FuzzifyFlag; FuzzificationMode: $This-&gt;{FuzzificationMode}; FuzzificationMethodology: $This-&gt;{FuzzificationMethodology}; FuzzFactor: $This-&gt;{FuzzFactor}&quot;</span><span class="sc">;</span>
1033 1020
1034 1021 <span class="c"># Total number of pharmacophore atom pairs...</span>
1035 1022 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; NumOfAtomPairs: &quot;</span> . <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1036 1023
1037 1024 <span class="c"># FingerprintsVector...</span>
1038 1025 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FingerprintsVector: &lt; $This-&gt;{FingerprintsVector} &gt;&quot;</span><span class="sc">;</span>
1039 1026
1040 1027 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span>
1041 1028 <span class="s">}</span>
1042 1029
1043 <a name="EOF-"></a></pre>
1044 <p>&nbsp;</p>
1045 <br />
1046 <center>
1047 <img src="../../../images/h2o2.png">
1048 </center>
1049 </body>
1050 </html>