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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> | |
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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 <msud@san.rr.com></span> | |
21 8 <span class="c">#</span> | |
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
23 10 <span class="c">#</span> | |
24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
25 12 <span class="c">#</span> | |
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
29 16 <span class="c"># later version.</span> | |
30 17 <span class="c">#</span> | |
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
34 21 <span class="c"># details.</span> | |
35 22 <span class="c">#</span> | |
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
40 27 <span class="c">#</span> | |
41 28 | |
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
45 32 <span class="k">use</span> <span class="w">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">=></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">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTopologicalPharmacophoreAtomPairsFingerprints'</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">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
72 59 <span class="k">bless</span> <span class="i">$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">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
74 61 | |
75 62 <span class="i">$This</span><span class="i">->_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">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalPharmacophoreAtomPairs'</span><span class="sc">;</span> | |
87 74 | |
88 75 <span class="c"># Type of vector...</span> | |
89 76 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</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">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">''</span><span class="sc">;</span> | |
99 86 | |
100 87 <span class="c"># Type of FingerprintsVector...</span> | |
101 88 <span class="c">#</span> | |
102 89 <span class="c"># OrderedNumericalValues - For ArbitrarySize value of AtomPairsSetSizeToUse</span> | |
103 90 <span class="c"># NumericalValues - For FixedSize value of AtomPairsSetSizeToUse</span> | |
104 91 <span class="c">#</span> | |
105 92 <span class="c"># Possible values: OrderedNumericalValues or NumericalValues. Default: NumericalValues</span> | |
106 93 <span class="c">#</span> | |
107 94 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</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">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="n">2</span><span class="sc">;</span> | |
112 99 | |
113 100 <span class="c"># Minimum and maximum bond distance between pharmacophore atom paris...</span> | |
114 101 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> | |
115 102 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> | |
116 103 | |
117 104 <span class="c"># Initialize atom types and weight information...</span> | |
118 105 <span class="i">$This</span><span class="i">->_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">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span> | |
126 113 | |
127 114 <span class="c"># Initialize fuzzification parameters...</span> | |
128 115 <span class="c">#</span> | |
129 116 <span class="i">$This</span><span class="i">->_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">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
134 121 | |
135 122 <span class="c"># Assigned Atom types count of each type in the molecule...</span> | |
136 123 <span class="c">#</span> | |
137 124 <span class="i">%</span>{<span class="i">$This</span>->{<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">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
142 129 <span class="i">%</span>{<span class="i">$This</span>->{<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>->{<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">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="k">sort</span> <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="s">)</span><span class="sc">;</span> | |
155 142 | |
156 143 <span class="c"># Weight of the various pharmacophore atom types to use for their contribution to atom</span> | |
157 144 <span class="c"># pair interaction. It allows to increase the importance of specific pharmacophore atom</span> | |
158 145 <span class="c"># types in the generted fingerprints.</span> | |
159 146 <span class="c">#</span> | |
160 147 <span class="c"># A value of 0 eliminates the contribution by a particular pharmacophore atom</span> | |
161 148 <span class="c"># type and 2 doubles its contribution.</span> | |
162 149 <span class="c">#</span> | |
163 150 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>->{<span class="w">AtomTypesWeight</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
168 155 <span class="k">for</span> <span class="i">$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">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$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">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} = <span class="n">0</span><span class="sc">;</span> | |
182 169 | |
183 170 <span class="c"># When to fuzz atom pair count...</span> | |
184 171 <span class="c">#</span> | |
185 172 <span class="c"># Possible values: BeforeNormalization or AfterNormalization. Default: AfterNormalization</span> | |
186 173 <span class="c">#</span> | |
187 174 <span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} = <span class="q">'AfterNormalization'</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">$This</span>->{<span class="w">FuzzificationMethodology</span>} = <span class="q">'FuzzyBinning'</span><span class="sc">;</span> | |
194 181 | |
195 182 <span class="c"># By how much to fuzz atom pairs count...</span> | |
196 183 <span class="c">#</span> | |
197 184 <span class="i">$This</span>->{<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">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
215 202 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
216 203 <span class="s">}</span> | |
217 204 | |
218 205 <span class="c"># Make sure molecule object was specified...</span> | |
219 206 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$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">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> | |
221 208 <span class="s">}</span> | |
222 209 | |
223 210 <span class="i">$This</span><span class="i">->_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">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span> | |
234 221 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">'ArbitrarySize'</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">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
239 226 | |
240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<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>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</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">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> | |
245 232 <span class="s">}</span> | |
246 233 | |
247 234 <span class="i">$This</span><span class="i">->_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>->{<span class="w">AtomPairsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span> | |
256 243 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomPairsSetSizeToUse: Can't change size: It's already set..."</span><span class="sc">;</span> | |
257 244 <span class="s">}</span> | |
258 245 | |
259 246 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: ${ClassName}->SetAtomPairsSetSizeToUse: Unknown AtomPairsSetSizeToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span> | |
261 248 <span class="s">}</span> | |
262 249 | |
263 250 <span class="i">$This</span>->{<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">"Warning: ${ClassName}->SetAvailableAtomTypes: AvailableAtomTypes value can't be set..."</span><span class="sc">;</span> | |
274 261 | |
275 262 <span class="k">return</span> <span class="i">$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">"Warning: ${ClassName}->SetAtomTypesToUse: No values specified..."</span><span class="sc">;</span> | |
286 273 <span class="k">return</span><span class="sc">;</span> | |
287 274 <span class="s">}</span> | |
288 275 | |
289 276 <span class="i">$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">"Error: ${ClassName}->SetAtomTypesToUse: Specified atom type, $SpecifiedAtomType, is not supported...\n "</span><span class="sc">;</span> | |
306 293 <span class="s">}</span> | |
307 294 <span class="i">$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">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
313 300 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<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">"Error: ${ClassName}->SetValuesPrecision: ValuesPrecision value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
326 313 <span class="s">}</span> | |
327 314 <span class="i">$This</span>->{<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">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> | |
339 326 <span class="s">}</span> | |
340 327 <span class="i">$This</span>->{<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">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
352 339 <span class="s">}</span> | |
353 340 <span class="i">$This</span>->{<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">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByAtomTypesCount..."</span><span class="sc">;</span> | |
366 353 <span class="s">}</span> | |
367 354 | |
368 355 <span class="i">$This</span>->{<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>->{<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">"Error: ${ClassName}->SetAtomTypesWeight: AtomTypeWeight for $AtomType couldn't be set: Unknown atom type..."</span><span class="sc">;</span> | |
389 376 <span class="s">}</span> | |
390 377 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Weight</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Weight</span> >= <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">"Error: ${ClassName}->SetAtomTypesWeight: Specified weight value, $Weight, for AtomType, $AtomType, muts be >= 0..."</span><span class="sc">;</span> | |
392 379 <span class="s">}</span> | |
393 380 <span class="i">$This</span>->{<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">"Error: ${ClassName}->SetFuzzificationMethodology: FuzzificationMethodology value, $Value, is not valid. Supported values: FuzzyBinning or FuzzyBinSmoothing..."</span><span class="sc">;</span> | |
404 391 <span class="s">}</span> | |
405 392 | |
406 393 <span class="i">$This</span>->{<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">"Error: ${ClassName}->SetFuzzificationMode: FuzzificationMode value, $Value, is not valid. Supported values: BeforeNormalization or AfterNormalization..."</span><span class="sc">;</span> | |
418 405 <span class="s">}</span> | |
419 406 | |
420 407 <span class="i">$This</span>->{<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">$This</span>->{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinning$/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">$Value</span><span class="s">)</span> && <span class="i">$Value</span> >=<span class="n">0</span> && <span class="i">$Value</span> <= <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">"Error: ${ClassName}->SetFuzzFactor: Specified fuzz factor value, $Value, must be >= 0 and <= 1..."</span><span class="sc">;</span> | |
433 420 <span class="s">}</span> | |
434 421 <span class="s">}</span> | |
435 422 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<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> && <span class="i">$Value</span> >=<span class="n">0</span> && <span class="i">$Value</span> <= <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">"Error: ${ClassName}->SetFuzzFactor: Specified fuzz factor value, $Value, must be >= 0 and <= 0.5..."</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">"Error: ${ClassName}->SetFuzzFactor: Fuzz factor value can't be changed: Uknown FuzzificationMethodology: $This->{FuzzificationMethodology}..."</span><span class="sc">;</span> | |
442 429 <span class="s">}</span> | |
443 430 | |
444 431 <span class="i">$This</span>->{<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>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> | |
456 443 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> | |
457 444 <span class="s">}</span> | |
458 445 | |
459 446 <span class="c"># Generate fingerprints description...</span> | |
460 447 | |
461 448 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomPairsSetSizeToUse}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</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">$This</span>->{<span class="w">MinDistance</span>} > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
492 479 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalPharmacophoreAtomPairsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span> | |
493 480 <span class="s">}</span> | |
494 481 | |
495 482 <span class="c"># Cache appropriate molecule data...</span> | |
496 483 <span class="i">$This</span><span class="i">->_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">->_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">"Warning: ${ClassName}->GenerateFingerprints: Fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span> | |
501 488 <span class="k">return</span> <span class="i">$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">$This</span><span class="i">->_AssignPharmacophoreAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
506 493 | |
507 494 <span class="c"># Initialize values of all possible pharmacohore atom pairs...</span> | |
508 495 <span class="i">$This</span><span class="i">->_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">$This</span><span class="i">->_CountPharmacohoreAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
512 499 | |
513 500 <span class="c"># Fuzzify atom pairs count...</span> | |
514 501 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<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">->_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">$This</span><span class="i">->_NormalizePharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
520 507 | |
521 508 <span class="c"># Fuzzify atom pairs count...</span> | |
522 509 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<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">->_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">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
528 515 | |
529 516 <span class="c"># Clear cached molecule data...</span> | |
530 517 <span class="i">$This</span><span class="i">->_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">$This</span>->{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->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">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span> | |
543 530 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
544 531 <span class="s">}</span> | |
545 532 | |
546 533 <span class="k">return</span> <span class="i">$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">$FunctionalClassAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}<span class="s">)</span><span class="sc">;</span> | |
558 545 <span class="i">$FunctionalClassAtomTypes</span><span class="i">->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">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
561 548 | |
562 549 <span class="c"># Initialize assigned atom types count...</span> | |
563 550 <span class="i">%</span>{<span class="i">$This</span>->{<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>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
565 552 <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType</span>} = <span class="n">0</span><span class="sc">;</span> | |
566 553 <span class="s">}</span> | |
567 554 | |
568 555 <span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} = <span class="n">0</span><span class="sc">;</span> | |
569 556 | |
570 557 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
571 558 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->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">$This</span>->{<span class="w">HeavyAtomCount</span>} += <span class="n">1</span><span class="sc">;</span> | |
575 562 | |
576 563 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
577 564 | |
578 565 <span class="c"># Collect all possible pharmacophore atom types which could be assigned to atom...</span> | |
579 566 <span class="k">my</span><span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span><span class="sc">;</span> | |
580 567 | |
581 568 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
582 569 <span class="i">$AssignedAtomType</span> = <span class="i">$FunctionalClassAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
583 570 <span class="k">if</span> <span class="s">(</span><span class="i">$AssignedAtomType</span> && <span class="i">$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>->{<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">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
592 579 <span class="i">$This</span>->{<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">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
629 616 | |
630 617 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
631 618 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
634 621 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span> | |
635 622 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
638 625 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span> | |
639 626 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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>->{<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">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
672 659 <span class="i">$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>->{<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>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span> && <span class="i">@</span>{<span class="i">$This</span>->{<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>->{<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>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span> && <span class="i">@</span>{<span class="i">$This</span>->{<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">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$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">$Distance</span> < <span class="i">$This</span>->{<span class="w">MinDistance</span>} || <span class="i">$Distance</span> > <span class="i">$This</span>->{<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>->{<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>->{<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">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}}<span class="s">)</span> <span class="s">{</span> | |
696 683 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$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>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType1</span>} * <span class="i">$This</span>->{<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>->{<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">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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>->{<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>->{<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">->_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">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByAtomTypesCount$/i</span><span class="s">)</span> <span class="s">{</span> | |
728 715 <span class="i">$This</span><span class="i">->_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">"Error: ${ClassName}->_NormalizePharmacohoreAtomPairsCount: Unknown NormalizationMethodology: $This->{NormalizationMethodology}..."</span><span class="sc">;</span> | |
732 719 <span class="s">}</span> | |
733 720 <span class="k">return</span> <span class="i">$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">$This</span>->{<span class="w">HeavyAtomCount</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
745 732 <span class="k">return</span> <span class="i">$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>->{<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>->{<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">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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>->{<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>->{<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>->{<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>->{<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>->{<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">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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>->{<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">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType1</span>} + <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span> | |
776 763 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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 < Dn < 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">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} && <span class="i">$This</span>->{<span class="w">FuzzFactor</span>} > <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">$This</span>->{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinSmoothing$/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">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
839 826 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$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>->{<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>->{<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">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span> | |
846 833 <span class="i">$NextCount</span> = <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
849 836 <span class="i">$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">$CurrentDistance</span> < <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> ? <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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>->{<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">$CurrentDistance</span> > <span class="i">$This</span>->{<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">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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">$CurrentDistance</span> > <span class="i">$This</span>->{<span class="w">MinDistance</span>} && <span class="i">$CurrentDistance</span> < <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
870 857 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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>->{<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">$CurrentDistance</span> < <span class="i">$This</span>->{<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">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
895 882 | |
896 883 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
897 884 <span class="i">@</span>{<span class="i">$This</span>->{<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>->{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> || <span class="s">(</span><span class="i">$This</span>->{<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>->{<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>->{<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">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<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">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
909 896 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$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>->{<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>->{<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">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$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>->{<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">$UseArbitrarySetSize</span> && <span class="i">$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">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="cm">,</span> <span class="q">"${AtomType1}-D${Distance}-${AtomType2}"</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>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="s">)</span><span class="sc">;</span> | |
932 919 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->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">$This</span>->{<span class="w">AtomPairsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<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>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
959 946 | |
960 947 <span class="c"># Get all atom IDs...</span> | |
961 948 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
962 949 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
963 950 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> | |
964 951 | |
965 952 <span class="c"># Set AtomIndex to AtomID hash...</span> | |
966 953 <span class="i">%</span>{<span class="i">$This</span>->{<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">$This</span>->{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#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">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
978 965 | |
979 966 <span class="k">return</span> <span class="i">$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">"Fingerprint type: $This->{Type}; AtomPairsSetSizeToUse: $This->{AtomPairsSetSizeToUse}"</span><span class="sc">;</span> | |
990 977 | |
991 978 <span class="c"># Min and max distance...</span> | |
992 979 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}"</span><span class="sc">;</span> | |
993 980 | |
994 981 <span class="c"># Pharmacophore type labels and description...</span> | |
995 982 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesOrder</span><span class="s">)</span> <span class="s">{</span> | |
1002 989 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="q">"$AtomType: $AvailableAtomTypes{$AtomType}"</span><span class="sc">;</span> | |
1003 990 <span class="s">}</span> | |
1004 991 | |
1005 992 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
1006 993 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
1007 994 <span class="i">$FingerprintsString</span> .= <span class="q">"; AvailableAtomTypes: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypes</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</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">"; NormalizationMethodology: $This->{NormalizationMethodology}"</span><span class="sc">;</span> | |
1011 998 | |
1012 999 <span class="c"># Weights...</span> | |
1013 1000 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FingerprintsString</span> .= <span class="q">"; AtomTypesWeight <Labels: Weight>: <"</span><span class="sc">;</span> | |
1016 1003 <span class="i">$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>->{<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>->{<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">" ${Label}: ${Weight}"</span><span class="sc">;</span> | |
1022 1009 <span class="s">}</span> | |
1023 1010 <span class="k">else</span> <span class="s">{</span> | |
1024 1011 <span class="i">$FingerprintsString</span> .= <span class="q">"; ${Label}: ${Weight}"</span><span class="sc">;</span> | |
1025 1012 <span class="s">}</span> | |
1026 1013 <span class="s">}</span> | |
1027 1014 <span class="i">$FingerprintsString</span> .= <span class="q">">"</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">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> | |
1032 1019 <span class="i">$FingerprintsString</span> .= <span class="q">"; FuzzifyAtomPairsCount: $FuzzifyFlag; FuzzificationMode: $This->{FuzzificationMode}; FuzzificationMethodology: $This->{FuzzificationMethodology}; FuzzFactor: $This->{FuzzFactor}"</span><span class="sc">;</span> | |
1033 1020 | |
1034 1021 <span class="c"># Total number of pharmacophore atom pairs...</span> | |
1035 1022 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomPairs: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1036 1023 | |
1037 1024 <span class="c"># FingerprintsVector...</span> | |
1038 1025 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> | |
1039 1026 | |
1040 1027 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span> | |
1041 1028 <span class="s">}</span> | |
1042 1029 | |
1043 <a name="EOF-"></a></pre> | |
1044 <p> </p> | |
1045 <br /> | |
1046 <center> | |
1047 <img src="../../../images/h2o2.png"> | |
1048 </center> | |
1049 </body> | |
1050 </html> |