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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:MolecularDescriptors::MolecularComplexityDescriptors.pm</title> | |
4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
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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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13 <pre> | |
14 <a name="package-MolecularDescriptors::MolecularComplexityDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularComplexityDescriptors</span><span class="sc">;</span> | |
15 2 <span class="c">#</span> | |
16 3 <span class="c"># $RCSfile: MolecularComplexityDescriptors.pm,v $</span> | |
17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> | |
18 5 <span class="c"># $Revision: 1.15 $</span> | |
19 6 <span class="c">#</span> | |
20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
21 8 <span class="c">#</span> | |
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
23 10 <span class="c">#</span> | |
24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
25 12 <span class="c">#</span> | |
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
29 16 <span class="c"># later version.</span> | |
30 17 <span class="c">#</span> | |
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
34 21 <span class="c"># details.</span> | |
35 22 <span class="c">#</span> | |
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
40 27 <span class="c">#</span> | |
41 28 | |
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
46 33 <span class="k">use</span> <span class="w">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">Atom</span><span class="sc">;</span> | |
49 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
50 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> | |
51 38 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> | |
52 39 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> | |
53 40 <span class="k">use</span> <span class="w">Fingerprints::AtomTypesFingerprints</span><span class="sc">;</span> | |
54 41 <span class="k">use</span> <span class="w">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span> | |
55 42 <span class="k">use</span> <span class="w">Fingerprints::MACCSKeys</span><span class="sc">;</span> | |
56 43 <span class="k">use</span> <span class="w">Fingerprints::PathLengthFingerprints</span><span class="sc">;</span> | |
57 44 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="sc">;</span> | |
58 45 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="sc">;</span> | |
59 46 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="sc">;</span> | |
60 47 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span> | |
61 48 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span> | |
62 49 | |
63 50 <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> | |
64 51 | |
65 52 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> | |
66 53 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
67 54 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames GetMolecularComplexityTypeAbbreviation)</span><span class="sc">;</span> | |
68 55 | |
69 56 <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> | |
70 57 | |
71 58 <span class="c"># Setup class variables...</span> | |
72 59 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
73 60 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
74 61 | |
75 62 <span class="c"># Overload Perl functions...</span> | |
76 63 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecularComplexityDescriptors'</span><span class="sc">;</span> | |
77 64 | |
78 65 <span class="c"># Class constructor...</span> | |
79 <a name="new-"></a> 66 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
80 67 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
81 68 | |
82 69 <span class="c"># Initialize object...</span> | |
83 70 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
84 71 <span class="k">bless</span> <span class="i">$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> | |
85 72 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
86 73 | |
87 74 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
88 75 | |
89 76 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
90 77 <span class="s">}</span> | |
91 78 | |
92 79 <span class="c"># Initialize class ...</span> | |
93 <a name="_InitializeClass-"></a> 80 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
94 81 <span class="c">#Class name...</span> | |
95 82 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
96 83 | |
97 84 <span class="c"># Descriptor names...</span> | |
98 85 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'MolecularComplexity'</span><span class="s">)</span><span class="sc">;</span> | |
99 86 | |
100 87 <span class="s">}</span> | |
101 88 | |
102 89 <span class="c"># Get descriptor names as an array.</span> | |
103 90 <span class="c">#</span> | |
104 91 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
105 92 <span class="c"># object method.</span> | |
106 93 <span class="c">#</span> | |
107 <a name="GetDescriptorNames-"></a> 94 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> | |
108 95 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
109 96 <span class="s">}</span> | |
110 97 | |
111 98 <span class="c"># Initialize object data...</span> | |
112 99 <span class="c">#</span> | |
113 <a name="_InitializeMolecularComplexityDescriptors-"></a> 100 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptors</span> <span class="s">{</span> | |
114 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
115 102 | |
116 103 <span class="c"># Type of MolecularDescriptor...</span> | |
117 104 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'MolecularComplexity'</span><span class="sc">;</span> | |
118 105 | |
119 106 <span class="c">#</span> | |
120 107 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span> | |
121 108 <span class="c"># corresponding to number of bits-set or unique keys [ Ref 117-119 ] in molecular</span> | |
122 109 <span class="c"># fingerprints. The following types of fingerprints based molecular complexity measures</span> | |
123 110 <span class="c"># are supported:</span> | |
124 111 <span class="c">#</span> | |
125 112 <span class="c"># AtomTypesFingerprints</span> | |
126 113 <span class="c"># ExtendedConnectivityFingerprints</span> | |
127 114 <span class="c"># MACCSKeys</span> | |
128 115 <span class="c"># PathLengthFingerprints</span> | |
129 116 <span class="c"># TopologicalAtomPairsFingerprints</span> | |
130 117 <span class="c"># TopologicalAtomTripletsFingerprints</span> | |
131 118 <span class="c"># TopologicalAtomTorsionsFingerprints</span> | |
132 119 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> | |
133 120 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
134 121 <span class="c">#</span> | |
135 122 <span class="c"># Default: MACCSKeys</span> | |
136 123 <span class="c">#</span> | |
137 124 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">''</span><span class="sc">;</span> | |
138 125 | |
139 126 <span class="c"># Atom types to use for generating fingerprints...</span> | |
140 127 <span class="c">#</span> | |
141 128 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> | |
142 129 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> | |
143 130 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> | |
144 131 <span class="c">#</span> | |
145 132 <span class="c"># Notes:</span> | |
146 133 <span class="c"># . AtomicInvariantsAtomTypes for all supported MolecularComplexityType except for</span> | |
147 134 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints and TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
148 135 <span class="c"># . This value is not used for MACCSKeys</span> | |
149 136 <span class="c"># . FunctionalClassAtomTypes is the only valid value during topological pharmacophore fingerprints.</span> | |
150 137 <span class="c">#</span> | |
151 138 <span class="c"># . Default values for AtomicInvariantsToUse and FunctionalClassesToUse are set appropriately</span> | |
152 139 <span class="c"># for different types of fingerprints as shown below.</span> | |
153 140 <span class="c">#</span> | |
154 141 <span class="c"># MolecularComplexityType AtomicInvariantsToUse</span> | |
155 142 <span class="c">#</span> | |
156 143 <span class="c"># AtomTypesFingerprints AS, X, BO, H, FC</span> | |
157 144 <span class="c"># TopologicalAtomPairsFingerprints AS, X, BO, H, FC</span> | |
158 145 <span class="c"># TopologicalAtomTripletsFingerprints AS, X, BO, H, FC</span> | |
159 146 <span class="c"># TopologicalAtomTorsionsFingerprints AS, X, BO, H, FC</span> | |
160 147 <span class="c">#</span> | |
161 148 <span class="c"># ExtendedConnectivityFingerprints AS, X, BO, H, FC, MN</span> | |
162 149 <span class="c"># PathLengthFingerprints AS</span> | |
163 150 <span class="c">#</span> | |
164 151 <span class="c"># Default for FunctionalClassesToUse for all fingerprints is set to:</span> | |
165 152 <span class="c">#</span> | |
166 153 <span class="c"># HBD, HBA, PI, NI, Ar, Hal</span> | |
167 154 <span class="c">#</span> | |
168 155 <span class="c"># except for the following two MolecularComplexityType fingerprints:</span> | |
169 156 <span class="c">#</span> | |
170 157 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints HBD, HBA, PI, NI, H</span> | |
171 158 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints HBD, HBA, PI, NI, H, Ar</span> | |
172 159 <span class="c">#</span> | |
173 160 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> | |
174 161 | |
175 162 <span class="c"># Size of MACCS key set: 166 or 322...</span> | |
176 163 <span class="c">#</span> | |
177 164 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="n">166</span><span class="sc">;</span> | |
178 165 | |
179 166 <span class="c"># Atomic neighborhoods radius for extended connectivity fingerprints...</span> | |
180 167 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span> | |
181 168 | |
182 169 <span class="c"># Minimum and maximum path lengths to use for path length fingerprints...</span> | |
183 170 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="n">1</span><span class="sc">;</span> | |
184 171 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="n">8</span><span class="sc">;</span> | |
185 172 | |
186 173 <span class="c"># By default bond symbols are included in atom path strings used to generate path length</span> | |
187 174 <span class="c"># fingerprints... ...</span> | |
188 175 <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} = <span class="n">1</span><span class="sc">;</span> | |
189 176 | |
190 177 <span class="c"># Minimum and maximum bond distance between atom pairs during topological</span> | |
191 178 <span class="c"># atom pairs/triplets fingerprints...</span> | |
192 179 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> | |
193 180 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> | |
194 181 | |
195 182 <span class="c"># Determines whether to apply triangle inequality to distance triplets...</span> | |
196 183 <span class="c">#</span> | |
197 184 <span class="c"># Default for TopologicalAtomTripletsFingerprints: 0</span> | |
198 185 <span class="c"># Default for TopologicalPharmacophoreAtomTripletsFingerprints: 1</span> | |
199 186 <span class="c">#</span> | |
200 187 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="q">''</span><span class="sc">;</span> | |
201 188 | |
202 189 <span class="c"># Distance bin size used for binning distances during generation of</span> | |
203 190 <span class="c"># topological pharmacophore atom triplets fingerprints...</span> | |
204 191 <span class="c">#</span> | |
205 192 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="n">2</span><span class="sc">;</span> | |
206 193 | |
207 194 <span class="c"># Normalization methodology to use for scaling the number of bits-set or unique keys</span> | |
208 195 <span class="c"># for:</span> | |
209 196 <span class="c">#</span> | |
210 197 <span class="c"># ExtendedConnectivityFingerprints</span> | |
211 198 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> | |
212 199 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
213 200 <span class="c">#</span> | |
214 201 <span class="c"># This option is gnored for all other types of fingerprints.</span> | |
215 202 <span class="c">#</span> | |
216 203 <span class="c"># Possible values during extended connectivity fingerprints: None or ByHeavyAtomsCount. Default:</span> | |
217 204 <span class="c"># None.</span> | |
218 205 <span class="c">#</span> | |
219 206 <span class="c"># Possible values during topological pharmacophore atom pairs and tripletes fingerprints: None,</span> | |
220 207 <span class="c"># or ByPossibleKeysCount. Default: None. ByPossibleKeysCount corresponds to total number of</span> | |
221 208 <span class="c"># possible topological pharmacophore atom pairs or triplets in a molecule.</span> | |
222 209 <span class="c">#</span> | |
223 210 <span class="c">#</span> | |
224 211 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span> | |
225 212 | |
226 213 <span class="c"># Intialize descriptor names and values...</span> | |
227 214 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
228 215 | |
229 216 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
230 217 <span class="s">}</span> | |
231 218 | |
232 219 <span class="c"># Initialize object properties...</span> | |
233 220 <span class="c">#</span> | |
234 <a name="_InitializeMolecularComplexityDescriptorsProperties-"></a> 221 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptorsProperties</span> <span class="s">{</span> | |
235 222 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
236 223 | |
237 224 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
238 225 <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> | |
239 226 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
240 227 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
241 228 <span class="s">}</span> | |
242 229 | |
243 230 <span class="c"># Make sure MolecularComplexityType is set...</span> | |
244 231 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span> | |
245 232 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">'MACCSKeys'</span><span class="sc">;</span> | |
246 233 <span class="s">}</span> | |
247 234 | |
248 235 <span class="c"># Make sure AtomIdentifierType is set...</span> | |
249 236 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> | |
250 237 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
251 238 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
252 239 <span class="s">}</span> | |
253 240 <span class="s">}</span> | |
254 241 | |
255 242 <span class="c"># Make sure UseTriangleInequality is set...</span> | |
256 243 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalAtomTripletsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> | |
257 244 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">UseTriangleInequality</span>}<span class="s">)</span> <span class="s">{</span> | |
258 245 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
259 246 <span class="s">}</span> | |
260 247 <span class="s">}</span> | |
261 248 | |
262 249 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
263 250 <span class="s">}</span> | |
264 251 | |
265 252 <span class="c"># Initialize atom identifer type...</span> | |
266 253 <span class="c">#</span> | |
267 <a name="_InitializeAtomIdentifierType-"></a> 254 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierType</span> <span class="s">{</span> | |
268 255 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
269 256 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span> | |
270 257 | |
271 258 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> | |
272 259 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
273 260 <span class="s">}</span> | |
274 261 | |
275 262 <span class="i">$AtomIdentifierType</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> ? <span class="q">'FunctionalClassAtomTypes'</span> <span class="co">:</span> <span class="q">'AtomicInvariantsAtomTypes'</span><span class="sc">;</span> | |
276 263 | |
277 264 <span class="i">$This</span><span class="i">->SetAtomIdentifierType</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span> | |
278 265 | |
279 266 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
280 267 <span class="s">}</span> | |
281 268 | |
282 269 <span class="c"># Get abbreviation for specified molecular complexity type or using descriptors object...</span> | |
283 270 <span class="c">#</span> | |
284 271 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
285 272 <span class="c"># object method.</span> | |
286 273 <span class="c">#</span> | |
287 <a name="GetMolecularComplexityTypeAbbreviation-"></a> 274 <span class="k">sub </span><span class="m">GetMolecularComplexityTypeAbbreviation</span> <span class="s">{</span> | |
288 275 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
289 276 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ComplexityType</span><span class="cm">,</span> <span class="i">%ComplexityTypeToAbbrev</span><span class="s">)</span><span class="sc">;</span> | |
290 277 | |
291 278 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecularComplexityDescriptors</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
292 279 <span class="i">$This</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
293 280 <span class="i">$ComplexityType</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span> | |
294 281 <span class="s">}</span> | |
295 282 <span class="k">else</span> <span class="s">{</span> | |
296 283 <span class="i">$ComplexityType</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
297 284 <span class="s">}</span> | |
298 285 | |
299 286 <span class="i">%ComplexityTypeToAbbrev</span> = <span class="s">(</span><span class="k">lc</span> <span class="q">'AtomTypesFingerprints'</span> <span class="cm">=></span> <span class="q">'ATFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'ExtendedConnectivityFingerprints'</span> <span class="cm">=></span> <span class="q">'ECFP'</span><span class="cm">,</span> | |
300 287 <span class="k">lc</span> <span class="q">'MACCSKeys'</span> <span class="cm">=></span> <span class="q">'MACCSKeys'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'PathLengthFingerprints'</span> <span class="cm">=></span> <span class="q">'PLFP'</span><span class="cm">,</span> | |
301 288 <span class="k">lc</span> <span class="q">'TopologicalAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TAPFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'TopologicalAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span> | |
302 289 <span class="k">lc</span> <span class="q">'TopologicalAtomTorsionsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span> | |
303 290 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPAPFP'</span><span class="cm">,</span> | |
304 291 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPATFP'</span><span class="s">)</span><span class="sc">;</span> | |
305 292 | |
306 293 <span class="k">return</span> <span class="k">exists</span> <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} ? <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> | |
307 294 <span class="s">}</span> | |
308 295 | |
309 296 <span class="c"># Set MACCS key set size...</span> | |
310 297 <span class="c">#</span> | |
311 <a name="SetMACCSKeysSize-"></a> 298 <span class="k">sub </span><span class="m">SetMACCSKeysSize</span> <span class="s">{</span> | |
312 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
313 300 | |
314 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
315 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: Size value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
316 303 <span class="s">}</span> | |
317 304 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(166|322)/i</span><span class="s">)</span> <span class="s">{</span> | |
318 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: The current release of MayaChemTools doesn't support MDL MACCS $Value keys..."</span><span class="sc">;</span> | |
319 306 <span class="s">}</span> | |
320 307 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
321 308 | |
322 309 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
323 310 <span class="s">}</span> | |
324 311 | |
325 312 <span class="c"># Set minimum path length...</span> | |
326 313 <span class="c">#</span> | |
327 <a name="SetMinPathLength-"></a> 314 <span class="k">sub </span><span class="m">SetMinPathLength</span> <span class="s">{</span> | |
328 315 <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> | |
329 316 | |
330 317 <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> | |
331 318 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinPathLength: MinPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
332 319 <span class="s">}</span> | |
333 320 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
334 321 | |
335 322 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
336 323 <span class="s">}</span> | |
337 324 | |
338 325 <span class="c"># Set maximum path length...</span> | |
339 326 <span class="c">#</span> | |
340 <a name="SetMaxPathLength-"></a> 327 <span class="k">sub </span><span class="m">SetMaxPathLength</span> <span class="s">{</span> | |
341 328 <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> | |
342 329 | |
343 330 <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> | |
344 331 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxPathLength: MaxPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
345 332 <span class="s">}</span> | |
346 333 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
347 334 | |
348 335 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
349 336 <span class="s">}</span> | |
350 337 | |
351 338 <span class="c"># Set minimum bond distance between atom pairs during topological and topological</span> | |
352 339 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span> | |
353 340 <span class="c">#</span> | |
354 <a name="SetMinDistance-"></a> 341 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> | |
355 342 <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> | |
356 343 | |
357 344 <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> | |
358 345 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
359 346 <span class="s">}</span> | |
360 347 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
361 348 | |
362 349 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
363 350 <span class="s">}</span> | |
364 351 | |
365 352 <span class="c"># Set maximum bond distance between atom pairs during topological and topological</span> | |
366 353 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span> | |
367 354 <span class="c">#</span> | |
368 <a name="SetMaxDistance-"></a> 355 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> | |
369 356 <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> | |
370 357 | |
371 358 <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> | |
372 359 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
373 360 <span class="s">}</span> | |
374 361 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
375 362 | |
376 363 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
377 364 <span class="s">}</span> | |
378 365 | |
379 366 <span class="c"># Set atom neighborhood radius...</span> | |
380 367 <span class="c">#</span> | |
381 <a name="SetNeighborhoodRadius-"></a> 368 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span> | |
382 369 <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> | |
383 370 | |
384 371 <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> | |
385 372 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> | |
386 373 <span class="s">}</span> | |
387 374 | |
388 375 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span> | |
389 376 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span> | |
390 377 <span class="s">}</span> | |
391 378 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
392 379 | |
393 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
394 381 <span class="s">}</span> | |
395 382 | |
396 383 <span class="c"># Set molecular complexity type...</span> | |
397 384 <span class="c">#</span> | |
398 <a name="SetMolecularComplexityType-"></a> 385 <span class="k">sub </span><span class="m">SetMolecularComplexityType</span> <span class="s">{</span> | |
399 386 <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> | |
400 387 | |
401 388 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|MACCSKeys|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> | |
402 389 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecularComplexityType: MolecularComplexityType value, $Value, is not valid. Supported values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..."</span><span class="sc">;</span> | |
403 390 <span class="s">}</span> | |
404 391 | |
405 392 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
406 393 | |
407 394 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
408 395 <span class="s">}</span> | |
409 396 | |
410 397 <span class="c"># Set distance bin size for binning pharmacophore atom pair distances in atom triplets...</span> | |
411 398 <span class="c">#</span> | |
412 <a name="SetDistanceBinSize-"></a> 399 <span class="k">sub </span><span class="m">SetDistanceBinSize</span> <span class="s">{</span> | |
413 400 <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> | |
414 401 | |
415 402 <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> | |
416 403 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDistanceBinSize: DistanceBinSize value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
417 404 <span class="s">}</span> | |
418 405 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
419 406 | |
420 407 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
421 408 <span class="s">}</span> | |
422 409 | |
423 410 <span class="c"># Set normalization methodology to use for scaling the number of bits-set or unique keys</span> | |
424 411 <span class="c"># in fingerprints...</span> | |
425 412 <span class="c">#</span> | |
426 <a name="SetNormalizationMethodology-"></a> 413 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span> | |
427 414 <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> | |
428 415 | |
429 416 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|ByPossibleKeysCount|None)$/i</span><span class="s">)</span> <span class="s">{</span> | |
430 417 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span> | |
431 418 <span class="s">}</span> | |
432 419 | |
433 420 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span> | |
434 421 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^(ExtendedConnectivityFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> | |
435 422 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: Normalization is not supported for MolecularComplexityType: $This->{MolecularComplexityType}. Valid MolecularComplexityType values: ExtendedConnectivityFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints...\n"</span><span class="sc">;</span> | |
436 423 <span class="s">}</span> | |
437 424 | |
438 425 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|None)$/i</span><span class="s">)</span> <span class="s">{</span> | |
439 426 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByHeavyAtomsCount..."</span><span class="sc">;</span> | |
440 427 <span class="s">}</span> | |
441 428 | |
442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByPossibleKeysCount|None)$/i</span><span class="s">)</span> <span class="s">{</span> | |
443 430 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByPossibleKeysCount..."</span><span class="sc">;</span> | |
444 431 <span class="s">}</span> | |
445 432 <span class="s">}</span> | |
446 433 | |
447 434 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
448 435 | |
449 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
450 437 <span class="s">}</span> | |
451 438 | |
452 439 <span class="c"># Set intial atom identifier type..</span> | |
453 440 <span class="c">#</span> | |
454 <a name="SetAtomIdentifierType-"></a> 441 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> | |
455 442 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
456 443 | |
457 444 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> | |
458 445 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span> | |
459 446 <span class="s">}</span> | |
460 447 | |
461 448 <span class="c"># FunctionalClassAtomTypes is the only valid atom identifier type for pharmacophore fingerprints...</span> | |
462 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> | |
463 450 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
464 451 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported type for $This->{MolecularComplexityType} complexity type: FunctionalClassAtomTypes."</span><span class="sc">;</span> | |
465 452 <span class="s">}</span> | |
466 453 <span class="s">}</span> | |
467 454 | |
468 455 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
469 456 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> | |
470 457 <span class="s">}</span> | |
471 458 | |
472 459 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> | |
473 460 | |
474 461 <span class="c"># Initialize identifier type information...</span> | |
475 462 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
476 463 | |
477 464 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
478 465 <span class="s">}</span> | |
479 466 | |
480 467 <span class="c"># Calculate molecular complexity [ Ref 117-119 ] of a molecule using its fingerprints.</span> | |
481 468 <span class="c">#</span> | |
482 469 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span> | |
483 470 <span class="c"># corresponding to the number of bits-set or unique keys in molecular fingerprints. The</span> | |
484 471 <span class="c"># following types of fingerprints based molecular complexity measures are supported:</span> | |
485 472 <span class="c">#</span> | |
486 473 <span class="c"># AtomTypesFingerprints</span> | |
487 474 <span class="c"># ExtendedConnectivityFingerprints</span> | |
488 475 <span class="c"># MACCSKeys</span> | |
489 476 <span class="c"># PathLengthFingerprints</span> | |
490 477 <span class="c"># TopologicalAtomPairsFingerprints</span> | |
491 478 <span class="c"># TopologicalAtomTripletsFingerprints</span> | |
492 479 <span class="c"># TopologicalAtomTorsionsFingerprints</span> | |
493 480 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> | |
494 481 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
495 482 <span class="c">#</span> | |
496 483 <span class="c"># After the molecular complexity value has been calculated, it can also be normalized by</span> | |
497 484 <span class="c"># by scaling the number of bits-set or unique keys for following types of fingerprints:</span> | |
498 485 <span class="c">#</span> | |
499 486 <span class="c"># ExtendedConnectivityFingerprints</span> | |
500 487 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> | |
501 488 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
502 489 <span class="c">#</span> | |
503 490 <span class="c"># Two types of normalization methodologies are supported: by heavy atoms count for</span> | |
504 491 <span class="c"># extended connectivity fingerprints; by possible keys count for topological pharmacophore</span> | |
505 492 <span class="c"># atom pairs and triplets fingerprints.</span> | |
506 493 <span class="c">#</span> | |
507 <a name="GenerateDescriptors-"></a> 494 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> | |
508 495 <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> | |
509 496 | |
510 497 <span class="c"># Initialize descriptor values...</span> | |
511 498 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
512 499 | |
513 500 <span class="c"># Check availability of molecule...</span> | |
514 501 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
515 502 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> | |
516 503 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
517 504 <span class="s">}</span> | |
518 505 | |
519 506 <span class="c"># Calculate descriptor values...</span> | |
520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
521 508 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate MolecularComplexity values corresponding to assigned MolecularComplexity atom types..."</span><span class="sc">;</span> | |
522 509 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
523 510 <span class="s">}</span> | |
524 511 | |
525 512 <span class="c"># Set final descriptor values...</span> | |
526 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
527 514 | |
528 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
529 516 <span class="s">}</span> | |
530 517 | |
531 518 <span class="c"># Calculate molecular complexity value...</span> | |
532 519 <span class="c">#</span> | |
533 <a name="_CalculateDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> | |
534 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
535 522 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
536 523 | |
537 524 <span class="c"># Setup fingerprints object and generate fingerprints...</span> | |
538 525 <span class="i">$MethodName</span> = <span class="q">"_Setup"</span> . <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span> | |
539 526 <span class="i">$FingerprintsObject</span> = <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
540 527 | |
541 528 <span class="i">$FingerprintsObject</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
542 529 | |
543 530 <span class="c"># Make sure atom types fingerprints generation is successful...</span> | |
544 531 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsObject</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
545 532 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
546 533 <span class="s">}</span> | |
547 534 | |
548 535 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
549 536 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
550 537 <span class="s">}</span> | |
551 538 | |
552 539 <span class="c"># Normalize molecular complexity...</span> | |
553 540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> | |
554 541 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_NormalizeMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
555 542 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
556 543 <span class="s">}</span> | |
557 544 <span class="s">}</span> | |
558 545 | |
559 546 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
560 547 <span class="s">}</span> | |
561 548 | |
562 549 <span class="c"># Setup atom types fingerprints...</span> | |
563 550 <span class="c">#</span> | |
564 <a name="_SetupAtomTypesFingerprints-"></a> 551 <span class="k">sub </span><span class="m">_SetupAtomTypesFingerprints</span> <span class="s">{</span> | |
565 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
566 553 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
567 554 | |
568 555 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::AtomTypesFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'AtomTypesCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
569 556 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
570 557 | |
571 558 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
572 559 <span class="s">}</span> | |
573 560 | |
574 561 <span class="c"># Setup extended connectivity fingerprints...</span> | |
575 562 <span class="c">#</span> | |
576 <a name="_SetupExtendedConnectivityFingerprints-"></a> 563 <span class="k">sub </span><span class="m">_SetupExtendedConnectivityFingerprints</span> <span class="s">{</span> | |
577 564 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
578 565 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
579 566 | |
580 567 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'ExtendedConnectivity'</span><span class="cm">,</span> <span class="q">'NeighborhoodRadius'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> | |
581 568 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
582 569 | |
583 570 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
584 571 <span class="s">}</span> | |
585 572 | |
586 573 <span class="c"># Setup MACCS keys...</span> | |
587 574 <span class="c">#</span> | |
588 <a name="_SetupMACCSKeys-"></a> 575 <span class="k">sub </span><span class="m">_SetupMACCSKeys</span> <span class="s">{</span> | |
589 576 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
590 577 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
591 578 | |
592 579 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::MACCSKeys</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'MACCSKeyBits'</span><span class="cm">,</span> <span class="q">'Size'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>}<span class="s">)</span><span class="sc">;</span> | |
593 580 | |
594 581 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
595 582 <span class="s">}</span> | |
596 583 | |
597 584 <span class="c"># Set up path length fingerprints...</span> | |
598 585 <span class="c">#</span> | |
599 <a name="_SetupPathLengthFingerprints-"></a> 586 <span class="k">sub </span><span class="m">_SetupPathLengthFingerprints</span> <span class="s">{</span> | |
600 587 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
601 588 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
602 589 | |
603 590 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::PathLengthFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'PathLengthCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'MinLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinPathLength</span>}<span class="cm">,</span> <span class="q">'MaxLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxPathLength</span>}<span class="cm">,</span> <span class="q">'AllowRings'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'AllowSharedBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'UseBondSymbols'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">'UseUniquePaths'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
604 591 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
605 592 | |
606 593 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
607 594 <span class="s">}</span> | |
608 595 | |
609 596 <span class="c"># Setup topological atom pairs fingerprints...</span> | |
610 597 <span class="c">#</span> | |
611 <a name="_SetupTopologicalAtomPairsFingerprints-"></a> 598 <span class="k">sub </span><span class="m">_SetupTopologicalAtomPairsFingerprints</span> <span class="s">{</span> | |
612 599 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
613 600 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
614 601 | |
615 602 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> | |
616 603 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
617 604 | |
618 605 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
619 606 <span class="s">}</span> | |
620 607 | |
621 608 <span class="c"># Setup topological atom triplets fingerprints...</span> | |
622 609 <span class="c">#</span> | |
623 <a name="_SetupTopologicalAtomTripletsFingerprints-"></a> 610 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTripletsFingerprints</span> <span class="s">{</span> | |
624 611 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
625 612 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
626 613 | |
627 614 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> | |
628 615 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
629 616 | |
630 617 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
631 618 <span class="s">}</span> | |
632 619 | |
633 620 <span class="c"># Setup topological atom torsions fingerprints...</span> | |
634 621 <span class="c">#</span> | |
635 <a name="_SetupTopologicalAtomTorsionsFingerprints-"></a> 622 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTorsionsFingerprints</span> <span class="s">{</span> | |
636 623 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
637 624 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
638 625 | |
639 626 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> | |
640 627 | |
641 628 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
642 629 | |
643 630 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
644 631 <span class="s">}</span> | |
645 632 | |
646 633 <span class="c"># Setup TopologicalPharmacophoreAtomPairsFingerprints...</span> | |
647 634 <span class="c">#</span> | |
648 <a name="_SetupTopologicalPharmacophoreAtomPairsFingerprints-"></a> 635 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span> | |
649 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
650 637 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomPairsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span> | |
651 638 | |
652 639 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span> | |
653 640 <span class="i">$AtomPairsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span> | |
654 641 | |
655 642 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomPairsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomPairsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="q">'None'</span><span class="cm">,</span> <span class="q">'ValuesPrecision'</span> <span class="cm">=></span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> | |
656 643 | |
657 644 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
658 645 <span class="s">}</span> | |
659 646 | |
660 647 <span class="c"># Setup TopologicalPharmacophoreAtomTripletsFingerprints...</span> | |
661 648 <span class="c">#</span> | |
662 <a name="_SetupTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 649 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span> | |
663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
664 651 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span> | |
665 652 | |
666 653 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span> | |
667 654 <span class="i">$AtomTripletsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span> | |
668 655 | |
669 656 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomTripletsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'DistanceBinSize'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span> | |
670 657 | |
671 658 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
672 659 <span class="s">}</span> | |
673 660 | |
674 661 <span class="c"># Normalize molecular complexity value...</span> | |
675 662 <span class="c">#</span> | |
676 <a name="_NormalizeMolecularComplexity-"></a> 663 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexity</span> <span class="s">{</span> | |
677 664 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
678 665 | |
679 666 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByHeavyAtomsCount$/i</span><span class="s">)</span> <span class="s">{</span> | |
680 667 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByHeavyAtomsCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
681 668 <span class="s">}</span> | |
682 669 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> <span class="s">{</span> | |
683 670 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByPossibleKeysCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
684 671 <span class="s">}</span> | |
685 672 <span class="k">else</span> <span class="s">{</span> | |
686 673 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_NormalizeMolecularComplexity: NormalizationMethodology value, $This->{NormalizationMethodology}, is not valid. Supported values: ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span> | |
687 674 <span class="s">}</span> | |
688 675 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
689 676 <span class="s">}</span> | |
690 677 | |
691 678 <span class="c"># Normalize molecular complexity value by heavy atom count...</span> | |
692 679 <span class="c">#</span> | |
693 <a name="_NormalizeMolecularComplexityByHeavyAtomsCount-"></a> 680 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByHeavyAtomsCount</span> <span class="s">{</span> | |
694 681 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
695 682 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfHeavyAtoms</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span> | |
696 683 | |
697 684 <span class="i">$NumOfHeavyAtoms</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetNumOfHeavyAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
698 685 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfHeavyAtoms</span><span class="s">)</span> <span class="s">{</span> | |
699 686 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
700 687 <span class="s">}</span> | |
701 688 | |
702 689 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfHeavyAtoms</span><span class="sc">;</span> | |
703 690 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> | |
704 691 | |
705 692 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
706 693 <span class="s">}</span> | |
707 694 | |
708 695 <span class="c"># Normalize molecular complexity value by possible keys count...</span> | |
709 696 <span class="c">#</span> | |
710 <a name="_NormalizeMolecularComplexityByPossibleKeysCount-"></a> 697 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByPossibleKeysCount</span> <span class="s">{</span> | |
711 698 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
712 699 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPossibleKeys</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span> | |
713 700 | |
714 701 <span class="i">$NumOfPossibleKeys</span> = <span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
715 702 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfPossibleKeys</span><span class="s">)</span> <span class="s">{</span> | |
716 703 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
717 704 <span class="s">}</span> | |
718 705 | |
719 706 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfPossibleKeys</span><span class="sc">;</span> | |
720 707 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> | |
721 708 | |
722 709 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
723 710 <span class="s">}</span> | |
724 711 | |
725 712 <span class="c"># Calculate molecular complexity value using fingerprints objects...</span> | |
726 713 <span class="c">#</span> | |
727 <a name="_CalculateMolecularComplexity-"></a> 714 <span class="k">sub </span><span class="m">_CalculateMolecularComplexity</span> <span class="s">{</span> | |
728 715 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
729 716 | |
730 717 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span> | |
731 718 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsBitVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
732 719 <span class="s">}</span> | |
733 720 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span> | |
734 721 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
735 722 <span class="s">}</span> | |
736 723 <span class="k">else</span> <span class="s">{</span> | |
737 724 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_CalculateMolecularComplexity: Fingerprints vector type is not valid. Supported values: FingerprintsBitVector or FingerprintsVector..."</span><span class="sc">;</span> | |
738 725 <span class="s">}</span> | |
739 726 | |
740 727 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
741 728 <span class="s">}</span> | |
742 729 | |
743 730 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span> | |
744 731 <span class="c">#</span> | |
745 <a name="_CalculateMolecularComplexityUsingFingerprintsVector-"></a> 732 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsVector</span> <span class="s">{</span> | |
746 733 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
747 734 | |
748 735 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="s">(</span><span class="i">$FingerprintsVector</span><span class="i">->GetType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^(OrderedNumericalValues|NumericalValues)$/i</span><span class="s">)</span> ? <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfNonZeroValues</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
749 736 | |
750 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
751 738 <span class="s">}</span> | |
752 739 | |
753 740 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span> | |
754 741 <span class="c">#</span> | |
755 <a name="_CalculateMolecularComplexityUsingFingerprintsBitVector-"></a> 742 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsBitVector</span> <span class="s">{</span> | |
756 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
757 744 | |
758 745 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">$FingerprintsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
759 746 | |
760 747 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
761 748 <span class="s">}</span> | |
762 749 | |
763 750 <span class="c"># Setup final descriptor values...</span> | |
764 751 <span class="c">#</span> | |
765 <a name="_SetFinalDescriptorValues-"></a> 752 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> | |
766 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
767 754 | |
768 755 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
769 756 | |
770 757 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexity</span>}<span class="s">)</span><span class="sc">;</span> | |
771 758 | |
772 759 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
773 760 <span class="s">}</span> | |
774 761 | |
775 762 <span class="c"># Set atom identifier type to use for generating fingerprints...</span> | |
776 763 <span class="c">#</span> | |
777 <a name="_SetAtomIdentifierTypeValuesToUse-"></a> 764 <span class="k">sub </span><span class="m">_SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span> | |
778 765 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
779 766 | |
780 767 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
781 768 <span class="i">$FingerprintsObject</span><span class="i">->SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span> | |
782 769 <span class="s">}</span> | |
783 770 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
784 771 <span class="i">$FingerprintsObject</span><span class="i">->SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span> | |
785 772 <span class="s">}</span> | |
786 773 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> | |
787 774 <span class="c"># Nothing to do for now...</span> | |
788 775 <span class="s">}</span> | |
789 776 <span class="k">else</span> <span class="s">{</span> | |
790 777 <span class="w">croak</span> <span class="q">"Error: The value specified, $This->{AtomIdentifierType}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span> | |
791 778 <span class="s">}</span> | |
792 779 <span class="s">}</span> | |
793 780 | |
794 781 <span class="c"># Initialize atom indentifier type information...</span> | |
795 782 <span class="c">#</span> | |
796 783 <span class="c"># Current supported values:</span> | |
797 784 <span class="c">#</span> | |
798 785 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span> | |
799 786 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> | |
800 787 <span class="c">#</span> | |
801 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 788 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> | |
802 789 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
803 790 | |
804 791 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> | |
805 792 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
806 793 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
807 794 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
808 795 <span class="s">}</span> | |
809 796 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
810 797 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
811 798 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
812 799 <span class="s">}</span> | |
813 800 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> | |
814 801 <span class="c"># Nothing to do for now...</span> | |
815 802 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
816 803 <span class="s">}</span> | |
817 804 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
818 805 <span class="s">}</span> | |
819 806 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
820 807 <span class="s">}</span> | |
821 808 | |
822 809 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span> | |
823 810 <span class="c"># class, to use for generating initial atom identifiers...</span> | |
824 811 <span class="c">#</span> | |
825 812 <span class="c"># Let:</span> | |
826 813 <span class="c"># AS = Atom symbol corresponding to element symbol</span> | |
827 814 <span class="c">#</span> | |
828 815 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
829 816 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
830 817 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
831 818 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
832 819 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
833 820 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
834 821 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> | |
835 822 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> | |
836 823 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> | |
837 824 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> | |
838 825 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> | |
839 826 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> | |
840 827 <span class="c">#</span> | |
841 828 <span class="c"># Then:</span> | |
842 829 <span class="c">#</span> | |
843 830 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> | |
844 831 <span class="c">#</span> | |
845 832 <span class="c"># AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></span> | |
846 833 <span class="c">#</span> | |
847 834 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> | |
848 835 <span class="c"># optional.</span> | |
849 836 <span class="c">#</span> | |
850 837 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span> | |
851 838 <span class="c">#</span> | |
852 839 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span> | |
853 840 <span class="c">#</span> | |
854 841 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span> | |
855 842 <span class="c"># are also allowed:</span> | |
856 843 <span class="c">#</span> | |
857 844 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span> | |
858 845 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span> | |
859 846 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span> | |
860 847 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span> | |
861 848 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span> | |
862 849 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span> | |
863 850 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span> | |
864 851 <span class="c"># Ar : Aromatic</span> | |
865 852 <span class="c"># RA : RingAtom</span> | |
866 853 <span class="c"># FC : FormalCharge</span> | |
867 854 <span class="c"># MN : MassNumber</span> | |
868 855 <span class="c"># SM : SpinMultiplicity</span> | |
869 856 <span class="c">#</span> | |
870 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 857 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> | |
871 858 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
872 859 | |
873 860 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
874 861 | |
875 862 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> | |
876 863 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> | |
877 864 <span class="s">}</span> | |
878 865 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
879 866 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="cm">,</span> <span class="q">'MN'</span><span class="s">)</span><span class="sc">;</span> | |
880 867 <span class="s">}</span> | |
881 868 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
882 869 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="s">)</span><span class="sc">;</span> | |
883 870 <span class="s">}</span> | |
884 871 | |
885 872 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
886 873 <span class="s">}</span> | |
887 874 | |
888 875 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> | |
889 876 <span class="c"># class, to use for generating initial atom identifiers...</span> | |
890 877 <span class="c">#</span> | |
891 878 <span class="c"># Let:</span> | |
892 879 <span class="c"># HBD: HydrogenBondDonor</span> | |
893 880 <span class="c"># HBA: HydrogenBondAcceptor</span> | |
894 881 <span class="c"># PI : PositivelyIonizable</span> | |
895 882 <span class="c"># NI : NegativelyIonizable</span> | |
896 883 <span class="c"># Ar : Aromatic</span> | |
897 884 <span class="c"># Hal : Halogen</span> | |
898 885 <span class="c"># H : Hydrophobic</span> | |
899 886 <span class="c"># RA : RingAtom</span> | |
900 887 <span class="c"># CA : ChainAtom</span> | |
901 888 <span class="c">#</span> | |
902 889 <span class="c"># Then:</span> | |
903 890 <span class="c">#</span> | |
904 891 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> | |
905 892 <span class="c">#</span> | |
906 893 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> | |
907 894 <span class="c">#</span> | |
908 895 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> | |
909 896 <span class="c">#</span> | |
910 897 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> | |
911 898 <span class="c">#</span> | |
912 899 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> | |
913 900 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> | |
914 901 <span class="c"># PositivelyIonizable: +, NH2</span> | |
915 902 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> | |
916 903 <span class="c">#</span> | |
917 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 904 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> | |
918 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
919 906 | |
920 907 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
921 908 | |
922 909 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> | |
923 910 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> | |
924 911 <span class="s">}</span> | |
925 912 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
926 913 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</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> | |
927 914 <span class="s">}</span> | |
928 915 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
929 916 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="s">)</span><span class="sc">;</span> | |
930 917 <span class="s">}</span> | |
931 918 | |
932 919 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
933 920 <span class="s">}</span> | |
934 921 | |
935 922 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span> | |
936 923 <span class="c">#</span> | |
937 <a name="SetAtomicInvariantsToUse-"></a> 924 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> | |
938 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
939 926 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span> | |
940 927 | |
941 928 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
942 929 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> | |
943 930 <span class="k">return</span><span class="sc">;</span> | |
944 931 <span class="s">}</span> | |
945 932 | |
946 933 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
947 934 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
948 935 <span class="k">return</span><span class="sc">;</span> | |
949 936 <span class="s">}</span> | |
950 937 | |
951 938 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
952 939 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
953 940 | |
954 941 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
955 942 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
956 943 | |
957 944 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
958 945 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
959 946 <span class="s">}</span> | |
960 947 <span class="k">else</span> <span class="s">{</span> | |
961 948 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
962 949 <span class="s">}</span> | |
963 950 | |
964 951 <span class="c"># Make sure specified AtomicInvariants are valid...</span> | |
965 952 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> | |
966 953 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
967 954 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> | |
968 955 <span class="s">}</span> | |
969 956 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> | |
970 957 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> | |
971 958 <span class="s">}</span> | |
972 959 | |
973 960 <span class="c"># Set atomic invariants to use...</span> | |
974 961 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
975 962 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> | |
976 963 | |
977 964 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
978 965 <span class="s">}</span> | |
979 966 | |
980 967 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span> | |
981 968 <span class="c">#</span> | |
982 <a name="SetFunctionalClassesToUse-"></a> 969 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> | |
983 970 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
984 971 <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">$FunctionalClass</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="cm">,</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span> | |
985 972 | |
986 973 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
987 974 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> | |
988 975 <span class="k">return</span><span class="sc">;</span> | |
989 976 <span class="s">}</span> | |
990 977 | |
991 978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
992 979 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
993 980 <span class="k">return</span><span class="sc">;</span> | |
994 981 <span class="s">}</span> | |
995 982 | |
996 983 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
997 984 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
998 985 | |
999 986 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1000 987 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1001 988 | |
1002 989 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
1003 990 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
1004 991 <span class="s">}</span> | |
1005 992 <span class="k">else</span> <span class="s">{</span> | |
1006 993 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
1007 994 <span class="s">}</span> | |
1008 995 | |
1009 996 <span class="c"># Make sure specified FunctionalClasses are valid...</span> | |
1010 997 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> | |
1011 998 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedFunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1012 999 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> | |
1013 1000 <span class="s">}</span> | |
1014 1001 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> | |
1015 1002 <span class="s">}</span> | |
1016 1003 | |
1017 1004 <span class="c"># Set functional classes to use...</span> | |
1018 1005 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1019 1006 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> | |
1020 1007 | |
1021 1008 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
1022 1009 <span class="s">}</span> | |
1023 1010 | |
1024 1011 <span class="c"># Return a string containg data for MolecularComplexityDescriptors object...</span> | |
1025 1012 <span class="c">#</span> | |
1026 <a name="StringifyMolecularComplexityDescriptors-"></a>1013 <span class="k">sub </span><span class="m">StringifyMolecularComplexityDescriptors</span> <span class="s">{</span> | |
1027 1014 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
1028 1015 <span class="k">my</span><span class="s">(</span><span class="i">$ComplexityDescriptorsString</span><span class="cm">,</span> <span class="i">$Nothing</span><span class="s">)</span><span class="sc">;</span> | |
1029 1016 | |
1030 1017 <span class="i">$ComplexityDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; MolecularComplexityType: $This->{MolecularComplexityType}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1031 1018 | |
1032 1019 <span class="c"># Setup fingerprints specific information...</span> | |
1033 1020 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> | |
1034 1021 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MACCSKeysSize = $This->{MACCSKeysSize}"</span><span class="sc">;</span> | |
1035 1022 <span class="s">}</span> | |
1036 1023 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
1037 1024 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; NeighborhoodRadius = $This->{NeighborhoodRadius}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span> | |
1038 1025 <span class="s">}</span> | |
1039 1026 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
1040 1027 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinPathLength = $This->{MinPathLength}; MaxPathLength = $This->{MaxPathLength}; UseBondSymbols: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> | |
1041 1028 <span class="s">}</span> | |
1042 1029 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
1043 1030 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span> | |
1044 1031 <span class="s">}</span> | |
1045 1032 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
1046 1033 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> | |
1047 1034 <span class="s">}</span> | |
1048 1035 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTorsionsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
1049 1036 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span> | |
1050 1037 <span class="s">}</span> | |
1051 1038 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
1052 1039 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span> | |
1053 1040 <span class="s">}</span> | |
1054 1041 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
1055 1042 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}; DistanceBinSize: $This->{DistanceBinSize}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> | |
1056 1043 <span class="s">}</span> | |
1057 1044 | |
1058 1045 <span class="c"># Setup atom identifier information...</span> | |
1059 1046 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> | |
1060 1047 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomIdentifierType = $This->{AtomIdentifierType}"</span><span class="sc">;</span> | |
1061 1048 | |
1062 1049 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
1063 1050 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span> | |
1064 1051 | |
1065 1052 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1066 1053 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1067 1054 | |
1068 1055 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> | |
1069 1056 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> | |
1070 1057 <span class="s">}</span> | |
1071 1058 | |
1072 1059 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</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> | |
1073 1060 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
1074 1061 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableAtomicInvariants: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</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> | |
1075 1062 <span class="s">}</span> | |
1076 1063 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
1077 1064 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> | |
1078 1065 | |
1079 1066 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1080 1067 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1081 1068 | |
1082 1069 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> | |
1083 1070 <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">"$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}"</span><span class="sc">;</span> | |
1084 1071 <span class="s">}</span> | |
1085 1072 | |
1086 1073 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</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> | |
1087 1074 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
1088 1075 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableFunctionalClasses: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</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> | |
1089 1076 <span class="s">}</span> | |
1090 1077 <span class="s">}</span> | |
1091 1078 <span class="k">return</span> <span class="i">$ComplexityDescriptorsString</span><span class="sc">;</span> | |
1092 1079 <span class="s">}</span> | |
1093 1080 | |
1094 1081 <span class="c"># Is it a MolecularComplexityDescriptors object?</span> | |
1095 <a name="_IsMolecularComplexityDescriptors-"></a>1082 <span class="k">sub </span><span class="m">_IsMolecularComplexityDescriptors</span> <span class="s">{</span> | |
1096 1083 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
1097 1084 | |
1098 1085 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
1099 1086 <span class="s">}</span> | |
1100 1087 | |
1101 <a name="EOF-"></a></pre> | |
1102 <p> </p> | |
1103 <br /> | |
1104 <center> | |
1105 <img src="../../../images/h2o2.png"> | |
1106 </center> | |
1107 </body> | |
1108 </html> |