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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:Fingerprints::TopologicalAtomPairsFingerprints.pm</title> | |
4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
6 </head> | |
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
8 <br/> | |
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12 <br/> | |
13 <pre> | |
14 <a name="package-Fingerprints::TopologicalAtomPairsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="sc">;</span> | |
15 2 <span class="c">#</span> | |
16 3 <span class="c"># $RCSfile: TopologicalAtomPairsFingerprints.pm,v $</span> | |
17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> | |
18 5 <span class="c"># $Revision: 1.30 $</span> | |
19 6 <span class="c">#</span> | |
20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
21 8 <span class="c">#</span> | |
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
23 10 <span class="c">#</span> | |
24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
25 12 <span class="c">#</span> | |
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
29 16 <span class="c"># later version.</span> | |
30 17 <span class="c">#</span> | |
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
34 21 <span class="c"># details.</span> | |
35 22 <span class="c">#</span> | |
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
40 27 <span class="c">#</span> | |
41 28 | |
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
45 32 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> | |
46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
47 34 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
48 35 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> | |
49 36 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span> | |
50 37 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> | |
51 38 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> | |
52 39 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span> | |
53 40 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span> | |
54 41 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span> | |
55 42 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> | |
56 43 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span> | |
57 44 | |
58 45 <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> | |
59 46 | |
60 47 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> | |
61 48 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
62 49 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
63 50 | |
64 51 <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> | |
65 52 | |
66 53 <span class="c"># Setup class variables...</span> | |
67 54 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
68 55 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
69 56 | |
70 57 <span class="c"># Overload Perl functions...</span> | |
71 58 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTopologicalAtomPairsFingerprints'</span><span class="sc">;</span> | |
72 59 | |
73 60 <span class="c"># Class constructor...</span> | |
74 <a name="new-"></a> 61 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
75 62 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
76 63 | |
77 64 <span class="c"># Initialize object...</span> | |
78 65 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
79 66 <span class="k">bless</span> <span class="i">$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> | |
80 67 <span class="i">$This</span><span class="i">->_InitializeTopologicalAtomPairsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
81 68 | |
82 69 <span class="i">$This</span><span class="i">->_InitializeTopologicalAtomPairsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
83 70 | |
84 71 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
85 72 <span class="s">}</span> | |
86 73 | |
87 74 <span class="c"># Initialize object data...</span> | |
88 75 <span class="c">#</span> | |
89 <a name="_InitializeTopologicalAtomPairsFingerprints-"></a> 76 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomPairsFingerprints</span> <span class="s">{</span> | |
90 77 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
91 78 | |
92 79 <span class="c"># Type of fingerprint...</span> | |
93 80 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalAtomPairs'</span><span class="sc">;</span> | |
94 81 | |
95 82 <span class="c"># Type of vector...</span> | |
96 83 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
97 84 | |
98 85 <span class="c"># Type of FingerprintsVector...</span> | |
99 86 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> | |
100 87 | |
101 88 <span class="c"># Minimum and maximum bond distance between atom paris...</span> | |
102 89 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> | |
103 90 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> | |
104 91 | |
105 92 <span class="c"># Atom identifier type to use for atom IDs in atom pairs...</span> | |
106 93 <span class="c">#</span> | |
107 94 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> | |
108 95 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> | |
109 96 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> | |
110 97 <span class="c">#</span> | |
111 98 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> | |
112 99 | |
113 100 <span class="c"># Atom types assigned to each heavy atom...</span> | |
114 101 <span class="c">#</span> | |
115 102 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
116 103 | |
117 104 <span class="c"># All atom pairs between minimum and maximum distance...</span> | |
118 105 <span class="c">#</span> | |
119 106 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
120 107 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
121 108 <span class="s">}</span> | |
122 109 | |
123 110 <span class="c"># Initialize class ...</span> | |
124 <a name="_InitializeClass-"></a> 111 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
125 112 <span class="c">#Class name...</span> | |
126 113 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
127 114 <span class="s">}</span> | |
128 115 | |
129 116 <span class="c"># Initialize object properties....</span> | |
130 <a name="_InitializeTopologicalAtomPairsFingerprintsProperties-"></a> 117 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomPairsFingerprintsProperties</span> <span class="s">{</span> | |
131 118 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
132 119 | |
133 120 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
134 121 <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> | |
135 122 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
136 123 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
137 124 <span class="s">}</span> | |
138 125 | |
139 126 <span class="c"># Make sure molecule object was specified...</span> | |
140 127 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
141 128 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> | |
142 129 <span class="s">}</span> | |
143 130 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
144 131 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span> | |
145 132 <span class="s">}</span> | |
146 133 | |
147 134 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
148 135 | |
149 136 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
150 137 <span class="s">}</span> | |
151 138 | |
152 139 <span class="c"># Set minimum distance for atom pairs...</span> | |
153 140 <span class="c">#</span> | |
154 <a name="SetMinDistance-"></a> 141 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> | |
155 142 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
156 143 | |
157 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
158 145 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
159 146 <span class="s">}</span> | |
160 147 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
161 148 | |
162 149 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
163 150 <span class="s">}</span> | |
164 151 | |
165 152 <span class="c"># Set maximum distance for atom pairs...</span> | |
166 153 <span class="c">#</span> | |
167 <a name="SetMaxDistance-"></a> 154 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> | |
168 155 <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> | |
169 156 | |
170 157 <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> | |
171 158 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
172 159 <span class="s">}</span> | |
173 160 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
174 161 | |
175 162 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
176 163 <span class="s">}</span> | |
177 164 | |
178 165 <span class="c"># Set atom identifier type..</span> | |
179 166 <span class="c">#</span> | |
180 <a name="SetAtomIdentifierType-"></a> 167 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> | |
181 168 <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> | |
182 169 | |
183 170 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> | |
184 171 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes."</span><span class="sc">;</span> | |
185 172 <span class="s">}</span> | |
186 173 | |
187 174 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
188 175 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SeAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> | |
189 176 <span class="s">}</span> | |
190 177 | |
191 178 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> | |
192 179 | |
193 180 <span class="c"># Initialize atom identifier type information...</span> | |
194 181 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
195 182 | |
196 183 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
197 184 <span class="s">}</span> | |
198 185 | |
199 186 <span class="c"># Generate fingerprints description...</span> | |
200 187 <span class="c">#</span> | |
201 <a name="GetDescription-"></a> 188 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> | |
202 189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
203 190 | |
204 191 <span class="c"># Is description explicity set?</span> | |
205 192 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> | |
206 193 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> | |
207 194 <span class="s">}</span> | |
208 195 | |
209 196 <span class="c"># Generate fingerprints description...</span> | |
210 197 | |
211 198 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span> | |
212 199 <span class="s">}</span> | |
213 200 | |
214 201 <span class="c"># Generate topological atom pairs [ Ref 57, Ref 59, Ref 72 ] fingerprints...</span> | |
215 202 <span class="c">#</span> | |
216 203 <span class="c"># Methodology:</span> | |
217 204 <span class="c"># . Generate a distance matrix.</span> | |
218 205 <span class="c"># . Assign atom types to all the atoms.</span> | |
219 206 <span class="c"># . Using distance matrix and atom types, count occurrence of</span> | |
220 207 <span class="c"># unique atom pairs within specified distance range - It corresponds to the</span> | |
221 208 <span class="c"># correlation-vector for the atom pairs.</span> | |
222 209 <span class="c">#</span> | |
223 210 <span class="c"># Notes:</span> | |
224 211 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span> | |
225 212 <span class="c">#</span> | |
226 <a name="GenerateFingerprints-"></a> 213 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> | |
227 214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
228 215 | |
229 216 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
230 217 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalAtomPairsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span> | |
231 218 <span class="s">}</span> | |
232 219 | |
233 220 <span class="c"># Cache appropriate molecule data...</span> | |
234 221 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
235 222 | |
236 223 <span class="c"># Generate distance matrix...</span> | |
237 224 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_SetupDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
238 225 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span> | |
239 226 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
240 227 <span class="s">}</span> | |
241 228 | |
242 229 <span class="c"># Assign atom types to all heavy atoms...</span> | |
243 230 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
244 231 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span> | |
245 232 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
246 233 <span class="s">}</span> | |
247 234 | |
248 235 <span class="c"># Intialize values of toplogical atom pairs...</span> | |
249 236 <span class="i">$This</span><span class="i">->_InitializeToplogicalAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
250 237 | |
251 238 <span class="c"># Count atom pairs...</span> | |
252 239 <span class="i">$This</span><span class="i">->_GenerateAndCountAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
253 240 | |
254 241 <span class="c"># Set final fingerprints...</span> | |
255 242 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
256 243 | |
257 244 <span class="c"># Clear cached molecule data...</span> | |
258 245 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
259 246 | |
260 247 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
261 248 <span class="s">}</span> | |
262 249 | |
263 250 <span class="c"># Setup distance matrix...</span> | |
264 251 <span class="c">#</span> | |
265 <a name="_SetupDistanceMatrix-"></a> 252 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span> | |
266 253 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
267 254 | |
268 255 <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
269 256 | |
270 257 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span> | |
271 258 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
272 259 <span class="s">}</span> | |
273 260 | |
274 261 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
275 262 <span class="s">}</span> | |
276 263 | |
277 264 <span class="c"># Assign appropriate atom types to all heavy atoms...</span> | |
278 265 <span class="c">#</span> | |
279 <a name="_AssignAtomTypes-"></a> 266 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span> | |
280 267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
281 268 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
282 269 | |
283 270 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
284 271 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span> | |
285 272 | |
286 273 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span> | |
287 274 | |
288 275 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> | |
289 276 <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> | |
290 277 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::AtomicInvariantsAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'AtomicInvariantsToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="sc">;</span> | |
291 278 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
292 279 <span class="s">}</span> | |
293 280 | |
294 281 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^DREIDINGAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
295 282 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::DREIDINGAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
296 283 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
297 284 <span class="s">}</span> | |
298 285 | |
299 286 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
300 287 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
301 288 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
302 289 <span class="s">}</span> | |
303 290 | |
304 291 <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> | |
305 292 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="sc">;</span> | |
306 293 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
307 294 <span class="s">}</span> | |
308 295 | |
309 296 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^MMFF94AtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
310 297 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::MMFF94AtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
311 298 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
312 299 <span class="s">}</span> | |
313 300 | |
314 301 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
315 302 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SLogPAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
316 303 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
317 304 <span class="s">}</span> | |
318 305 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SYBYLAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
319 306 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SYBYLAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
320 307 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
321 308 <span class="s">}</span> | |
322 309 | |
323 310 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
324 311 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> | |
325 312 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
326 313 <span class="s">}</span> | |
327 314 | |
328 315 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
329 316 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::UFFAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
330 317 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
331 318 <span class="s">}</span> | |
332 319 | |
333 320 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignAtomTypes: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
334 321 <span class="s">}</span> | |
335 322 | |
336 323 <span class="c"># Assign atom types...</span> | |
337 324 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
338 325 | |
339 326 <span class="c"># Make sure atom types assignment is successful...</span> | |
340 327 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
341 328 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
342 329 <span class="s">}</span> | |
343 330 | |
344 331 <span class="c"># Collect assigned atom types...</span> | |
345 332 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
346 333 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
347 334 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
348 335 <span class="s">}</span> | |
349 336 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
350 337 <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$SpecifiedAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
351 338 <span class="s">}</span> | |
352 339 | |
353 340 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
354 341 <span class="s">}</span> | |
355 342 | |
356 343 <span class="c"># Initialize topological atom pairs between specified distance range...</span> | |
357 344 <span class="c">#</span> | |
358 <a name="_InitializeToplogicalAtomPairs-"></a> 345 <span class="k">sub </span><span class="m">_InitializeToplogicalAtomPairs</span> <span class="s">{</span> | |
359 346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
360 347 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="s">)</span><span class="sc">;</span> | |
361 348 | |
362 349 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
363 350 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
364 351 | |
365 352 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
366 353 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
367 354 <span class="s">}</span> | |
368 355 | |
369 356 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
370 357 <span class="s">}</span> | |
371 358 | |
372 359 <span class="c"># Count atom pairs between mininum and maximum distance at each</span> | |
373 360 <span class="c"># distance using distance matrix and atom types assiged to each heavy</span> | |
374 361 <span class="c"># atom.</span> | |
375 362 <span class="c">#</span> | |
376 363 <span class="c"># Notes:</span> | |
377 364 <span class="c"># . The row and column indices of distance matrix correspond to atom indices.</span> | |
378 365 <span class="c"># . Distance value of BigNumber implies the atom is not connected to any other atom.</span> | |
379 366 <span class="c"># . Due to symmetric nature of distance matrix, only upper or lower triangular matrix</span> | |
380 367 <span class="c"># needs to be processed during identification and count of atom pairs.</span> | |
381 368 <span class="c">#</span> | |
382 <a name="_GenerateAndCountAtomPairs-"></a> 369 <span class="k">sub </span><span class="m">_GenerateAndCountAtomPairs</span> <span class="s">{</span> | |
383 370 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
384 371 | |
385 372 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$CountIncrement</span><span class="s">)</span><span class="sc">;</span> | |
386 373 | |
387 374 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span> | |
388 375 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
389 376 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span> | |
390 377 | |
391 378 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
392 379 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span> | |
393 380 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
394 381 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span> | |
395 382 <span class="s">}</span> | |
396 383 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="sc">;</span> | |
397 384 | |
398 385 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$RowIndex</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
399 386 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span> | |
400 387 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
401 388 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> | |
402 389 <span class="s">}</span> | |
403 390 <span class="i">$Distance</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
404 391 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> < <span class="i">$This</span>->{<span class="w">MinDistance</span>} || <span class="i">$Distance</span> > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
405 392 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> | |
406 393 <span class="s">}</span> | |
407 394 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="sc">;</span> | |
408 395 | |
409 396 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType1</span> <span class="k">le</span> <span class="i">$AtomType2</span><span class="s">)</span> <span class="s">{</span> | |
410 397 <span class="i">$This</span><span class="i">->_SetAtomPairsCount</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span> | |
411 398 <span class="s">}</span> | |
412 399 <span class="k">else</span> <span class="s">{</span> | |
413 400 <span class="i">$This</span><span class="i">->_SetAtomPairsCount</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="s">)</span><span class="sc">;</span> | |
414 401 <span class="s">}</span> | |
415 402 <span class="s">}</span> | |
416 403 <span class="s">}</span> | |
417 404 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
418 405 <span class="s">}</span> | |
419 406 | |
420 407 <span class="c"># Set atom paris count for a specific atom ID pair at a specific distance...</span> | |
421 408 <span class="c">#</span> | |
422 <a name="_SetAtomPairsCount-"></a> 409 <span class="k">sub </span><span class="m">_SetAtomPairsCount</span> <span class="s">{</span> | |
423 410 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
424 411 | |
425 412 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}<span class="s">)</span> <span class="s">{</span> | |
426 413 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
427 414 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">1</span><span class="sc">;</span> | |
428 415 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
429 416 <span class="s">}</span> | |
430 417 | |
431 418 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="s">)</span> <span class="s">{</span> | |
432 419 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="n">1</span><span class="sc">;</span> | |
433 420 <span class="s">}</span> | |
434 421 <span class="k">else</span> <span class="s">{</span> | |
435 422 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">1</span><span class="sc">;</span> | |
436 423 <span class="s">}</span> | |
437 424 | |
438 425 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
439 426 <span class="s">}</span> | |
440 427 | |
441 428 <span class="c"># Set final fingerpritns vector...</span> | |
442 429 <span class="c">#</span> | |
443 <a name="_SetFinalFingerprints-"></a> 430 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> | |
444 431 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
445 432 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> | |
446 433 | |
447 434 <span class="c"># Mark successful generation of fingerprints...</span> | |
448 435 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
449 436 | |
450 437 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
451 438 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
452 439 | |
453 440 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
454 441 <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span> | |
455 442 <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span> | |
456 443 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="cm">,</span> <span class="q">"${AtomType1}-D${Distance}-${AtomType2}"</span><span class="sc">;</span> | |
457 444 <span class="i">$Value</span> = <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span> | |
458 445 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span> | |
459 446 <span class="s">}</span> | |
460 447 <span class="s">}</span> | |
461 448 <span class="s">}</span> | |
462 449 | |
463 450 <span class="c"># Add AtomPairsIDs and values to fingerprint vector...</span> | |
464 451 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="s">)</span><span class="sc">;</span> | |
465 452 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> | |
466 453 | |
467 454 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
468 455 <span class="s">}</span> | |
469 456 | |
470 457 <span class="c"># Get atom pair IDs corresponding to atom pairs count values in fingerprint</span> | |
471 458 <span class="c"># vector as an array or reference to an array...</span> | |
472 459 <span class="c">#</span> | |
473 460 <span class="c"># AtomPairIDs list differes in molecules and is generated during finalization</span> | |
474 461 <span class="c"># of fingerprints to make sure the fingerprint vector containing count values</span> | |
475 462 <span class="c"># matches the atom pairs array.</span> | |
476 463 <span class="c">#</span> | |
477 <a name="GetAtomPairIDs-"></a> 464 <span class="k">sub </span><span class="m">GetAtomPairIDs</span> <span class="s">{</span> | |
478 465 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
479 466 | |
480 467 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="sc">;</span> | |
481 468 <span class="s">}</span> | |
482 469 | |
483 470 <span class="c"># Cache appropriate molecule data...</span> | |
484 471 <span class="c">#</span> | |
485 <a name="_SetupMoleculeDataCache-"></a> 472 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> | |
486 473 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
487 474 | |
488 475 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span> | |
489 476 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span> | |
490 477 <span class="c">#</span> | |
491 478 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
492 479 | |
493 480 <span class="c"># Get all atom IDs...</span> | |
494 481 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
495 482 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
496 483 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> | |
497 484 | |
498 485 <span class="c"># Set AtomIndex to AtomID hash...</span> | |
499 486 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
500 487 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span> | |
501 488 | |
502 489 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
503 490 <span class="s">}</span> | |
504 491 | |
505 492 <span class="c"># Clear cached molecule data...</span> | |
506 493 <span class="c">#</span> | |
507 <a name="_ClearMoleculeDataCache-"></a> 494 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> | |
508 495 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
509 496 | |
510 497 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
511 498 | |
512 499 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
513 500 <span class="s">}</span> | |
514 501 | |
515 502 <span class="c"># Set atomic invariants to use for atom identifiers...</span> | |
516 503 <span class="c">#</span> | |
517 <a name="SetAtomicInvariantsToUse-"></a> 504 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> | |
518 505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
519 506 <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">$AtomicInvariantValue</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> | |
520 507 | |
521 508 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
522 509 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> | |
523 510 <span class="k">return</span><span class="sc">;</span> | |
524 511 <span class="s">}</span> | |
525 512 | |
526 513 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
527 514 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
528 515 | |
529 516 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
530 517 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
531 518 | |
532 519 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
533 520 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
534 521 <span class="s">}</span> | |
535 522 <span class="k">else</span> <span class="s">{</span> | |
536 523 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
537 524 <span class="s">}</span> | |
538 525 | |
539 526 <span class="c"># Make sure specified AtomicInvariants are valid...</span> | |
540 527 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> | |
541 528 <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> | |
542 529 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> | |
543 530 <span class="s">}</span> | |
544 531 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> | |
545 532 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> | |
546 533 <span class="s">}</span> | |
547 534 | |
548 535 <span class="c"># Set atomic invariants to use...</span> | |
549 536 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
550 537 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> | |
551 538 | |
552 539 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
553 540 <span class="s">}</span> | |
554 541 | |
555 542 <span class="c"># Set functional classes to use for atom identifiers...</span> | |
556 543 <span class="c">#</span> | |
557 <a name="SetFunctionalClassesToUse-"></a> 544 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> | |
558 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
559 546 <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> | |
560 547 | |
561 548 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
562 549 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> | |
563 550 <span class="k">return</span><span class="sc">;</span> | |
564 551 <span class="s">}</span> | |
565 552 | |
566 553 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
567 554 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
568 555 <span class="k">return</span><span class="sc">;</span> | |
569 556 <span class="s">}</span> | |
570 557 | |
571 558 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
572 559 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
573 560 | |
574 561 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
575 562 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
576 563 | |
577 564 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
578 565 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
579 566 <span class="s">}</span> | |
580 567 <span class="k">else</span> <span class="s">{</span> | |
581 568 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
582 569 <span class="s">}</span> | |
583 570 | |
584 571 <span class="c"># Make sure specified FunctionalClasses are valid...</span> | |
585 572 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> | |
586 573 <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> | |
587 574 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> | |
588 575 <span class="s">}</span> | |
589 576 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> | |
590 577 <span class="s">}</span> | |
591 578 | |
592 579 <span class="c"># Set functional classes to use...</span> | |
593 580 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
594 581 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> | |
595 582 | |
596 583 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
597 584 <span class="s">}</span> | |
598 585 | |
599 586 <span class="c"># Initialize atom indentifier type information...</span> | |
600 587 <span class="c">#</span> | |
601 588 <span class="c"># Current supported values:</span> | |
602 589 <span class="c">#</span> | |
603 590 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span> | |
604 591 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> | |
605 592 <span class="c">#</span> | |
606 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 593 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> | |
607 594 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
608 595 | |
609 596 <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> | |
610 597 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
611 598 <span class="s">}</span> | |
612 599 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
613 600 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
614 601 <span class="s">}</span> | |
615 602 <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> | |
616 603 <span class="c"># Nothing to do for now...</span> | |
617 604 <span class="s">}</span> | |
618 605 <span class="k">else</span> <span class="s">{</span> | |
619 606 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
620 607 <span class="s">}</span> | |
621 608 | |
622 609 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
623 610 <span class="s">}</span> | |
624 611 | |
625 612 <span class="c"># Initialize atomic invariants atom types to use for generating atom identifiers...</span> | |
626 613 <span class="c">#</span> | |
627 614 <span class="c"># Let:</span> | |
628 615 <span class="c"># AS = Atom symbol corresponding to element symbol</span> | |
629 616 <span class="c">#</span> | |
630 617 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
631 618 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
632 619 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
633 620 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
634 621 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
635 622 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
636 623 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> | |
637 624 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> | |
638 625 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> | |
639 626 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> | |
640 627 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> | |
641 628 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> | |
642 629 <span class="c">#</span> | |
643 630 <span class="c"># AtomTypeIDx = Atomic invariants atom type for atom x</span> | |
644 631 <span class="c"># AtomTypeIDy = Atomic invariants atom type for atom y</span> | |
645 632 <span class="c"># Dn = Topological distance between atom x and y</span> | |
646 633 <span class="c">#</span> | |
647 634 <span class="c"># Then:</span> | |
648 635 <span class="c">#</span> | |
649 636 <span class="c"># Atom pair AtomID generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> | |
650 637 <span class="c">#</span> | |
651 638 <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> | |
652 639 <span class="c">#</span> | |
653 640 <span class="c"># AtomPairID corresponds to:</span> | |
654 641 <span class="c">#</span> | |
655 642 <span class="c"># AtomTypeIDx-D<n>-AtomTypeIDy</span> | |
656 643 <span class="c">#</span> | |
657 644 <span class="c"># Except for AS which is a required atomic invariant in atom pair AtomIDs, all other atomic invariants are</span> | |
658 645 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X<n>, BO<n>, H<n>, FC<+n/-n>.</span> | |
659 646 <span class="c"># AtomID specification doesn't include atomic invariants with zero or undefined values.</span> | |
660 647 <span class="c">#</span> | |
661 648 <span class="c"># Examples of atom pair AtomIDs:</span> | |
662 649 <span class="c">#</span> | |
663 650 <span class="c"># O.X1.BO1.H1 - Hydroxyl oxygen in carboxylate with attached hydrogen and no explicit charge</span> | |
664 651 <span class="c"># O.X1.BO1.FC-1 - Hydroxyl ozygen in carboxylate with explicit negative charge</span> | |
665 652 <span class="c"># O.X1.BO2 - Carbonyl oxygen in carboxylate with double bond to carbon</span> | |
666 653 <span class="c"># O.X2.BO2 - Hydroxyl ozygen in carboxylate attached to carbonyl carbon and another heavy atom</span> | |
667 654 <span class="c">#</span> | |
668 655 <span class="c"># C.X2.BO3.H1.Ar - Aromatic carbon</span> | |
669 656 <span class="c">#</span> | |
670 657 <span class="c"># Examples of AtomPairIDs:</span> | |
671 658 <span class="c">#</span> | |
672 659 <span class="c"># C.X2.BO2.H3-D1-O.X1.BO1 - Carbon with two heavy atom neighbors attached to oxygen at bond distance 1(methanol)</span> | |
673 660 <span class="c">#</span> | |
674 661 <span class="c"># C.X2.BO3.H1.Ar-D3-C.X2.BO3.H1.Ar - Two aromatic carbons at bond distance 3 where each carbon has</span> | |
675 662 <span class="c"># two heavy atom neighbors and bond order of 3 (benzene)</span> | |
676 663 <span class="c">#</span> | |
677 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 664 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> | |
678 665 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
679 666 | |
680 667 <span class="c"># Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC</span> | |
681 668 <span class="c">#</span> | |
682 669 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
683 670 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> | |
684 671 | |
685 672 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
686 673 <span class="s">}</span> | |
687 674 | |
688 675 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> | |
689 676 <span class="c"># class, to use for generating atom identifiers...</span> | |
690 677 <span class="c">#</span> | |
691 678 <span class="c"># Let:</span> | |
692 679 <span class="c"># HBD: HydrogenBondDonor</span> | |
693 680 <span class="c"># HBA: HydrogenBondAcceptor</span> | |
694 681 <span class="c"># PI : PositivelyIonizable</span> | |
695 682 <span class="c"># NI : NegativelyIonizable</span> | |
696 683 <span class="c"># Ar : Aromatic</span> | |
697 684 <span class="c"># Hal : Halogen</span> | |
698 685 <span class="c"># H : Hydrophobic</span> | |
699 686 <span class="c"># RA : RingAtom</span> | |
700 687 <span class="c"># CA : ChainAtom</span> | |
701 688 <span class="c">#</span> | |
702 689 <span class="c"># Then:</span> | |
703 690 <span class="c">#</span> | |
704 691 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> | |
705 692 <span class="c">#</span> | |
706 693 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> | |
707 694 <span class="c">#</span> | |
708 695 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> | |
709 696 <span class="c">#</span> | |
710 697 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> | |
711 698 <span class="c">#</span> | |
712 699 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> | |
713 700 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> | |
714 701 <span class="c"># PositivelyIonizable: +, NH2</span> | |
715 702 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> | |
716 703 <span class="c">#</span> | |
717 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 704 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> | |
718 705 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
719 706 | |
720 707 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span> | |
721 708 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span> | |
722 709 <span class="c">#</span> | |
723 710 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
724 711 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> | |
725 712 | |
726 713 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
727 714 <span class="s">}</span> | |
728 715 | |
729 716 <span class="c"># Return a string containg data for TopologicalAtomPairsFingerprints object...</span> | |
730 717 <span class="c">#</span> | |
731 <a name="StringifyTopologicalAtomPairsFingerprints-"></a> 718 <span class="k">sub </span><span class="m">StringifyTopologicalAtomPairsFingerprints</span> <span class="s">{</span> | |
732 719 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
733 720 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span> | |
734 721 | |
735 722 <span class="c"># Type of fingerprint...</span> | |
736 723 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}"</span><span class="sc">;</span> | |
737 724 | |
738 725 <span class="c"># Min and max distance...</span> | |
739 726 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}"</span><span class="sc">;</span> | |
740 727 | |
741 728 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
742 729 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
743 730 | |
744 731 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
745 732 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
746 733 | |
747 734 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> | |
748 735 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> | |
749 736 <span class="s">}</span> | |
750 737 | |
751 738 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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> | |
752 739 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
753 740 <span class="i">$FingerprintsString</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> | |
754 741 <span class="s">}</span> | |
755 742 <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> | |
756 743 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> | |
757 744 | |
758 745 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
759 746 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
760 747 | |
761 748 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> | |
762 749 <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> | |
763 750 <span class="s">}</span> | |
764 751 | |
765 752 <span class="i">$FingerprintsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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> | |
766 753 <span class="i">$FingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
767 754 <span class="i">$FingerprintsString</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> | |
768 755 <span class="s">}</span> | |
769 756 | |
770 757 <span class="c"># Total number of atom pairs...</span> | |
771 758 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomPairs: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
772 759 | |
773 760 <span class="c"># FingerprintsVector...</span> | |
774 761 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> | |
775 762 | |
776 763 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span> | |
777 764 <span class="s">}</span> | |
778 765 | |
779 <a name="EOF-"></a></pre> | |
780 <p> </p> | |
781 <br /> | |
782 <center> | |
783 <img src="../../../images/h2o2.png"> | |
784 </center> | |
785 </body> | |
786 </html> |