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14 <a name="package-Fingerprints::TopologicalAtomTripletsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="sc">;</span>
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: TopologicalAtomTripletsFingerprints.pm,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
18 5 <span class="c"># $Revision: 1.15 $</span>
19 6 <span class="c">#</span>
20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
21 8 <span class="c">#</span>
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
23 10 <span class="c">#</span>
24 11 <span class="c"># This file is part of MayaChemTools.</span>
25 12 <span class="c">#</span>
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
29 16 <span class="c"># later version.</span>
30 17 <span class="c">#</span>
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
34 21 <span class="c"># details.</span>
35 22 <span class="c">#</span>
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
40 27 <span class="c">#</span>
41 28
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
45 32 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span>
46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">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">=&gt;</span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
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">&#39;&quot;&quot;&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;StringifyTopologicalAtomTripletsFingerprints&#39;</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">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
79 66 <span class="k">bless</span> <span class="i">$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">$This</span><span class="i">-&gt;_InitializeTopologicalAtomTripletsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
81 68
82 69 <span class="i">$This</span><span class="i">-&gt;_InitializeTopologicalAtomTripletsFingerprintsProperties</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">$This</span><span class="sc">;</span>
85 72 <span class="s">}</span>
86 73
87 74 <span class="c"># Initialize object data...</span>
88 75 <span class="c">#</span>
89 <a name="_InitializeTopologicalAtomTripletsFingerprints-"></a> 76 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomTripletsFingerprints</span> <span class="s">{</span>
90 77 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;TopologicalAtomTriplets&#39;</span><span class="sc">;</span>
94 81
95 82 <span class="c"># Type of vector...</span>
96 83 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsVector&#39;</span><span class="sc">;</span>
97 84
98 85 <span class="c"># Type of FingerprintsVector...</span>
99 86 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;NumericalValues&#39;</span><span class="sc">;</span>
100 87
101 88 <span class="c"># Minimum and maximum bond distance between atom paris...</span>
102 89 <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span>
103 90 <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span>
104 91
105 92 <span class="c"># Determines whether to apply triangle inequality to distance triplets...</span>
106 93 <span class="c">#</span>
107 94 <span class="i">$This</span>-&gt;{<span class="w">UseTriangleInequality</span>} = <span class="n">0</span><span class="sc">;</span>
108 95
109 96 <span class="c"># Atom identifier type to use for atom IDs in atom triplets...</span>
110 97 <span class="c">#</span>
111 98 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span>
112 99 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span>
113 100 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
114 101 <span class="c">#</span>
115 102 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
116 103
117 104 <span class="c"># Atom types assigned to each heavy atom...</span>
118 105 <span class="c">#</span>
119 106 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
120 107
121 108 <span class="c"># All atom triplets between minimum and maximum distance...</span>
122 109 <span class="c">#</span>
123 110 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
124 111 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
125 112 <span class="s">}</span>
126 113
127 114 <span class="c"># Initialize class ...</span>
128 <a name="_InitializeClass-"></a> 115 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
129 116 <span class="c">#Class name...</span>
130 117 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
131 118 <span class="s">}</span>
132 119
133 120 <span class="c"># Initialize object properties....</span>
134 <a name="_InitializeTopologicalAtomTripletsFingerprintsProperties-"></a> 121 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomTripletsFingerprintsProperties</span> <span class="s">{</span>
135 122 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
136 123
137 124 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
138 125 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
139 126 <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
140 127 <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
141 128 <span class="s">}</span>
142 129
143 130 <span class="c"># Make sure molecule object was specified...</span>
144 131 <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>
145 132 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying molecule...&quot;</span><span class="sc">;</span>
146 133 <span class="s">}</span>
147 134 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
148 135 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying AtomIdentifierType...&quot;</span><span class="sc">;</span>
149 136 <span class="s">}</span>
150 137
151 138 <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
152 139
153 140 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
154 141 <span class="s">}</span>
155 142
156 143 <span class="c"># Set minimum distance for atom triplets...</span>
157 144 <span class="c">#</span>
158 <a name="SetMinDistance-"></a> 145 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span>
159 146 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
160 147
161 148 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
162 149 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer...&quot;</span><span class="sc">;</span>
163 150 <span class="s">}</span>
164 151 <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
165 152
166 153 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
167 154 <span class="s">}</span>
168 155
169 156 <span class="c"># Set maximum distance for atom triplets...</span>
170 157 <span class="c">#</span>
171 <a name="SetMaxDistance-"></a> 158 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span>
172 159 <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>
173 160
174 161 <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>
175 162 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer...&quot;</span><span class="sc">;</span>
176 163 <span class="s">}</span>
177 164 <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
178 165
179 166 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
180 167 <span class="s">}</span>
181 168
182 169 <span class="c"># Set atom identifier type..</span>
183 170 <span class="c">#</span>
184 <a name="SetAtomIdentifierType-"></a> 171 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
185 172 <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>
186 173
187 174 <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>
188 175 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes.&quot;</span><span class="sc">;</span>
189 176 <span class="s">}</span>
190 177
191 178 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
192 179 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SeAtomIdentifierType: Can&#39;t change intial atom identifier type: It&#39;s already set...&quot;</span><span class="sc">;</span>
193 180 <span class="s">}</span>
194 181
195 182 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
196 183
197 184 <span class="c"># Initialize atom identifier type information...</span>
198 185 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
199 186
200 187 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
201 188 <span class="s">}</span>
202 189
203 190 <span class="c"># Generate fingerprints description...</span>
204 191 <span class="c">#</span>
205 <a name="GetDescription-"></a> 192 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
206 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
207 194
208 195 <span class="c"># Is description explicity set?</span>
209 196 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
210 197 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="sc">;</span>
211 198 <span class="s">}</span>
212 199
213 200 <span class="c"># Generate fingerprints description...</span>
214 201
215 202 <span class="k">return</span> <span class="q">&quot;$This-&gt;{Type}:$This-&gt;{AtomIdentifierType}:MinDistance$This-&gt;{MinDistance}:MaxDistance$This-&gt;{MaxDistance}&quot;</span><span class="sc">;</span>
216 203 <span class="s">}</span>
217 204
218 205 <span class="c"># Generate topological atom triplets fingerprints...</span>
219 206 <span class="c">#</span>
220 207 <span class="c"># Let:</span>
221 208 <span class="c">#</span>
222 209 <span class="c"># AT = Any of the supported atom types</span>
223 210 <span class="c">#</span>
224 211 <span class="c"># ATx = Atom type for atom x</span>
225 212 <span class="c"># ATy = Atom type for atom y</span>
226 213 <span class="c"># ATz = Atom type for atom z</span>
227 214 <span class="c">#</span>
228 215 <span class="c"># Dxy = Distance between Px and Py</span>
229 216 <span class="c"># Dxz = Distance between Px and Pz</span>
230 217 <span class="c"># Dyz = Distance between Py and Pz</span>
231 218 <span class="c">#</span>
232 219 <span class="c"># Then:</span>
233 220 <span class="c">#</span>
234 221 <span class="c"># ATx-Dyz-ATy-Dxz-ATz-Dxy = Atom triplet ID for atom types ATx, ATy and Atz</span>
235 222 <span class="c">#</span>
236 223 <span class="c"># Methodology:</span>
237 224 <span class="c"># . Generate a distance matrix.</span>
238 225 <span class="c"># . Assign atom types to all the atoms.</span>
239 226 <span class="c"># . Using distance matrix and atom types, count occurrence of unique atom triplets</span>
240 227 <span class="c"># within specified distance range along with optional trinagle inequality</span>
241 228 <span class="c">#</span>
242 229 <span class="c"># Notes:</span>
243 230 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span>
244 231 <span class="c"># . For a molecule containing N atoms with all different atom type, the total number of</span>
245 232 <span class="c"># possible unique atom triplets without applying triangle inquality check corresponds to:</span>
246 233 <span class="c">#</span>
247 234 <span class="c"># Factorial( N ) / ( Factorial( N - 3 ) * Factorial (3) )</span>
248 235 <span class="c">#</span>
249 236 <span class="c"># However, due to similar atom types assigned to atoms in a molecule for a specific atom</span>
250 237 <span class="c"># typing methodology and specified distance range used during fingerprints generation, the</span>
251 238 <span class="c"># actual number of unique triplets is usually smaller than the theoretical limit.</span>
252 239 <span class="c">#</span>
253 <a name="GenerateFingerprints-"></a> 240 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
254 241 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
255 242
256 243 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
257 244 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;GenerateTopologicalAtomTripletsFingerprints: No fingerpritns generated: MinDistance, $This-&gt;{MinDistance}, must be &lt;= MaxDistance, $This-&gt;{MaxDistance}...&quot;</span><span class="sc">;</span>
258 245 <span class="s">}</span>
259 246
260 247 <span class="c"># Cache appropriate molecule data...</span>
261 248 <span class="i">$This</span><span class="i">-&gt;_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
262 249
263 250 <span class="c"># Generate distance matrix...</span>
264 251 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_SetupDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
265 252 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateFingerprints: $This-&gt;{AtomIdentifierType} fingerprints generation didn&#39;t succeed: Couldn&#39;t generate distance matrix...&quot;</span><span class="sc">;</span>
266 253 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
267 254 <span class="s">}</span>
268 255
269 256 <span class="c"># Assign atom types to all heavy atoms...</span>
270 257 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
271 258 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateFingerprints: $This-&gt;{AtomIdentifierType} fingerprints generation didn&#39;t succeed: Couldn&#39;t assign valid $This-&gt;{AtomIdentifierType} to all atoms...&quot;</span><span class="sc">;</span>
272 259 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
273 260 <span class="s">}</span>
274 261
275 262 <span class="c"># Intialize values of toplogical atom triplets...</span>
276 263 <span class="i">$This</span><span class="i">-&gt;_InitializeToplogicalAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
277 264
278 265 <span class="c"># Count atom triplets...</span>
279 266 <span class="i">$This</span><span class="i">-&gt;_GenerateAndCountAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
280 267
281 268 <span class="c"># Set final fingerprints...</span>
282 269 <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
283 270
284 271 <span class="c"># Clear cached molecule data...</span>
285 272 <span class="i">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
286 273
287 274 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
288 275 <span class="s">}</span>
289 276
290 277 <span class="c"># Setup distance matrix...</span>
291 278 <span class="c">#</span>
292 <a name="_SetupDistanceMatrix-"></a> 279 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span>
293 280 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
294 281
295 282 <span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
296 283
297 284 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span>
298 285 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
299 286 <span class="s">}</span>
300 287
301 288 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
302 289 <span class="s">}</span>
303 290
304 291 <span class="c"># Assign appropriate atom types to all heavy atoms...</span>
305 292 <span class="c">#</span>
306 <a name="_AssignAtomTypes-"></a> 293 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span>
307 294 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
308 295 <span class="k">my</span><span class="s">(</span><span class="i">$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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
309 296
310 297 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
311 298 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span>
312 299
313 300 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span>
314 301
315 302 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
316 303 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
317 304 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::AtomicInvariantsAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">&#39;AtomicInvariantsToUse&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="sc">;</span>
318 305 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
319 306 <span class="s">}</span>
320 307
321 308 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^DREIDINGAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
322 309 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::DREIDINGAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
323 310 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
324 311 <span class="s">}</span>
325 312
326 313 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
327 314 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
328 315 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
329 316 <span class="s">}</span>
330 317
331 318 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
332 319 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">&#39;FunctionalClassesToUse&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="sc">;</span>
333 320 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
334 321 <span class="s">}</span>
335 322
336 323 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^MMFF94AtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
337 324 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::MMFF94AtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
338 325 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
339 326 <span class="s">}</span>
340 327
341 328 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
342 329 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SLogPAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
343 330 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
344 331 <span class="s">}</span>
345 332 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SYBYLAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
346 333 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SYBYLAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
347 334 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
348 335 <span class="s">}</span>
349 336
350 337 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
351 338 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnorePhosphorus&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="cm">,</span> <span class="q">&#39;IgnoreSulfur&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
352 339 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
353 340 <span class="s">}</span>
354 341
355 342 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
356 343 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::UFFAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
357 344 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
358 345 <span class="s">}</span>
359 346
360 347 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_AssignAtomTypes: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
361 348 <span class="s">}</span>
362 349
363 350 <span class="c"># Assign atom types...</span>
364 351 <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
365 352
366 353 <span class="c"># Make sure atom types assignment is successful...</span>
367 354 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
368 355 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
369 356 <span class="s">}</span>
370 357
371 358 <span class="c"># Collect assigned atom types...</span>
372 359 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
373 360 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
374 361 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
375 362 <span class="s">}</span>
376 363 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
377 364 <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
378 365 <span class="s">}</span>
379 366
380 367 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
381 368 <span class="s">}</span>
382 369
383 370 <span class="c"># Initialize topological atom triplets between specified distance range...</span>
384 371 <span class="c">#</span>
385 <a name="_InitializeToplogicalAtomTriplets-"></a> 372 <span class="k">sub </span><span class="m">_InitializeToplogicalAtomTriplets</span> <span class="s">{</span>
386 373 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
387 374 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="s">)</span><span class="sc">;</span>
388 375
389 376 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
390 377 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
391 378
392 379 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
393 380 <span class="s">}</span>
394 381
395 382 <span class="c"># Count atom triplets between mininum and maximum distance at each</span>
396 383 <span class="c"># distance using distance matrix and atom types assiged to each heavy</span>
397 384 <span class="c"># atom.</span>
398 385 <span class="c">#</span>
399 <a name="_GenerateAndCountAtomTriplets-"></a> 386 <span class="k">sub </span><span class="m">_GenerateAndCountAtomTriplets</span> <span class="s">{</span>
400 387 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
401 388 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfAtoms</span><span class="cm">,</span> <span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomIndex3</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomID3</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">$AtomType3</span><span class="cm">,</span> <span class="i">$Distance12</span><span class="cm">,</span> <span class="i">$Distance13</span><span class="cm">,</span> <span class="i">$Distance23</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="s">)</span><span class="sc">;</span>
402 389
403 390 <span class="i">$NumOfAtoms</span> = <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="sc">;</span>
404 391 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>}<span class="sc">;</span>
405 392 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span>
406 393
407 394 <span class="j">ATOMINDEX1:</span> <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
408 395 <span class="i">$AtomID1</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex1</span>}<span class="sc">;</span>
409 396 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
410 397 <span class="k">next</span> <span class="j">ATOMINDEX1</span><span class="sc">;</span>
411 398 <span class="s">}</span>
412 399 <span class="i">$AtomType1</span> = <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="sc">;</span>
413 400
414 401 <span class="j">ATOMINDEX2:</span> <span class="k">for</span> <span class="i">$AtomIndex2</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
415 402 <span class="i">$AtomID2</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex2</span>}<span class="sc">;</span>
416 403 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
417 404 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span>
418 405 <span class="s">}</span>
419 406 <span class="i">$AtomType2</span> = <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="sc">;</span>
420 407
421 408 <span class="i">$Distance12</span> = <span class="i">$DistanceMatrix</span><span class="i">-&gt;GetValue</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
422 409 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance12</span> &lt; <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} || <span class="i">$Distance12</span> &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
423 410 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span>
424 411 <span class="s">}</span>
425 412
426 413 <span class="j">ATOMINDEX3:</span> <span class="k">for</span> <span class="i">$AtomIndex3</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomIndex2</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
427 414 <span class="i">$AtomID3</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex3</span>}<span class="sc">;</span>
428 415 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID3</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
429 416 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span>
430 417 <span class="s">}</span>
431 418 <span class="i">$AtomType3</span> = <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID3</span>}<span class="sc">;</span>
432 419
433 420 <span class="i">$Distance13</span> = <span class="i">$DistanceMatrix</span><span class="i">-&gt;GetValue</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex3</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
434 421 <span class="i">$Distance23</span> = <span class="i">$DistanceMatrix</span><span class="i">-&gt;GetValue</span><span class="s">(</span><span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomIndex3</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
435 422
436 423 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance13</span> &lt; <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} || <span class="i">$Distance13</span> &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
437 424 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span>
438 425 <span class="s">}</span>
439 426 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance23</span> &lt; <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} || <span class="i">$Distance23</span> &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
440 427 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span>
441 428 <span class="s">}</span>
442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">UseTriangleInequality</span>} &amp;&amp; !<span class="i">$This</span><span class="i">-&gt;_DoDistancesSatisfyTriangleInequality</span><span class="s">(</span><span class="i">$Distance12</span><span class="cm">,</span> <span class="i">$Distance13</span><span class="cm">,</span> <span class="i">$Distance23</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
443 430 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span>
444 431 <span class="s">}</span>
445 432
446 433 <span class="i">$AtomTripletID</span> = <span class="i">$This</span><span class="i">-&gt;_GetAtomTripletID</span><span class="s">(</span><span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$Distance23</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$Distance13</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$Distance12</span><span class="s">)</span><span class="sc">;</span>
447 434 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomTripletsCount</span>}{<span class="i">$AtomTripletID</span>}<span class="s">)</span> <span class="s">{</span>
448 435 <span class="i">$This</span>-&gt;{<span class="w">AtomTripletsCount</span>}{<span class="i">$AtomTripletID</span>} = <span class="n">0</span><span class="sc">;</span>
449 436 <span class="s">}</span>
450 437 <span class="i">$This</span>-&gt;{<span class="w">AtomTripletsCount</span>}{<span class="i">$AtomTripletID</span>} += <span class="n">1</span><span class="sc">;</span>
451 438 <span class="s">}</span>
452 439 <span class="s">}</span>
453 440 <span class="s">}</span>
454 441 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
455 442 <span class="s">}</span>
456 443
457 444 <span class="c"># Check triangle inequality...</span>
458 445 <span class="c">#</span>
459 <a name="_DoDistancesSatisfyTriangleInequality-"></a> 446 <span class="k">sub </span><span class="m">_DoDistancesSatisfyTriangleInequality</span> <span class="s">{</span>
460 447 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Distance1</span><span class="cm">,</span> <span class="i">$Distance2</span><span class="cm">,</span> <span class="i">$Distance3</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
461 448
462 449 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$Distance1</span> &gt; <span class="k">abs</span><span class="s">(</span><span class="i">$Distance2</span> - <span class="i">$Distance3</span><span class="s">)</span> &amp;&amp; <span class="i">$Distance1</span> &lt; <span class="s">(</span><span class="i">$Distance2</span> + <span class="i">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
463 450 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
464 451 <span class="s">}</span>
465 452 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$Distance2</span> &gt; <span class="k">abs</span><span class="s">(</span><span class="i">$Distance1</span> - <span class="i">$Distance3</span><span class="s">)</span> &amp;&amp; <span class="i">$Distance2</span> &lt; <span class="s">(</span><span class="i">$Distance1</span> + <span class="i">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
466 453 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
467 454 <span class="s">}</span>
468 455 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$Distance3</span> &gt; <span class="k">abs</span><span class="s">(</span><span class="i">$Distance1</span> - <span class="i">$Distance2</span><span class="s">)</span> &amp;&amp; <span class="i">$Distance3</span> &lt; <span class="s">(</span><span class="i">$Distance1</span> + <span class="i">$Distance2</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
469 456 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
470 457 <span class="s">}</span>
471 458 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
472 459 <span class="s">}</span>
473 460
474 461 <span class="c"># Get atom triplet ID corresponding to atom types and distances corresponding to atom triplet...</span>
475 462 <span class="c">#</span>
476 <a name="_GetAtomTripletID-"></a> 463 <span class="k">sub </span><span class="m">_GetAtomTripletID</span> <span class="s">{</span>
477 464 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ATx</span><span class="cm">,</span> <span class="i">$Dyz</span><span class="cm">,</span> <span class="i">$ATy</span><span class="cm">,</span> <span class="i">$Dxz</span><span class="cm">,</span> <span class="i">$ATz</span><span class="cm">,</span> <span class="i">$Dxy</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
478 465 <span class="k">my</span><span class="s">(</span><span class="i">$AtomTripletID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
479 466
480 467 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
481 468
482 469 <span class="i">@AtomIDs</span> = <span class="k">sort</span><span class="s">(</span><span class="q">&quot;${ATx}-D${Dyz}&quot;</span><span class="cm">,</span> <span class="q">&quot;${ATy}-D${Dxz}&quot;</span><span class="cm">,</span> <span class="q">&quot;${ATz}-D${Dxy}&quot;</span><span class="s">)</span><span class="sc">;</span>
483 470 <span class="i">$AtomTripletID</span> = <span class="k">join</span> <span class="q">&quot;-&quot;</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="sc">;</span>
484 471
485 472 <span class="k">return</span> <span class="i">$AtomTripletID</span><span class="sc">;</span>
486 473 <span class="s">}</span>
487 474
488 475 <span class="c"># Set final fingerpritns vector...</span>
489 476 <span class="c">#</span>
490 <a name="_SetFinalFingerprints-"></a> 477 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
491 478 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
492 479 <span class="k">my</span><span class="s">(</span><span class="i">$AtomTripletID</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
493 480
494 481 <span class="c"># Mark successful generation of fingerprints...</span>
495 482 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
496 483
497 484 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
498 485 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
499 486
500 487 <span class="k">for</span> <span class="i">$AtomTripletID</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsCount</span>}}<span class="s">)</span> <span class="s">{</span>
501 488 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsIDs</span>}}<span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="sc">;</span>
502 489 <span class="i">$Value</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTripletsCount</span>}{<span class="i">$AtomTripletID</span>}<span class="sc">;</span>
503 490 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span>
504 491 <span class="s">}</span>
505 492
506 493 <span class="c"># Add AtomTripletsIDs and values to fingerprint vector...</span>
507 494 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsIDs</span>}}<span class="s">)</span><span class="sc">;</span>
508 495 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
509 496
510 497 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
511 498 <span class="s">}</span>
512 499
513 500 <span class="c"># Get atom triplet IDs corresponding to atom triplets count values in fingerprint</span>
514 501 <span class="c"># vector as an array or reference to an array...</span>
515 502 <span class="c">#</span>
516 503 <span class="c"># AtomTripletIDs list differes in molecules and is generated during finalization</span>
517 504 <span class="c"># of fingerprints to make sure the fingerprint vector containing count values</span>
518 505 <span class="c"># matches the atom triplets array.</span>
519 506 <span class="c">#</span>
520 <a name="GetAtomTripletIDs-"></a> 507 <span class="k">sub </span><span class="m">GetAtomTripletIDs</span> <span class="s">{</span>
521 508 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
522 509
523 510 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTripletsIDs</span>}}<span class="sc">;</span>
524 511 <span class="s">}</span>
525 512
526 513 <span class="c"># Cache appropriate molecule data...</span>
527 514 <span class="c">#</span>
528 <a name="_SetupMoleculeDataCache-"></a> 515 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
529 516 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
530 517
531 518 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span>
532 519 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span>
533 520 <span class="c">#</span>
534 521 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
535 522
536 523 <span class="c"># Get all atom IDs...</span>
537 524 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
538 525 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
539 526 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="sc">;</span>
540 527
541 528 <span class="c"># Set AtomIndex to AtomID hash...</span>
542 529 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
543 530 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span>
544 531
545 532 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
546 533 <span class="s">}</span>
547 534
548 535 <span class="c"># Set atomic invariants to use for atom identifiers...</span>
549 536 <span class="c">#</span>
550 <a name="SetAtomicInvariantsToUse-"></a> 537 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
551 538 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
552 539 <span class="k">my</span><span class="s">(</span><span class="i">$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>
553 540
554 541 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
555 542 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetAtomicInvariantsToUse: No values specified...&quot;</span><span class="sc">;</span>
556 543 <span class="k">return</span><span class="sc">;</span>
557 544 <span class="s">}</span>
558 545
559 546 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
560 547 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
561 548
562 549 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
563 550 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
564 551
565 552 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
566 553 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
567 554 <span class="s">}</span>
568 555 <span class="k">else</span> <span class="s">{</span>
569 556 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
570 557 <span class="s">}</span>
571 558
572 559 <span class="c"># Make sure specified AtomicInvariants are valid...</span>
573 560 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
574 561 <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>
575 562 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n &quot;</span><span class="sc">;</span>
576 563 <span class="s">}</span>
577 564 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
578 565 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
579 566 <span class="s">}</span>
580 567
581 568 <span class="c"># Set atomic invariants to use...</span>
582 569 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
583 570 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
584 571
585 572 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
586 573 <span class="s">}</span>
587 574
588 575 <span class="c"># Set functional classes to use for atom identifiers...</span>
589 576 <span class="c">#</span>
590 <a name="SetFunctionalClassesToUse-"></a> 577 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
591 578 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
592 579 <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>
593 580
594 581 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
595 582 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: No values specified...&quot;</span><span class="sc">;</span>
596 583 <span class="k">return</span><span class="sc">;</span>
597 584 <span class="s">}</span>
598 585
599 586 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
600 587 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: FunctionalClassesToUse can&#39;t be set for InitialAtomIdentifierType of $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
601 588 <span class="k">return</span><span class="sc">;</span>
602 589 <span class="s">}</span>
603 590
604 591 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
605 592 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
606 593
607 594 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
608 595 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
609 596
610 597 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
611 598 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
612 599 <span class="s">}</span>
613 600 <span class="k">else</span> <span class="s">{</span>
614 601 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
615 602 <span class="s">}</span>
616 603
617 604 <span class="c"># Make sure specified FunctionalClasses are valid...</span>
618 605 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
619 606 <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>
620 607 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n &quot;</span><span class="sc">;</span>
621 608 <span class="s">}</span>
622 609 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
623 610 <span class="s">}</span>
624 611
625 612 <span class="c"># Set functional classes to use...</span>
626 613 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
627 614 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
628 615
629 616 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
630 617 <span class="s">}</span>
631 618
632 619 <span class="c"># Initialize atom indentifier type information...</span>
633 620 <span class="c">#</span>
634 621 <span class="c"># Current supported values:</span>
635 622 <span class="c">#</span>
636 623 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span>
637 624 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
638 625 <span class="c">#</span>
639 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 626 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
640 627 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
641 628
642 629 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
643 630 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
644 631 <span class="s">}</span>
645 632 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
646 633 <span class="i">$This</span><span class="i">-&gt;_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
647 634 <span class="s">}</span>
648 635 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
649 636 <span class="c"># Nothing to do for now...</span>
650 637 <span class="s">}</span>
651 638 <span class="k">else</span> <span class="s">{</span>
652 639 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
653 640 <span class="s">}</span>
654 641
655 642 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
656 643 <span class="s">}</span>
657 644
658 645 <span class="c"># Initialize atomic invariants atom types to use for generating atom IDs in atom triplets...</span>
659 646 <span class="c">#</span>
660 647 <span class="c"># Let:</span>
661 648 <span class="c"># AS = Atom symbol corresponding to element symbol</span>
662 649 <span class="c">#</span>
663 650 <span class="c"># X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
664 651 <span class="c"># BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
665 652 <span class="c"># LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
666 653 <span class="c"># SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
667 654 <span class="c"># DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
668 655 <span class="c"># TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
669 656 <span class="c"># H&lt;n&gt; = Number of implicit and explicit hydrogens for atom</span>
670 657 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
671 658 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span>
672 659 <span class="c"># FC&lt;+n/-n&gt; = Formal charge assigned to atom</span>
673 660 <span class="c"># MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope</span>
674 661 <span class="c"># SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
675 662 <span class="c">#</span>
676 663 <span class="c"># ATx = Atomic invariants atom type for atom x</span>
677 664 <span class="c"># ATy = Atomic invariants atom type for atom y</span>
678 665 <span class="c"># ATz = Atomic invariants atom type for atom z</span>
679 666 <span class="c">#</span>
680 667 <span class="c"># Dxy = Distance between Px and Py</span>
681 668 <span class="c"># Dxz = Distance between Px and Pz</span>
682 669 <span class="c"># Dyz = Distance between Py and Pz</span>
683 670 <span class="c">#</span>
684 671 <span class="c"># Then:</span>
685 672 <span class="c">#</span>
686 673 <span class="c"># Atom triplet AtomID generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
687 674 <span class="c">#</span>
688 675 <span class="c"># AS.X&lt;n&gt;.BO&lt;n&gt;.LBO&lt;n&gt;.&lt;SB&gt;&lt;n&gt;.&lt;DB&gt;&lt;n&gt;.&lt;TB&gt;&lt;n&gt;.H&lt;n&gt;.Ar.RA.FC&lt;+n/-n&gt;.MN&lt;n&gt;.SM&lt;n&gt;</span>
689 676 <span class="c">#</span>
690 677 <span class="c"># Toplogical atom triplet ID between atom IDs ATx, ATy and ATz corresponds to:</span>
691 678 <span class="c">#</span>
692 679 <span class="c"># ATx-Dyz-ATy-Dxz-ATz-Dxy</span>
693 680 <span class="c">#</span>
694 681 <span class="c"># Except for AS which is a required atomic invariant in atom triplet AtomIDs, all other atomic invariants are</span>
695 682 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X&lt;n&gt;, BO&lt;n&gt;, H&lt;n&gt;, FC&lt;+n/-n&gt;.</span>
696 683 <span class="c"># AtomID specification doesn&#39;t include atomic invariants with zero or undefined values.</span>
697 684 <span class="c">#</span>
698 685 <span class="c"># Examples of atom triplet AtomIDs:</span>
699 686 <span class="c">#</span>
700 687 <span class="c"># O.X1.BO1.H1 - Hydroxyl oxygen in carboxylate with attached hydrogen and no explicit charge</span>
701 688 <span class="c"># O.X1.BO1.FC-1 - Hydroxyl ozygen in carboxylate with explicit negative charge</span>
702 689 <span class="c"># O.X1.BO2 - Carbonyl oxygen in carboxylate with double bond to carbon</span>
703 690 <span class="c"># O.X2.BO2 - Hydroxyl ozygen in carboxylate attached to carbonyl carbon and another heavy atom</span>
704 691 <span class="c">#</span>
705 692 <span class="c"># C.X2.BO3.H1.Ar - Aromatic carbon</span>
706 693 <span class="c">#</span>
707 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 694 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
708 695 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
709 696
710 697 <span class="c"># Default atomic invariants to use for generating atom triplet atom IDs: AS, X, BO, H, FC</span>
711 698 <span class="c">#</span>
712 699 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
713 700 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">&#39;AS&#39;</span><span class="cm">,</span> <span class="q">&#39;X&#39;</span><span class="cm">,</span> <span class="q">&#39;BO&#39;</span><span class="cm">,</span> <span class="q">&#39;H&#39;</span><span class="cm">,</span> <span class="q">&#39;FC&#39;</span><span class="s">)</span><span class="sc">;</span>
714 701
715 702 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
716 703 <span class="s">}</span>
717 704
718 705 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
719 706 <span class="c"># class, to use for generating atom identifiers...</span>
720 707 <span class="c">#</span>
721 708 <span class="c"># Let:</span>
722 709 <span class="c"># HBD: HydrogenBondDonor</span>
723 710 <span class="c"># HBA: HydrogenBondAcceptor</span>
724 711 <span class="c"># PI : PositivelyIonizable</span>
725 712 <span class="c"># NI : NegativelyIonizable</span>
726 713 <span class="c"># Ar : Aromatic</span>
727 714 <span class="c"># Hal : Halogen</span>
728 715 <span class="c"># H : Hydrophobic</span>
729 716 <span class="c"># RA : RingAtom</span>
730 717 <span class="c"># CA : ChainAtom</span>
731 718 <span class="c">#</span>
732 719 <span class="c"># Then:</span>
733 720 <span class="c">#</span>
734 721 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span>
735 722 <span class="c">#</span>
736 723 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
737 724 <span class="c">#</span>
738 725 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
739 726 <span class="c">#</span>
740 727 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
741 728 <span class="c">#</span>
742 729 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span>
743 730 <span class="c"># HydrogenBondAcceptor: N[!H], O</span>
744 731 <span class="c"># PositivelyIonizable: +, NH2</span>
745 732 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
746 733 <span class="c">#</span>
747 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 734 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
748 735 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
749 736
750 737 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span>
751 738 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span>
752 739 <span class="c">#</span>
753 740 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
754 741 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">&#39;HBD&#39;</span><span class="cm">,</span> <span class="q">&#39;HBA&#39;</span><span class="cm">,</span> <span class="q">&#39;PI&#39;</span><span class="cm">,</span> <span class="q">&#39;NI&#39;</span><span class="cm">,</span> <span class="q">&#39;Ar&#39;</span><span class="cm">,</span> <span class="q">&#39;Hal&#39;</span><span class="s">)</span><span class="sc">;</span>
755 742
756 743 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
757 744 <span class="s">}</span>
758 745
759 746 <span class="c"># Clear cached molecule data...</span>
760 747 <span class="c">#</span>
761 <a name="_ClearMoleculeDataCache-"></a> 748 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
762 749 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
763 750
764 751 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
765 752
766 753 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
767 754 <span class="s">}</span>
768 755
769 756 <span class="c"># Return a string containg data for TopologicalAtomTripletsFingerprints object...</span>
770 757 <span class="c">#</span>
771 <a name="StringifyTopologicalAtomTripletsFingerprints-"></a> 758 <span class="k">sub </span><span class="m">StringifyTopologicalAtomTripletsFingerprints</span> <span class="s">{</span>
772 759 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
773 760 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span>
774 761
775 762 <span class="c"># Type of fingerprint...</span>
776 763 <span class="i">$FingerprintsString</span> = <span class="q">&quot;Fingerprint type: $This-&gt;{Type}; AtomIdentifierType: $This-&gt;{AtomIdentifierType}&quot;</span><span class="sc">;</span>
777 764
778 765 <span class="c"># Min and max distance...</span>
779 766 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; MinDistance: $This-&gt;{MinDistance}; MaxDistance: $This-&gt;{MaxDistance}; UseTriangleInequality: &quot;</span> . <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">UseTriangleInequality</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="s">)</span><span class="sc">;</span>
780 767
781 768 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
782 769 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span>
783 770
784 771 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
785 772 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
786 773
787 774 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
788 775 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">&quot;$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}&quot;</span><span class="sc">;</span>
789 776 <span class="s">}</span>
790 777
791 778 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsToUse: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
792 779 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
793 780 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AvailableAtomicInvariants: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
794 781 <span class="s">}</span>
795 782 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
796 783 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
797 784
798 785 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
799 786 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
800 787
801 788 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
802 789 <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">&quot;$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}&quot;</span><span class="sc">;</span>
803 790 <span class="s">}</span>
804 791
805 792 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesToUse: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
806 793 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
807 794 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AvailableFunctionalClasses: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
808 795 <span class="s">}</span>
809 796
810 797 <span class="c"># Total number of atom triplets...</span>
811 798 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; NumOfAtomTriplets: &quot;</span> . <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
812 799
813 800 <span class="c"># FingerprintsVector...</span>
814 801 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FingerprintsVector: &lt; $This-&gt;{FingerprintsVector} &gt;&quot;</span><span class="sc">;</span>
815 802
816 803 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span>
817 804 <span class="s">}</span>
818 805
819 <a name="EOF-"></a></pre>
820 <p>&nbsp;</p>
821 <br />
822 <center>
823 <img src="../../../images/h2o2.png">
824 </center>
825 </body>
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