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14 <a name="package-Fingerprints::AtomNeighborhoodsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::AtomNeighborhoodsFingerprints</span><span class="sc">;</span>
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: AtomNeighborhoodsFingerprints.pm,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:48:53 $</span>
18 5 <span class="c"># $Revision: 1.27 $</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;StringifyAtomNeighborhoodsFingerprints&#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">$This</span><span class="i">-&gt;_InitializeAtomNeighborhoodsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
81 68
82 69 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomNeighborhoodsFingerprintsProperties</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">$This</span><span class="sc">;</span>
85 72 <span class="s">}</span>
86 73
87 74 <span class="c"># Initialize object data...</span>
88 75 <span class="c">#</span>
89 <a name="_InitializeAtomNeighborhoodsFingerprints-"></a> 76 <span class="k">sub </span><span class="m">_InitializeAtomNeighborhoodsFingerprints</span> <span class="s">{</span>
90 77 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;AtomNeighborhoods&#39;</span><span class="sc">;</span>
94 81
95 82 <span class="c"># Type of vector...</span>
96 83 <span class="i">$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">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;AlphaNumericalValues&#39;</span><span class="sc">;</span>
100 87
101 88 <span class="c"># Minimum and maximum atomic neighborhoods radii...</span>
102 89 <span class="i">$This</span>-&gt;{<span class="w">MinNeighborhoodRadius</span>} = <span class="n">0</span><span class="sc">;</span>
103 90 <span class="i">$This</span>-&gt;{<span class="w">MaxNeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span>
104 91
105 92 <span class="c"># Atom identifier type to use for atom IDs in atom neighborhood atoms...</span>
106 93 <span class="c">#</span>
107 94 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span>
108 95 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span>
109 96 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
110 97 <span class="c">#</span>
111 98 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
112 99
113 100 <span class="c"># Atom types assigned to each heavy atom...</span>
114 101 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
115 102
116 103 <span class="c"># Atom neighorhoods with in specified atom radii..</span>
117 104 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
118 105
119 106 <span class="c"># Atom neighborhoods atom types count at different neighborhoods...</span>
120 107 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
121 108
122 109 <span class="c"># Atom neighborhood identifiers using specified atom identifier types methodology...</span>
123 110 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoodsIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
124 111 <span class="s">}</span>
125 112
126 113 <span class="c"># Initialize class ...</span>
127 <a name="_InitializeClass-"></a> 114 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
128 115 <span class="c">#Class name...</span>
129 116 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
130 117 <span class="s">}</span>
131 118
132 119 <span class="c"># Initialize object properties....</span>
133 <a name="_InitializeAtomNeighborhoodsFingerprintsProperties-"></a> 120 <span class="k">sub </span><span class="m">_InitializeAtomNeighborhoodsFingerprintsProperties</span> <span class="s">{</span>
134 121 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
135 122
136 123 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
137 124 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
138 125 <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
139 126 <span class="i">$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>
140 127 <span class="s">}</span>
141 128
142 129 <span class="c"># Make sure molecule object was specified...</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">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
144 131 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying molecule...&quot;</span><span class="sc">;</span>
145 132 <span class="s">}</span>
146 133 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span>
147 134 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated with a user specified size: It&#39;s an arbitrary length vector...&quot;</span><span class="sc">;</span>
148 135 <span class="s">}</span>
149 136 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
150 137 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying AtomIdentifierType...&quot;</span><span class="sc">;</span>
151 138 <span class="s">}</span>
152 139
153 140 <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
154 141
155 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
156 143 <span class="s">}</span>
157 144
158 145 <span class="c"># Set atom identifier type..</span>
159 146 <span class="c">#</span>
160 <a name="SetAtomIdentifierType-"></a> 147 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
161 148 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
162 149
163 150 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
164 151 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes.&quot;</span><span class="sc">;</span>
165 152 <span class="s">}</span>
166 153
167 154 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
168 155 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomIdentifierType: Can&#39;t change intial atom identifier type: It&#39;s already set...&quot;</span><span class="sc">;</span>
169 156 <span class="s">}</span>
170 157
171 158 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
172 159
173 160 <span class="c"># Initialize atom identifier type information...</span>
174 161 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
175 162
176 163 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
177 164 <span class="s">}</span>
178 165
179 166 <span class="c"># Set minimum atom neighborhood radius...</span>
180 167 <span class="c">#</span>
181 <a name="SetMinNeighborhoodRadius-"></a> 168 <span class="k">sub </span><span class="m">SetMinNeighborhoodRadius</span> <span class="s">{</span>
182 169 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
183 170
184 171 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
185 172 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMinNeighborhoodRadius: MinNeighborhoodRadius value, $Value, is not valid: It must be an integer...&quot;</span><span class="sc">;</span>
186 173 <span class="s">}</span>
187 174
188 175 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> &lt; <span class="n">0</span> <span class="s">)</span> <span class="s">{</span>
189 176 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMinNeighborhoodRadius: MinNeighborhoodRadius value, $Value, is not valid: It must be &gt;= 0...&quot;</span><span class="sc">;</span>
190 177 <span class="s">}</span>
191 178 <span class="i">$This</span>-&gt;{<span class="w">MinNeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span>
192 179
193 180 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
194 181 <span class="s">}</span>
195 182
196 183 <span class="c"># Set maximum atom neighborhood radius...</span>
197 184 <span class="c">#</span>
198 <a name="SetMaxNeighborhoodRadius-"></a> 185 <span class="k">sub </span><span class="m">SetMaxNeighborhoodRadius</span> <span class="s">{</span>
199 186 <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>
200 187
201 188 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
202 189 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMaxNeighborhoodRadius: MaxNeighborhoodRadius value, $Value, is not valid: It must be an integer...&quot;</span><span class="sc">;</span>
203 190 <span class="s">}</span>
204 191
205 192 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> &lt; <span class="n">0</span> <span class="s">)</span> <span class="s">{</span>
206 193 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMaxNeighborhoodRadius: MaxNeighborhoodRadius value, $Value, is not valid: It must be &gt;= 0...&quot;</span><span class="sc">;</span>
207 194 <span class="s">}</span>
208 195 <span class="i">$This</span>-&gt;{<span class="w">MaxNeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span>
209 196
210 197 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
211 198 <span class="s">}</span>
212 199
213 200 <span class="c"># Generate fingerprints description...</span>
214 201 <span class="c">#</span>
215 <a name="GetDescription-"></a> 202 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
216 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
217 204
218 205 <span class="c"># Is description explicity set?</span>
219 206 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
220 207 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="sc">;</span>
221 208 <span class="s">}</span>
222 209
223 210 <span class="c"># Generate fingerprints description...</span>
224 211
225 212 <span class="k">return</span> <span class="q">&quot;$This-&gt;{Type}:$This-&gt;{AtomIdentifierType}:MinRadius$This-&gt;{MinNeighborhoodRadius}:MaxRadius$This-&gt;{MaxNeighborhoodRadius}&quot;</span><span class="sc">;</span>
226 213 <span class="s">}</span>
227 214
228 215 <span class="c"># Generate atom neighborhood [ Ref 53-56, Ref 73 ] fingerprints...</span>
229 216 <span class="c">#</span>
230 217 <span class="c"># Methodology:</span>
231 218 <span class="c"># . Assign atom types to all non-hydrogen atoms in the molecule</span>
232 219 <span class="c"># . Get atom neighborhoods up to MaxNeighborhoodRadis</span>
233 220 <span class="c"># . Count unqiue atom types at each neighborhood radii for all heavy atoms</span>
234 221 <span class="c"># . Generate neighborhood identifiers for all neighborhoods around central</span>
235 222 <span class="c"># heavy atom</span>
236 223 <span class="c"># . Atom neighborhood identifier for a specific radii is generated using neighborhood</span>
237 224 <span class="c"># radius, assigned atom type and its count as follows:</span>
238 225 <span class="c">#</span>
239 226 <span class="c"># NR&lt;n&gt;-&lt;AtomType&gt;-ATC&lt;n&gt;</span>
240 227 <span class="c">#</span>
241 228 <span class="c"># . Atom neighborhood identifier for a central atom at all specified radii is generated</span>
242 229 <span class="c"># by concatenating neighborhood identifiers at each radii by colon:</span>
243 230 <span class="c">#</span>
244 231 <span class="c"># NR&lt;n&gt;-&lt;AtomType&gt;-ATC&lt;n&gt;:NR&lt;n&gt;-&lt;AtomType&gt;-ATC&lt;n&gt;:</span>
245 232 <span class="c">#</span>
246 233 <span class="c"># . Set final fingerprints as list of neighborhood atom indentifiers</span>
247 234 <span class="c">#</span>
248 <a name="GenerateFingerprints-"></a> 235 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
249 236 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
250 237
251 238 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinNeighborhoodRadius</span>} &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
252 239 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;GenerateFingerprints: No fingerpritns generated: MinLength, $This-&gt;{MinNeighborhoodRadius}, must be less than MaxLength, $This-&gt;{MaxNeighborhoodRadius}...&quot;</span><span class="sc">;</span>
253 240 <span class="s">}</span>
254 241
255 242 <span class="c"># Cache appropriate molecule data...</span>
256 243 <span class="i">$This</span><span class="i">-&gt;_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
257 244
258 245 <span class="c"># Assign atom types to all heavy atoms...</span>
259 246 <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>
260 247 <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 $This-&gt;{AtomIdentifierType} to all atoms...&quot;</span><span class="sc">;</span>
261 248 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
262 249 <span class="s">}</span>
263 250
264 251 <span class="c"># Intialize atom neighborhoods information...</span>
265 252 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
266 253
267 254 <span class="c"># Identify atom neighborhoods with in specified radii...</span>
268 255 <span class="i">$This</span><span class="i">-&gt;_GetAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
269 256
270 257 <span class="c"># Count atom neighborhoods atom types...</span>
271 258 <span class="i">$This</span><span class="i">-&gt;_CountAtomNeighborhoodsAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
272 259
273 260 <span class="c"># Genenerate atom neighborhood identifiers...</span>
274 261 <span class="i">$This</span><span class="i">-&gt;_GenerateAtomNeighborhoodIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
275 262
276 263 <span class="c"># Set final fingerprints...</span>
277 264 <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
278 265
279 266 <span class="c"># Clear cached molecule data...</span>
280 267 <span class="i">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
281 268
282 269 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
283 270 <span class="s">}</span>
284 271
285 272 <span class="c"># Assign appropriate atom types to all heavy atoms...</span>
286 273 <span class="c">#</span>
287 <a name="_AssignAtomTypes-"></a> 274 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span>
288 275 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
289 276 <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>
290 277
291 278 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
292 279 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span>
293 280
294 281 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span>
295 282
296 283 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
297 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
298 285 <span class="i">$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">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="sc">;</span>
299 286 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
300 287 <span class="s">}</span>
301 288
302 289 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^DREIDINGAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
303 290 <span class="i">$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>
304 291 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
305 292 <span class="s">}</span>
306 293
307 294 <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>
308 295 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
309 296 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
310 297 <span class="s">}</span>
311 298
312 299 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
313 300 <span class="i">$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">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="sc">;</span>
314 301 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
315 302 <span class="s">}</span>
316 303
317 304 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^MMFF94AtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
318 305 <span class="i">$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>
319 306 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
320 307 <span class="s">}</span>
321 308
322 309 <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>
323 310 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
324 311 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
325 312 <span class="s">}</span>
326 313 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SYBYLAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
327 314 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::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>
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">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
332 319 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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>
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">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
337 324 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::UFFAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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>
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="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_AssignAtomTypes: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
342 329 <span class="s">}</span>
343 330
344 331 <span class="c"># Assign atom types...</span>
345 332 <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
346 333
347 334 <span class="c"># Make sure atom types assignment is successful...</span>
348 335 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
349 336 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
350 337 <span class="s">}</span>
351 338
352 339 <span class="c"># Collect assigned atom types...</span>
353 340 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
354 341 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
355 342 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
356 343 <span class="s">}</span>
357 344 <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>
358 345 <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>
359 346 <span class="s">}</span>
360 347
361 348 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
362 349 <span class="s">}</span>
363 350
364 351 <span class="c"># Initialize topological atom pairs between specified distance range...</span>
365 352 <span class="c">#</span>
366 <a name="_InitializeAtomNeighborhoods-"></a> 353 <span class="k">sub </span><span class="m">_InitializeAtomNeighborhoods</span> <span class="s">{</span>
367 354 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
368 355 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span>
369 356
370 357 <span class="c"># Initialize atom neighborhood count information between specified radii...</span>
371 358 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
372 359
373 360 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinNeighborhoodRadius</span>} .. <span class="i">$This</span>-&gt;{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
374 361 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
375 362 <span class="s">}</span>
376 363
377 364 <span class="c"># Initialize atom neighborhoods atoms information at all specified radii...</span>
378 365 <span class="c">#</span>
379 366 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
380 367
381 368 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>-&gt;{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
382 369 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
383 370 <span class="s">}</span>
384 371
385 372 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
386 373 <span class="s">}</span>
387 374
388 375 <span class="c"># Collect atom neighborhoods upto maximum neighborhood radius...</span>
389 376 <span class="c">#</span>
390 377 <span class="c"># Notes:</span>
391 378 <span class="c"># . Fingerprints are only generated for neighborhoods between specified minimum</span>
392 379 <span class="c"># and maximum neighborhood radii.</span>
393 380 <span class="c">#</span>
394 <a name="_GetAtomNeighborhoods-"></a> 381 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span>
395 382 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
396 383 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$MaxRadius</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
397 384
398 385 <span class="i">$MaxRadius</span> = <span class="i">$This</span>-&gt;{<span class="w">MaxNeighborhoodRadius</span>}<span class="sc">;</span>
399 386 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
400 387
401 388 <span class="c"># Collect atom neighborhoods...</span>
402 389
403 390 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
404 391 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
405 392 <span class="i">$Radius</span> = <span class="n">0</span><span class="sc">;</span>
406 393
407 394 <span class="k">if</span> <span class="s">(</span><span class="i">$MaxRadius</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
408 395 <span class="c"># Atom is its own neighborhood at 0 radius...</span>
409 396 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighborhoodsAtoms</span><span class="s">)</span><span class="sc">;</span>
410 397
411 398 <span class="i">@AtomNeighborhoodsAtoms</span> = <span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
412 399 <span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = \<span class="i">@AtomNeighborhoodsAtoms</span><span class="sc">;</span>
413 400
414 401 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
415 402 <span class="s">}</span>
416 403
417 404 <span class="c"># Collect available atom neighborhoods at different neighborhood radii levels...</span>
418 405 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighborhoodAtomsRef</span><span class="s">)</span><span class="sc">;</span>
419 406
420 407 <span class="k">for</span> <span class="i">$AtomNeighborhoodAtomsRef</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">-&gt;GetAtomNeighborhoodsWithRadiusUpto</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$MaxRadius</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
421 408 <span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomNeighborhoodAtomsRef</span><span class="sc">;</span>
422 409 <span class="i">$Radius</span>++<span class="sc">;</span>
423 410 <span class="s">}</span>
424 411 <span class="s">}</span>
425 412 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
426 413 <span class="s">}</span>
427 414
428 415 <span class="c"># Count atom neighborhoods atom types for each non-hydrogen central atoms with</span>
429 416 <span class="c"># neighborhoods in specified radii range...</span>
430 417 <span class="c">#</span>
431 <a name="_CountAtomNeighborhoodsAtomTypes-"></a> 418 <span class="k">sub </span><span class="m">_CountAtomNeighborhoodsAtomTypes</span> <span class="s">{</span>
432 419 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
433 420 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomType</span><span class="cm">,</span> <span class="i">$AtomNeighborhoodAtomsRef</span><span class="s">)</span><span class="sc">;</span>
434 421
435 422 <span class="j">RADIUS:</span> <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}} <span class="s">)</span> <span class="s">{</span>
436 423 <span class="k">if</span> <span class="s">(</span><span class="i">$Radius</span> &lt; <span class="i">$This</span>-&gt;{<span class="w">MinNeighborhoodRadius</span>} || <span class="i">$Radius</span> &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
437 424 <span class="k">next</span> <span class="j">RADIUS</span><span class="sc">;</span>
438 425 <span class="s">}</span>
439 426 <span class="c"># Go over the neighborhoods of each atom at the current radius...</span>
440 427 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
441 428 <span class="i">$AtomNeighborhoodAtomsRef</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
442 429 <span class="j">NEIGHBORHOODATOM:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$AtomNeighborhoodAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
443 430 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
444 431 <span class="k">next</span> <span class="j">NEIGHBORHOODATOM</span><span class="sc">;</span>
445 432 <span class="s">}</span>
446 433 <span class="i">$NeighborhoodAtomID</span> = <span class="i">$NeighborhoodAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
447 434 <span class="i">$NeighborhoodAtomType</span> = <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$NeighborhoodAtomID</span>}<span class="sc">;</span>
448 435
449 436 <span class="c"># Count neighbothood atom types for each atom at different radii...</span>
450 437 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span>
451 438 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
452 439 <span class="s">}</span>
453 440 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}{<span class="i">$NeighborhoodAtomType</span>}<span class="s">)</span> <span class="s">{</span>
454 441 <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}{<span class="i">$NeighborhoodAtomType</span>} += <span class="n">1</span><span class="sc">;</span>
455 442 <span class="s">}</span>
456 443 <span class="k">else</span> <span class="s">{</span>
457 444 <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}{<span class="i">$NeighborhoodAtomType</span>} = <span class="n">1</span><span class="sc">;</span>
458 445 <span class="s">}</span>
459 446 <span class="s">}</span>
460 447 <span class="s">}</span>
461 448 <span class="s">}</span>
462 449 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
463 450 <span class="s">}</span>
464 451
465 452 <span class="c"># Generate atom neighborhood identifiers for each non-hydrogen atom using atom</span>
466 453 <span class="c"># neighborhood atom types and their count information...</span>
467 454 <span class="c">#</span>
468 455 <span class="c"># Let:</span>
469 456 <span class="c"># NR&lt;n&gt; = Neighborhood radius</span>
470 457 <span class="c"># AtomType = Assigned atom type</span>
471 458 <span class="c"># ATC&lt;n&gt; = AtomType count</span>
472 459 <span class="c">#</span>
473 460 <span class="c"># Then:</span>
474 461 <span class="c">#</span>
475 462 <span class="c"># AtomNeighborhoodAtomIdentifier for a neighborhood atom generated for</span>
476 463 <span class="c"># AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
477 464 <span class="c">#</span>
478 465 <span class="c"># NR&lt;n&gt;-&lt;AtomType&gt;-ATC&lt;n&gt;</span>
479 466 <span class="c">#</span>
480 467 <span class="c"># AtomNeighborhoodsIdentifier for all specified atom neighbothoods of an atom generated for</span>
481 468 <span class="c"># AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
482 469 <span class="c">#</span>
483 470 <span class="c"># NR&lt;n&gt;-&lt;AtomType&gt;-ATC&lt;n&gt;;NR&lt;n&gt;-&lt;AtomType&gt;-ATC&lt;n&gt;;...</span>
484 471 <span class="c">#</span>
485 <a name="_GenerateAtomNeighborhoodIdentifiers-"></a> 472 <span class="k">sub </span><span class="m">_GenerateAtomNeighborhoodIdentifiers</span> <span class="s">{</span>
486 473 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
487 474 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$AtomTypeCount</span><span class="cm">,</span> <span class="i">$AtomNeighborhoodIdentifier</span><span class="cm">,</span> <span class="i">@AtomNeighborhoodIdentifiers</span><span class="s">)</span><span class="sc">;</span>
488 475
489 476 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoodsIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
490 477
491 478 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
492 479 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
493 480 <span class="i">@AtomNeighborhoodIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
494 481 <span class="j">RADIUS:</span> <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinNeighborhoodRadius</span>} .. <span class="i">$This</span>-&gt;{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
495 482 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span>
496 483 <span class="k">next</span> <span class="j">RADIUS</span><span class="sc">;</span>
497 484 <span class="s">}</span>
498 485 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span>
499 486 <span class="i">$AtomTypeCount</span> = <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}{<span class="i">$AtomType</span>}<span class="sc">;</span>
500 487 <span class="k">push</span> <span class="i">@AtomNeighborhoodIdentifiers</span><span class="cm">,</span> <span class="q">&quot;NR${Radius}-${AtomType}-ATC${AtomTypeCount}&quot;</span><span class="sc">;</span>
501 488 <span class="s">}</span>
502 489 <span class="s">}</span>
503 490 <span class="i">$AtomNeighborhoodIdentifier</span> = <span class="k">join</span><span class="s">(</span><span class="q">&quot;:&quot;</span><span class="cm">,</span> <span class="i">@AtomNeighborhoodIdentifiers</span><span class="s">)</span><span class="sc">;</span>
504 491 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoodsIdentifiers</span>}}<span class="cm">,</span> <span class="i">$AtomNeighborhoodIdentifier</span><span class="sc">;</span>
505 492 <span class="s">}</span>
506 493
507 494 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
508 495 <span class="s">}</span>
509 496
510 497 <span class="c"># Set final fingerprits vector...</span>
511 498 <span class="c">#</span>
512 <a name="_SetFinalFingerprints-"></a> 499 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
513 500 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
514 501
515 502 <span class="c"># Mark successful generation of fingerprints...</span>
516 503 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
517 504
518 505 <span class="c"># Sort AtomNeighborhoodsIdentifiers..</span>
519 506 <span class="c">#</span>
520 507 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoodsIdentifiers</span>}} = <span class="k">sort</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoodsIdentifiers</span>}}<span class="sc">;</span>
521 508
522 509 <span class="c"># Add sorted atom neighborhood identifiers to FingerprintsVector which is already defined</span>
523 510 <span class="c"># during initialization containing AlphaNumericalValues...</span>
524 511 <span class="c">#</span>
525 512 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValues</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoodsIdentifiers</span>}}<span class="s">)</span><span class="sc">;</span>
526 513
527 514 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
528 515 <span class="s">}</span>
529 516
530 517 <span class="c"># Cache appropriate molecule data...</span>
531 518 <span class="c">#</span>
532 <a name="_SetupMoleculeDataCache-"></a> 519 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
533 520 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
534 521
535 522 <span class="c"># Get all non-hydrogen atoms...</span>
536 523 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
537 524 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span>
538 525 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="q">&quot;IsHydrogen&quot;</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
539 526
540 527 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
541 528 <span class="s">}</span>
542 529
543 530 <span class="c"># Clear cached molecule data...</span>
544 531 <span class="c">#</span>
545 <a name="_ClearMoleculeDataCache-"></a> 532 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
546 533 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
547 534
548 535 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
549 536
550 537 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
551 538 <span class="s">}</span>
552 539
553 540 <span class="c"># Set atomic invariants to use for atom identifiers...</span>
554 541 <span class="c">#</span>
555 <a name="SetAtomicInvariantsToUse-"></a> 542 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
556 543 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
557 544 <span class="k">my</span><span class="s">(</span><span class="i">$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>
558 545
559 546 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
560 547 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetAtomicInvariantsToUse: No values specified...&quot;</span><span class="sc">;</span>
561 548 <span class="k">return</span><span class="sc">;</span>
562 549 <span class="s">}</span>
563 550
564 551 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
565 552 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
566 553
567 554 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
568 555 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
569 556
570 557 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
571 558 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
572 559 <span class="s">}</span>
573 560 <span class="k">else</span> <span class="s">{</span>
574 561 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
575 562 <span class="s">}</span>
576 563
577 564 <span class="c"># Make sure specified AtomicInvariants are valid...</span>
578 565 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
579 566 <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>
580 567 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n &quot;</span><span class="sc">;</span>
581 568 <span class="s">}</span>
582 569 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
583 570 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
584 571 <span class="s">}</span>
585 572
586 573 <span class="c"># Set atomic invariants to use...</span>
587 574 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
588 575 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
589 576
590 577 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
591 578 <span class="s">}</span>
592 579
593 580 <span class="c"># Set functional classes to use for atom identifiers...</span>
594 581 <span class="c">#</span>
595 <a name="SetFunctionalClassesToUse-"></a> 582 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
596 583 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
597 584 <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>
598 585
599 586 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
600 587 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: No values specified...&quot;</span><span class="sc">;</span>
601 588 <span class="k">return</span><span class="sc">;</span>
602 589 <span class="s">}</span>
603 590
604 591 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
605 592 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: FunctionalClassesToUse can&#39;t be set for InitialAtomIdentifierType of $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
606 593 <span class="k">return</span><span class="sc">;</span>
607 594 <span class="s">}</span>
608 595
609 596 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
610 597 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
611 598
612 599 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
613 600 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
614 601
615 602 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
616 603 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
617 604 <span class="s">}</span>
618 605 <span class="k">else</span> <span class="s">{</span>
619 606 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
620 607 <span class="s">}</span>
621 608
622 609 <span class="c"># Make sure specified FunctionalClasses are valid...</span>
623 610 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
624 611 <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>
625 612 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n &quot;</span><span class="sc">;</span>
626 613 <span class="s">}</span>
627 614 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
628 615 <span class="s">}</span>
629 616
630 617 <span class="c"># Set functional classes to use...</span>
631 618 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
632 619 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
633 620
634 621 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
635 622 <span class="s">}</span>
636 623
637 624 <span class="c"># Initialize atom indentifier type information...</span>
638 625 <span class="c">#</span>
639 626 <span class="c"># Current supported values:</span>
640 627 <span class="c">#</span>
641 628 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span>
642 629 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
643 630 <span class="c">#</span>
644 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 631 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
645 632 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
646 633
647 634 <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>
648 635 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
649 636 <span class="s">}</span>
650 637 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
651 638 <span class="i">$This</span><span class="i">-&gt;_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
652 639 <span class="s">}</span>
653 640 <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>
654 641 <span class="c"># Nothing to do for now...</span>
655 642 <span class="s">}</span>
656 643 <span class="k">else</span> <span class="s">{</span>
657 644 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
658 645 <span class="s">}</span>
659 646
660 647 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
661 648 <span class="s">}</span>
662 649
663 650 <span class="c"># Initialize atomic invariants atom types to use for generating atom identifiers...</span>
664 651 <span class="c">#</span>
665 652 <span class="c"># Let:</span>
666 653 <span class="c"># AS = Atom symbol corresponding to element symbol</span>
667 654 <span class="c">#</span>
668 655 <span class="c"># X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
669 656 <span class="c"># BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
670 657 <span class="c"># LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
671 658 <span class="c"># SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
672 659 <span class="c"># DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
673 660 <span class="c"># TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
674 661 <span class="c"># H&lt;n&gt; = Number of implicit and explicit hydrogens for atom</span>
675 662 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
676 663 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span>
677 664 <span class="c"># FC&lt;+n/-n&gt; = Formal charge assigned to atom</span>
678 665 <span class="c"># MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope</span>
679 666 <span class="c"># SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
680 667 <span class="c">#</span>
681 668 <span class="c"># Then:</span>
682 669 <span class="c">#</span>
683 670 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
684 671 <span class="c">#</span>
685 672 <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>
686 673 <span class="c">#</span>
687 674 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span>
688 675 <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>
689 676 <span class="c"># AtomID specification doesn&#39;t include atomic invariants with zero or undefined values.</span>
690 677 <span class="c">#</span>
691 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 678 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
692 679 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
693 680
694 681 <span class="c"># Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC</span>
695 682 <span class="c">#</span>
696 683 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
697 684 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">&#39;AS&#39;</span><span class="cm">,</span> <span class="q">&#39;X&#39;</span><span class="cm">,</span> <span class="q">&#39;BO&#39;</span><span class="cm">,</span> <span class="q">&#39;H&#39;</span><span class="cm">,</span> <span class="q">&#39;FC&#39;</span><span class="s">)</span><span class="sc">;</span>
698 685
699 686 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
700 687 <span class="s">}</span>
701 688
702 689 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
703 690 <span class="c"># class, to use for generating atom identifiers...</span>
704 691 <span class="c">#</span>
705 692 <span class="c"># Let:</span>
706 693 <span class="c"># HBD: HydrogenBondDonor</span>
707 694 <span class="c"># HBA: HydrogenBondAcceptor</span>
708 695 <span class="c"># PI : PositivelyIonizable</span>
709 696 <span class="c"># NI : NegativelyIonizable</span>
710 697 <span class="c"># Ar : Aromatic</span>
711 698 <span class="c"># Hal : Halogen</span>
712 699 <span class="c"># H : Hydrophobic</span>
713 700 <span class="c"># RA : RingAtom</span>
714 701 <span class="c"># CA : ChainAtom</span>
715 702 <span class="c">#</span>
716 703 <span class="c"># Then:</span>
717 704 <span class="c">#</span>
718 705 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span>
719 706 <span class="c">#</span>
720 707 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
721 708 <span class="c">#</span>
722 709 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
723 710 <span class="c">#</span>
724 711 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
725 712 <span class="c">#</span>
726 713 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span>
727 714 <span class="c"># HydrogenBondAcceptor: N[!H], O</span>
728 715 <span class="c"># PositivelyIonizable: +, NH2</span>
729 716 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
730 717 <span class="c">#</span>
731 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 718 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
732 719 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
733 720
734 721 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span>
735 722 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span>
736 723 <span class="c">#</span>
737 724 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
738 725 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">&#39;HBD&#39;</span><span class="cm">,</span> <span class="q">&#39;HBA&#39;</span><span class="cm">,</span> <span class="q">&#39;PI&#39;</span><span class="cm">,</span> <span class="q">&#39;NI&#39;</span><span class="cm">,</span> <span class="q">&#39;Ar&#39;</span><span class="cm">,</span> <span class="q">&#39;Hal&#39;</span><span class="s">)</span><span class="sc">;</span>
739 726
740 727 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
741 728 <span class="s">}</span>
742 729
743 730 <span class="c"># Return a string containg data for AtomNeighborhoodsFingerprints object...</span>
744 731 <span class="c">#</span>
745 <a name="StringifyAtomNeighborhoodsFingerprints-"></a> 732 <span class="k">sub </span><span class="m">StringifyAtomNeighborhoodsFingerprints</span> <span class="s">{</span>
746 733 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
747 734 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span>
748 735
749 736 <span class="c"># Type of fingerprint...</span>
750 737 <span class="i">$FingerprintsString</span> = <span class="q">&quot;Fingerprint type: $This-&gt;{Type}; AtomIdentifierType: $This-&gt;{AtomIdentifierType}; MinNeighborhoodRadius: $This-&gt;{MinNeighborhoodRadius}; MaxNeighborhoodRadius: $This-&gt;{MaxNeighborhoodRadius}&quot;</span><span class="sc">;</span>
751 738
752 739 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
753 740 <span class="k">my</span><span class="s">(</span><span class="i">$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>
754 741
755 742 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
756 743 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
757 744
758 745 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
759 746 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">&quot;$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}&quot;</span><span class="sc">;</span>
760 747 <span class="s">}</span>
761 748
762 749 <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>
763 750 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
764 751 <span class="i">$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>
765 752 <span class="s">}</span>
766 753 <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>
767 754 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
768 755
769 756 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
770 757 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
771 758
772 759 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
773 760 <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>
774 761 <span class="s">}</span>
775 762
776 763 <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>
777 764 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
778 765 <span class="i">$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>
779 766 <span class="s">}</span>
780 767
781 768 <span class="c"># Total number of atom neighborhood atom IDs...</span>
782 769 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; NumOfAtomNeighborhoodAtomIdentifiers: &quot;</span> . <span class="i">$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>
783 770
784 771 <span class="c"># FingerprintsVector...</span>
785 772 <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FingerprintsVector: &lt; $This-&gt;{FingerprintsVector} &gt;&quot;</span><span class="sc">;</span>
786 773
787 774 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span>
788 775 <span class="s">}</span>
789 776
790 <a name="EOF-"></a></pre>
791 <p>&nbsp;</p>
792 <br />
793 <center>
794 <img src="../../../images/h2o2.png">
795 </center>
796 </body>
797 </html>