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