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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/MolecularComplexityDescriptors.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,1108 @@ +<html> +<head> +<title>MayaChemTools:Code:MolecularDescriptors::MolecularComplexityDescriptors.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> +<a name="package-MolecularDescriptors::MolecularComplexityDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularComplexityDescriptors</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: MolecularComplexityDescriptors.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> + 5 <span class="c"># $Revision: 1.15 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> + 38 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> + 39 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> + 40 <span class="k">use</span> <span class="w">Fingerprints::AtomTypesFingerprints</span><span class="sc">;</span> + 41 <span class="k">use</span> <span class="w">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span> + 42 <span class="k">use</span> <span class="w">Fingerprints::MACCSKeys</span><span class="sc">;</span> + 43 <span class="k">use</span> <span class="w">Fingerprints::PathLengthFingerprints</span><span class="sc">;</span> + 44 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="sc">;</span> + 45 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="sc">;</span> + 46 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="sc">;</span> + 47 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span> + 48 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span> + 49 + 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> + 51 + 52 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> + 53 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> + 54 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames GetMolecularComplexityTypeAbbreviation)</span><span class="sc">;</span> + 55 + 56 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> + 57 + 58 <span class="c"># Setup class variables...</span> + 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> + 60 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 61 + 62 <span class="c"># Overload Perl functions...</span> + 63 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecularComplexityDescriptors'</span><span class="sc">;</span> + 64 + 65 <span class="c"># Class constructor...</span> +<a name="new-"></a> 66 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> + 67 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 68 + 69 <span class="c"># Initialize object...</span> + 70 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 71 <span class="k">bless</span> <span class="i">$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> + 72 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 73 + 74 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 75 + 76 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 77 <span class="s">}</span> + 78 + 79 <span class="c"># Initialize class ...</span> +<a name="_InitializeClass-"></a> 80 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> + 81 <span class="c">#Class name...</span> + 82 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> + 83 + 84 <span class="c"># Descriptor names...</span> + 85 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'MolecularComplexity'</span><span class="s">)</span><span class="sc">;</span> + 86 + 87 <span class="s">}</span> + 88 + 89 <span class="c"># Get descriptor names as an array.</span> + 90 <span class="c">#</span> + 91 <span class="c"># This functionality can be either invoked as a class function or an</span> + 92 <span class="c"># object method.</span> + 93 <span class="c">#</span> +<a name="GetDescriptorNames-"></a> 94 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> + 95 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> + 96 <span class="s">}</span> + 97 + 98 <span class="c"># Initialize object data...</span> + 99 <span class="c">#</span> +<a name="_InitializeMolecularComplexityDescriptors-"></a> 100 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptors</span> <span class="s">{</span> + 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 102 + 103 <span class="c"># Type of MolecularDescriptor...</span> + 104 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'MolecularComplexity'</span><span class="sc">;</span> + 105 + 106 <span class="c">#</span> + 107 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span> + 108 <span class="c"># corresponding to number of bits-set or unique keys [ Ref 117-119 ] in molecular</span> + 109 <span class="c"># fingerprints. The following types of fingerprints based molecular complexity measures</span> + 110 <span class="c"># are supported:</span> + 111 <span class="c">#</span> + 112 <span class="c"># AtomTypesFingerprints</span> + 113 <span class="c"># ExtendedConnectivityFingerprints</span> + 114 <span class="c"># MACCSKeys</span> + 115 <span class="c"># PathLengthFingerprints</span> + 116 <span class="c"># TopologicalAtomPairsFingerprints</span> + 117 <span class="c"># TopologicalAtomTripletsFingerprints</span> + 118 <span class="c"># TopologicalAtomTorsionsFingerprints</span> + 119 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> + 120 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> + 121 <span class="c">#</span> + 122 <span class="c"># Default: MACCSKeys</span> + 123 <span class="c">#</span> + 124 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">''</span><span class="sc">;</span> + 125 + 126 <span class="c"># Atom types to use for generating fingerprints...</span> + 127 <span class="c">#</span> + 128 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> + 129 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> + 130 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> + 131 <span class="c">#</span> + 132 <span class="c"># Notes:</span> + 133 <span class="c"># . AtomicInvariantsAtomTypes for all supported MolecularComplexityType except for</span> + 134 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints and TopologicalPharmacophoreAtomTripletsFingerprints</span> + 135 <span class="c"># . This value is not used for MACCSKeys</span> + 136 <span class="c"># . FunctionalClassAtomTypes is the only valid value during topological pharmacophore fingerprints.</span> + 137 <span class="c">#</span> + 138 <span class="c"># . Default values for AtomicInvariantsToUse and FunctionalClassesToUse are set appropriately</span> + 139 <span class="c"># for different types of fingerprints as shown below.</span> + 140 <span class="c">#</span> + 141 <span class="c"># MolecularComplexityType AtomicInvariantsToUse</span> + 142 <span class="c">#</span> + 143 <span class="c"># AtomTypesFingerprints AS, X, BO, H, FC</span> + 144 <span class="c"># TopologicalAtomPairsFingerprints AS, X, BO, H, FC</span> + 145 <span class="c"># TopologicalAtomTripletsFingerprints AS, X, BO, H, FC</span> + 146 <span class="c"># TopologicalAtomTorsionsFingerprints AS, X, BO, H, FC</span> + 147 <span class="c">#</span> + 148 <span class="c"># ExtendedConnectivityFingerprints AS, X, BO, H, FC, MN</span> + 149 <span class="c"># PathLengthFingerprints AS</span> + 150 <span class="c">#</span> + 151 <span class="c"># Default for FunctionalClassesToUse for all fingerprints is set to:</span> + 152 <span class="c">#</span> + 153 <span class="c"># HBD, HBA, PI, NI, Ar, Hal</span> + 154 <span class="c">#</span> + 155 <span class="c"># except for the following two MolecularComplexityType fingerprints:</span> + 156 <span class="c">#</span> + 157 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints HBD, HBA, PI, NI, H</span> + 158 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints HBD, HBA, PI, NI, H, Ar</span> + 159 <span class="c">#</span> + 160 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> + 161 + 162 <span class="c"># Size of MACCS key set: 166 or 322...</span> + 163 <span class="c">#</span> + 164 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="n">166</span><span class="sc">;</span> + 165 + 166 <span class="c"># Atomic neighborhoods radius for extended connectivity fingerprints...</span> + 167 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span> + 168 + 169 <span class="c"># Minimum and maximum path lengths to use for path length fingerprints...</span> + 170 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="n">1</span><span class="sc">;</span> + 171 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="n">8</span><span class="sc">;</span> + 172 + 173 <span class="c"># By default bond symbols are included in atom path strings used to generate path length</span> + 174 <span class="c"># fingerprints... ...</span> + 175 <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} = <span class="n">1</span><span class="sc">;</span> + 176 + 177 <span class="c"># Minimum and maximum bond distance between atom pairs during topological</span> + 178 <span class="c"># atom pairs/triplets fingerprints...</span> + 179 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> + 180 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> + 181 + 182 <span class="c"># Determines whether to apply triangle inequality to distance triplets...</span> + 183 <span class="c">#</span> + 184 <span class="c"># Default for TopologicalAtomTripletsFingerprints: 0</span> + 185 <span class="c"># Default for TopologicalPharmacophoreAtomTripletsFingerprints: 1</span> + 186 <span class="c">#</span> + 187 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="q">''</span><span class="sc">;</span> + 188 + 189 <span class="c"># Distance bin size used for binning distances during generation of</span> + 190 <span class="c"># topological pharmacophore atom triplets fingerprints...</span> + 191 <span class="c">#</span> + 192 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="n">2</span><span class="sc">;</span> + 193 + 194 <span class="c"># Normalization methodology to use for scaling the number of bits-set or unique keys</span> + 195 <span class="c"># for:</span> + 196 <span class="c">#</span> + 197 <span class="c"># ExtendedConnectivityFingerprints</span> + 198 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> + 199 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> + 200 <span class="c">#</span> + 201 <span class="c"># This option is gnored for all other types of fingerprints.</span> + 202 <span class="c">#</span> + 203 <span class="c"># Possible values during extended connectivity fingerprints: None or ByHeavyAtomsCount. Default:</span> + 204 <span class="c"># None.</span> + 205 <span class="c">#</span> + 206 <span class="c"># Possible values during topological pharmacophore atom pairs and tripletes fingerprints: None,</span> + 207 <span class="c"># or ByPossibleKeysCount. Default: None. ByPossibleKeysCount corresponds to total number of</span> + 208 <span class="c"># possible topological pharmacophore atom pairs or triplets in a molecule.</span> + 209 <span class="c">#</span> + 210 <span class="c">#</span> + 211 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span> + 212 + 213 <span class="c"># Intialize descriptor names and values...</span> + 214 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> + 215 + 216 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 217 <span class="s">}</span> + 218 + 219 <span class="c"># Initialize object properties...</span> + 220 <span class="c">#</span> +<a name="_InitializeMolecularComplexityDescriptorsProperties-"></a> 221 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptorsProperties</span> <span class="s">{</span> + 222 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 223 + 224 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 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> + 226 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> + 227 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 228 <span class="s">}</span> + 229 + 230 <span class="c"># Make sure MolecularComplexityType is set...</span> + 231 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span> + 232 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">'MACCSKeys'</span><span class="sc">;</span> + 233 <span class="s">}</span> + 234 + 235 <span class="c"># Make sure AtomIdentifierType is set...</span> + 236 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> + 237 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> + 238 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 239 <span class="s">}</span> + 240 <span class="s">}</span> + 241 + 242 <span class="c"># Make sure UseTriangleInequality is set...</span> + 243 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalAtomTripletsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> + 244 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">UseTriangleInequality</span>}<span class="s">)</span> <span class="s">{</span> + 245 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 246 <span class="s">}</span> + 247 <span class="s">}</span> + 248 + 249 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 250 <span class="s">}</span> + 251 + 252 <span class="c"># Initialize atom identifer type...</span> + 253 <span class="c">#</span> +<a name="_InitializeAtomIdentifierType-"></a> 254 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierType</span> <span class="s">{</span> + 255 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 256 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span> + 257 + 258 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> + 259 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 260 <span class="s">}</span> + 261 + 262 <span class="i">$AtomIdentifierType</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> ? <span class="q">'FunctionalClassAtomTypes'</span> <span class="co">:</span> <span class="q">'AtomicInvariantsAtomTypes'</span><span class="sc">;</span> + 263 + 264 <span class="i">$This</span><span class="i">->SetAtomIdentifierType</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span> + 265 + 266 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 267 <span class="s">}</span> + 268 + 269 <span class="c"># Get abbreviation for specified molecular complexity type or using descriptors object...</span> + 270 <span class="c">#</span> + 271 <span class="c"># This functionality can be either invoked as a class function or an</span> + 272 <span class="c"># object method.</span> + 273 <span class="c">#</span> +<a name="GetMolecularComplexityTypeAbbreviation-"></a> 274 <span class="k">sub </span><span class="m">GetMolecularComplexityTypeAbbreviation</span> <span class="s">{</span> + 275 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 277 + 278 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecularComplexityDescriptors</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 279 <span class="i">$This</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> + 280 <span class="i">$ComplexityType</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span> + 281 <span class="s">}</span> + 282 <span class="k">else</span> <span class="s">{</span> + 283 <span class="i">$ComplexityType</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> + 284 <span class="s">}</span> + 285 + 286 <span class="i">%ComplexityTypeToAbbrev</span> = <span class="s">(</span><span class="k">lc</span> <span class="q">'AtomTypesFingerprints'</span> <span class="cm">=></span> <span class="q">'ATFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'ExtendedConnectivityFingerprints'</span> <span class="cm">=></span> <span class="q">'ECFP'</span><span class="cm">,</span> + 287 <span class="k">lc</span> <span class="q">'MACCSKeys'</span> <span class="cm">=></span> <span class="q">'MACCSKeys'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'PathLengthFingerprints'</span> <span class="cm">=></span> <span class="q">'PLFP'</span><span class="cm">,</span> + 288 <span class="k">lc</span> <span class="q">'TopologicalAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TAPFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'TopologicalAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span> + 289 <span class="k">lc</span> <span class="q">'TopologicalAtomTorsionsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span> + 290 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPAPFP'</span><span class="cm">,</span> + 291 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPATFP'</span><span class="s">)</span><span class="sc">;</span> + 292 + 293 <span class="k">return</span> <span class="k">exists</span> <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} ? <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> + 294 <span class="s">}</span> + 295 + 296 <span class="c"># Set MACCS key set size...</span> + 297 <span class="c">#</span> +<a name="SetMACCSKeysSize-"></a> 298 <span class="k">sub </span><span class="m">SetMACCSKeysSize</span> <span class="s">{</span> + 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 300 + 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: Size value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 303 <span class="s">}</span> + 304 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(166|322)/i</span><span class="s">)</span> <span class="s">{</span> + 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: The current release of MayaChemTools doesn't support MDL MACCS $Value keys..."</span><span class="sc">;</span> + 306 <span class="s">}</span> + 307 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="i">$Value</span><span class="sc">;</span> + 308 + 309 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 310 <span class="s">}</span> + 311 + 312 <span class="c"># Set minimum path length...</span> + 313 <span class="c">#</span> +<a name="SetMinPathLength-"></a> 314 <span class="k">sub </span><span class="m">SetMinPathLength</span> <span class="s">{</span> + 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> + 316 + 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> + 318 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinPathLength: MinPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 319 <span class="s">}</span> + 320 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span> + 321 + 322 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 323 <span class="s">}</span> + 324 + 325 <span class="c"># Set maximum path length...</span> + 326 <span class="c">#</span> +<a name="SetMaxPathLength-"></a> 327 <span class="k">sub </span><span class="m">SetMaxPathLength</span> <span class="s">{</span> + 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> + 329 + 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> + 331 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxPathLength: MaxPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 332 <span class="s">}</span> + 333 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span> + 334 + 335 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 336 <span class="s">}</span> + 337 + 338 <span class="c"># Set minimum bond distance between atom pairs during topological and topological</span> + 339 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span> + 340 <span class="c">#</span> +<a name="SetMinDistance-"></a> 341 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> + 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> + 343 + 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> + 345 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 346 <span class="s">}</span> + 347 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> + 348 + 349 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 350 <span class="s">}</span> + 351 + 352 <span class="c"># Set maximum bond distance between atom pairs during topological and topological</span> + 353 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span> + 354 <span class="c">#</span> +<a name="SetMaxDistance-"></a> 355 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> + 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> + 357 + 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> + 359 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 360 <span class="s">}</span> + 361 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> + 362 + 363 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 364 <span class="s">}</span> + 365 + 366 <span class="c"># Set atom neighborhood radius...</span> + 367 <span class="c">#</span> +<a name="SetNeighborhoodRadius-"></a> 368 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span> + 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> + 370 + 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> + 372 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> + 373 <span class="s">}</span> + 374 + 375 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span> + 376 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span> + 377 <span class="s">}</span> + 378 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span> + 379 + 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 381 <span class="s">}</span> + 382 + 383 <span class="c"># Set molecular complexity type...</span> + 384 <span class="c">#</span> +<a name="SetMolecularComplexityType-"></a> 385 <span class="k">sub </span><span class="m">SetMolecularComplexityType</span> <span class="s">{</span> + 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> + 387 + 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> + 389 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecularComplexityType: MolecularComplexityType value, $Value, is not valid. Supported values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..."</span><span class="sc">;</span> + 390 <span class="s">}</span> + 391 + 392 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="i">$Value</span><span class="sc">;</span> + 393 + 394 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 395 <span class="s">}</span> + 396 + 397 <span class="c"># Set distance bin size for binning pharmacophore atom pair distances in atom triplets...</span> + 398 <span class="c">#</span> +<a name="SetDistanceBinSize-"></a> 399 <span class="k">sub </span><span class="m">SetDistanceBinSize</span> <span class="s">{</span> + 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> + 401 + 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> + 403 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDistanceBinSize: DistanceBinSize value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 404 <span class="s">}</span> + 405 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="i">$Value</span><span class="sc">;</span> + 406 + 407 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 408 <span class="s">}</span> + 409 + 410 <span class="c"># Set normalization methodology to use for scaling the number of bits-set or unique keys</span> + 411 <span class="c"># in fingerprints...</span> + 412 <span class="c">#</span> +<a name="SetNormalizationMethodology-"></a> 413 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span> + 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> + 415 + 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> + 417 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span> + 418 <span class="s">}</span> + 419 + 420 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span> + 421 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^(ExtendedConnectivityFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> + 422 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: Normalization is not supported for MolecularComplexityType: $This->{MolecularComplexityType}. Valid MolecularComplexityType values: ExtendedConnectivityFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints...\n"</span><span class="sc">;</span> + 423 <span class="s">}</span> + 424 + 425 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|None)$/i</span><span class="s">)</span> <span class="s">{</span> + 426 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByHeavyAtomsCount..."</span><span class="sc">;</span> + 427 <span class="s">}</span> + 428 + 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByPossibleKeysCount|None)$/i</span><span class="s">)</span> <span class="s">{</span> + 430 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByPossibleKeysCount..."</span><span class="sc">;</span> + 431 <span class="s">}</span> + 432 <span class="s">}</span> + 433 + 434 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span> + 435 + 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 437 <span class="s">}</span> + 438 + 439 <span class="c"># Set intial atom identifier type..</span> + 440 <span class="c">#</span> +<a name="SetAtomIdentifierType-"></a> 441 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> + 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> + 443 + 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> + 445 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span> + 446 <span class="s">}</span> + 447 + 448 <span class="c"># FunctionalClassAtomTypes is the only valid atom identifier type for pharmacophore fingerprints...</span> + 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> + 450 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 451 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported type for $This->{MolecularComplexityType} complexity type: FunctionalClassAtomTypes."</span><span class="sc">;</span> + 452 <span class="s">}</span> + 453 <span class="s">}</span> + 454 + 455 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> + 456 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> + 457 <span class="s">}</span> + 458 + 459 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> + 460 + 461 <span class="c"># Initialize identifier type information...</span> + 462 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 463 + 464 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 465 <span class="s">}</span> + 466 + 467 <span class="c"># Calculate molecular complexity [ Ref 117-119 ] of a molecule using its fingerprints.</span> + 468 <span class="c">#</span> + 469 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span> + 470 <span class="c"># corresponding to the number of bits-set or unique keys in molecular fingerprints. The</span> + 471 <span class="c"># following types of fingerprints based molecular complexity measures are supported:</span> + 472 <span class="c">#</span> + 473 <span class="c"># AtomTypesFingerprints</span> + 474 <span class="c"># ExtendedConnectivityFingerprints</span> + 475 <span class="c"># MACCSKeys</span> + 476 <span class="c"># PathLengthFingerprints</span> + 477 <span class="c"># TopologicalAtomPairsFingerprints</span> + 478 <span class="c"># TopologicalAtomTripletsFingerprints</span> + 479 <span class="c"># TopologicalAtomTorsionsFingerprints</span> + 480 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> + 481 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> + 482 <span class="c">#</span> + 483 <span class="c"># After the molecular complexity value has been calculated, it can also be normalized by</span> + 484 <span class="c"># by scaling the number of bits-set or unique keys for following types of fingerprints:</span> + 485 <span class="c">#</span> + 486 <span class="c"># ExtendedConnectivityFingerprints</span> + 487 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> + 488 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> + 489 <span class="c">#</span> + 490 <span class="c"># Two types of normalization methodologies are supported: by heavy atoms count for</span> + 491 <span class="c"># extended connectivity fingerprints; by possible keys count for topological pharmacophore</span> + 492 <span class="c"># atom pairs and triplets fingerprints.</span> + 493 <span class="c">#</span> +<a name="GenerateDescriptors-"></a> 494 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> + 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> + 496 + 497 <span class="c"># Initialize descriptor values...</span> + 498 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 499 + 500 <span class="c"># Check availability of molecule...</span> + 501 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> + 502 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> + 503 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 504 <span class="s">}</span> + 505 + 506 <span class="c"># Calculate descriptor values...</span> + 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 508 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate MolecularComplexity values corresponding to assigned MolecularComplexity atom types..."</span><span class="sc">;</span> + 509 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 510 <span class="s">}</span> + 511 + 512 <span class="c"># Set final descriptor values...</span> + 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 514 + 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 516 <span class="s">}</span> + 517 + 518 <span class="c"># Calculate molecular complexity value...</span> + 519 <span class="c">#</span> +<a name="_CalculateDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> + 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 523 + 524 <span class="c"># Setup fingerprints object and generate fingerprints...</span> + 525 <span class="i">$MethodName</span> = <span class="q">"_Setup"</span> . <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span> + 526 <span class="i">$FingerprintsObject</span> = <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 527 + 528 <span class="i">$FingerprintsObject</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 529 + 530 <span class="c"># Make sure atom types fingerprints generation is successful...</span> + 531 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsObject</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 532 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 533 <span class="s">}</span> + 534 + 535 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 536 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 537 <span class="s">}</span> + 538 + 539 <span class="c"># Normalize molecular complexity...</span> + 540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> + 541 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_NormalizeMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 542 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 543 <span class="s">}</span> + 544 <span class="s">}</span> + 545 + 546 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 547 <span class="s">}</span> + 548 + 549 <span class="c"># Setup atom types fingerprints...</span> + 550 <span class="c">#</span> +<a name="_SetupAtomTypesFingerprints-"></a> 551 <span class="k">sub </span><span class="m">_SetupAtomTypesFingerprints</span> <span class="s">{</span> + 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 553 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 554 + 555 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::AtomTypesFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'AtomTypesCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> + 556 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 557 + 558 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> + 559 <span class="s">}</span> + 560 + 561 <span class="c"># Setup extended connectivity fingerprints...</span> + 562 <span class="c">#</span> +<a name="_SetupExtendedConnectivityFingerprints-"></a> 563 <span class="k">sub </span><span class="m">_SetupExtendedConnectivityFingerprints</span> <span class="s">{</span> + 564 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 565 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 566 + 567 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'ExtendedConnectivity'</span><span class="cm">,</span> <span class="q">'NeighborhoodRadius'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> + 568 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 569 + 570 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> + 571 <span class="s">}</span> + 572 + 573 <span class="c"># Setup MACCS keys...</span> + 574 <span class="c">#</span> +<a name="_SetupMACCSKeys-"></a> 575 <span class="k">sub </span><span class="m">_SetupMACCSKeys</span> <span class="s">{</span> + 576 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 577 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 578 + 579 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::MACCSKeys</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'MACCSKeyBits'</span><span class="cm">,</span> <span class="q">'Size'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>}<span class="s">)</span><span class="sc">;</span> + 580 + 581 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> + 582 <span class="s">}</span> + 583 + 584 <span class="c"># Set up path length fingerprints...</span> + 585 <span class="c">#</span> +<a name="_SetupPathLengthFingerprints-"></a> 586 <span class="k">sub </span><span class="m">_SetupPathLengthFingerprints</span> <span class="s">{</span> + 587 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 588 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 589 + 590 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::PathLengthFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'PathLengthCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'MinLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinPathLength</span>}<span class="cm">,</span> <span class="q">'MaxLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxPathLength</span>}<span class="cm">,</span> <span class="q">'AllowRings'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'AllowSharedBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'UseBondSymbols'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">'UseUniquePaths'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> + 591 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 592 + 593 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> + 594 <span class="s">}</span> + 595 + 596 <span class="c"># Setup topological atom pairs fingerprints...</span> + 597 <span class="c">#</span> +<a name="_SetupTopologicalAtomPairsFingerprints-"></a> 598 <span class="k">sub </span><span class="m">_SetupTopologicalAtomPairsFingerprints</span> <span class="s">{</span> + 599 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 600 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 601 + 602 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> + 603 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 604 + 605 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> + 606 <span class="s">}</span> + 607 + 608 <span class="c"># Setup topological atom triplets fingerprints...</span> + 609 <span class="c">#</span> +<a name="_SetupTopologicalAtomTripletsFingerprints-"></a> 610 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTripletsFingerprints</span> <span class="s">{</span> + 611 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 612 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 613 + 614 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> + 615 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 616 + 617 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> + 618 <span class="s">}</span> + 619 + 620 <span class="c"># Setup topological atom torsions fingerprints...</span> + 621 <span class="c">#</span> +<a name="_SetupTopologicalAtomTorsionsFingerprints-"></a> 622 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTorsionsFingerprints</span> <span class="s">{</span> + 623 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 624 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 625 + 626 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> + 627 + 628 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 629 + 630 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> + 631 <span class="s">}</span> + 632 + 633 <span class="c"># Setup TopologicalPharmacophoreAtomPairsFingerprints...</span> + 634 <span class="c">#</span> +<a name="_SetupTopologicalPharmacophoreAtomPairsFingerprints-"></a> 635 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span> + 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 638 + 639 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span> + 640 <span class="i">$AtomPairsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span> + 641 + 642 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomPairsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomPairsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="q">'None'</span><span class="cm">,</span> <span class="q">'ValuesPrecision'</span> <span class="cm">=></span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> + 643 + 644 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> + 645 <span class="s">}</span> + 646 + 647 <span class="c"># Setup TopologicalPharmacophoreAtomTripletsFingerprints...</span> + 648 <span class="c">#</span> +<a name="_SetupTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 649 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span> + 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 651 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span> + 652 + 653 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span> + 654 <span class="i">$AtomTripletsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span> + 655 + 656 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomTripletsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'DistanceBinSize'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span> + 657 + 658 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> + 659 <span class="s">}</span> + 660 + 661 <span class="c"># Normalize molecular complexity value...</span> + 662 <span class="c">#</span> +<a name="_NormalizeMolecularComplexity-"></a> 663 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexity</span> <span class="s">{</span> + 664 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 665 + 666 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByHeavyAtomsCount$/i</span><span class="s">)</span> <span class="s">{</span> + 667 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByHeavyAtomsCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 668 <span class="s">}</span> + 669 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> <span class="s">{</span> + 670 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByPossibleKeysCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 671 <span class="s">}</span> + 672 <span class="k">else</span> <span class="s">{</span> + 673 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_NormalizeMolecularComplexity: NormalizationMethodology value, $This->{NormalizationMethodology}, is not valid. Supported values: ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span> + 674 <span class="s">}</span> + 675 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 676 <span class="s">}</span> + 677 + 678 <span class="c"># Normalize molecular complexity value by heavy atom count...</span> + 679 <span class="c">#</span> +<a name="_NormalizeMolecularComplexityByHeavyAtomsCount-"></a> 680 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByHeavyAtomsCount</span> <span class="s">{</span> + 681 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 682 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfHeavyAtoms</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span> + 683 + 684 <span class="i">$NumOfHeavyAtoms</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetNumOfHeavyAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 685 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfHeavyAtoms</span><span class="s">)</span> <span class="s">{</span> + 686 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 687 <span class="s">}</span> + 688 + 689 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfHeavyAtoms</span><span class="sc">;</span> + 690 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> + 691 + 692 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 693 <span class="s">}</span> + 694 + 695 <span class="c"># Normalize molecular complexity value by possible keys count...</span> + 696 <span class="c">#</span> +<a name="_NormalizeMolecularComplexityByPossibleKeysCount-"></a> 697 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByPossibleKeysCount</span> <span class="s">{</span> + 698 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 699 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPossibleKeys</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span> + 700 + 701 <span class="i">$NumOfPossibleKeys</span> = <span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 702 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfPossibleKeys</span><span class="s">)</span> <span class="s">{</span> + 703 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 704 <span class="s">}</span> + 705 + 706 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfPossibleKeys</span><span class="sc">;</span> + 707 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> + 708 + 709 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 710 <span class="s">}</span> + 711 + 712 <span class="c"># Calculate molecular complexity value using fingerprints objects...</span> + 713 <span class="c">#</span> +<a name="_CalculateMolecularComplexity-"></a> 714 <span class="k">sub </span><span class="m">_CalculateMolecularComplexity</span> <span class="s">{</span> + 715 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 716 + 717 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span> + 718 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsBitVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> + 719 <span class="s">}</span> + 720 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span> + 721 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> + 722 <span class="s">}</span> + 723 <span class="k">else</span> <span class="s">{</span> + 724 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_CalculateMolecularComplexity: Fingerprints vector type is not valid. Supported values: FingerprintsBitVector or FingerprintsVector..."</span><span class="sc">;</span> + 725 <span class="s">}</span> + 726 + 727 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 728 <span class="s">}</span> + 729 + 730 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span> + 731 <span class="c">#</span> +<a name="_CalculateMolecularComplexityUsingFingerprintsVector-"></a> 732 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsVector</span> <span class="s">{</span> + 733 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 734 + 735 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="s">(</span><span class="i">$FingerprintsVector</span><span class="i">->GetType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^(OrderedNumericalValues|NumericalValues)$/i</span><span class="s">)</span> ? <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfNonZeroValues</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 736 + 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 738 <span class="s">}</span> + 739 + 740 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span> + 741 <span class="c">#</span> +<a name="_CalculateMolecularComplexityUsingFingerprintsBitVector-"></a> 742 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsBitVector</span> <span class="s">{</span> + 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 744 + 745 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">$FingerprintsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 746 + 747 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 748 <span class="s">}</span> + 749 + 750 <span class="c"># Setup final descriptor values...</span> + 751 <span class="c">#</span> +<a name="_SetFinalDescriptorValues-"></a> 752 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> + 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 754 + 755 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> + 756 + 757 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexity</span>}<span class="s">)</span><span class="sc">;</span> + 758 + 759 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 760 <span class="s">}</span> + 761 + 762 <span class="c"># Set atom identifier type to use for generating fingerprints...</span> + 763 <span class="c">#</span> +<a name="_SetAtomIdentifierTypeValuesToUse-"></a> 764 <span class="k">sub </span><span class="m">_SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span> + 765 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 766 + 767 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 768 <span class="i">$FingerprintsObject</span><span class="i">->SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span> + 769 <span class="s">}</span> + 770 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 771 <span class="i">$FingerprintsObject</span><span class="i">->SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span> + 772 <span class="s">}</span> + 773 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> + 774 <span class="c"># Nothing to do for now...</span> + 775 <span class="s">}</span> + 776 <span class="k">else</span> <span class="s">{</span> + 777 <span class="w">croak</span> <span class="q">"Error: The value specified, $This->{AtomIdentifierType}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span> + 778 <span class="s">}</span> + 779 <span class="s">}</span> + 780 + 781 <span class="c"># Initialize atom indentifier type information...</span> + 782 <span class="c">#</span> + 783 <span class="c"># Current supported values:</span> + 784 <span class="c">#</span> + 785 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span> + 786 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> + 787 <span class="c">#</span> +<a name="_InitializeAtomIdentifierTypeInformation-"></a> 788 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> + 789 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 790 + 791 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> + 792 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 793 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 794 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 795 <span class="s">}</span> + 796 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 797 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 798 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 799 <span class="s">}</span> + 800 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> + 801 <span class="c"># Nothing to do for now...</span> + 802 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 803 <span class="s">}</span> + 804 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> + 805 <span class="s">}</span> + 806 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 807 <span class="s">}</span> + 808 + 809 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span> + 810 <span class="c"># class, to use for generating initial atom identifiers...</span> + 811 <span class="c">#</span> + 812 <span class="c"># Let:</span> + 813 <span class="c"># AS = Atom symbol corresponding to element symbol</span> + 814 <span class="c">#</span> + 815 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 816 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 817 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 818 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 819 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 820 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 821 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> + 822 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> + 823 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> + 824 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> + 825 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> + 826 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> + 827 <span class="c">#</span> + 828 <span class="c"># Then:</span> + 829 <span class="c">#</span> + 830 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> + 831 <span class="c">#</span> + 832 <span class="c"># AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></span> + 833 <span class="c">#</span> + 834 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> + 835 <span class="c"># optional.</span> + 836 <span class="c">#</span> + 837 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span> + 838 <span class="c">#</span> + 839 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span> + 840 <span class="c">#</span> + 841 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span> + 842 <span class="c"># are also allowed:</span> + 843 <span class="c">#</span> + 844 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span> + 845 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span> + 846 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span> + 847 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span> + 848 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span> + 849 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span> + 850 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span> + 851 <span class="c"># Ar : Aromatic</span> + 852 <span class="c"># RA : RingAtom</span> + 853 <span class="c"># FC : FormalCharge</span> + 854 <span class="c"># MN : MassNumber</span> + 855 <span class="c"># SM : SpinMultiplicity</span> + 856 <span class="c">#</span> +<a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 857 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> + 858 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 859 + 860 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 861 + 862 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> + 863 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> + 864 <span class="s">}</span> + 865 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> + 866 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="cm">,</span> <span class="q">'MN'</span><span class="s">)</span><span class="sc">;</span> + 867 <span class="s">}</span> + 868 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> + 869 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="s">)</span><span class="sc">;</span> + 870 <span class="s">}</span> + 871 + 872 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 873 <span class="s">}</span> + 874 + 875 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> + 876 <span class="c"># class, to use for generating initial atom identifiers...</span> + 877 <span class="c">#</span> + 878 <span class="c"># Let:</span> + 879 <span class="c"># HBD: HydrogenBondDonor</span> + 880 <span class="c"># HBA: HydrogenBondAcceptor</span> + 881 <span class="c"># PI : PositivelyIonizable</span> + 882 <span class="c"># NI : NegativelyIonizable</span> + 883 <span class="c"># Ar : Aromatic</span> + 884 <span class="c"># Hal : Halogen</span> + 885 <span class="c"># H : Hydrophobic</span> + 886 <span class="c"># RA : RingAtom</span> + 887 <span class="c"># CA : ChainAtom</span> + 888 <span class="c">#</span> + 889 <span class="c"># Then:</span> + 890 <span class="c">#</span> + 891 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> + 892 <span class="c">#</span> + 893 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> + 894 <span class="c">#</span> + 895 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> + 896 <span class="c">#</span> + 897 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> + 898 <span class="c">#</span> + 899 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> + 900 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> + 901 <span class="c"># PositivelyIonizable: +, NH2</span> + 902 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> + 903 <span class="c">#</span> +<a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 904 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> + 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 906 + 907 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 908 + 909 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> + 910 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> + 911 <span class="s">}</span> + 912 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> + 913 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="s">)</span><span class="sc">;</span> + 914 <span class="s">}</span> + 915 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> + 916 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="s">)</span><span class="sc">;</span> + 917 <span class="s">}</span> + 918 + 919 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 920 <span class="s">}</span> + 921 + 922 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span> + 923 <span class="c">#</span> +<a name="SetAtomicInvariantsToUse-"></a> 924 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> + 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 926 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 927 + 928 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> + 929 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> + 930 <span class="k">return</span><span class="sc">;</span> + 931 <span class="s">}</span> + 932 + 933 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 934 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> + 935 <span class="k">return</span><span class="sc">;</span> + 936 <span class="s">}</span> + 937 + 938 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> + 939 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> + 940 + 941 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 942 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 943 + 944 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> + 945 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> + 946 <span class="s">}</span> + 947 <span class="k">else</span> <span class="s">{</span> + 948 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> + 949 <span class="s">}</span> + 950 + 951 <span class="c"># Make sure specified AtomicInvariants are valid...</span> + 952 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> + 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> + 954 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> + 955 <span class="s">}</span> + 956 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> + 957 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> + 958 <span class="s">}</span> + 959 + 960 <span class="c"># Set atomic invariants to use...</span> + 961 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 962 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> + 963 + 964 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 965 <span class="s">}</span> + 966 + 967 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span> + 968 <span class="c">#</span> +<a name="SetFunctionalClassesToUse-"></a> 969 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> + 970 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 972 + 973 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> + 974 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> + 975 <span class="k">return</span><span class="sc">;</span> + 976 <span class="s">}</span> + 977 + 978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 979 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> + 980 <span class="k">return</span><span class="sc">;</span> + 981 <span class="s">}</span> + 982 + 983 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> + 984 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> + 985 + 986 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 987 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 988 + 989 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> + 990 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> + 991 <span class="s">}</span> + 992 <span class="k">else</span> <span class="s">{</span> + 993 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> + 994 <span class="s">}</span> + 995 + 996 <span class="c"># Make sure specified FunctionalClasses are valid...</span> + 997 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> + 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> + 999 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> +1000 <span class="s">}</span> +1001 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> +1002 <span class="s">}</span> +1003 +1004 <span class="c"># Set functional classes to use...</span> +1005 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1006 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> +1007 +1008 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1009 <span class="s">}</span> +1010 +1011 <span class="c"># Return a string containg data for MolecularComplexityDescriptors object...</span> +1012 <span class="c">#</span> +<a name="StringifyMolecularComplexityDescriptors-"></a>1013 <span class="k">sub </span><span class="m">StringifyMolecularComplexityDescriptors</span> <span class="s">{</span> +1014 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +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> +1016 +1017 <span class="i">$ComplexityDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; MolecularComplexityType: $This->{MolecularComplexityType}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1018 +1019 <span class="c"># Setup fingerprints specific information...</span> +1020 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> +1021 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MACCSKeysSize = $This->{MACCSKeysSize}"</span><span class="sc">;</span> +1022 <span class="s">}</span> +1023 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> +1024 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; NeighborhoodRadius = $This->{NeighborhoodRadius}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span> +1025 <span class="s">}</span> +1026 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> +1027 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinPathLength = $This->{MinPathLength}; MaxPathLength = $This->{MaxPathLength}; UseBondSymbols: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> +1028 <span class="s">}</span> +1029 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> +1030 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span> +1031 <span class="s">}</span> +1032 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> +1033 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> +1034 <span class="s">}</span> +1035 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTorsionsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> +1036 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span> +1037 <span class="s">}</span> +1038 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> +1039 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span> +1040 <span class="s">}</span> +1041 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> +1042 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}; DistanceBinSize: $This->{DistanceBinSize}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> +1043 <span class="s">}</span> +1044 +1045 <span class="c"># Setup atom identifier information...</span> +1046 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> +1047 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomIdentifierType = $This->{AtomIdentifierType}"</span><span class="sc">;</span> +1048 +1049 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> +1050 <span class="k">my</span><span class="s">(</span><span class="i">$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> +1051 +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> +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> +1054 +1055 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> +1056 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> +1057 <span class="s">}</span> +1058 +1059 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1060 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1061 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableAtomicInvariants: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1062 <span class="s">}</span> +1063 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> +1064 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> +1065 +1066 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1067 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1068 +1069 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> +1070 <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">"$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}"</span><span class="sc">;</span> +1071 <span class="s">}</span> +1072 +1073 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1074 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1075 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableFunctionalClasses: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1076 <span class="s">}</span> +1077 <span class="s">}</span> +1078 <span class="k">return</span> <span class="i">$ComplexityDescriptorsString</span><span class="sc">;</span> +1079 <span class="s">}</span> +1080 +1081 <span class="c"># Is it a MolecularComplexityDescriptors object?</span> +<a name="_IsMolecularComplexityDescriptors-"></a>1082 <span class="k">sub </span><span class="m">_IsMolecularComplexityDescriptors</span> <span class="s">{</span> +1083 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1084 +1085 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> +1086 <span class="s">}</span> +1087 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>