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| author | deepakjadmin |
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| date | Thu, 15 Dec 2016 14:18:03 -0500 |
| parents | 73ae111cf86f |
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<html> <head> <title>MayaChemTools:Code:Fingerprints::AtomNeighborhoodsFingerprints.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-Fingerprints::AtomNeighborhoodsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::AtomNeighborhoodsFingerprints</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: AtomNeighborhoodsFingerprints.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:48:53 $</span> 5 <span class="c"># $Revision: 1.27 $</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">Fingerprints::Fingerprints</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">Molecule</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> 38 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> 39 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span> 40 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span> 41 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span> 42 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> 43 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span> 44 45 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> 46 47 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> 48 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 49 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> 50 51 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> 52 53 <span class="c"># Setup class variables...</span> 54 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> 55 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 56 57 <span class="c"># Overload Perl functions...</span> 58 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyAtomNeighborhoodsFingerprints'</span><span class="sc">;</span> 59 60 <span class="c"># Class constructor...</span> <a name="new-"></a> 61 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 62 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 63 64 <span class="c"># Initialize object...</span> 65 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 66 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> 67 <span class="i">$This</span><span class="i">->_InitializeAtomNeighborhoodsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 68 69 <span class="i">$This</span><span class="i">->_InitializeAtomNeighborhoodsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 70 71 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 72 <span class="s">}</span> 73 74 <span class="c"># Initialize object data...</span> 75 <span class="c">#</span> <a name="_InitializeAtomNeighborhoodsFingerprints-"></a> 76 <span class="k">sub </span><span class="m">_InitializeAtomNeighborhoodsFingerprints</span> <span class="s">{</span> 77 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 78 79 <span class="c"># Type of fingerprint...</span> 80 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'AtomNeighborhoods'</span><span class="sc">;</span> 81 82 <span class="c"># Type of vector...</span> 83 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> 84 85 <span class="c"># Type of FingerprintsVector...</span> 86 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'AlphaNumericalValues'</span><span class="sc">;</span> 87 88 <span class="c"># Minimum and maximum atomic neighborhoods radii...</span> 89 <span class="i">$This</span>->{<span class="w">MinNeighborhoodRadius</span>} = <span class="n">0</span><span class="sc">;</span> 90 <span class="i">$This</span>->{<span class="w">MaxNeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span> 91 92 <span class="c"># Atom identifier type to use for atom IDs in atom neighborhood atoms...</span> 93 <span class="c">#</span> 94 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> 95 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> 96 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> 97 <span class="c">#</span> 98 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> 99 100 <span class="c"># Atom types assigned to each heavy atom...</span> 101 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 102 103 <span class="c"># Atom neighorhoods with in specified atom radii..</span> 104 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 105 106 <span class="c"># Atom neighborhoods atom types count at different neighborhoods...</span> 107 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 108 109 <span class="c"># Atom neighborhood identifiers using specified atom identifier types methodology...</span> 110 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoodsIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 111 <span class="s">}</span> 112 113 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 114 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 115 <span class="c">#Class name...</span> 116 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 117 <span class="s">}</span> 118 119 <span class="c"># Initialize object properties....</span> <a name="_InitializeAtomNeighborhoodsFingerprintsProperties-"></a> 120 <span class="k">sub </span><span class="m">_InitializeAtomNeighborhoodsFingerprintsProperties</span> <span class="s">{</span> 121 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 122 123 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> 124 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 125 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 126 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 127 <span class="s">}</span> 128 129 <span class="c"># Make sure molecule object was specified...</span> 130 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 131 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> 132 <span class="s">}</span> 133 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span> 134 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated with a user specified size: It's an arbitrary length vector..."</span><span class="sc">;</span> 135 <span class="s">}</span> 136 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> 137 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span> 138 <span class="s">}</span> 139 140 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 141 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 143 <span class="s">}</span> 144 145 <span class="c"># Set atom identifier type..</span> 146 <span class="c">#</span> <a name="SetAtomIdentifierType-"></a> 147 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> 148 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 149 150 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> 151 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes."</span><span class="sc">;</span> 152 <span class="s">}</span> 153 154 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> 155 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> 156 <span class="s">}</span> 157 158 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> 159 160 <span class="c"># Initialize atom identifier type information...</span> 161 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 162 163 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 164 <span class="s">}</span> 165 166 <span class="c"># Set minimum atom neighborhood radius...</span> 167 <span class="c">#</span> <a name="SetMinNeighborhoodRadius-"></a> 168 <span class="k">sub </span><span class="m">SetMinNeighborhoodRadius</span> <span class="s">{</span> 169 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 170 171 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 172 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinNeighborhoodRadius: MinNeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> 173 <span class="s">}</span> 174 175 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span> 176 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinNeighborhoodRadius: MinNeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span> 177 <span class="s">}</span> 178 <span class="i">$This</span>->{<span class="w">MinNeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span> 179 180 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 181 <span class="s">}</span> 182 183 <span class="c"># Set maximum atom neighborhood radius...</span> 184 <span class="c">#</span> <a name="SetMaxNeighborhoodRadius-"></a> 185 <span class="k">sub </span><span class="m">SetMaxNeighborhoodRadius</span> <span class="s">{</span> 186 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 187 188 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 189 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxNeighborhoodRadius: MaxNeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> 190 <span class="s">}</span> 191 192 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span> 193 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxNeighborhoodRadius: MaxNeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span> 194 <span class="s">}</span> 195 <span class="i">$This</span>->{<span class="w">MaxNeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span> 196 197 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 198 <span class="s">}</span> 199 200 <span class="c"># Generate fingerprints description...</span> 201 <span class="c">#</span> <a name="GetDescription-"></a> 202 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 204 205 <span class="c"># Is description explicity set?</span> 206 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> 207 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> 208 <span class="s">}</span> 209 210 <span class="c"># Generate fingerprints description...</span> 211 212 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:MinRadius$This->{MinNeighborhoodRadius}:MaxRadius$This->{MaxNeighborhoodRadius}"</span><span class="sc">;</span> 213 <span class="s">}</span> 214 215 <span class="c"># Generate atom neighborhood [ Ref 53-56, Ref 73 ] fingerprints...</span> 216 <span class="c">#</span> 217 <span class="c"># Methodology:</span> 218 <span class="c"># . Assign atom types to all non-hydrogen atoms in the molecule</span> 219 <span class="c"># . Get atom neighborhoods up to MaxNeighborhoodRadis</span> 220 <span class="c"># . Count unqiue atom types at each neighborhood radii for all heavy atoms</span> 221 <span class="c"># . Generate neighborhood identifiers for all neighborhoods around central</span> 222 <span class="c"># heavy atom</span> 223 <span class="c"># . Atom neighborhood identifier for a specific radii is generated using neighborhood</span> 224 <span class="c"># radius, assigned atom type and its count as follows:</span> 225 <span class="c">#</span> 226 <span class="c"># NR<n>-<AtomType>-ATC<n></span> 227 <span class="c">#</span> 228 <span class="c"># . Atom neighborhood identifier for a central atom at all specified radii is generated</span> 229 <span class="c"># by concatenating neighborhood identifiers at each radii by colon:</span> 230 <span class="c">#</span> 231 <span class="c"># NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:</span> 232 <span class="c">#</span> 233 <span class="c"># . Set final fingerprints as list of neighborhood atom indentifiers</span> 234 <span class="c">#</span> <a name="GenerateFingerprints-"></a> 235 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> 236 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 237 238 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinNeighborhoodRadius</span>} > <span class="i">$This</span>->{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 239 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateFingerprints: No fingerpritns generated: MinLength, $This->{MinNeighborhoodRadius}, must be less than MaxLength, $This->{MaxNeighborhoodRadius}..."</span><span class="sc">;</span> 240 <span class="s">}</span> 241 242 <span class="c"># Cache appropriate molecule data...</span> 243 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 244 245 <span class="c"># Assign atom types to all heavy atoms...</span> 246 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 247 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span> 248 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 249 <span class="s">}</span> 250 251 <span class="c"># Intialize atom neighborhoods information...</span> 252 <span class="i">$This</span><span class="i">->_InitializeAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 253 254 <span class="c"># Identify atom neighborhoods with in specified radii...</span> 255 <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 256 257 <span class="c"># Count atom neighborhoods atom types...</span> 258 <span class="i">$This</span><span class="i">->_CountAtomNeighborhoodsAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 259 260 <span class="c"># Genenerate atom neighborhood identifiers...</span> 261 <span class="i">$This</span><span class="i">->_GenerateAtomNeighborhoodIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 262 263 <span class="c"># Set final fingerprints...</span> 264 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 265 266 <span class="c"># Clear cached molecule data...</span> 267 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 268 269 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 270 <span class="s">}</span> 271 272 <span class="c"># Assign appropriate atom types to all heavy atoms...</span> 273 <span class="c">#</span> <a name="_AssignAtomTypes-"></a> 274 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span> 275 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 276 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 277 278 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 279 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span> 280 281 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span> 282 283 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 285 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::AtomicInvariantsAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'AtomicInvariantsToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="sc">;</span> 286 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 287 <span class="s">}</span> 288 289 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^DREIDINGAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 290 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::DREIDINGAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 291 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 292 <span class="s">}</span> 293 294 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 295 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 296 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 297 <span class="s">}</span> 298 299 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 300 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="sc">;</span> 301 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 302 <span class="s">}</span> 303 304 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^MMFF94AtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 305 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::MMFF94AtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 306 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 307 <span class="s">}</span> 308 309 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 310 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SLogPAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 311 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 312 <span class="s">}</span> 313 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SYBYLAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 314 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SYBYLAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 315 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 316 <span class="s">}</span> 317 318 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 319 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> 320 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 321 <span class="s">}</span> 322 323 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 324 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::UFFAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 325 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 326 <span class="s">}</span> 327 328 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignAtomTypes: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 329 <span class="s">}</span> 330 331 <span class="c"># Assign atom types...</span> 332 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 333 334 <span class="c"># Make sure atom types assignment is successful...</span> 335 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 336 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 337 <span class="s">}</span> 338 339 <span class="c"># Collect assigned atom types...</span> 340 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 341 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 342 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 343 <span class="s">}</span> 344 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 345 <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$SpecifiedAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 346 <span class="s">}</span> 347 348 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 349 <span class="s">}</span> 350 351 <span class="c"># Initialize topological atom pairs between specified distance range...</span> 352 <span class="c">#</span> <a name="_InitializeAtomNeighborhoods-"></a> 353 <span class="k">sub </span><span class="m">_InitializeAtomNeighborhoods</span> <span class="s">{</span> 354 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 355 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span> 356 357 <span class="c"># Initialize atom neighborhood count information between specified radii...</span> 358 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 359 360 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinNeighborhoodRadius</span>} .. <span class="i">$This</span>->{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 361 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 362 <span class="s">}</span> 363 364 <span class="c"># Initialize atom neighborhoods atoms information at all specified radii...</span> 365 <span class="c">#</span> 366 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 367 368 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 369 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 370 <span class="s">}</span> 371 372 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 373 <span class="s">}</span> 374 375 <span class="c"># Collect atom neighborhoods upto maximum neighborhood radius...</span> 376 <span class="c">#</span> 377 <span class="c"># Notes:</span> 378 <span class="c"># . Fingerprints are only generated for neighborhoods between specified minimum</span> 379 <span class="c"># and maximum neighborhood radii.</span> 380 <span class="c">#</span> <a name="_GetAtomNeighborhoods-"></a> 381 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span> 382 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 383 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$MaxRadius</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 384 385 <span class="i">$MaxRadius</span> = <span class="i">$This</span>->{<span class="w">MaxNeighborhoodRadius</span>}<span class="sc">;</span> 386 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 387 388 <span class="c"># Collect atom neighborhoods...</span> 389 390 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 391 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 392 <span class="i">$Radius</span> = <span class="n">0</span><span class="sc">;</span> 393 394 <span class="k">if</span> <span class="s">(</span><span class="i">$MaxRadius</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 395 <span class="c"># Atom is its own neighborhood at 0 radius...</span> 396 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighborhoodsAtoms</span><span class="s">)</span><span class="sc">;</span> 397 398 <span class="i">@AtomNeighborhoodsAtoms</span> = <span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 399 <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = \<span class="i">@AtomNeighborhoodsAtoms</span><span class="sc">;</span> 400 401 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 402 <span class="s">}</span> 403 404 <span class="c"># Collect available atom neighborhoods at different neighborhood radii levels...</span> 405 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighborhoodAtomsRef</span><span class="s">)</span><span class="sc">;</span> 406 407 <span class="k">for</span> <span class="i">$AtomNeighborhoodAtomsRef</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->GetAtomNeighborhoodsWithRadiusUpto</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$MaxRadius</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 408 <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomNeighborhoodAtomsRef</span><span class="sc">;</span> 409 <span class="i">$Radius</span>++<span class="sc">;</span> 410 <span class="s">}</span> 411 <span class="s">}</span> 412 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 413 <span class="s">}</span> 414 415 <span class="c"># Count atom neighborhoods atom types for each non-hydrogen central atoms with</span> 416 <span class="c"># neighborhoods in specified radii range...</span> 417 <span class="c">#</span> <a name="_CountAtomNeighborhoodsAtomTypes-"></a> 418 <span class="k">sub </span><span class="m">_CountAtomNeighborhoodsAtomTypes</span> <span class="s">{</span> 419 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 420 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomType</span><span class="cm">,</span> <span class="i">$AtomNeighborhoodAtomsRef</span><span class="s">)</span><span class="sc">;</span> 421 422 <span class="j">RADIUS:</span> <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} <span class="s">)</span> <span class="s">{</span> 423 <span class="k">if</span> <span class="s">(</span><span class="i">$Radius</span> < <span class="i">$This</span>->{<span class="w">MinNeighborhoodRadius</span>} || <span class="i">$Radius</span> > <span class="i">$This</span>->{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 424 <span class="k">next</span> <span class="j">RADIUS</span><span class="sc">;</span> 425 <span class="s">}</span> 426 <span class="c"># Go over the neighborhoods of each atom at the current radius...</span> 427 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> 428 <span class="i">$AtomNeighborhoodAtomsRef</span> = <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> 429 <span class="j">NEIGHBORHOODATOM:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$AtomNeighborhoodAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 430 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 431 <span class="k">next</span> <span class="j">NEIGHBORHOODATOM</span><span class="sc">;</span> 432 <span class="s">}</span> 433 <span class="i">$NeighborhoodAtomID</span> = <span class="i">$NeighborhoodAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 434 <span class="i">$NeighborhoodAtomType</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$NeighborhoodAtomID</span>}<span class="sc">;</span> 435 436 <span class="c"># Count neighbothood atom types for each atom at different radii...</span> 437 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span> 438 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 439 <span class="s">}</span> 440 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}{<span class="i">$NeighborhoodAtomType</span>}<span class="s">)</span> <span class="s">{</span> 441 <span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}{<span class="i">$NeighborhoodAtomType</span>} += <span class="n">1</span><span class="sc">;</span> 442 <span class="s">}</span> 443 <span class="k">else</span> <span class="s">{</span> 444 <span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}{<span class="i">$NeighborhoodAtomType</span>} = <span class="n">1</span><span class="sc">;</span> 445 <span class="s">}</span> 446 <span class="s">}</span> 447 <span class="s">}</span> 448 <span class="s">}</span> 449 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 450 <span class="s">}</span> 451 452 <span class="c"># Generate atom neighborhood identifiers for each non-hydrogen atom using atom</span> 453 <span class="c"># neighborhood atom types and their count information...</span> 454 <span class="c">#</span> 455 <span class="c"># Let:</span> 456 <span class="c"># NR<n> = Neighborhood radius</span> 457 <span class="c"># AtomType = Assigned atom type</span> 458 <span class="c"># ATC<n> = AtomType count</span> 459 <span class="c">#</span> 460 <span class="c"># Then:</span> 461 <span class="c">#</span> 462 <span class="c"># AtomNeighborhoodAtomIdentifier for a neighborhood atom generated for</span> 463 <span class="c"># AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> 464 <span class="c">#</span> 465 <span class="c"># NR<n>-<AtomType>-ATC<n></span> 466 <span class="c">#</span> 467 <span class="c"># AtomNeighborhoodsIdentifier for all specified atom neighbothoods of an atom generated for</span> 468 <span class="c"># AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> 469 <span class="c">#</span> 470 <span class="c"># NR<n>-<AtomType>-ATC<n>;NR<n>-<AtomType>-ATC<n>;...</span> 471 <span class="c">#</span> <a name="_GenerateAtomNeighborhoodIdentifiers-"></a> 472 <span class="k">sub </span><span class="m">_GenerateAtomNeighborhoodIdentifiers</span> <span class="s">{</span> 473 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 474 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$AtomTypeCount</span><span class="cm">,</span> <span class="i">$AtomNeighborhoodIdentifier</span><span class="cm">,</span> <span class="i">@AtomNeighborhoodIdentifiers</span><span class="s">)</span><span class="sc">;</span> 475 476 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoodsIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 477 478 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 479 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 480 <span class="i">@AtomNeighborhoodIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 481 <span class="j">RADIUS:</span> <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinNeighborhoodRadius</span>} .. <span class="i">$This</span>->{<span class="w">MaxNeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 482 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span> 483 <span class="k">next</span> <span class="j">RADIUS</span><span class="sc">;</span> 484 <span class="s">}</span> 485 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span> 486 <span class="i">$AtomTypeCount</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodAtomTypesCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}{<span class="i">$AtomType</span>}<span class="sc">;</span> 487 <span class="k">push</span> <span class="i">@AtomNeighborhoodIdentifiers</span><span class="cm">,</span> <span class="q">"NR${Radius}-${AtomType}-ATC${AtomTypeCount}"</span><span class="sc">;</span> 488 <span class="s">}</span> 489 <span class="s">}</span> 490 <span class="i">$AtomNeighborhoodIdentifier</span> = <span class="k">join</span><span class="s">(</span><span class="q">":"</span><span class="cm">,</span> <span class="i">@AtomNeighborhoodIdentifiers</span><span class="s">)</span><span class="sc">;</span> 491 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoodsIdentifiers</span>}}<span class="cm">,</span> <span class="i">$AtomNeighborhoodIdentifier</span><span class="sc">;</span> 492 <span class="s">}</span> 493 494 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 495 <span class="s">}</span> 496 497 <span class="c"># Set final fingerprits vector...</span> 498 <span class="c">#</span> <a name="_SetFinalFingerprints-"></a> 499 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> 500 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 501 502 <span class="c"># Mark successful generation of fingerprints...</span> 503 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 504 505 <span class="c"># Sort AtomNeighborhoodsIdentifiers..</span> 506 <span class="c">#</span> 507 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoodsIdentifiers</span>}} = <span class="k">sort</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoodsIdentifiers</span>}}<span class="sc">;</span> 508 509 <span class="c"># Add sorted atom neighborhood identifiers to FingerprintsVector which is already defined</span> 510 <span class="c"># during initialization containing AlphaNumericalValues...</span> 511 <span class="c">#</span> 512 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoodsIdentifiers</span>}}<span class="s">)</span><span class="sc">;</span> 513 514 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 515 <span class="s">}</span> 516 517 <span class="c"># Cache appropriate molecule data...</span> 518 <span class="c">#</span> <a name="_SetupMoleculeDataCache-"></a> 519 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> 520 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 521 522 <span class="c"># Get all non-hydrogen atoms...</span> 523 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> 524 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span> 525 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="q">"IsHydrogen"</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> 526 527 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 528 <span class="s">}</span> 529 530 <span class="c"># Clear cached molecule data...</span> 531 <span class="c">#</span> <a name="_ClearMoleculeDataCache-"></a> 532 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> 533 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 534 535 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 536 537 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 538 <span class="s">}</span> 539 540 <span class="c"># Set atomic invariants to use for atom identifiers...</span> 541 <span class="c">#</span> <a name="SetAtomicInvariantsToUse-"></a> 542 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> 543 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 544 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomicInvariantValue</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span> 545 546 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 547 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> 548 <span class="k">return</span><span class="sc">;</span> 549 <span class="s">}</span> 550 551 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 552 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 553 554 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 555 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 556 557 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 558 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 559 <span class="s">}</span> 560 <span class="k">else</span> <span class="s">{</span> 561 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 562 <span class="s">}</span> 563 564 <span class="c"># Make sure specified AtomicInvariants are valid...</span> 565 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> 566 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 567 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> 568 <span class="s">}</span> 569 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> 570 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> 571 <span class="s">}</span> 572 573 <span class="c"># Set atomic invariants to use...</span> 574 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 575 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> 576 577 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 578 <span class="s">}</span> 579 580 <span class="c"># Set functional classes to use for atom identifiers...</span> 581 <span class="c">#</span> <a name="SetFunctionalClassesToUse-"></a> 582 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> 583 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 584 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="cm">,</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span> 585 586 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 587 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> 588 <span class="k">return</span><span class="sc">;</span> 589 <span class="s">}</span> 590 591 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 592 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 593 <span class="k">return</span><span class="sc">;</span> 594 <span class="s">}</span> 595 596 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 597 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 598 599 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 600 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 601 602 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 603 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 604 <span class="s">}</span> 605 <span class="k">else</span> <span class="s">{</span> 606 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 607 <span class="s">}</span> 608 609 <span class="c"># Make sure specified FunctionalClasses are valid...</span> 610 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> 611 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedFunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 612 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> 613 <span class="s">}</span> 614 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> 615 <span class="s">}</span> 616 617 <span class="c"># Set functional classes to use...</span> 618 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 619 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> 620 621 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 622 <span class="s">}</span> 623 624 <span class="c"># Initialize atom indentifier type information...</span> 625 <span class="c">#</span> 626 <span class="c"># Current supported values:</span> 627 <span class="c">#</span> 628 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span> 629 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> 630 <span class="c">#</span> <a name="_InitializeAtomIdentifierTypeInformation-"></a> 631 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> 632 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 633 634 <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> 635 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 636 <span class="s">}</span> 637 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 638 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 639 <span class="s">}</span> 640 <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> 641 <span class="c"># Nothing to do for now...</span> 642 <span class="s">}</span> 643 <span class="k">else</span> <span class="s">{</span> 644 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 645 <span class="s">}</span> 646 647 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 648 <span class="s">}</span> 649 650 <span class="c"># Initialize atomic invariants atom types to use for generating atom identifiers...</span> 651 <span class="c">#</span> 652 <span class="c"># Let:</span> 653 <span class="c"># AS = Atom symbol corresponding to element symbol</span> 654 <span class="c">#</span> 655 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 656 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 657 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 658 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 659 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 660 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 661 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> 662 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> 663 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> 664 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> 665 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> 666 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> 667 <span class="c">#</span> 668 <span class="c"># Then:</span> 669 <span class="c">#</span> 670 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> 671 <span class="c">#</span> 672 <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> 673 <span class="c">#</span> 674 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> 675 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X<n>, BO<n>, H<n>, FC<+n/-n>.</span> 676 <span class="c"># AtomID specification doesn't include atomic invariants with zero or undefined values.</span> 677 <span class="c">#</span> <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 678 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> 679 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 680 681 <span class="c"># Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC</span> 682 <span class="c">#</span> 683 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 684 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> 685 686 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 687 <span class="s">}</span> 688 689 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> 690 <span class="c"># class, to use for generating atom identifiers...</span> 691 <span class="c">#</span> 692 <span class="c"># Let:</span> 693 <span class="c"># HBD: HydrogenBondDonor</span> 694 <span class="c"># HBA: HydrogenBondAcceptor</span> 695 <span class="c"># PI : PositivelyIonizable</span> 696 <span class="c"># NI : NegativelyIonizable</span> 697 <span class="c"># Ar : Aromatic</span> 698 <span class="c"># Hal : Halogen</span> 699 <span class="c"># H : Hydrophobic</span> 700 <span class="c"># RA : RingAtom</span> 701 <span class="c"># CA : ChainAtom</span> 702 <span class="c">#</span> 703 <span class="c"># Then:</span> 704 <span class="c">#</span> 705 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> 706 <span class="c">#</span> 707 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> 708 <span class="c">#</span> 709 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> 710 <span class="c">#</span> 711 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> 712 <span class="c">#</span> 713 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> 714 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> 715 <span class="c"># PositivelyIonizable: +, NH2</span> 716 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> 717 <span class="c">#</span> <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 718 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> 719 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 720 721 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span> 722 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span> 723 <span class="c">#</span> 724 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 725 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> 726 727 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 728 <span class="s">}</span> 729 730 <span class="c"># Return a string containg data for AtomNeighborhoodsFingerprints object...</span> 731 <span class="c">#</span> <a name="StringifyAtomNeighborhoodsFingerprints-"></a> 732 <span class="k">sub </span><span class="m">StringifyAtomNeighborhoodsFingerprints</span> <span class="s">{</span> 733 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 734 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span> 735 736 <span class="c"># Type of fingerprint...</span> 737 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}; MinNeighborhoodRadius: $This->{MinNeighborhoodRadius}; MaxNeighborhoodRadius: $This->{MaxNeighborhoodRadius}"</span><span class="sc">;</span> 738 739 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 740 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span> 741 742 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 743 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 744 745 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> 746 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> 747 <span class="s">}</span> 748 749 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 750 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 751 <span class="i">$FingerprintsString</span> .= <span class="q">"; AvailableAtomicInvariants: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 752 <span class="s">}</span> 753 <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> 754 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> 755 756 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 757 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 758 759 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> 760 <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> 761 <span class="s">}</span> 762 763 <span class="i">$FingerprintsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 764 <span class="i">$FingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 765 <span class="i">$FingerprintsString</span> .= <span class="q">"; AvailableFunctionalClasses: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 766 <span class="s">}</span> 767 768 <span class="c"># Total number of atom neighborhood atom IDs...</span> 769 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomNeighborhoodAtomIdentifiers: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 770 771 <span class="c"># FingerprintsVector...</span> 772 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> 773 774 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span> 775 <span class="s">}</span> 776 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>