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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/AtomNeighborhoodsFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,797 @@ +<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>