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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/PathLengthFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,1469 @@ +<html> +<head> +<title>MayaChemTools:Code:Fingerprints::PathLengthFingerprints.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::PathLengthFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::PathLengthFingerprints</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: PathLengthFingerprints.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> + 5 <span class="c"># $Revision: 1.39 $</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">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span> + 38 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> + 39 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> + 40 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span> + 41 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span> + 42 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span> + 43 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> + 44 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span> + 45 + 46 <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> + 47 + 48 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> + 49 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> + 50 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> + 51 + 52 <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> + 53 + 54 <span class="c"># Setup class variables...</span> + 55 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> + 56 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 57 + 58 <span class="c"># Overload Perl functions...</span> + 59 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyPathLengthFingerprints'</span><span class="sc">;</span> + 60 + 61 <span class="c"># Class constructor...</span> +<a name="new-"></a> 62 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> + 63 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 64 + 65 <span class="c"># Initialize object...</span> + 66 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 67 <span class="k">bless</span> <span class="i">$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> + 68 <span class="i">$This</span><span class="i">->_InitializePathLengthFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 69 + 70 <span class="i">$This</span><span class="i">->_InitializePathLengthFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 71 + 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 73 <span class="s">}</span> + 74 + 75 <span class="c"># Initialize object data...</span> + 76 <span class="c">#</span> +<a name="_InitializePathLengthFingerprints-"></a> 77 <span class="k">sub </span><span class="m">_InitializePathLengthFingerprints</span> <span class="s">{</span> + 78 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 79 + 80 <span class="c"># Type of fingerprint to generate...</span> + 81 <span class="c">#</span> + 82 <span class="c"># PathLengthBits - A bit vector indicating presence/absence of atom paths</span> + 83 <span class="c"># PathLengthCount - A vector containing count of atom paths</span> + 84 <span class="c">#</span> + 85 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span> + 86 + 87 <span class="c"># Type of vector: FingerprintsBitVector or FingerprintsVector</span> + 88 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">''</span><span class="sc">;</span> + 89 + 90 <span class="c"># Set default mininum, maximum, and default size. Although any arbitrary size can</span> + 91 <span class="c"># be specified, bit vector used to store bits work on a vector size which is</span> + 92 <span class="c"># power of 2 and additonal bits are automatically added and cleared.</span> + 93 <span class="c">#</span> + 94 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="n">1024</span><span class="sc">;</span> + 95 + 96 <span class="i">$This</span>->{<span class="w">MinSize</span>} = <span class="n">32</span><span class="sc">;</span> + 97 <span class="i">$This</span>->{<span class="w">MaxSize</span>} = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span> + 98 + 99 <span class="c"># Minimum and maximum path lengths to use for fingerprints generation...</span> + 100 <span class="i">$This</span>->{<span class="w">MinLength</span>} = <span class="n">1</span><span class="sc">;</span> + 101 <span class="i">$This</span>->{<span class="w">MaxLength</span>} = <span class="n">8</span><span class="sc">;</span> + 102 + 103 <span class="c"># Numner of bits to set for each atom path for FingerprintsBitVector...</span> + 104 <span class="i">$This</span>->{<span class="w">NumOfBitsToSetPerPath</span>} = <span class="n">1</span><span class="sc">;</span> + 105 + 106 <span class="c"># Atom identifier type to use for path atoms during fingerprints generation...</span> + 107 <span class="c">#</span> + 108 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> + 109 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> + 110 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> + 111 <span class="c">#</span> + 112 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> + 113 + 114 <span class="c"># Atom types assigned to atoms...</span> + 115 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 116 + 117 <span class="c"># For molecules containing rings, atom paths starting from each atom can be traversed in four</span> + 118 <span class="c"># different ways:</span> + 119 <span class="c">#</span> + 120 <span class="c"># . Atom paths without any rings and sharing of bonds in traversed paths.</span> + 121 <span class="c"># . Atom paths containing rings and without any sharing of bonds in traversed paths</span> + 122 <span class="c"># . All possible atom paths without any rings and sharing of bonds in traversed paths</span> + 123 <span class="c"># . All possible atom paths containing rings and with sharing of bonds in traversed paths.</span> + 124 <span class="c">#</span> + 125 <span class="c"># Atom path traversal is terminated at the last ring atom. For molecules containing no rings,</span> + 126 <span class="c"># first two and last two types described above are equivalent.</span> + 127 <span class="c">#</span> + 128 <span class="c"># AllowSharedBonds and AllowRings variables allow generation of differen types of paths</span> + 129 <span class="c"># to be used for fingerprints generation.</span> + 130 <span class="c">#</span> + 131 <span class="c"># In addition to atom symbols, bond symbols are also used to generate a string</span> + 132 <span class="c"># for atom paths. These atom paths strings are hased to a 32 bit integer key which</span> + 133 <span class="c"># in turn is used as a seed for a random number generation in range of 1 to fingerprint</span> + 134 <span class="c"># size for setting corresponding bit in bit vector.</span> + 135 <span class="c">#</span> + 136 <span class="c"># UseBondSymbols variable allow generation of atom path strings and consequently fingerprints.</span> + 137 <span class="c">#</span> + 138 <span class="c"># Combination of AllowSharedBonds, AllowRings, and UseBondSymbols allow generation of</span> + 139 <span class="c"># 8 different types of path length fingerprints:</span> + 140 <span class="c">#</span> + 141 <span class="c"># AllowSharedBonds AllowRings UseBondSymbols PathLengthFingerprintsType</span> + 142 <span class="c">#</span> + 143 <span class="c"># No No Yes AtomPathsNoCyclesWithBondSymbols</span> + 144 <span class="c"># No Yes Yes AtomPathsWithCyclesWithBondSymbols</span> + 145 <span class="c">#</span> + 146 <span class="c"># Yes No Yes AllAtomPathsNoCyclesWithBondSymbols</span> + 147 <span class="c"># Yes Yes Yes AllAtomPathsWithCyclesWithBondSymbols [ DEFAULT ]</span> + 148 <span class="c">#</span> + 149 <span class="c"># No No No AtomPathsNoCyclesNoBondSymbols</span> + 150 <span class="c"># No Yes No AtomPathsWithCyclesNoBondSymbols</span> + 151 <span class="c">#</span> + 152 <span class="c"># Yes No No AllAtomPathsNoCyclesNoBondSymbols</span> + 153 <span class="c"># Yes Yes No AllAtomPathsWithCyclesNoWithBondSymbols</span> + 154 <span class="c">#</span> + 155 <span class="c">#</span> + 156 + 157 <span class="c"># By default, atom paths starting from atoms are allowed to share bonds already traversed...</span> + 158 <span class="i">$This</span>->{<span class="w">AllowSharedBonds</span>} = <span class="n">1</span><span class="sc">;</span> + 159 + 160 <span class="c"># By default rings are included in paths...</span> + 161 <span class="i">$This</span>->{<span class="w">AllowRings</span>} = <span class="n">1</span><span class="sc">;</span> + 162 + 163 <span class="c"># By default bond symbols are included in atom path strings...</span> + 164 <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} = <span class="n">1</span><span class="sc">;</span> + 165 + 166 <span class="c"># By default only structurally unique atom paths are used for generation</span> + 167 <span class="c"># atom path strings...</span> + 168 <span class="i">$This</span>->{<span class="w">UseUniquePaths</span>} = <span class="n">1</span><span class="sc">;</span> + 169 + 170 <span class="c"># Random number generator to use during generation of fingerprints bit-vector</span> + 171 <span class="c"># string: Perl CORE::rand or MayaChemTools MathUtil::random function.</span> + 172 <span class="c">#</span> + 173 <span class="c"># The random number generator implemented in MayaChemTools is a variant of</span> + 174 <span class="c"># linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].</span> + 175 <span class="c"># It is also referred to as Lehmer random number generator or Park-Miller</span> + 176 <span class="c"># random number generator.</span> + 177 <span class="c">#</span> + 178 <span class="c"># Unlike Perl's core random number generator function rand, the random number</span> + 179 <span class="c"># generator implemented in MayaChemTools, MathUtil::random, generates consistent</span> + 180 <span class="c"># random values across different platformsfor a specific random seed and leads</span> + 181 <span class="c"># to generation of portable fingerprints bit-vector strings.</span> + 182 <span class="c">#</span> + 183 <span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>} = <span class="n">1</span><span class="sc">;</span> + 184 + 185 <span class="c"># Bond symbols to use during generation of atom path strings...</span> + 186 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondOrderToSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 187 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondOrderToSymbol</span>}} = <span class="s">(</span><span class="q">'1'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span> <span class="q">'1.5'</span> <span class="cm">=></span> <span class="q">':'</span><span class="cm">,</span> <span class="q">'2'</span> <span class="cm">=></span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'3'</span> <span class="cm">=></span> <span class="q">'#'</span><span class="s">)</span><span class="sc">;</span> + 188 + 189 <span class="c"># BondSymbols map to use for bonded atom IDs to use during atom path strings...</span> + 190 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondSymbols</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 191 + 192 <span class="c"># Path atom IDs to remove duplicate paths...</span> + 193 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueLinearAtomPathsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 194 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueCyclicAtomPathsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 195 + 196 <span class="c"># Reference to all the atom paths upto specified path length...</span> + 197 <span class="i">$This</span>->{<span class="w">AtomPathsRef</span>} = <span class="q">''</span><span class="sc">;</span> + 198 + 199 <span class="c"># Atom paths strings created using specified atom types and bond symbols...</span> + 200 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 201 <span class="s">}</span> + 202 + 203 <span class="c"># Initialize class ...</span> +<a name="_InitializeClass-"></a> 204 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> + 205 <span class="c">#Class name...</span> + 206 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> + 207 <span class="s">}</span> + 208 + 209 <span class="c"># Initialize object properties....</span> +<a name="_InitializePathLengthFingerprintsProperties-"></a> 210 <span class="k">sub </span><span class="m">_InitializePathLengthFingerprintsProperties</span> <span class="s">{</span> + 211 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 212 + 213 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> + 214 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> + 215 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> + 216 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 217 <span class="s">}</span> + 218 + 219 <span class="c"># Make sure molecule object was specified...</span> + 220 <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> + 221 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> + 222 <span class="s">}</span> + 223 + 224 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> + 225 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying Type..."</span><span class="sc">;</span> + 226 <span class="s">}</span> + 227 + 228 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> + 229 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span> + 230 <span class="s">}</span> + 231 + 232 <span class="c"># Make sure it's power of 2...</span> + 233 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span> + 234 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 235 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Specified size value, $NamesAndValues{Size}, must be power of 2..."</span><span class="sc">;</span> + 236 <span class="s">}</span> + 237 <span class="s">}</span> + 238 + 239 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span> + 240 <span class="i">$This</span><span class="i">->_InitializePathLengthBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 241 <span class="s">}</span> + 242 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span> + 243 <span class="i">$This</span><span class="i">->_InitializePathLengthCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 244 <span class="s">}</span> + 245 <span class="k">else</span> <span class="s">{</span> + 246 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializePathLengthFingerprintsProperties: Unknown PathLength type: $This->{Type}; Supported PathLength type : PathLengthBits or PathLengthCount......"</span><span class="sc">;</span> + 247 <span class="s">}</span> + 248 + 249 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 250 <span class="s">}</span> + 251 + 252 <span class="c"># Initialize PathLength bits...</span> + 253 <span class="c">#</span> +<a name="_InitializePathLengthBits-"></a> 254 <span class="k">sub </span><span class="m">_InitializePathLengthBits</span> <span class="s">{</span> + 255 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 256 + 257 <span class="c"># Vector type...</span> + 258 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span> + 259 + 260 <span class="i">$This</span><span class="i">->_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 261 + 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 263 <span class="s">}</span> + 264 + 265 <span class="c"># Initialize PathLength key count...</span> + 266 <span class="c">#</span> +<a name="_InitializePathLengthCount-"></a> 267 <span class="k">sub </span><span class="m">_InitializePathLengthCount</span> <span class="s">{</span> + 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 269 + 270 <span class="c"># Vector type and type of values...</span> + 271 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> + 272 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> + 273 + 274 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 275 + 276 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 277 <span class="s">}</span> + 278 + 279 <span class="c"># Set type...</span> + 280 <span class="c">#</span> +<a name="SetType-"></a> 281 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> + 282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 283 + 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> + 285 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change type: It's already set..."</span><span class="sc">;</span> + 286 <span class="s">}</span> + 287 + 288 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span> + 289 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'PathLengthBits'</span><span class="sc">;</span><span class="sc">;</span> + 290 <span class="s">}</span> + 291 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span> + 292 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'PathLengthCount'</span><span class="sc">;</span><span class="sc">;</span> + 293 <span class="s">}</span> + 294 <span class="k">else</span> <span class="s">{</span> + 295 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Unknown PathLength keys: $Type; Supported PathLength types: PathLengthBits or PathLengthCount..."</span><span class="sc">;</span> + 296 <span class="s">}</span> + 297 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 298 <span class="s">}</span> + 299 + 300 <span class="c"># Disable vector type change...</span> + 301 <span class="c">#</span> +<a name="SetVectorType-"></a> 302 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span> + 303 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 304 + 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Can't change vector type..."</span><span class="sc">;</span> + 306 + 307 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 308 <span class="s">}</span> + 309 + 310 <span class="c"># Disable vector type change...</span> + 311 <span class="c">#</span> +<a name="SetFingerprintsVectorType-"></a> 312 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span> + 313 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 314 + 315 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVectorType: Can't change fingerprints vector type..."</span><span class="sc">;</span> + 316 + 317 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 318 <span class="s">}</span> + 319 + 320 <span class="c"># Set atom identifier type to use for path length atom identifiers...</span> + 321 <span class="c">#</span> +<a name="SetAtomIdentifierType-"></a> 322 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> + 323 <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> + 324 + 325 <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> + 326 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes."</span><span class="sc">;</span> + 327 <span class="s">}</span> + 328 + 329 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> + 330 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change atom identifier type: It's already set..."</span><span class="sc">;</span> + 331 <span class="s">}</span> + 332 + 333 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> + 334 + 335 <span class="c"># Initialize atom identifier type information...</span> + 336 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 337 + 338 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 339 <span class="s">}</span> + 340 + 341 <span class="c"># Set minimum path length...</span> + 342 <span class="c">#</span> +<a name="SetMinLength-"></a> 343 <span class="k">sub </span><span class="m">SetMinLength</span> <span class="s">{</span> + 344 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 345 + 346 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 347 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinLength: MinLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 348 <span class="s">}</span> + 349 <span class="i">$This</span>->{<span class="w">MinLength</span>} = <span class="i">$Value</span><span class="sc">;</span> + 350 + 351 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 352 <span class="s">}</span> + 353 + 354 <span class="c"># Set maximum path length...</span> + 355 <span class="c">#</span> +<a name="SetMaxLength-"></a> 356 <span class="k">sub </span><span class="m">SetMaxLength</span> <span class="s">{</span> + 357 <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> + 358 + 359 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 360 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxLength: MaxLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 361 <span class="s">}</span> + 362 <span class="i">$This</span>->{<span class="w">MaxLength</span>} = <span class="i">$Value</span><span class="sc">;</span> + 363 + 364 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 365 <span class="s">}</span> + 366 + 367 <span class="c"># Set number of bits to set for each path...</span> + 368 <span class="c">#</span> +<a name="SetNumOfBitsToSetPerPath-"></a> 369 <span class="k">sub </span><span class="m">SetNumOfBitsToSetPerPath</span> <span class="s">{</span> + 370 <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> + 371 + 372 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 373 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNumOfBitsToSetPerPath: NumOfBitsToSetPerPath value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 374 <span class="s">}</span> + 375 <span class="i">$This</span>->{<span class="w">NumOfBitsToSetPerPath</span>} = <span class="i">$Value</span><span class="sc">;</span> + 376 + 377 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 378 <span class="s">}</span> + 379 + 380 <span class="c"># Generate fingerprints description...</span> + 381 <span class="c">#</span> +<a name="GetDescription-"></a> 382 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> + 383 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 384 + 385 <span class="c"># Is description explicity set?</span> + 386 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> + 387 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> + 388 <span class="s">}</span> + 389 + 390 <span class="c"># Generate fingerprints description...</span> + 391 + 392 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:MinLength$This->{MinLength}:MaxLength$This->{MaxLength}"</span><span class="sc">;</span> + 393 <span class="s">}</span> + 394 + 395 <span class="c"># Generate path length fingerprints...</span> + 396 <span class="c">#</span> +<a name="GenerateFingerprints-"></a> 397 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> + 398 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 399 + 400 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinLength</span>} > <span class="i">$This</span>->{<span class="w">MaxLength</span>}<span class="s">)</span> <span class="s">{</span> + 401 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateFingerprints: No fingerpritns generated: MinLength, $This->{MinLength}, must be <= MaxLength, $This->{MaxLength}..."</span><span class="sc">;</span> + 402 <span class="s">}</span> + 403 + 404 <span class="c"># Cache appropriate molecule data...</span> + 405 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 406 + 407 <span class="c"># Assign atom types to all atoms...</span> + 408 <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> + 409 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span> + 410 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 411 <span class="s">}</span> + 412 + 413 <span class="c"># Setup bond symbol map...</span> + 414 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span> + 415 <span class="i">$This</span><span class="i">->_InitializeBondSymbols</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 416 <span class="s">}</span> + 417 + 418 <span class="c"># Generate appropriate atom paths...</span> + 419 <span class="i">$This</span><span class="i">->_GenerateAtomPathsUpToMaxLength</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 420 + 421 <span class="c"># Initialize atom path strings...</span> + 422 <span class="i">$This</span><span class="i">->_InitializeAtomPathsStrings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 423 + 424 <span class="c"># Generate appropriate atom path strings for unique atom paths...</span> + 425 <span class="i">$This</span><span class="i">->_GenerateAtomPathsStrings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 426 + 427 <span class="c"># Set final fingerprints...</span> + 428 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 429 + 430 <span class="c"># Clear cached molecule data...</span> + 431 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 432 + 433 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 434 <span class="s">}</span> + 435 + 436 <span class="c"># Assign appropriate atom types to all atoms...</span> + 437 <span class="c">#</span> +<a name="_AssignAtomTypes-"></a> 438 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span> + 439 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 440 <span class="k">my</span><span class="s">(</span><span class="i">$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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 441 + 442 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 443 <span class="i">$IgnoreHydrogens</span> = <span class="n">0</span><span class="sc">;</span> + 444 + 445 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span> + 446 + 447 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> + 448 <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> + 449 <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> + 450 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 451 <span class="s">}</span> + 452 + 453 <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> + 454 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 455 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 456 <span class="s">}</span> + 457 + 458 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 459 <span class="i">$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> + 460 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 461 <span class="s">}</span> + 462 + 463 <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> + 464 <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> + 465 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 466 <span class="s">}</span> + 467 + 468 <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> + 469 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 470 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 471 <span class="s">}</span> + 472 + 473 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 474 <span class="i">$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> + 475 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 476 <span class="s">}</span> + 477 <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> + 478 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 479 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 480 <span class="s">}</span> + 481 + 482 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 483 <span class="i">$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">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> + 484 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 485 <span class="s">}</span> + 486 + 487 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 488 <span class="i">$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> + 489 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 490 <span class="s">}</span> + 491 + 492 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignAtomTypes: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> + 493 <span class="s">}</span> + 494 + 495 <span class="c"># Assign atom types...</span> + 496 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 497 + 498 <span class="c"># Make sure atom types assignment is successful...</span> + 499 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 500 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 501 <span class="s">}</span> + 502 + 503 <span class="c"># Collect assigned atom types...</span> + 504 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> + 505 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 506 <span class="i">$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">$Atom</span><span class="s">)</span><span class="sc">;</span> + 507 <span class="s">}</span> + 508 + 509 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 510 <span class="s">}</span> + 511 + 512 <span class="c"># Setup bond symbol map for atoms to speed up generation of path length identifiers</span> + 513 <span class="c"># during fingerprints generation...</span> + 514 <span class="c">#</span> +<a name="_InitializeBondSymbols-"></a> 515 <span class="k">sub </span><span class="m">_InitializeBondSymbols</span> <span class="s">{</span> + 516 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 517 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondSymbol</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="s">)</span><span class="sc">;</span> + 518 + 519 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondSymbols</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 520 + 521 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span> + 522 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 523 <span class="s">}</span> + 524 + 525 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 526 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 527 <span class="i">$BondSymbol</span> = <span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="q">':'</span> <span class="co">:</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrderToSymbol</span>}{<span class="i">$BondOrder</span>}<span class="s">)</span> ? <span class="i">$This</span>->{<span class="w">BondOrderToSymbol</span>}{<span class="i">$BondOrder</span>} <span class="co">:</span> <span class="i">$BondOrder</span><span class="s">)</span><span class="sc">;</span> + 528 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 529 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 530 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID1</span> > <span class="i">$AtomID2</span><span class="s">)</span> <span class="s">{</span> + 531 <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="s">)</span><span class="sc">;</span> + 532 <span class="s">}</span> + 533 + 534 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span> <span class="s">{</span> + 535 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$AtomID1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 536 <span class="s">}</span> + 537 <span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$AtomID1</span>}{<span class="i">$AtomID2</span>} = <span class="i">$BondSymbol</span><span class="sc">;</span> + 538 <span class="s">}</span> + 539 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 540 <span class="s">}</span> + 541 + 542 <span class="c"># Get appropriate atom paths with length up to MaxLength...</span> + 543 <span class="c">#</span> +<a name="_GenerateAtomPathsUpToMaxLength-"></a> 544 <span class="k">sub </span><span class="m">_GenerateAtomPathsUpToMaxLength</span> <span class="s">{</span> + 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 546 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AllowRings</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$AtomPathsRef</span><span class="s">)</span><span class="sc">;</span> + 547 + 548 <span class="i">$PathLength</span> = <span class="i">$This</span>->{<span class="w">MaxLength</span>}<span class="sc">;</span> + 549 <span class="i">$AllowRings</span> = <span class="i">$This</span>->{<span class="w">AllowRings</span>}<span class="sc">;</span> + 550 <span class="i">$Molecule</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="sc">;</span> + 551 + 552 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AllowSharedBonds</span>}<span class="s">)</span> <span class="s">{</span> + 553 <span class="i">$AtomPathsRef</span> = <span class="i">$Molecule</span><span class="i">->GetAllAtomPathsWithLengthUpto</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AllowRings</span><span class="s">)</span><span class="sc">;</span> + 554 <span class="s">}</span> + 555 <span class="k">else</span> <span class="s">{</span> + 556 <span class="i">$AtomPathsRef</span> = <span class="i">$Molecule</span><span class="i">->GetAtomPathsWithLengthUpto</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AllowRings</span><span class="s">)</span><span class="sc">;</span> + 557 <span class="s">}</span> + 558 <span class="i">$This</span>->{<span class="w">AtomPathsRef</span>} = <span class="i">$AtomPathsRef</span><span class="sc">;</span> + 559 + 560 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 561 <span class="s">}</span> + 562 + 563 <span class="c"># Initialize atom paths strings at various pathlength levels...</span> + 564 <span class="c">#</span> +<a name="_InitializeAtomPathsStrings-"></a> 565 <span class="k">sub </span><span class="m">_InitializeAtomPathsStrings</span> <span class="s">{</span> + 566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 567 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="s">)</span><span class="sc">;</span> + 568 + 569 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 570 + 571 <span class="k">for</span> <span class="i">$PathLength</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinLength</span>} .. <span class="i">$This</span>->{<span class="w">MaxLength</span>}<span class="s">)</span> <span class="s">{</span> + 572 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 573 <span class="s">}</span> + 574 + 575 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 576 <span class="s">}</span> + 577 + 578 <span class="c"># Generate appropriate atom path strings for unique atom paths...</span> + 579 <span class="c">#</span> +<a name="_GenerateAtomPathsStrings-"></a> 580 <span class="k">sub </span><span class="m">_GenerateAtomPathsStrings</span> <span class="s">{</span> + 581 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 582 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$MinPathLength</span><span class="cm">,</span> <span class="i">$UseUniquePaths</span><span class="s">)</span><span class="sc">;</span> + 583 + 584 <span class="i">$MinPathLength</span> = <span class="i">$This</span>->{<span class="w">MinLength</span>}<span class="sc">;</span> + 585 <span class="i">$UseUniquePaths</span> = <span class="i">$This</span>->{<span class="w">UseUniquePaths</span>}<span class="sc">;</span> + 586 + 587 <span class="j">PATHATOMS:</span> <span class="k">for</span> <span class="i">$PathAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPathsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 588 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> + 589 <span class="k">if</span> <span class="s">(</span><span class="i">$PathLength</span> < <span class="i">$MinPathLength</span><span class="s">)</span> <span class="s">{</span> + 590 <span class="k">next</span> <span class="j">PATHATOMS</span><span class="sc">;</span> + 591 <span class="s">}</span> + 592 <span class="k">if</span> <span class="s">(</span><span class="i">$UseUniquePaths</span><span class="s">)</span> <span class="s">{</span> + 593 <span class="i">$This</span><span class="i">->_GenerateAtomPathStringUsingUniquePath</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 594 <span class="s">}</span> + 595 <span class="k">else</span> <span class="s">{</span> + 596 <span class="i">$This</span><span class="i">->_GenerateAtomPathString</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 597 <span class="s">}</span> + 598 <span class="s">}</span> + 599 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 600 <span class="s">}</span> + 601 + 602 <span class="c"># Generate atom path string using unique path...</span> + 603 <span class="c">#</span> +<a name="_GenerateAtomPathStringUsingUniquePath-"></a> 604 <span class="k">sub </span><span class="m">_GenerateAtomPathStringUsingUniquePath</span> <span class="s">{</span> + 605 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 606 + 607 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AllowRings</span>} && <span class="i">$This</span><span class="i">->_DoesAtomPathContainsCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 608 <span class="i">$This</span><span class="i">->_GenerateAtomPathStringUsingUniquePathContainingCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 609 <span class="s">}</span> + 610 <span class="k">else</span> <span class="s">{</span> + 611 <span class="i">$This</span><span class="i">->_GenerateAtomPathStringUsingUniqueLinearPath</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 612 <span class="s">}</span> + 613 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 614 <span class="s">}</span> + 615 + 616 <span class="c"># Generate atom path string for specified path containing no cycle...</span> + 617 <span class="c">#</span> +<a name="_GenerateAtomPathStringUsingUniqueLinearPath-"></a> 618 <span class="k">sub </span><span class="m">_GenerateAtomPathStringUsingUniqueLinearPath</span> <span class="s">{</span> + 619 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 620 + 621 <span class="c"># Is it a unique linear atom path?</span> + 622 <span class="c">#</span> + 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_IsUniqueLinearAtomPath</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 624 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 625 <span class="s">}</span> + 626 <span class="i">$This</span><span class="i">->_GenerateAtomPathString</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 627 + 628 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 629 <span class="s">}</span> + 630 + 631 <span class="c"># Is it a structurally unique linear path?</span> + 632 <span class="c">#</span> + 633 <span class="c"># For a path to be structurally unique, all of its atom IDs must be diffferent from any</span> + 634 <span class="c"># earlier path atom IDs. In order to generate atom path atom ID invariant of the atom</span> + 635 <span class="c"># order in the molecule, atom IDs are sorted numerically before generating the path ID.</span> + 636 <span class="c">#</span> + 637 <span class="c"># Notes:</span> + 638 <span class="c"># . Atom path ID doesn't reflect the order of atoms in the atom path.</span> + 639 <span class="c">#</span> +<a name="_IsUniqueLinearAtomPath-"></a> 640 <span class="k">sub </span><span class="m">_IsUniqueLinearAtomPath</span> <span class="s">{</span> + 641 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 642 <span class="k">my</span><span class="s">(</span><span class="i">$AtomPathID</span><span class="cm">,</span> <span class="i">$PathLength</span><span class="cm">,</span> <span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> + 643 + 644 <span class="i">@PathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 645 <span class="i">@PathAtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> + 646 + 647 <span class="i">$AtomPathID</span> = <span class="k">join</span> <span class="q">'-'</span><span class="cm">,</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="i">@PathAtomIDs</span><span class="sc">;</span> + 648 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">UniqueLinearAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>}<span class="s">)</span> <span class="s">{</span> + 649 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 650 <span class="s">}</span> + 651 + 652 <span class="c"># It's a unique atom path...</span> + 653 <span class="i">$This</span>->{<span class="w">UniqueLinearAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>} = <span class="n">1</span><span class="sc">;</span> + 654 + 655 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> + 656 <span class="s">}</span> + 657 + 658 <span class="c"># Generate atom path string for specified path containing a cycle...</span> + 659 <span class="c">#</span> +<a name="_GenerateAtomPathStringUsingUniquePathContainingCycle-"></a> 660 <span class="k">sub </span><span class="m">_GenerateAtomPathStringUsingUniquePathContainingCycle</span> <span class="s">{</span> + 661 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 662 + 663 <span class="c"># Is it a unique atom path containing a cycle?</span> + 664 <span class="c">#</span> + 665 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_IsUniqueAtomPathContainingCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 666 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 667 <span class="s">}</span> + 668 + 669 <span class="k">my</span><span class="s">(</span><span class="i">$CycleClosingPathAtomIndex</span><span class="s">)</span><span class="sc">;</span> + 670 <span class="s">(</span><span class="i">$CycleClosingPathAtomIndex</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetAtomPathCycleClosingAtomIndex</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 671 + 672 <span class="k">if</span> <span class="s">(</span><span class="i">$CycleClosingPathAtomIndex</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 673 <span class="i">$This</span><span class="i">->_GenerateUniqueAtomPathStringForPathCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 674 <span class="s">}</span> + 675 <span class="k">else</span> <span class="s">{</span> + 676 <span class="i">$This</span><span class="i">->_GenerateUniqueAtomPathStringForPathContainingCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$CycleClosingPathAtomIndex</span><span class="s">)</span><span class="sc">;</span> + 677 <span class="s">}</span> + 678 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 679 <span class="s">}</span> + 680 + 681 <span class="c"># Generate a unique atom path string for a cyclic path by generating atom path</span> + 682 <span class="c"># strings for all possible paths in the cycle and keeping the lexicographically smallest</span> + 683 <span class="c"># one.</span> + 684 <span class="c">#</span> + 685 <span class="c"># Although all the paths enumerated during atom path string generation are also</span> + 686 <span class="c"># present in the intial paths list, but structural uniqueness check would detect</span> + 687 <span class="c"># 'em earlier and this method ends being invoked only once for the first cyclic path.</span> + 688 <span class="c">#</span> + 689 <span class="c"># For atom paths containg same atom types and bond symbols, atom path strings</span> + 690 <span class="c"># would be same for the paths.</span> + 691 <span class="c">#</span> +<a name="_GenerateUniqueAtomPathStringForPathCycle-"></a> 692 <span class="k">sub </span><span class="m">_GenerateUniqueAtomPathStringForPathCycle</span> <span class="s">{</span> + 693 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 694 + 695 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_AreAllPathAtomsSymbolsSame</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->_AreAllPathBondSymbolsSame</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 696 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GenerateAtomPathString</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 697 <span class="s">}</span> + 698 + 699 <span class="c"># Generate all possible atom path strings and select the lexicographically smallest one...</span> + 700 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$FinalAtomPathString</span><span class="cm">,</span> <span class="i">$FirstAtomPathString</span><span class="cm">,</span> <span class="i">$LastIndex</span><span class="cm">,</span> <span class="i">$FirstPartIndex</span><span class="cm">,</span> <span class="i">$FirstPartStartIndex</span><span class="cm">,</span> <span class="i">$FirstPartEndIndex</span><span class="cm">,</span> <span class="i">$SecondPartIndex</span><span class="cm">,</span> <span class="i">$SecondPartStartIndex</span><span class="cm">,</span> <span class="i">$SecondPartEndIndex</span><span class="cm">,</span> <span class="i">$AtomPathSymbolsRef</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$ReverseAtomPathString</span><span class="cm">,</span> <span class="i">@FirstPartPathAtoms</span><span class="cm">,</span> <span class="i">@SecondPartPathAtoms</span><span class="cm">,</span> <span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> + 701 + 702 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> + 703 <span class="i">$LastIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span> + 704 + 705 <span class="i">$FinalAtomPathString</span> = <span class="q">''</span><span class="sc">;</span> + 706 <span class="i">$FirstAtomPathString</span> = <span class="n">1</span><span class="sc">;</span> + 707 + 708 <span class="i">@FirstPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@SecondPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 709 + 710 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$LastIndex</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 711 <span class="i">@FirstPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@SecondPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 712 + 713 <span class="i">$FirstPartStartIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$FirstPartEndIndex</span> = <span class="i">$Index</span> - <span class="n">1</span><span class="sc">;</span> + 714 <span class="i">$SecondPartStartIndex</span> = <span class="i">$Index</span><span class="sc">;</span> <span class="i">$SecondPartEndIndex</span> = <span class="i">$LastIndex</span> - <span class="n">1</span><span class="sc">;</span> + 715 + 716 <span class="c"># Get first part atoms...</span> + 717 <span class="k">for</span> <span class="i">$FirstPartIndex</span> <span class="s">(</span><span class="i">$FirstPartStartIndex</span> .. <span class="i">$FirstPartEndIndex</span><span class="s">)</span> <span class="s">{</span> + 718 <span class="k">push</span> <span class="i">@FirstPartPathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>->[<span class="i">$FirstPartIndex</span>]<span class="sc">;</span> + 719 <span class="s">}</span> + 720 + 721 <span class="c"># Get second part atoms...</span> + 722 <span class="k">for</span> <span class="i">$SecondPartIndex</span> <span class="s">(</span><span class="i">$SecondPartStartIndex</span> .. <span class="i">$SecondPartEndIndex</span><span class="s">)</span> <span class="s">{</span> + 723 <span class="k">push</span> <span class="i">@SecondPartPathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>->[<span class="i">$SecondPartIndex</span>]<span class="sc">;</span> + 724 <span class="s">}</span> + 725 + 726 <span class="c"># Get final list of path atoms...</span> + 727 <span class="k">if</span> <span class="s">(</span><span class="i">@SecondPartPathAtoms</span><span class="s">)</span> <span class="s">{</span> + 728 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">@SecondPartPathAtoms</span><span class="sc">;</span> + 729 <span class="s">}</span> + 730 <span class="k">if</span> <span class="s">(</span><span class="i">@FirstPartPathAtoms</span><span class="s">)</span> <span class="s">{</span> + 731 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">@FirstPartPathAtoms</span><span class="sc">;</span> + 732 <span class="s">}</span> + 733 + 734 <span class="c"># Complete the cycle by adding first atom as the last atom...</span> + 735 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>->[<span class="i">$SecondPartStartIndex</span>]<span class="sc">;</span> + 736 + 737 <span class="c"># Generate atom path string...</span> + 738 <span class="i">$AtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">->_GenerateAtomPathSymbols</span><span class="s">(</span>\<span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> + 739 + 740 <span class="i">$AtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span> + 741 <span class="i">$ReverseAtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span> + 742 + 743 <span class="k">if</span> <span class="s">(</span><span class="i">$ReverseAtomPathString</span> <span class="k">le</span> <span class="i">$AtomPathString</span><span class="s">)</span> <span class="s">{</span> + 744 <span class="i">$AtomPathString</span> = <span class="i">$ReverseAtomPathString</span><span class="sc">;</span> + 745 <span class="s">}</span> + 746 + 747 <span class="c"># Update final atom path string...</span> + 748 + 749 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomPathString</span><span class="s">)</span> <span class="s">{</span> + 750 <span class="i">$FirstAtomPathString</span> = <span class="n">0</span><span class="sc">;</span> + 751 <span class="i">$FinalAtomPathString</span> = <span class="i">$AtomPathString</span><span class="sc">;</span> + 752 <span class="s">}</span> + 753 <span class="k">else</span> <span class="s">{</span> + 754 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomPathString</span> <span class="k">le</span> <span class="i">$FinalAtomPathString</span><span class="s">)</span> <span class="s">{</span> + 755 <span class="i">$FinalAtomPathString</span> = <span class="i">$AtomPathString</span><span class="sc">;</span> + 756 <span class="s">}</span> + 757 <span class="s">}</span> + 758 <span class="s">}</span> + 759 + 760 <span class="c"># Set final atom path string...</span> + 761 <span class="c">#</span> + 762 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$FinalAtomPathString</span>}<span class="s">)</span> <span class="s">{</span> + 763 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$FinalAtomPathString</span>} += <span class="n">1</span><span class="sc">;</span> + 764 <span class="s">}</span> + 765 <span class="k">else</span> <span class="s">{</span> + 766 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$FinalAtomPathString</span>} = <span class="n">1</span><span class="sc">;</span> + 767 <span class="s">}</span> + 768 + 769 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 770 <span class="s">}</span> + 771 + 772 <span class="c">#</span> + 773 <span class="c"># Generate a unique atom path string for paths containing a cycle closed by</span> + 774 <span class="c"># the specified atom index and the last atom index.</span> + 775 <span class="c">#</span> + 776 <span class="c"># The following methodology is used to generate atom path string which is</span> + 777 <span class="c"># independemt of initial atom ordering:</span> + 778 <span class="c"># . Generate atom paths string from first atom to the atom before the first cycle</span> + 779 <span class="c"># closing atom.</span> + 780 <span class="c"># . Generate atom path string from atoms from first cycle closing atom index to</span> + 781 <span class="c"># the last path atom in both forward and reverse order. And select the lexicographically</span> + 782 <span class="c"># smallest atom path string.</span> + 783 <span class="c"># . Combine atom path string generated in first step with second step to generate</span> + 784 <span class="c"># final atom path string.</span> + 785 <span class="c">#</span> +<a name="_GenerateUniqueAtomPathStringForPathContainingCycle-"></a> 786 <span class="k">sub </span><span class="m">_GenerateUniqueAtomPathStringForPathContainingCycle</span> <span class="s">{</span> + 787 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$CycleClosingAtomIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 788 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$LastIndex</span><span class="cm">,</span> <span class="i">$LinearPartStartIndex</span><span class="cm">,</span> <span class="i">$LinearPartEndIndex</span><span class="cm">,</span> <span class="i">$CyclicPartStartIndex</span><span class="cm">,</span> <span class="i">$CyclicPartEndIndex</span><span class="cm">,</span> <span class="i">$CyclicPartAtomPathSymbolsRef</span><span class="cm">,</span> <span class="i">$CyclicPartAtomPathString</span><span class="cm">,</span> <span class="i">$ReverseCyclicPartAtomPathString</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$AtomPathSymbolsRef</span><span class="cm">,</span> <span class="i">@CyclicPartPathAtoms</span><span class="cm">,</span> <span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> + 789 + 790 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> + 791 <span class="i">$LastIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span> + 792 + 793 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 794 + 795 <span class="c"># Get path atoms corresponding to linear part of the path...</span> + 796 <span class="i">$LinearPartStartIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$LinearPartEndIndex</span> = <span class="i">$CycleClosingAtomIndex</span> - <span class="n">1</span><span class="sc">;</span> + 797 + 798 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="i">$LinearPartStartIndex</span> .. <span class="i">$LinearPartEndIndex</span><span class="s">)</span> <span class="s">{</span> + 799 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> + 800 <span class="s">}</span> + 801 + 802 <span class="c"># Get atoms correcponding to cyclic part of the path...</span> + 803 <span class="i">@CyclicPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 804 <span class="i">$CyclicPartStartIndex</span> = <span class="i">$CycleClosingAtomIndex</span><span class="sc">;</span> <span class="i">$CyclicPartEndIndex</span> = <span class="i">$LastIndex</span><span class="sc">;</span> + 805 + 806 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="i">$CyclicPartStartIndex</span> .. <span class="i">$CyclicPartEndIndex</span><span class="s">)</span> <span class="s">{</span> + 807 <span class="k">push</span> <span class="i">@CyclicPartPathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> + 808 <span class="s">}</span> + 809 + 810 <span class="c"># Setup a lexicographically smaller atom path string for cyclic part...</span> + 811 + 812 <span class="i">$CyclicPartAtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">->_GenerateAtomPathSymbols</span><span class="s">(</span>\<span class="i">@CyclicPartPathAtoms</span><span class="s">)</span><span class="sc">;</span> + 813 <span class="i">$CyclicPartAtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$CyclicPartAtomPathSymbolsRef</span>}<span class="sc">;</span> + 814 <span class="i">$ReverseCyclicPartAtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@</span>{<span class="i">$CyclicPartAtomPathSymbolsRef</span>}<span class="sc">;</span> + 815 + 816 <span class="c"># Setup atom path corresponding to linear part and lexigraphicall smaller cyclic part...</span> + 817 + 818 <span class="k">if</span> <span class="s">(</span><span class="i">$ReverseCyclicPartAtomPathString</span> <span class="k">le</span> <span class="i">$CyclicPartAtomPathString</span><span class="s">)</span> <span class="s">{</span> + 819 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@CyclicPartPathAtoms</span><span class="sc">;</span> + 820 <span class="s">}</span> + 821 <span class="k">else</span> <span class="s">{</span> + 822 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">@CyclicPartPathAtoms</span><span class="sc">;</span> + 823 <span class="s">}</span> + 824 + 825 <span class="c"># Setup final atom path string...</span> + 826 + 827 <span class="i">$AtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">->_GenerateAtomPathSymbols</span><span class="s">(</span>\<span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> + 828 <span class="i">$AtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span> + 829 + 830 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>}<span class="s">)</span> <span class="s">{</span> + 831 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} += <span class="n">1</span><span class="sc">;</span> + 832 <span class="s">}</span> + 833 <span class="k">else</span> <span class="s">{</span> + 834 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} = <span class="n">1</span><span class="sc">;</span> + 835 <span class="s">}</span> + 836 + 837 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 838 <span class="s">}</span> + 839 + 840 <span class="c"># Does atom path contain a cycle?</span> + 841 <span class="c">#</span> + 842 <span class="c"># For an atom path to contain cycle, it must satisfy the following conditions:</span> + 843 <span class="c"># . Pathlength >= 3</span> + 844 <span class="c"># . Last atom ID is equal to first atom ID or some other atom ID besides itself</span> + 845 <span class="c">#</span> +<a name="_DoesAtomPathContainsCycle-"></a> 846 <span class="k">sub </span><span class="m">_DoesAtomPathContainsCycle</span> <span class="s">{</span> + 847 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 848 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="s">)</span><span class="sc">;</span> + 849 + 850 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> + 851 <span class="k">if</span> <span class="s">(</span><span class="i">$PathLength</span> <= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 852 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 853 <span class="s">}</span> + 854 + 855 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIndex</span><span class="cm">,</span> <span class="i">$LastAtomIndex</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$LastAtom</span><span class="cm">,</span> <span class="i">$LastAtomID</span><span class="s">)</span><span class="sc">;</span> + 856 + 857 <span class="i">$LastAtomIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span> + 858 <span class="i">$LastAtom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$LastAtomIndex</span>]<span class="sc">;</span> + 859 <span class="i">$LastAtomID</span> = <span class="i">$LastAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 860 + 861 <span class="c"># Look for atomID similar to last atom ID...</span> + 862 <span class="k">for</span> <span class="i">$AtomIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$LastAtomIndex</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 863 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$AtomIndex</span>]<span class="sc">;</span> + 864 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 865 + 866 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID</span> == <span class="i">$LastAtomID</span><span class="s">)</span> <span class="s">{</span> + 867 <span class="c"># It's a cycle...</span> + 868 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> + 869 <span class="s">}</span> + 870 <span class="s">}</span> + 871 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 872 <span class="s">}</span> + 873 + 874 <span class="c"># Get atom path cycle closing atom index...</span> + 875 <span class="c">#</span> +<a name="_GetAtomPathCycleClosingAtomIndex-"></a> 876 <span class="k">sub </span><span class="m">_GetAtomPathCycleClosingAtomIndex</span> <span class="s">{</span> + 877 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 878 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIndex</span><span class="cm">,</span> <span class="i">$LastAtomIndex</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$LastAtom</span><span class="cm">,</span> <span class="i">$LastAtomID</span><span class="cm">,</span> <span class="i">$PathLength</span><span class="s">)</span><span class="sc">;</span> + 879 + 880 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> + 881 + 882 <span class="i">$LastAtomIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span> + 883 <span class="i">$LastAtom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$LastAtomIndex</span>]<span class="sc">;</span> <span class="i">$LastAtomID</span> = <span class="i">$LastAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 884 + 885 <span class="c"># Look for atomID similar to last atom ID...</span> + 886 <span class="k">for</span> <span class="i">$AtomIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$LastAtomIndex</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 887 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$AtomIndex</span>]<span class="sc">;</span> <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> + 888 + 889 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID</span> == <span class="i">$LastAtomID</span><span class="s">)</span> <span class="s">{</span> + 890 <span class="c"># It's a cycle closing atom...</span> + 891 <span class="k">return</span> <span class="i">$AtomIndex</span><span class="sc">;</span> + 892 <span class="s">}</span> + 893 <span class="s">}</span> + 894 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 895 <span class="s">}</span> + 896 + 897 <span class="c"># Is it a structurally unique path containing a cycle?</span> + 898 <span class="c">#</span> + 899 <span class="c"># For atom paths containing cycles, last atom ID is either equal to first atom ID or</span> + 900 <span class="c"># some other atom ID besides itself.</span> + 901 <span class="c">#</span> + 902 <span class="c"># In order to determine its structurally unqiue independent of initial atom ordering,</span> + 903 <span class="c"># the following methodolgy is used:</span> + 904 <span class="c">#</span> + 905 <span class="c"># . For paths with same first and atom IDs:</span> + 906 <span class="c"># . Remove the last atom ID from atom path</span> + 907 <span class="c"># . Sort atom IDs in the path</span> + 908 <span class="c"># . Add first atom ID from the sorted list to the end of list to complete the cycle</span> + 909 <span class="c"># . Generate a atom path ID</span> + 910 <span class="c"># . Use final path ID to track uniqueness of path containing cycle.</span> + 911 <span class="c">#</span> + 912 <span class="c"># . For paths with last atom ID equal to some other atom ID besidies itself:</span> + 913 <span class="c"># . Sort atom IDs in atom path</span> + 914 <span class="c"># . Generate atom path ID and use it to track unqiueness of atom paths.</span> + 915 <span class="c">#</span> +<a name="_IsUniqueAtomPathContainingCycle-"></a> 916 <span class="k">sub </span><span class="m">_IsUniqueAtomPathContainingCycle</span> <span class="s">{</span> + 917 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 918 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AtomPathID</span><span class="cm">,</span> <span class="i">$FirstAtom</span><span class="cm">,</span> <span class="i">$LastAtom</span><span class="cm">,</span> <span class="i">$FirstAtomID</span><span class="cm">,</span> <span class="i">$LastAtomID</span><span class="cm">,</span> <span class="i">@PathAtomIDs</span><span class="cm">,</span> <span class="i">@SortedPathAtomIDs</span><span class="s">)</span><span class="sc">;</span> + 919 + 920 <span class="i">@PathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 921 <span class="i">@PathAtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> + 922 + 923 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> + 924 + 925 <span class="i">$FirstAtom</span> = <span class="i">$PathAtomsRef</span>->[<span class="n">0</span>]<span class="sc">;</span> <span class="i">$FirstAtomID</span> = <span class="i">$FirstAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 926 <span class="i">$LastAtom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$PathLength</span> - <span class="n">1</span>]<span class="sc">;</span> <span class="i">$LastAtomID</span> = <span class="i">$LastAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 927 + 928 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomID</span> == <span class="i">$LastAtomID</span><span class="s">)</span> <span class="s">{</span> + 929 <span class="k">pop</span> <span class="i">@PathAtomIDs</span><span class="sc">;</span> + 930 + 931 <span class="i">@SortedPathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 932 <span class="i">@SortedPathAtomIDs</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="i">@PathAtomIDs</span><span class="sc">;</span> + 933 + 934 <span class="k">push</span> <span class="i">@SortedPathAtomIDs</span><span class="cm">,</span> <span class="i">$SortedPathAtomIDs</span>[<span class="n">0</span>]<span class="sc">;</span> + 935 + 936 <span class="i">$AtomPathID</span> = <span class="k">join</span> <span class="q">'-'</span><span class="cm">,</span> <span class="i">@SortedPathAtomIDs</span><span class="sc">;</span> + 937 <span class="s">}</span> + 938 <span class="k">else</span> <span class="s">{</span> + 939 <span class="i">$AtomPathID</span> = <span class="k">join</span> <span class="q">'-'</span><span class="cm">,</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="i">@PathAtomIDs</span><span class="sc">;</span> + 940 <span class="s">}</span> + 941 + 942 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">UniqueCyclicAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>}<span class="s">)</span> <span class="s">{</span> + 943 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 944 <span class="s">}</span> + 945 + 946 <span class="c"># It's a unique atom path containing a cycle...</span> + 947 <span class="i">$This</span>->{<span class="w">UniqueCyclicAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>} = <span class="n">1</span><span class="sc">;</span> + 948 + 949 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> + 950 <span class="s">}</span> + 951 + 952 <span class="c"># Generate atom path string for specified atom path...</span> + 953 <span class="c">#</span> +<a name="_GenerateAtomPathString-"></a> 954 <span class="k">sub </span><span class="m">_GenerateAtomPathString</span> <span class="s">{</span> + 955 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 956 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$ReverseAtomPathString</span><span class="cm">,</span> <span class="i">$AtomPathSymbolsRef</span><span class="s">)</span><span class="sc">;</span> + 957 + 958 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> + 959 + 960 <span class="c"># Generate path atom and bond symbols...</span> + 961 <span class="c">#</span> + 962 <span class="i">$AtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">->_GenerateAtomPathSymbols</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 963 + 964 <span class="c"># Check presence of path using path ID created by atom path symbols...</span> + 965 <span class="i">$AtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span> + 966 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>}<span class="s">)</span> <span class="s">{</span> + 967 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} += <span class="n">1</span><span class="sc">;</span> + 968 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 969 <span class="s">}</span> + 970 + 971 <span class="c"># Check presence of reverse path using path ID created by atom path symbols...</span> + 972 <span class="c">#</span> + 973 <span class="i">$ReverseAtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span> + 974 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$ReverseAtomPathString</span>}<span class="s">)</span> <span class="s">{</span> + 975 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$ReverseAtomPathString</span>} += <span class="n">1</span><span class="sc">;</span> + 976 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 977 <span class="s">}</span> + 978 + 979 <span class="c"># Use lexicographically smaller atom path string as PathID...</span> + 980 <span class="c">#</span> + 981 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomPathString</span> <span class="k">le</span> <span class="i">$ReverseAtomPathString</span><span class="s">)</span> <span class="s">{</span> + 982 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} = <span class="n">1</span><span class="sc">;</span> + 983 <span class="s">}</span> + 984 <span class="k">else</span> <span class="s">{</span> + 985 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$ReverseAtomPathString</span>} = <span class="n">1</span><span class="sc">;</span> + 986 <span class="s">}</span> + 987 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 988 <span class="s">}</span> + 989 + 990 <span class="c"># Are atom types for all path atoms same?</span> + 991 <span class="c">#</span> +<a name="_AreAllPathAtomsSymbolsSame-"></a> 992 <span class="k">sub </span><span class="m">_AreAllPathAtomsSymbolsSame</span> <span class="s">{</span> + 993 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 994 <span class="k">my</span><span class="s">(</span><span class="i">$Index</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">$AtomType</span><span class="cm">,</span> <span class="i">$FirstAtomType</span><span class="s">)</span><span class="sc">;</span> + 995 + 996 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="n">0</span>]<span class="sc">;</span> <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> + 997 <span class="i">$FirstAtomType</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> + 998 + 999 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> +1000 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1001 <span class="i">$AtomType</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> +1002 +1003 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> <span class="k">ne</span> <span class="i">$FirstAtomType</span><span class="s">)</span> <span class="s">{</span> +1004 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> +1005 <span class="s">}</span> +1006 <span class="s">}</span> +1007 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> +1008 <span class="s">}</span> +1009 +1010 <span class="c"># Are bond symbols for all path bonds same?</span> +1011 <span class="c">#</span> +<a name="_AreAllPathBondSymbolsSame-"></a>1012 <span class="k">sub </span><span class="m">_AreAllPathBondSymbolsSame</span> <span class="s">{</span> +1013 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1014 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="cm">,</span> <span class="i">$FirstBondSymbol</span><span class="cm">,</span> <span class="i">$BondSymbol</span><span class="s">)</span><span class="sc">;</span> +1015 +1016 <span class="c"># During no usage of bond symbols, just ignore them and assume they are same...</span> +1017 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span> +1018 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> +1019 <span class="s">}</span> +1020 +1021 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="n">0</span>]<span class="sc">;</span> <span class="i">$BondedAtom</span> = <span class="i">$PathAtomsRef</span>->[<span class="n">1</span>]<span class="sc">;</span> +1022 <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> <span class="i">$BondedAtomID</span> = <span class="i">$BondedAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1023 +1024 <span class="s">(</span><span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomID</span> < <span class="i">$BondedAtomID</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> +1025 <span class="i">$FirstBondSymbol</span> = <span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$BondAtomID1</span>}{<span class="i">$BondAtomID2</span>}<span class="sc">;</span> +1026 +1027 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="s">(</span><span class="i">$#</span>{<span class="i">$PathAtomsRef</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1028 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$BondedAtom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> +1029 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$BondedAtomID</span> = <span class="i">$BondedAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1030 +1031 <span class="s">(</span><span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomID</span> < <span class="i">$BondedAtomID</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> +1032 <span class="i">$BondSymbol</span> = <span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$BondAtomID1</span>}{<span class="i">$BondAtomID2</span>}<span class="sc">;</span> +1033 +1034 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> <span class="k">ne</span> <span class="i">$FirstBondSymbol</span><span class="s">)</span> <span class="s">{</span> +1035 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> +1036 <span class="s">}</span> +1037 <span class="s">}</span> +1038 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> +1039 <span class="s">}</span> +1040 +1041 <span class="c"># Generate atom path symbols...</span> +1042 <span class="c">#</span> +<a name="_GenerateAtomPathSymbols-"></a>1043 <span class="k">sub </span><span class="m">_GenerateAtomPathSymbols</span> <span class="s">{</span> +1044 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1045 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@AtomPathSymbols</span><span class="s">)</span><span class="sc">;</span> +1046 +1047 <span class="i">@AtomPathSymbols</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1048 +1049 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>} == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> +1050 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="n">0</span>]<span class="sc">;</span> <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> +1051 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> +1052 <span class="k">return</span> \<span class="i">@AtomPathSymbols</span><span class="sc">;</span> +1053 <span class="s">}</span> +1054 +1055 <span class="c"># Ignore bond information...</span> +1056 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span> +1057 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> +1058 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1059 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> +1060 <span class="s">}</span> +1061 <span class="k">return</span> \<span class="i">@AtomPathSymbols</span><span class="sc">;</span> +1062 <span class="s">}</span> +1063 +1064 <span class="c"># Use atoms and bonds to generate atom path string...</span> +1065 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="s">)</span><span class="sc">;</span> +1066 +1067 <span class="c"># Process atom type of first atom in path...</span> +1068 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="n">0</span>]<span class="sc">;</span> <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> +1069 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> +1070 +1071 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$#</span>{<span class="i">$PathAtomsRef</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1072 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$BondedAtom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> +1073 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$BondedAtomID</span> = <span class="i">$BondedAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1074 +1075 <span class="s">(</span><span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomID</span> < <span class="i">$BondedAtomID</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> +1076 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$BondAtomID1</span>}{<span class="i">$BondAtomID2</span>}<span class="sc">;</span> +1077 +1078 <span class="c"># Process atom type of next atom in path...</span> +1079 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$BondedAtomID</span>}<span class="sc">;</span> +1080 <span class="s">}</span> +1081 <span class="k">return</span> \<span class="i">@AtomPathSymbols</span><span class="sc">;</span> +1082 <span class="s">}</span> +1083 +1084 <span class="c"># Set final fingerprits...</span> +1085 <span class="c">#</span> +<a name="_SetFinalFingerprints-"></a>1086 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> +1087 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1088 +1089 <span class="c"># Mark successful generation of fingerprints...</span> +1090 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> +1091 +1092 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span> +1093 <span class="i">$This</span><span class="i">->_SetFinalFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1094 <span class="s">}</span> +1095 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span> +1096 <span class="i">$This</span><span class="i">->_SetFinalFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1097 <span class="s">}</span> +1098 +1099 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1100 <span class="s">}</span> +1101 +1102 <span class="c"># Set final fingerprits bit vector...</span> +1103 <span class="c">#</span> +<a name="_SetFinalFingerprintsBitVector-"></a>1104 <span class="k">sub </span><span class="m">_SetFinalFingerprintsBitVector</span> <span class="s">{</span> +1105 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1106 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$Size</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$AtomPathHashCode</span><span class="cm">,</span> <span class="i">$AtomPathBitPos</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="cm">,</span> <span class="i">$NumOfBitsToSetPerPath</span><span class="cm">,</span> <span class="i">$SetBitNum</span><span class="s">)</span><span class="sc">;</span> +1107 +1108 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span> +1109 +1110 <span class="i">$Size</span> = <span class="i">$This</span>->{<span class="w">Size</span>}<span class="sc">;</span> +1111 +1112 <span class="i">$SkipBitPosCheck</span> = <span class="n">1</span><span class="sc">;</span> +1113 <span class="i">$NumOfBitsToSetPerPath</span> = <span class="i">$This</span>->{<span class="w">NumOfBitsToSetPerPath</span>}<span class="sc">;</span> +1114 +1115 <span class="k">for</span> <span class="i">$PathLength</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}}<span class="s">)</span> <span class="s">{</span> +1116 <span class="k">for</span> <span class="i">$AtomPathString</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}}<span class="s">)</span> <span class="s">{</span> +1117 <span class="i">$AtomPathHashCode</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$AtomPathString</span><span class="s">)</span><span class="sc">;</span> +1118 +1119 <span class="c"># Set random number seed...</span> +1120 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span> <span class="s">{</span> +1121 <span class="i">CORE::</span><span class="k">srand</span><span class="s">(</span><span class="i">$AtomPathHashCode</span><span class="s">)</span><span class="sc">;</span> +1122 <span class="s">}</span> +1123 <span class="k">else</span> <span class="s">{</span> +1124 <span class="i">MathUtil::srandom</span><span class="s">(</span><span class="i">$AtomPathHashCode</span><span class="s">)</span><span class="sc">;</span> +1125 <span class="s">}</span> +1126 +1127 <span class="k">for</span> <span class="i">$SetBitNum</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$NumOfBitsToSetPerPath</span><span class="s">)</span> <span class="s">{</span> +1128 <span class="i">$AtomPathBitPos</span> = <span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>} ? <span class="k">int</span><span class="s">(</span><span class="i">CORE::</span><span class="k">rand</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="k">int</span><span class="s">(</span><span class="i">MathUtil::random</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> +1129 <span class="i">$FingerprintsBitVector</span><span class="i">->SetBit</span><span class="s">(</span><span class="i">$AtomPathBitPos</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="s">)</span><span class="sc">;</span> +1130 <span class="s">}</span> +1131 <span class="s">}</span> +1132 <span class="s">}</span> +1133 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1134 <span class="s">}</span> +1135 +1136 <span class="c"># Set final fingerprits vector...</span> +1137 <span class="c">#</span> +<a name="_SetFinalFingerprintsVector-"></a>1138 <span class="k">sub </span><span class="m">_SetFinalFingerprintsVector</span> <span class="s">{</span> +1139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1140 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="cm">,</span> <span class="i">$AtomPathCount</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span> +1141 +1142 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1143 <span class="i">@ValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1144 +1145 <span class="k">for</span> <span class="i">$PathLength</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">$This</span>->{<span class="w">AtomPathsStrings</span>}}<span class="s">)</span> <span class="s">{</span> +1146 <span class="k">for</span> <span class="i">$AtomPathString</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}}<span class="s">)</span> <span class="s">{</span> +1147 <span class="i">$AtomPathCount</span> = <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>}<span class="sc">;</span> +1148 +1149 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$AtomPathCount</span><span class="sc">;</span> +1150 <span class="k">push</span> <span class="i">@ValueIDs</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="sc">;</span> +1151 <span class="s">}</span> +1152 <span class="s">}</span> +1153 +1154 <span class="c"># Add PathLengthIDs and values to fingerprint vector...</span> +1155 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span> +1156 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> +1157 +1158 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1159 <span class="s">}</span> +1160 +1161 <span class="c"># Cache appropriate molecule data...</span> +1162 <span class="c">#</span> +<a name="_SetupMoleculeDataCache-"></a>1163 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> +1164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1165 +1166 <span class="c"># Get all atoms...</span> +1167 <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="s">)</span><span class="sc">;</span> +1168 +1169 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1170 <span class="s">}</span> +1171 +1172 <span class="c"># Clear cached molecule data...</span> +1173 <span class="c">#</span> +<a name="_ClearMoleculeDataCache-"></a>1174 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> +1175 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1176 +1177 <span class="c"># Clear atoms...</span> +1178 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1179 +1180 <span class="c"># Clear path atoms..</span> +1181 <span class="i">$This</span>->{<span class="w">AtomPathsRef</span>} = <span class="q">''</span><span class="sc">;</span> +1182 +1183 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1184 <span class="s">}</span> +1185 +1186 <span class="c"># Set atomic invariants to use atom identifiers...</span> +1187 <span class="c">#</span> +<a name="SetAtomicInvariantsToUse-"></a>1188 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> +1189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1190 <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> +1191 +1192 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> +1193 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> +1194 <span class="k">return</span><span class="sc">;</span> +1195 <span class="s">}</span> +1196 +1197 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> +1198 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> +1199 +1200 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1201 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1202 +1203 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> +1204 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> +1205 <span class="s">}</span> +1206 <span class="k">else</span> <span class="s">{</span> +1207 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> +1208 <span class="s">}</span> +1209 +1210 <span class="c"># Make sure specified AtomicInvariants are valid...</span> +1211 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> +1212 <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> +1213 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> +1214 <span class="s">}</span> +1215 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> +1216 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> +1217 <span class="s">}</span> +1218 +1219 <span class="c"># Set atomic invariants to use...</span> +1220 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1221 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> +1222 +1223 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1224 <span class="s">}</span> +1225 +1226 <span class="c"># Set functional classes to use for atom identifiers...</span> +1227 <span class="c">#</span> +<a name="SetFunctionalClassesToUse-"></a>1228 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> +1229 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1230 <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> +1231 +1232 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> +1233 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> +1234 <span class="k">return</span><span class="sc">;</span> +1235 <span class="s">}</span> +1236 +1237 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> +1238 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> +1239 <span class="k">return</span><span class="sc">;</span> +1240 <span class="s">}</span> +1241 +1242 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> +1243 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> +1244 +1245 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1246 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1247 +1248 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> +1249 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> +1250 <span class="s">}</span> +1251 <span class="k">else</span> <span class="s">{</span> +1252 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> +1253 <span class="s">}</span> +1254 +1255 <span class="c"># Make sure specified FunctionalClasses are valid...</span> +1256 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> +1257 <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> +1258 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> +1259 <span class="s">}</span> +1260 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> +1261 <span class="s">}</span> +1262 +1263 <span class="c"># Set functional classes to use...</span> +1264 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1265 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> +1266 +1267 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1268 <span class="s">}</span> +1269 +1270 <span class="c"># Initialize atom indentifier type information...</span> +1271 <span class="c">#</span> +1272 <span class="c"># Current supported values:</span> +1273 <span class="c">#</span> +1274 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span> +1275 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> +1276 <span class="c">#</span> +<a name="_InitializeAtomIdentifierTypeInformation-"></a>1277 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> +1278 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1279 +1280 <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> +1281 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1282 <span class="s">}</span> +1283 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> +1284 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1285 <span class="s">}</span> +1286 <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> +1287 <span class="c"># Nothing to do for now...</span> +1288 <span class="s">}</span> +1289 <span class="k">else</span> <span class="s">{</span> +1290 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> +1291 <span class="s">}</span> +1292 +1293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1294 <span class="s">}</span> +1295 +1296 <span class="c"># Initialize atomic invariants atom types to use for generating atom identifiers...</span> +1297 <span class="c">#</span> +1298 <span class="c"># Let:</span> +1299 <span class="c"># AS = Atom symbol corresponding to element symbol</span> +1300 <span class="c">#</span> +1301 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> +1302 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> +1303 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> +1304 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> +1305 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> +1306 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> +1307 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> +1308 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> +1309 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> +1310 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> +1311 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> +1312 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> +1313 <span class="c">#</span> +1314 <span class="c"># Then:</span> +1315 <span class="c">#</span> +1316 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> +1317 <span class="c">#</span> +1318 <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> +1319 <span class="c">#</span> +1320 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> +1321 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X<n>, BO<n>, H<n>, FC<+n/-n>.</span> +1322 <span class="c"># AtomID specification doesn't include atomic invariants with zero or undefined values.</span> +1323 <span class="c">#</span> +<a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a>1324 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> +1325 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1326 +1327 <span class="c"># Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC</span> +1328 <span class="c">#</span> +1329 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1330 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> +1331 +1332 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1333 <span class="s">}</span> +1334 +1335 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> +1336 <span class="c"># class, to use for generating atom identifiers...</span> +1337 <span class="c">#</span> +1338 <span class="c"># Let:</span> +1339 <span class="c"># HBD: HydrogenBondDonor</span> +1340 <span class="c"># HBA: HydrogenBondAcceptor</span> +1341 <span class="c"># PI : PositivelyIonizable</span> +1342 <span class="c"># NI : NegativelyIonizable</span> +1343 <span class="c"># Ar : Aromatic</span> +1344 <span class="c"># Hal : Halogen</span> +1345 <span class="c"># H : Hydrophobic</span> +1346 <span class="c"># RA : RingAtom</span> +1347 <span class="c"># CA : ChainAtom</span> +1348 <span class="c">#</span> +1349 <span class="c"># Then:</span> +1350 <span class="c">#</span> +1351 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> +1352 <span class="c">#</span> +1353 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> +1354 <span class="c">#</span> +1355 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> +1356 <span class="c">#</span> +1357 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> +1358 <span class="c">#</span> +1359 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> +1360 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> +1361 <span class="c"># PositivelyIonizable: +, NH2</span> +1362 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> +1363 <span class="c">#</span> +<a name="_InitializeFunctionalClassAtomTypesInformation-"></a>1364 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> +1365 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1366 +1367 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span> +1368 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span> +1369 <span class="c">#</span> +1370 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1371 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> +1372 +1373 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1374 <span class="s">}</span> +1375 +1376 <span class="c"># Return a string containg data for PathLengthFingerprints object...</span> +1377 <span class="c">#</span> +<a name="StringifyPathLengthFingerprints-"></a>1378 <span class="k">sub </span><span class="m">StringifyPathLengthFingerprints</span> <span class="s">{</span> +1379 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1380 <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthsFingerprintsString</span><span class="s">)</span><span class="sc">;</span> +1381 +1382 <span class="c"># Type of fingerprint...</span> +1383 <span class="i">$PathLengthsFingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}"</span><span class="sc">;</span> +1384 +1385 <span class="c"># Path length...</span> +1386 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; MinPathLength: $This->{MinLength}; MaxPathLength: $This->{MaxLength}"</span><span class="sc">;</span> +1387 +1388 <span class="c"># Fingerprint generation control...</span> +1389 <span class="k">my</span><span class="s">(</span><span class="i">$AllowSharedBonds</span><span class="cm">,</span> <span class="i">$AllowRings</span><span class="cm">,</span> <span class="i">$UseBondSymbols</span><span class="cm">,</span> <span class="i">$UseUniquePaths</span><span class="s">)</span><span class="sc">;</span> +1390 +1391 <span class="i">$AllowSharedBonds</span> = <span class="i">$This</span>->{<span class="w">AllowSharedBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> +1392 <span class="i">$AllowRings</span> = <span class="i">$This</span>->{<span class="w">AllowRings</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> +1393 <span class="i">$UseBondSymbols</span> = <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> +1394 <span class="i">$UseUniquePaths</span> = <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> +1395 +1396 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; UseUniquePaths: $UseUniquePaths; AllowSharedBonds: $AllowSharedBonds; AllowRings: $AllowRings; UseBondSymbols: $UseBondSymbols"</span><span class="sc">;</span> +1397 +1398 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> +1399 <span class="k">my</span><span class="s">(</span><span class="i">$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> +1400 +1401 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1402 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1403 +1404 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> +1405 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> +1406 <span class="s">}</span> +1407 +1408 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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> +1409 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1410 <span class="i">$PathLengthsFingerprintsString</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> +1411 <span class="s">}</span> +1412 <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> +1413 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> +1414 +1415 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1416 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1417 +1418 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> +1419 <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> +1420 <span class="s">}</span> +1421 +1422 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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> +1423 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1424 <span class="i">$PathLengthsFingerprintsString</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> +1425 <span class="s">}</span> +1426 +1427 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span> +1428 <span class="c"># Size...</span> +1429 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; Size: $This->{Size}; MinSize: $This->{MinSize}; MaxSize: $This->{MaxSize}"</span><span class="sc">;</span> +1430 +1431 <span class="c"># NumOfBitsToSetPerPath...</span> +1432 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; NumOfBitsToSetPerPath: $This->{NumOfBitsToSetPerPath}"</span><span class="sc">;</span> +1433 +1434 <span class="c"># Fingerprint bit density and num of bits set...</span> +1435 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span> +1436 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1437 <span class="i">$BitDensity</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1438 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity"</span><span class="sc">;</span> +1439 +1440 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; FingerprintsBitVector: < $This->{FingerprintsBitVector} >"</span><span class="sc">;</span> +1441 <span class="s">}</span> +1442 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span> +1443 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> +1444 <span class="s">}</span> +1445 +1446 <span class="k">return</span> <span class="i">$PathLengthsFingerprintsString</span><span class="sc">;</span> +1447 <span class="s">}</span> +1448 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>