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<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>