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comparison mayachemtools/docs/modules/html/code/PathLengthFingerprints.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:Fingerprints::PathLengthFingerprints.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-Fingerprints::PathLengthFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::PathLengthFingerprints</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: PathLengthFingerprints.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> | |
| 18 5 <span class="c"># $Revision: 1.39 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> | |
| 52 39 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> | |
| 53 40 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span> | |
| 54 41 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span> | |
| 55 42 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span> | |
| 56 43 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> | |
| 57 44 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span> | |
| 58 45 | |
| 59 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> | |
| 60 47 | |
| 61 48 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> | |
| 62 49 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 63 50 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 64 51 | |
| 65 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> | |
| 66 53 | |
| 67 54 <span class="c"># Setup class variables...</span> | |
| 68 55 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 69 56 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 70 57 | |
| 71 58 <span class="c"># Overload Perl functions...</span> | |
| 72 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> | |
| 73 60 | |
| 74 61 <span class="c"># Class constructor...</span> | |
| 75 <a name="new-"></a> 62 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 76 63 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 77 64 | |
| 78 65 <span class="c"># Initialize object...</span> | |
| 79 66 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 80 67 <span class="k">bless</span> <span class="i">$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> | |
| 81 68 <span class="i">$This</span><span class="i">->_InitializePathLengthFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 82 69 | |
| 83 70 <span class="i">$This</span><span class="i">->_InitializePathLengthFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 84 71 | |
| 85 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 86 73 <span class="s">}</span> | |
| 87 74 | |
| 88 75 <span class="c"># Initialize object data...</span> | |
| 89 76 <span class="c">#</span> | |
| 90 <a name="_InitializePathLengthFingerprints-"></a> 77 <span class="k">sub </span><span class="m">_InitializePathLengthFingerprints</span> <span class="s">{</span> | |
| 91 78 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 92 79 | |
| 93 80 <span class="c"># Type of fingerprint to generate...</span> | |
| 94 81 <span class="c">#</span> | |
| 95 82 <span class="c"># PathLengthBits - A bit vector indicating presence/absence of atom paths</span> | |
| 96 83 <span class="c"># PathLengthCount - A vector containing count of atom paths</span> | |
| 97 84 <span class="c">#</span> | |
| 98 85 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 99 86 | |
| 100 87 <span class="c"># Type of vector: FingerprintsBitVector or FingerprintsVector</span> | |
| 101 88 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 102 89 | |
| 103 90 <span class="c"># Set default mininum, maximum, and default size. Although any arbitrary size can</span> | |
| 104 91 <span class="c"># be specified, bit vector used to store bits work on a vector size which is</span> | |
| 105 92 <span class="c"># power of 2 and additonal bits are automatically added and cleared.</span> | |
| 106 93 <span class="c">#</span> | |
| 107 94 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="n">1024</span><span class="sc">;</span> | |
| 108 95 | |
| 109 96 <span class="i">$This</span>->{<span class="w">MinSize</span>} = <span class="n">32</span><span class="sc">;</span> | |
| 110 97 <span class="i">$This</span>->{<span class="w">MaxSize</span>} = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span> | |
| 111 98 | |
| 112 99 <span class="c"># Minimum and maximum path lengths to use for fingerprints generation...</span> | |
| 113 100 <span class="i">$This</span>->{<span class="w">MinLength</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 114 101 <span class="i">$This</span>->{<span class="w">MaxLength</span>} = <span class="n">8</span><span class="sc">;</span> | |
| 115 102 | |
| 116 103 <span class="c"># Numner of bits to set for each atom path for FingerprintsBitVector...</span> | |
| 117 104 <span class="i">$This</span>->{<span class="w">NumOfBitsToSetPerPath</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 118 105 | |
| 119 106 <span class="c"># Atom identifier type to use for path atoms during fingerprints generation...</span> | |
| 120 107 <span class="c">#</span> | |
| 121 108 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> | |
| 122 109 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> | |
| 123 110 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> | |
| 124 111 <span class="c">#</span> | |
| 125 112 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 126 113 | |
| 127 114 <span class="c"># Atom types assigned to atoms...</span> | |
| 128 115 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 129 116 | |
| 130 117 <span class="c"># For molecules containing rings, atom paths starting from each atom can be traversed in four</span> | |
| 131 118 <span class="c"># different ways:</span> | |
| 132 119 <span class="c">#</span> | |
| 133 120 <span class="c"># . Atom paths without any rings and sharing of bonds in traversed paths.</span> | |
| 134 121 <span class="c"># . Atom paths containing rings and without any sharing of bonds in traversed paths</span> | |
| 135 122 <span class="c"># . All possible atom paths without any rings and sharing of bonds in traversed paths</span> | |
| 136 123 <span class="c"># . All possible atom paths containing rings and with sharing of bonds in traversed paths.</span> | |
| 137 124 <span class="c">#</span> | |
| 138 125 <span class="c"># Atom path traversal is terminated at the last ring atom. For molecules containing no rings,</span> | |
| 139 126 <span class="c"># first two and last two types described above are equivalent.</span> | |
| 140 127 <span class="c">#</span> | |
| 141 128 <span class="c"># AllowSharedBonds and AllowRings variables allow generation of differen types of paths</span> | |
| 142 129 <span class="c"># to be used for fingerprints generation.</span> | |
| 143 130 <span class="c">#</span> | |
| 144 131 <span class="c"># In addition to atom symbols, bond symbols are also used to generate a string</span> | |
| 145 132 <span class="c"># for atom paths. These atom paths strings are hased to a 32 bit integer key which</span> | |
| 146 133 <span class="c"># in turn is used as a seed for a random number generation in range of 1 to fingerprint</span> | |
| 147 134 <span class="c"># size for setting corresponding bit in bit vector.</span> | |
| 148 135 <span class="c">#</span> | |
| 149 136 <span class="c"># UseBondSymbols variable allow generation of atom path strings and consequently fingerprints.</span> | |
| 150 137 <span class="c">#</span> | |
| 151 138 <span class="c"># Combination of AllowSharedBonds, AllowRings, and UseBondSymbols allow generation of</span> | |
| 152 139 <span class="c"># 8 different types of path length fingerprints:</span> | |
| 153 140 <span class="c">#</span> | |
| 154 141 <span class="c"># AllowSharedBonds AllowRings UseBondSymbols PathLengthFingerprintsType</span> | |
| 155 142 <span class="c">#</span> | |
| 156 143 <span class="c"># No No Yes AtomPathsNoCyclesWithBondSymbols</span> | |
| 157 144 <span class="c"># No Yes Yes AtomPathsWithCyclesWithBondSymbols</span> | |
| 158 145 <span class="c">#</span> | |
| 159 146 <span class="c"># Yes No Yes AllAtomPathsNoCyclesWithBondSymbols</span> | |
| 160 147 <span class="c"># Yes Yes Yes AllAtomPathsWithCyclesWithBondSymbols [ DEFAULT ]</span> | |
| 161 148 <span class="c">#</span> | |
| 162 149 <span class="c"># No No No AtomPathsNoCyclesNoBondSymbols</span> | |
| 163 150 <span class="c"># No Yes No AtomPathsWithCyclesNoBondSymbols</span> | |
| 164 151 <span class="c">#</span> | |
| 165 152 <span class="c"># Yes No No AllAtomPathsNoCyclesNoBondSymbols</span> | |
| 166 153 <span class="c"># Yes Yes No AllAtomPathsWithCyclesNoWithBondSymbols</span> | |
| 167 154 <span class="c">#</span> | |
| 168 155 <span class="c">#</span> | |
| 169 156 | |
| 170 157 <span class="c"># By default, atom paths starting from atoms are allowed to share bonds already traversed...</span> | |
| 171 158 <span class="i">$This</span>->{<span class="w">AllowSharedBonds</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 172 159 | |
| 173 160 <span class="c"># By default rings are included in paths...</span> | |
| 174 161 <span class="i">$This</span>->{<span class="w">AllowRings</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 175 162 | |
| 176 163 <span class="c"># By default bond symbols are included in atom path strings...</span> | |
| 177 164 <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 178 165 | |
| 179 166 <span class="c"># By default only structurally unique atom paths are used for generation</span> | |
| 180 167 <span class="c"># atom path strings...</span> | |
| 181 168 <span class="i">$This</span>->{<span class="w">UseUniquePaths</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 182 169 | |
| 183 170 <span class="c"># Random number generator to use during generation of fingerprints bit-vector</span> | |
| 184 171 <span class="c"># string: Perl CORE::rand or MayaChemTools MathUtil::random function.</span> | |
| 185 172 <span class="c">#</span> | |
| 186 173 <span class="c"># The random number generator implemented in MayaChemTools is a variant of</span> | |
| 187 174 <span class="c"># linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].</span> | |
| 188 175 <span class="c"># It is also referred to as Lehmer random number generator or Park-Miller</span> | |
| 189 176 <span class="c"># random number generator.</span> | |
| 190 177 <span class="c">#</span> | |
| 191 178 <span class="c"># Unlike Perl's core random number generator function rand, the random number</span> | |
| 192 179 <span class="c"># generator implemented in MayaChemTools, MathUtil::random, generates consistent</span> | |
| 193 180 <span class="c"># random values across different platformsfor a specific random seed and leads</span> | |
| 194 181 <span class="c"># to generation of portable fingerprints bit-vector strings.</span> | |
| 195 182 <span class="c">#</span> | |
| 196 183 <span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 197 184 | |
| 198 185 <span class="c"># Bond symbols to use during generation of atom path strings...</span> | |
| 199 186 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondOrderToSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 200 187 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondOrderToSymbol</span>}} = <span class="s">(</span><span class="q">'1'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span> <span class="q">'1.5'</span> <span class="cm">=></span> <span class="q">':'</span><span class="cm">,</span> <span class="q">'2'</span> <span class="cm">=></span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'3'</span> <span class="cm">=></span> <span class="q">'#'</span><span class="s">)</span><span class="sc">;</span> | |
| 201 188 | |
| 202 189 <span class="c"># BondSymbols map to use for bonded atom IDs to use during atom path strings...</span> | |
| 203 190 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondSymbols</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 204 191 | |
| 205 192 <span class="c"># Path atom IDs to remove duplicate paths...</span> | |
| 206 193 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueLinearAtomPathsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 207 194 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueCyclicAtomPathsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 208 195 | |
| 209 196 <span class="c"># Reference to all the atom paths upto specified path length...</span> | |
| 210 197 <span class="i">$This</span>->{<span class="w">AtomPathsRef</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 211 198 | |
| 212 199 <span class="c"># Atom paths strings created using specified atom types and bond symbols...</span> | |
| 213 200 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 214 201 <span class="s">}</span> | |
| 215 202 | |
| 216 203 <span class="c"># Initialize class ...</span> | |
| 217 <a name="_InitializeClass-"></a> 204 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 218 205 <span class="c">#Class name...</span> | |
| 219 206 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 220 207 <span class="s">}</span> | |
| 221 208 | |
| 222 209 <span class="c"># Initialize object properties....</span> | |
| 223 <a name="_InitializePathLengthFingerprintsProperties-"></a> 210 <span class="k">sub </span><span class="m">_InitializePathLengthFingerprintsProperties</span> <span class="s">{</span> | |
| 224 211 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 225 212 | |
| 226 213 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 227 214 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 228 215 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 229 216 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 230 217 <span class="s">}</span> | |
| 231 218 | |
| 232 219 <span class="c"># Make sure molecule object was specified...</span> | |
| 233 220 <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> | |
| 234 221 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> | |
| 235 222 <span class="s">}</span> | |
| 236 223 | |
| 237 224 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> | |
| 238 225 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying Type..."</span><span class="sc">;</span> | |
| 239 226 <span class="s">}</span> | |
| 240 227 | |
| 241 228 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 242 229 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span> | |
| 243 230 <span class="s">}</span> | |
| 244 231 | |
| 245 232 <span class="c"># Make sure it's power of 2...</span> | |
| 246 233 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span> | |
| 247 234 <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> | |
| 248 235 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Specified size value, $NamesAndValues{Size}, must be power of 2..."</span><span class="sc">;</span> | |
| 249 236 <span class="s">}</span> | |
| 250 237 <span class="s">}</span> | |
| 251 238 | |
| 252 239 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 253 240 <span class="i">$This</span><span class="i">->_InitializePathLengthBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 254 241 <span class="s">}</span> | |
| 255 242 <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> | |
| 256 243 <span class="i">$This</span><span class="i">->_InitializePathLengthCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 257 244 <span class="s">}</span> | |
| 258 245 <span class="k">else</span> <span class="s">{</span> | |
| 259 246 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializePathLengthFingerprintsProperties: Unknown PathLength type: $This->{Type}; Supported PathLength type : PathLengthBits or PathLengthCount......"</span><span class="sc">;</span> | |
| 260 247 <span class="s">}</span> | |
| 261 248 | |
| 262 249 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 263 250 <span class="s">}</span> | |
| 264 251 | |
| 265 252 <span class="c"># Initialize PathLength bits...</span> | |
| 266 253 <span class="c">#</span> | |
| 267 <a name="_InitializePathLengthBits-"></a> 254 <span class="k">sub </span><span class="m">_InitializePathLengthBits</span> <span class="s">{</span> | |
| 268 255 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 269 256 | |
| 270 257 <span class="c"># Vector type...</span> | |
| 271 258 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span> | |
| 272 259 | |
| 273 260 <span class="i">$This</span><span class="i">->_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 274 261 | |
| 275 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 276 263 <span class="s">}</span> | |
| 277 264 | |
| 278 265 <span class="c"># Initialize PathLength key count...</span> | |
| 279 266 <span class="c">#</span> | |
| 280 <a name="_InitializePathLengthCount-"></a> 267 <span class="k">sub </span><span class="m">_InitializePathLengthCount</span> <span class="s">{</span> | |
| 281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 282 269 | |
| 283 270 <span class="c"># Vector type and type of values...</span> | |
| 284 271 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
| 285 272 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> | |
| 286 273 | |
| 287 274 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 288 275 | |
| 289 276 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 290 277 <span class="s">}</span> | |
| 291 278 | |
| 292 279 <span class="c"># Set type...</span> | |
| 293 280 <span class="c">#</span> | |
| 294 <a name="SetType-"></a> 281 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> | |
| 295 282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 296 283 | |
| 297 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> | |
| 298 285 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change type: It's already set..."</span><span class="sc">;</span> | |
| 299 286 <span class="s">}</span> | |
| 300 287 | |
| 301 288 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 302 289 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'PathLengthBits'</span><span class="sc">;</span><span class="sc">;</span> | |
| 303 290 <span class="s">}</span> | |
| 304 291 <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> | |
| 305 292 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'PathLengthCount'</span><span class="sc">;</span><span class="sc">;</span> | |
| 306 293 <span class="s">}</span> | |
| 307 294 <span class="k">else</span> <span class="s">{</span> | |
| 308 295 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Unknown PathLength keys: $Type; Supported PathLength types: PathLengthBits or PathLengthCount..."</span><span class="sc">;</span> | |
| 309 296 <span class="s">}</span> | |
| 310 297 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 311 298 <span class="s">}</span> | |
| 312 299 | |
| 313 300 <span class="c"># Disable vector type change...</span> | |
| 314 301 <span class="c">#</span> | |
| 315 <a name="SetVectorType-"></a> 302 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span> | |
| 316 303 <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> | |
| 317 304 | |
| 318 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Can't change vector type..."</span><span class="sc">;</span> | |
| 319 306 | |
| 320 307 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 321 308 <span class="s">}</span> | |
| 322 309 | |
| 323 310 <span class="c"># Disable vector type change...</span> | |
| 324 311 <span class="c">#</span> | |
| 325 <a name="SetFingerprintsVectorType-"></a> 312 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span> | |
| 326 313 <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> | |
| 327 314 | |
| 328 315 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVectorType: Can't change fingerprints vector type..."</span><span class="sc">;</span> | |
| 329 316 | |
| 330 317 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 331 318 <span class="s">}</span> | |
| 332 319 | |
| 333 320 <span class="c"># Set atom identifier type to use for path length atom identifiers...</span> | |
| 334 321 <span class="c">#</span> | |
| 335 <a name="SetAtomIdentifierType-"></a> 322 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> | |
| 336 323 <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> | |
| 337 324 | |
| 338 325 <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> | |
| 339 326 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes."</span><span class="sc">;</span> | |
| 340 327 <span class="s">}</span> | |
| 341 328 | |
| 342 329 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 343 330 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change atom identifier type: It's already set..."</span><span class="sc">;</span> | |
| 344 331 <span class="s">}</span> | |
| 345 332 | |
| 346 333 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> | |
| 347 334 | |
| 348 335 <span class="c"># Initialize atom identifier type information...</span> | |
| 349 336 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 350 337 | |
| 351 338 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 352 339 <span class="s">}</span> | |
| 353 340 | |
| 354 341 <span class="c"># Set minimum path length...</span> | |
| 355 342 <span class="c">#</span> | |
| 356 <a name="SetMinLength-"></a> 343 <span class="k">sub </span><span class="m">SetMinLength</span> <span class="s">{</span> | |
| 357 344 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 358 345 | |
| 359 346 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 360 347 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinLength: MinLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 361 348 <span class="s">}</span> | |
| 362 349 <span class="i">$This</span>->{<span class="w">MinLength</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 363 350 | |
| 364 351 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 365 352 <span class="s">}</span> | |
| 366 353 | |
| 367 354 <span class="c"># Set maximum path length...</span> | |
| 368 355 <span class="c">#</span> | |
| 369 <a name="SetMaxLength-"></a> 356 <span class="k">sub </span><span class="m">SetMaxLength</span> <span class="s">{</span> | |
| 370 357 <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> | |
| 371 358 | |
| 372 359 <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> | |
| 373 360 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxLength: MaxLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 374 361 <span class="s">}</span> | |
| 375 362 <span class="i">$This</span>->{<span class="w">MaxLength</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 376 363 | |
| 377 364 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 378 365 <span class="s">}</span> | |
| 379 366 | |
| 380 367 <span class="c"># Set number of bits to set for each path...</span> | |
| 381 368 <span class="c">#</span> | |
| 382 <a name="SetNumOfBitsToSetPerPath-"></a> 369 <span class="k">sub </span><span class="m">SetNumOfBitsToSetPerPath</span> <span class="s">{</span> | |
| 383 370 <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> | |
| 384 371 | |
| 385 372 <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> | |
| 386 373 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNumOfBitsToSetPerPath: NumOfBitsToSetPerPath value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 387 374 <span class="s">}</span> | |
| 388 375 <span class="i">$This</span>->{<span class="w">NumOfBitsToSetPerPath</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 389 376 | |
| 390 377 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 391 378 <span class="s">}</span> | |
| 392 379 | |
| 393 380 <span class="c"># Generate fingerprints description...</span> | |
| 394 381 <span class="c">#</span> | |
| 395 <a name="GetDescription-"></a> 382 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> | |
| 396 383 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 397 384 | |
| 398 385 <span class="c"># Is description explicity set?</span> | |
| 399 386 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> | |
| 400 387 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> | |
| 401 388 <span class="s">}</span> | |
| 402 389 | |
| 403 390 <span class="c"># Generate fingerprints description...</span> | |
| 404 391 | |
| 405 392 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:MinLength$This->{MinLength}:MaxLength$This->{MaxLength}"</span><span class="sc">;</span> | |
| 406 393 <span class="s">}</span> | |
| 407 394 | |
| 408 395 <span class="c"># Generate path length fingerprints...</span> | |
| 409 396 <span class="c">#</span> | |
| 410 <a name="GenerateFingerprints-"></a> 397 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> | |
| 411 398 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 412 399 | |
| 413 400 <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> | |
| 414 401 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateFingerprints: No fingerpritns generated: MinLength, $This->{MinLength}, must be <= MaxLength, $This->{MaxLength}..."</span><span class="sc">;</span> | |
| 415 402 <span class="s">}</span> | |
| 416 403 | |
| 417 404 <span class="c"># Cache appropriate molecule data...</span> | |
| 418 405 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 419 406 | |
| 420 407 <span class="c"># Assign atom types to all atoms...</span> | |
| 421 408 <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> | |
| 422 409 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span> | |
| 423 410 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 424 411 <span class="s">}</span> | |
| 425 412 | |
| 426 413 <span class="c"># Setup bond symbol map...</span> | |
| 427 414 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span> | |
| 428 415 <span class="i">$This</span><span class="i">->_InitializeBondSymbols</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 429 416 <span class="s">}</span> | |
| 430 417 | |
| 431 418 <span class="c"># Generate appropriate atom paths...</span> | |
| 432 419 <span class="i">$This</span><span class="i">->_GenerateAtomPathsUpToMaxLength</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 433 420 | |
| 434 421 <span class="c"># Initialize atom path strings...</span> | |
| 435 422 <span class="i">$This</span><span class="i">->_InitializeAtomPathsStrings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 436 423 | |
| 437 424 <span class="c"># Generate appropriate atom path strings for unique atom paths...</span> | |
| 438 425 <span class="i">$This</span><span class="i">->_GenerateAtomPathsStrings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 439 426 | |
| 440 427 <span class="c"># Set final fingerprints...</span> | |
| 441 428 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 442 429 | |
| 443 430 <span class="c"># Clear cached molecule data...</span> | |
| 444 431 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 445 432 | |
| 446 433 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 447 434 <span class="s">}</span> | |
| 448 435 | |
| 449 436 <span class="c"># Assign appropriate atom types to all atoms...</span> | |
| 450 437 <span class="c">#</span> | |
| 451 <a name="_AssignAtomTypes-"></a> 438 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span> | |
| 452 439 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 453 440 <span class="k">my</span><span class="s">(</span><span class="i">$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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
| 454 441 | |
| 455 442 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 456 443 <span class="i">$IgnoreHydrogens</span> = <span class="n">0</span><span class="sc">;</span> | |
| 457 444 | |
| 458 445 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 459 446 | |
| 460 447 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> | |
| 461 448 <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> | |
| 462 449 <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> | |
| 463 450 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 464 451 <span class="s">}</span> | |
| 465 452 | |
| 466 453 <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> | |
| 467 454 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
| 468 455 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 469 456 <span class="s">}</span> | |
| 470 457 | |
| 471 458 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 472 459 <span class="i">$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> | |
| 473 460 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 474 461 <span class="s">}</span> | |
| 475 462 | |
| 476 463 <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> | |
| 477 464 <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> | |
| 478 465 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 479 466 <span class="s">}</span> | |
| 480 467 | |
| 481 468 <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> | |
| 482 469 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
| 483 470 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 484 471 <span class="s">}</span> | |
| 485 472 | |
| 486 473 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 487 474 <span class="i">$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> | |
| 488 475 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 489 476 <span class="s">}</span> | |
| 490 477 <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> | |
| 491 478 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
| 492 479 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 493 480 <span class="s">}</span> | |
| 494 481 | |
| 495 482 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 496 483 <span class="i">$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">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> | |
| 497 484 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 498 485 <span class="s">}</span> | |
| 499 486 | |
| 500 487 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 501 488 <span class="i">$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> | |
| 502 489 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 503 490 <span class="s">}</span> | |
| 504 491 | |
| 505 492 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignAtomTypes: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
| 506 493 <span class="s">}</span> | |
| 507 494 | |
| 508 495 <span class="c"># Assign atom types...</span> | |
| 509 496 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 510 497 | |
| 511 498 <span class="c"># Make sure atom types assignment is successful...</span> | |
| 512 499 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 513 500 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 514 501 <span class="s">}</span> | |
| 515 502 | |
| 516 503 <span class="c"># Collect assigned atom types...</span> | |
| 517 504 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 518 505 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 519 506 <span class="i">$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">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 520 507 <span class="s">}</span> | |
| 521 508 | |
| 522 509 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 523 510 <span class="s">}</span> | |
| 524 511 | |
| 525 512 <span class="c"># Setup bond symbol map for atoms to speed up generation of path length identifiers</span> | |
| 526 513 <span class="c"># during fingerprints generation...</span> | |
| 527 514 <span class="c">#</span> | |
| 528 <a name="_InitializeBondSymbols-"></a> 515 <span class="k">sub </span><span class="m">_InitializeBondSymbols</span> <span class="s">{</span> | |
| 529 516 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 530 517 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 531 518 | |
| 532 519 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondSymbols</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 533 520 | |
| 534 521 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span> | |
| 535 522 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 536 523 <span class="s">}</span> | |
| 537 524 | |
| 538 525 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 539 526 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 540 527 <span class="i">$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> | |
| 541 528 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 542 529 <span class="i">$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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 543 530 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID1</span> > <span class="i">$AtomID2</span><span class="s">)</span> <span class="s">{</span> | |
| 544 531 <span class="s">(</span><span class="i">$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">$AtomID1</span><span class="s">)</span><span class="sc">;</span> | |
| 545 532 <span class="s">}</span> | |
| 546 533 | |
| 547 534 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span> <span class="s">{</span> | |
| 548 535 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$AtomID1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 549 536 <span class="s">}</span> | |
| 550 537 <span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$AtomID1</span>}{<span class="i">$AtomID2</span>} = <span class="i">$BondSymbol</span><span class="sc">;</span> | |
| 551 538 <span class="s">}</span> | |
| 552 539 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 553 540 <span class="s">}</span> | |
| 554 541 | |
| 555 542 <span class="c"># Get appropriate atom paths with length up to MaxLength...</span> | |
| 556 543 <span class="c">#</span> | |
| 557 <a name="_GenerateAtomPathsUpToMaxLength-"></a> 544 <span class="k">sub </span><span class="m">_GenerateAtomPathsUpToMaxLength</span> <span class="s">{</span> | |
| 558 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 559 546 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomPathsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 560 547 | |
| 561 548 <span class="i">$PathLength</span> = <span class="i">$This</span>->{<span class="w">MaxLength</span>}<span class="sc">;</span> | |
| 562 549 <span class="i">$AllowRings</span> = <span class="i">$This</span>->{<span class="w">AllowRings</span>}<span class="sc">;</span> | |
| 563 550 <span class="i">$Molecule</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="sc">;</span> | |
| 564 551 | |
| 565 552 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AllowSharedBonds</span>}<span class="s">)</span> <span class="s">{</span> | |
| 566 553 <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> | |
| 567 554 <span class="s">}</span> | |
| 568 555 <span class="k">else</span> <span class="s">{</span> | |
| 569 556 <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> | |
| 570 557 <span class="s">}</span> | |
| 571 558 <span class="i">$This</span>->{<span class="w">AtomPathsRef</span>} = <span class="i">$AtomPathsRef</span><span class="sc">;</span> | |
| 572 559 | |
| 573 560 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 574 561 <span class="s">}</span> | |
| 575 562 | |
| 576 563 <span class="c"># Initialize atom paths strings at various pathlength levels...</span> | |
| 577 564 <span class="c">#</span> | |
| 578 <a name="_InitializeAtomPathsStrings-"></a> 565 <span class="k">sub </span><span class="m">_InitializeAtomPathsStrings</span> <span class="s">{</span> | |
| 579 566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 580 567 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="s">)</span><span class="sc">;</span> | |
| 581 568 | |
| 582 569 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 583 570 | |
| 584 571 <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">$This</span>->{<span class="w">MaxLength</span>}<span class="s">)</span> <span class="s">{</span> | |
| 585 572 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 586 573 <span class="s">}</span> | |
| 587 574 | |
| 588 575 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 589 576 <span class="s">}</span> | |
| 590 577 | |
| 591 578 <span class="c"># Generate appropriate atom path strings for unique atom paths...</span> | |
| 592 579 <span class="c">#</span> | |
| 593 <a name="_GenerateAtomPathsStrings-"></a> 580 <span class="k">sub </span><span class="m">_GenerateAtomPathsStrings</span> <span class="s">{</span> | |
| 594 581 <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> | |
| 595 582 <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">$UseUniquePaths</span><span class="s">)</span><span class="sc">;</span> | |
| 596 583 | |
| 597 584 <span class="i">$MinPathLength</span> = <span class="i">$This</span>->{<span class="w">MinLength</span>}<span class="sc">;</span> | |
| 598 585 <span class="i">$UseUniquePaths</span> = <span class="i">$This</span>->{<span class="w">UseUniquePaths</span>}<span class="sc">;</span> | |
| 599 586 | |
| 600 587 <span class="j">PATHATOMS:</span> <span class="k">for</span> <span class="i">$PathAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPathsRef</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 601 588 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> | |
| 602 589 <span class="k">if</span> <span class="s">(</span><span class="i">$PathLength</span> < <span class="i">$MinPathLength</span><span class="s">)</span> <span class="s">{</span> | |
| 603 590 <span class="k">next</span> <span class="j">PATHATOMS</span><span class="sc">;</span> | |
| 604 591 <span class="s">}</span> | |
| 605 592 <span class="k">if</span> <span class="s">(</span><span class="i">$UseUniquePaths</span><span class="s">)</span> <span class="s">{</span> | |
| 606 593 <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> | |
| 607 594 <span class="s">}</span> | |
| 608 595 <span class="k">else</span> <span class="s">{</span> | |
| 609 596 <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> | |
| 610 597 <span class="s">}</span> | |
| 611 598 <span class="s">}</span> | |
| 612 599 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 613 600 <span class="s">}</span> | |
| 614 601 | |
| 615 602 <span class="c"># Generate atom path string using unique path...</span> | |
| 616 603 <span class="c">#</span> | |
| 617 <a name="_GenerateAtomPathStringUsingUniquePath-"></a> 604 <span class="k">sub </span><span class="m">_GenerateAtomPathStringUsingUniquePath</span> <span class="s">{</span> | |
| 618 605 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 619 606 | |
| 620 607 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 621 608 <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> | |
| 622 609 <span class="s">}</span> | |
| 623 610 <span class="k">else</span> <span class="s">{</span> | |
| 624 611 <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> | |
| 625 612 <span class="s">}</span> | |
| 626 613 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 627 614 <span class="s">}</span> | |
| 628 615 | |
| 629 616 <span class="c"># Generate atom path string for specified path containing no cycle...</span> | |
| 630 617 <span class="c">#</span> | |
| 631 <a name="_GenerateAtomPathStringUsingUniqueLinearPath-"></a> 618 <span class="k">sub </span><span class="m">_GenerateAtomPathStringUsingUniqueLinearPath</span> <span class="s">{</span> | |
| 632 619 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 633 620 | |
| 634 621 <span class="c"># Is it a unique linear atom path?</span> | |
| 635 622 <span class="c">#</span> | |
| 636 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_IsUniqueLinearAtomPath</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 637 624 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 638 625 <span class="s">}</span> | |
| 639 626 <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> | |
| 640 627 | |
| 641 628 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 642 629 <span class="s">}</span> | |
| 643 630 | |
| 644 631 <span class="c"># Is it a structurally unique linear path?</span> | |
| 645 632 <span class="c">#</span> | |
| 646 633 <span class="c"># For a path to be structurally unique, all of its atom IDs must be diffferent from any</span> | |
| 647 634 <span class="c"># earlier path atom IDs. In order to generate atom path atom ID invariant of the atom</span> | |
| 648 635 <span class="c"># order in the molecule, atom IDs are sorted numerically before generating the path ID.</span> | |
| 649 636 <span class="c">#</span> | |
| 650 637 <span class="c"># Notes:</span> | |
| 651 638 <span class="c"># . Atom path ID doesn't reflect the order of atoms in the atom path.</span> | |
| 652 639 <span class="c">#</span> | |
| 653 <a name="_IsUniqueLinearAtomPath-"></a> 640 <span class="k">sub </span><span class="m">_IsUniqueLinearAtomPath</span> <span class="s">{</span> | |
| 654 641 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 655 642 <span class="k">my</span><span class="s">(</span><span class="i">$AtomPathID</span><span class="cm">,</span> <span class="i">$PathLength</span><span class="cm">,</span> <span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 656 643 | |
| 657 644 <span class="i">@PathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 658 645 <span class="i">@PathAtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</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">$PathAtomsRef</span>}<span class="sc">;</span> | |
| 659 646 | |
| 660 647 <span class="i">$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> | |
| 661 648 <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> | |
| 662 649 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 663 650 <span class="s">}</span> | |
| 664 651 | |
| 665 652 <span class="c"># It's a unique atom path...</span> | |
| 666 653 <span class="i">$This</span>->{<span class="w">UniqueLinearAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 667 654 | |
| 668 655 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 669 656 <span class="s">}</span> | |
| 670 657 | |
| 671 658 <span class="c"># Generate atom path string for specified path containing a cycle...</span> | |
| 672 659 <span class="c">#</span> | |
| 673 <a name="_GenerateAtomPathStringUsingUniquePathContainingCycle-"></a> 660 <span class="k">sub </span><span class="m">_GenerateAtomPathStringUsingUniquePathContainingCycle</span> <span class="s">{</span> | |
| 674 661 <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> | |
| 675 662 | |
| 676 663 <span class="c"># Is it a unique atom path containing a cycle?</span> | |
| 677 664 <span class="c">#</span> | |
| 678 665 <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> | |
| 679 666 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 680 667 <span class="s">}</span> | |
| 681 668 | |
| 682 669 <span class="k">my</span><span class="s">(</span><span class="i">$CycleClosingPathAtomIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 683 670 <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">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 684 671 | |
| 685 672 <span class="k">if</span> <span class="s">(</span><span class="i">$CycleClosingPathAtomIndex</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 686 673 <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> | |
| 687 674 <span class="s">}</span> | |
| 688 675 <span class="k">else</span> <span class="s">{</span> | |
| 689 676 <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">$CycleClosingPathAtomIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 690 677 <span class="s">}</span> | |
| 691 678 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 692 679 <span class="s">}</span> | |
| 693 680 | |
| 694 681 <span class="c"># Generate a unique atom path string for a cyclic path by generating atom path</span> | |
| 695 682 <span class="c"># strings for all possible paths in the cycle and keeping the lexicographically smallest</span> | |
| 696 683 <span class="c"># one.</span> | |
| 697 684 <span class="c">#</span> | |
| 698 685 <span class="c"># Although all the paths enumerated during atom path string generation are also</span> | |
| 699 686 <span class="c"># present in the intial paths list, but structural uniqueness check would detect</span> | |
| 700 687 <span class="c"># 'em earlier and this method ends being invoked only once for the first cyclic path.</span> | |
| 701 688 <span class="c">#</span> | |
| 702 689 <span class="c"># For atom paths containg same atom types and bond symbols, atom path strings</span> | |
| 703 690 <span class="c"># would be same for the paths.</span> | |
| 704 691 <span class="c">#</span> | |
| 705 <a name="_GenerateUniqueAtomPathStringForPathCycle-"></a> 692 <span class="k">sub </span><span class="m">_GenerateUniqueAtomPathStringForPathCycle</span> <span class="s">{</span> | |
| 706 693 <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> | |
| 707 694 | |
| 708 695 <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> | |
| 709 696 <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> | |
| 710 697 <span class="s">}</span> | |
| 711 698 | |
| 712 699 <span class="c"># Generate all possible atom path strings and select the lexicographically smallest one...</span> | |
| 713 700 <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> | |
| 714 701 | |
| 715 702 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> | |
| 716 703 <span class="i">$LastIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span> | |
| 717 704 | |
| 718 705 <span class="i">$FinalAtomPathString</span> = <span class="q">''</span><span class="sc">;</span> | |
| 719 706 <span class="i">$FirstAtomPathString</span> = <span class="n">1</span><span class="sc">;</span> | |
| 720 707 | |
| 721 708 <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> | |
| 722 709 | |
| 723 710 <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> | |
| 724 711 <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> | |
| 725 712 | |
| 726 713 <span class="i">$FirstPartStartIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$FirstPartEndIndex</span> = <span class="i">$Index</span> - <span class="n">1</span><span class="sc">;</span> | |
| 727 714 <span class="i">$SecondPartStartIndex</span> = <span class="i">$Index</span><span class="sc">;</span> <span class="i">$SecondPartEndIndex</span> = <span class="i">$LastIndex</span> - <span class="n">1</span><span class="sc">;</span> | |
| 728 715 | |
| 729 716 <span class="c"># Get first part atoms...</span> | |
| 730 717 <span class="k">for</span> <span class="i">$FirstPartIndex</span> <span class="s">(</span><span class="i">$FirstPartStartIndex</span> .. <span class="i">$FirstPartEndIndex</span><span class="s">)</span> <span class="s">{</span> | |
| 731 718 <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> | |
| 732 719 <span class="s">}</span> | |
| 733 720 | |
| 734 721 <span class="c"># Get second part atoms...</span> | |
| 735 722 <span class="k">for</span> <span class="i">$SecondPartIndex</span> <span class="s">(</span><span class="i">$SecondPartStartIndex</span> .. <span class="i">$SecondPartEndIndex</span><span class="s">)</span> <span class="s">{</span> | |
| 736 723 <span class="k">push</span> <span class="i">@SecondPartPathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>->[<span class="i">$SecondPartIndex</span>]<span class="sc">;</span> | |
| 737 724 <span class="s">}</span> | |
| 738 725 | |
| 739 726 <span class="c"># Get final list of path atoms...</span> | |
| 740 727 <span class="k">if</span> <span class="s">(</span><span class="i">@SecondPartPathAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 741 728 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">@SecondPartPathAtoms</span><span class="sc">;</span> | |
| 742 729 <span class="s">}</span> | |
| 743 730 <span class="k">if</span> <span class="s">(</span><span class="i">@FirstPartPathAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 744 731 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">@FirstPartPathAtoms</span><span class="sc">;</span> | |
| 745 732 <span class="s">}</span> | |
| 746 733 | |
| 747 734 <span class="c"># Complete the cycle by adding first atom as the last atom...</span> | |
| 748 735 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>->[<span class="i">$SecondPartStartIndex</span>]<span class="sc">;</span> | |
| 749 736 | |
| 750 737 <span class="c"># Generate atom path string...</span> | |
| 751 738 <span class="i">$AtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">->_GenerateAtomPathSymbols</span><span class="s">(</span>\<span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 752 739 | |
| 753 740 <span class="i">$AtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span> | |
| 754 741 <span class="i">$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">$AtomPathSymbolsRef</span>}<span class="sc">;</span> | |
| 755 742 | |
| 756 743 <span class="k">if</span> <span class="s">(</span><span class="i">$ReverseAtomPathString</span> <span class="k">le</span> <span class="i">$AtomPathString</span><span class="s">)</span> <span class="s">{</span> | |
| 757 744 <span class="i">$AtomPathString</span> = <span class="i">$ReverseAtomPathString</span><span class="sc">;</span> | |
| 758 745 <span class="s">}</span> | |
| 759 746 | |
| 760 747 <span class="c"># Update final atom path string...</span> | |
| 761 748 | |
| 762 749 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomPathString</span><span class="s">)</span> <span class="s">{</span> | |
| 763 750 <span class="i">$FirstAtomPathString</span> = <span class="n">0</span><span class="sc">;</span> | |
| 764 751 <span class="i">$FinalAtomPathString</span> = <span class="i">$AtomPathString</span><span class="sc">;</span> | |
| 765 752 <span class="s">}</span> | |
| 766 753 <span class="k">else</span> <span class="s">{</span> | |
| 767 754 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomPathString</span> <span class="k">le</span> <span class="i">$FinalAtomPathString</span><span class="s">)</span> <span class="s">{</span> | |
| 768 755 <span class="i">$FinalAtomPathString</span> = <span class="i">$AtomPathString</span><span class="sc">;</span> | |
| 769 756 <span class="s">}</span> | |
| 770 757 <span class="s">}</span> | |
| 771 758 <span class="s">}</span> | |
| 772 759 | |
| 773 760 <span class="c"># Set final atom path string...</span> | |
| 774 761 <span class="c">#</span> | |
| 775 762 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$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> | |
| 776 763 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$FinalAtomPathString</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 777 764 <span class="s">}</span> | |
| 778 765 <span class="k">else</span> <span class="s">{</span> | |
| 779 766 <span class="i">$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> | |
| 780 767 <span class="s">}</span> | |
| 781 768 | |
| 782 769 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 783 770 <span class="s">}</span> | |
| 784 771 | |
| 785 772 <span class="c">#</span> | |
| 786 773 <span class="c"># Generate a unique atom path string for paths containing a cycle closed by</span> | |
| 787 774 <span class="c"># the specified atom index and the last atom index.</span> | |
| 788 775 <span class="c">#</span> | |
| 789 776 <span class="c"># The following methodology is used to generate atom path string which is</span> | |
| 790 777 <span class="c"># independemt of initial atom ordering:</span> | |
| 791 778 <span class="c"># . Generate atom paths string from first atom to the atom before the first cycle</span> | |
| 792 779 <span class="c"># closing atom.</span> | |
| 793 780 <span class="c"># . Generate atom path string from atoms from first cycle closing atom index to</span> | |
| 794 781 <span class="c"># the last path atom in both forward and reverse order. And select the lexicographically</span> | |
| 795 782 <span class="c"># smallest atom path string.</span> | |
| 796 783 <span class="c"># . Combine atom path string generated in first step with second step to generate</span> | |
| 797 784 <span class="c"># final atom path string.</span> | |
| 798 785 <span class="c">#</span> | |
| 799 <a name="_GenerateUniqueAtomPathStringForPathContainingCycle-"></a> 786 <span class="k">sub </span><span class="m">_GenerateUniqueAtomPathStringForPathContainingCycle</span> <span class="s">{</span> | |
| 800 787 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 801 788 <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> | |
| 802 789 | |
| 803 790 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> | |
| 804 791 <span class="i">$LastIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span> | |
| 805 792 | |
| 806 793 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 807 794 | |
| 808 795 <span class="c"># Get path atoms corresponding to linear part of the path...</span> | |
| 809 796 <span class="i">$LinearPartStartIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$LinearPartEndIndex</span> = <span class="i">$CycleClosingAtomIndex</span> - <span class="n">1</span><span class="sc">;</span> | |
| 810 797 | |
| 811 798 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="i">$LinearPartStartIndex</span> .. <span class="i">$LinearPartEndIndex</span><span class="s">)</span> <span class="s">{</span> | |
| 812 799 <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> | |
| 813 800 <span class="s">}</span> | |
| 814 801 | |
| 815 802 <span class="c"># Get atoms correcponding to cyclic part of the path...</span> | |
| 816 803 <span class="i">@CyclicPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 817 804 <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> | |
| 818 805 | |
| 819 806 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="i">$CyclicPartStartIndex</span> .. <span class="i">$CyclicPartEndIndex</span><span class="s">)</span> <span class="s">{</span> | |
| 820 807 <span class="k">push</span> <span class="i">@CyclicPartPathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 821 808 <span class="s">}</span> | |
| 822 809 | |
| 823 810 <span class="c"># Setup a lexicographically smaller atom path string for cyclic part...</span> | |
| 824 811 | |
| 825 812 <span class="i">$CyclicPartAtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">->_GenerateAtomPathSymbols</span><span class="s">(</span>\<span class="i">@CyclicPartPathAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 826 813 <span class="i">$CyclicPartAtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$CyclicPartAtomPathSymbolsRef</span>}<span class="sc">;</span> | |
| 827 814 <span class="i">$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">$CyclicPartAtomPathSymbolsRef</span>}<span class="sc">;</span> | |
| 828 815 | |
| 829 816 <span class="c"># Setup atom path corresponding to linear part and lexigraphicall smaller cyclic part...</span> | |
| 830 817 | |
| 831 818 <span class="k">if</span> <span class="s">(</span><span class="i">$ReverseCyclicPartAtomPathString</span> <span class="k">le</span> <span class="i">$CyclicPartAtomPathString</span><span class="s">)</span> <span class="s">{</span> | |
| 832 819 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@CyclicPartPathAtoms</span><span class="sc">;</span> | |
| 833 820 <span class="s">}</span> | |
| 834 821 <span class="k">else</span> <span class="s">{</span> | |
| 835 822 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">@CyclicPartPathAtoms</span><span class="sc">;</span> | |
| 836 823 <span class="s">}</span> | |
| 837 824 | |
| 838 825 <span class="c"># Setup final atom path string...</span> | |
| 839 826 | |
| 840 827 <span class="i">$AtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">->_GenerateAtomPathSymbols</span><span class="s">(</span>\<span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 841 828 <span class="i">$AtomPathString</span> = <span class="k">join</span> <span class="q">''</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span> | |
| 842 829 | |
| 843 830 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$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> | |
| 844 831 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 845 832 <span class="s">}</span> | |
| 846 833 <span class="k">else</span> <span class="s">{</span> | |
| 847 834 <span class="i">$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> | |
| 848 835 <span class="s">}</span> | |
| 849 836 | |
| 850 837 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 851 838 <span class="s">}</span> | |
| 852 839 | |
| 853 840 <span class="c"># Does atom path contain a cycle?</span> | |
| 854 841 <span class="c">#</span> | |
| 855 842 <span class="c"># For an atom path to contain cycle, it must satisfy the following conditions:</span> | |
| 856 843 <span class="c"># . Pathlength >= 3</span> | |
| 857 844 <span class="c"># . Last atom ID is equal to first atom ID or some other atom ID besides itself</span> | |
| 858 845 <span class="c">#</span> | |
| 859 <a name="_DoesAtomPathContainsCycle-"></a> 846 <span class="k">sub </span><span class="m">_DoesAtomPathContainsCycle</span> <span class="s">{</span> | |
| 860 847 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 861 848 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="s">)</span><span class="sc">;</span> | |
| 862 849 | |
| 863 850 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> | |
| 864 851 <span class="k">if</span> <span class="s">(</span><span class="i">$PathLength</span> <= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 865 852 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 866 853 <span class="s">}</span> | |
| 867 854 | |
| 868 855 <span class="k">my</span><span class="s">(</span><span class="i">$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">$LastAtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 869 856 | |
| 870 857 <span class="i">$LastAtomIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span> | |
| 871 858 <span class="i">$LastAtom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$LastAtomIndex</span>]<span class="sc">;</span> | |
| 872 859 <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> | |
| 873 860 | |
| 874 861 <span class="c"># Look for atomID similar to last atom ID...</span> | |
| 875 862 <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> | |
| 876 863 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>->[<span class="i">$AtomIndex</span>]<span class="sc">;</span> | |
| 877 864 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 878 865 | |
| 879 866 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID</span> == <span class="i">$LastAtomID</span><span class="s">)</span> <span class="s">{</span> | |
| 880 867 <span class="c"># It's a cycle...</span> | |
| 881 868 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 882 869 <span class="s">}</span> | |
| 883 870 <span class="s">}</span> | |
| 884 871 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 885 872 <span class="s">}</span> | |
| 886 873 | |
| 887 874 <span class="c"># Get atom path cycle closing atom index...</span> | |
| 888 875 <span class="c">#</span> | |
| 889 <a name="_GetAtomPathCycleClosingAtomIndex-"></a> 876 <span class="k">sub </span><span class="m">_GetAtomPathCycleClosingAtomIndex</span> <span class="s">{</span> | |
| 890 877 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 891 878 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 892 879 | |
| 893 880 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> | |
| 894 881 | |
| 895 882 <span class="i">$LastAtomIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span> | |
| 896 883 <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">$LastAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 897 884 | |
| 898 885 <span class="c"># Look for atomID similar to last atom ID...</span> | |
| 899 886 <span class="k">for</span> <span class="i">$AtomIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$LastAtomIndex</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 900 887 <span class="i">$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> | |
| 901 888 | |
| 902 889 <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> | |
| 903 890 <span class="c"># It's a cycle closing atom...</span> | |
| 904 891 <span class="k">return</span> <span class="i">$AtomIndex</span><span class="sc">;</span> | |
| 905 892 <span class="s">}</span> | |
| 906 893 <span class="s">}</span> | |
| 907 894 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 908 895 <span class="s">}</span> | |
| 909 896 | |
| 910 897 <span class="c"># Is it a structurally unique path containing a cycle?</span> | |
| 911 898 <span class="c">#</span> | |
| 912 899 <span class="c"># For atom paths containing cycles, last atom ID is either equal to first atom ID or</span> | |
| 913 900 <span class="c"># some other atom ID besides itself.</span> | |
| 914 901 <span class="c">#</span> | |
| 915 902 <span class="c"># In order to determine its structurally unqiue independent of initial atom ordering,</span> | |
| 916 903 <span class="c"># the following methodolgy is used:</span> | |
| 917 904 <span class="c">#</span> | |
| 918 905 <span class="c"># . For paths with same first and atom IDs:</span> | |
| 919 906 <span class="c"># . Remove the last atom ID from atom path</span> | |
| 920 907 <span class="c"># . Sort atom IDs in the path</span> | |
| 921 908 <span class="c"># . Add first atom ID from the sorted list to the end of list to complete the cycle</span> | |
| 922 909 <span class="c"># . Generate a atom path ID</span> | |
| 923 910 <span class="c"># . Use final path ID to track uniqueness of path containing cycle.</span> | |
| 924 911 <span class="c">#</span> | |
| 925 912 <span class="c"># . For paths with last atom ID equal to some other atom ID besidies itself:</span> | |
| 926 913 <span class="c"># . Sort atom IDs in atom path</span> | |
| 927 914 <span class="c"># . Generate atom path ID and use it to track unqiueness of atom paths.</span> | |
| 928 915 <span class="c">#</span> | |
| 929 <a name="_IsUniqueAtomPathContainingCycle-"></a> 916 <span class="k">sub </span><span class="m">_IsUniqueAtomPathContainingCycle</span> <span class="s">{</span> | |
| 930 917 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 931 918 <span class="k">my</span><span class="s">(</span><span class="i">$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">$LastAtomID</span><span class="cm">,</span> <span class="i">@PathAtomIDs</span><span class="cm">,</span> <span class="i">@SortedPathAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 932 919 | |
| 933 920 <span class="i">@PathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 934 921 <span class="i">@PathAtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</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">$PathAtomsRef</span>}<span class="sc">;</span> | |
| 935 922 | |
| 936 923 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> | |
| 937 924 | |
| 938 925 <span class="i">$FirstAtom</span> = <span class="i">$PathAtomsRef</span>->[<span class="n">0</span>]<span class="sc">;</span> <span class="i">$FirstAtomID</span> = <span class="i">$FirstAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 939 926 <span class="i">$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> | |
| 940 927 | |
| 941 928 <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> | |
| 942 929 <span class="k">pop</span> <span class="i">@PathAtomIDs</span><span class="sc">;</span> | |
| 943 930 | |
| 944 931 <span class="i">@SortedPathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 945 932 <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> | |
| 946 933 | |
| 947 934 <span class="k">push</span> <span class="i">@SortedPathAtomIDs</span><span class="cm">,</span> <span class="i">$SortedPathAtomIDs</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 948 935 | |
| 949 936 <span class="i">$AtomPathID</span> = <span class="k">join</span> <span class="q">'-'</span><span class="cm">,</span> <span class="i">@SortedPathAtomIDs</span><span class="sc">;</span> | |
| 950 937 <span class="s">}</span> | |
| 951 938 <span class="k">else</span> <span class="s">{</span> | |
| 952 939 <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">$b</span> <span class="s">}</span> <span class="i">@PathAtomIDs</span><span class="sc">;</span> | |
| 953 940 <span class="s">}</span> | |
| 954 941 | |
| 955 942 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">UniqueCyclicAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 956 943 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 957 944 <span class="s">}</span> | |
| 958 945 | |
| 959 946 <span class="c"># It's a unique atom path containing a cycle...</span> | |
| 960 947 <span class="i">$This</span>->{<span class="w">UniqueCyclicAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 961 948 | |
| 962 949 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 963 950 <span class="s">}</span> | |
| 964 951 | |
| 965 952 <span class="c"># Generate atom path string for specified atom path...</span> | |
| 966 953 <span class="c">#</span> | |
| 967 <a name="_GenerateAtomPathString-"></a> 954 <span class="k">sub </span><span class="m">_GenerateAtomPathString</span> <span class="s">{</span> | |
| 968 955 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 969 956 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomPathSymbolsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 970 957 | |
| 971 958 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span> | |
| 972 959 | |
| 973 960 <span class="c"># Generate path atom and bond symbols...</span> | |
| 974 961 <span class="c">#</span> | |
| 975 962 <span class="i">$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> | |
| 976 963 | |
| 977 964 <span class="c"># Check presence of path using path ID created by atom path symbols...</span> | |
| 978 965 <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> | |
| 979 966 <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">$AtomPathString</span>}<span class="s">)</span> <span class="s">{</span> | |
| 980 967 <span class="i">$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> | |
| 981 968 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 982 969 <span class="s">}</span> | |
| 983 970 | |
| 984 971 <span class="c"># Check presence of reverse path using path ID created by atom path symbols...</span> | |
| 985 972 <span class="c">#</span> | |
| 986 973 <span class="i">$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">$AtomPathSymbolsRef</span>}<span class="sc">;</span> | |
| 987 974 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$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> | |
| 988 975 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$ReverseAtomPathString</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 989 976 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 990 977 <span class="s">}</span> | |
| 991 978 | |
| 992 979 <span class="c"># Use lexicographically smaller atom path string as PathID...</span> | |
| 993 980 <span class="c">#</span> | |
| 994 981 <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> | |
| 995 982 <span class="i">$This</span>->{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 996 983 <span class="s">}</span> | |
| 997 984 <span class="k">else</span> <span class="s">{</span> | |
| 998 985 <span class="i">$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> | |
| 999 986 <span class="s">}</span> | |
| 1000 987 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1001 988 <span class="s">}</span> | |
| 1002 989 | |
| 1003 990 <span class="c"># Are atom types for all path atoms same?</span> | |
| 1004 991 <span class="c">#</span> | |
| 1005 <a name="_AreAllPathAtomsSymbolsSame-"></a> 992 <span class="k">sub </span><span class="m">_AreAllPathAtomsSymbolsSame</span> <span class="s">{</span> | |
| 1006 993 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1007 994 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1008 995 | |
| 1009 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> | |
| 1010 997 <span class="i">$FirstAtomType</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 1011 998 | |
| 1012 999 <span class="k">for</span> <span class="i">$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> | |
| 1013 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">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1014 1001 <span class="i">$AtomType</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 1015 1002 | |
| 1016 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> | |
| 1017 1004 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1018 1005 <span class="s">}</span> | |
| 1019 1006 <span class="s">}</span> | |
| 1020 1007 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1021 1008 <span class="s">}</span> | |
| 1022 1009 | |
| 1023 1010 <span class="c"># Are bond symbols for all path bonds same?</span> | |
| 1024 1011 <span class="c">#</span> | |
| 1025 <a name="_AreAllPathBondSymbolsSame-"></a>1012 <span class="k">sub </span><span class="m">_AreAllPathBondSymbolsSame</span> <span class="s">{</span> | |
| 1026 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> | |
| 1027 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">$BondSymbol</span><span class="s">)</span><span class="sc">;</span> | |
| 1028 1015 | |
| 1029 1016 <span class="c"># During no usage of bond symbols, just ignore them and assume they are same...</span> | |
| 1030 1017 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1031 1018 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1032 1019 <span class="s">}</span> | |
| 1033 1020 | |
| 1034 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> | |
| 1035 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> | |
| 1036 1023 | |
| 1037 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> | |
| 1038 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> | |
| 1039 1026 | |
| 1040 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">$PathAtomsRef</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1041 1028 <span class="i">$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">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 1042 1029 <span class="i">$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">$BondedAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1043 1030 | |
| 1044 1031 <span class="s">(</span><span class="i">$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">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 1045 1032 <span class="i">$BondSymbol</span> = <span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$BondAtomID1</span>}{<span class="i">$BondAtomID2</span>}<span class="sc">;</span> | |
| 1046 1033 | |
| 1047 1034 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> <span class="k">ne</span> <span class="i">$FirstBondSymbol</span><span class="s">)</span> <span class="s">{</span> | |
| 1048 1035 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1049 1036 <span class="s">}</span> | |
| 1050 1037 <span class="s">}</span> | |
| 1051 1038 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1052 1039 <span class="s">}</span> | |
| 1053 1040 | |
| 1054 1041 <span class="c"># Generate atom path symbols...</span> | |
| 1055 1042 <span class="c">#</span> | |
| 1056 <a name="_GenerateAtomPathSymbols-"></a>1043 <span class="k">sub </span><span class="m">_GenerateAtomPathSymbols</span> <span class="s">{</span> | |
| 1057 1044 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1058 1045 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@AtomPathSymbols</span><span class="s">)</span><span class="sc">;</span> | |
| 1059 1046 | |
| 1060 1047 <span class="i">@AtomPathSymbols</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1061 1048 | |
| 1062 1049 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>} == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 1063 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> | |
| 1064 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> | |
| 1065 1052 <span class="k">return</span> \<span class="i">@AtomPathSymbols</span><span class="sc">;</span> | |
| 1066 1053 <span class="s">}</span> | |
| 1067 1054 | |
| 1068 1055 <span class="c"># Ignore bond information...</span> | |
| 1069 1056 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1070 1057 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1071 1058 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1072 1059 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 1073 1060 <span class="s">}</span> | |
| 1074 1061 <span class="k">return</span> \<span class="i">@AtomPathSymbols</span><span class="sc">;</span> | |
| 1075 1062 <span class="s">}</span> | |
| 1076 1063 | |
| 1077 1064 <span class="c"># Use atoms and bonds to generate atom path string...</span> | |
| 1078 1065 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1079 1066 | |
| 1080 1067 <span class="c"># Process atom type of first atom in path...</span> | |
| 1081 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> | |
| 1082 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> | |
| 1083 1070 | |
| 1084 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">$PathAtomsRef</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1085 1072 <span class="i">$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">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 1086 1073 <span class="i">$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">$BondedAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1087 1074 | |
| 1088 1075 <span class="s">(</span><span class="i">$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">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 1089 1076 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">BondSymbols</span>}{<span class="i">$BondAtomID1</span>}{<span class="i">$BondAtomID2</span>}<span class="sc">;</span> | |
| 1090 1077 | |
| 1091 1078 <span class="c"># Process atom type of next atom in path...</span> | |
| 1092 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> | |
| 1093 1080 <span class="s">}</span> | |
| 1094 1081 <span class="k">return</span> \<span class="i">@AtomPathSymbols</span><span class="sc">;</span> | |
| 1095 1082 <span class="s">}</span> | |
| 1096 1083 | |
| 1097 1084 <span class="c"># Set final fingerprits...</span> | |
| 1098 1085 <span class="c">#</span> | |
| 1099 <a name="_SetFinalFingerprints-"></a>1086 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> | |
| 1100 1087 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1101 1088 | |
| 1102 1089 <span class="c"># Mark successful generation of fingerprints...</span> | |
| 1103 1090 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 1104 1091 | |
| 1105 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> | |
| 1106 1093 <span class="i">$This</span><span class="i">->_SetFinalFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1107 1094 <span class="s">}</span> | |
| 1108 1095 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1109 1096 <span class="i">$This</span><span class="i">->_SetFinalFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1110 1097 <span class="s">}</span> | |
| 1111 1098 | |
| 1112 1099 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1113 1100 <span class="s">}</span> | |
| 1114 1101 | |
| 1115 1102 <span class="c"># Set final fingerprits bit vector...</span> | |
| 1116 1103 <span class="c">#</span> | |
| 1117 <a name="_SetFinalFingerprintsBitVector-"></a>1104 <span class="k">sub </span><span class="m">_SetFinalFingerprintsBitVector</span> <span class="s">{</span> | |
| 1118 1105 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1119 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">$SetBitNum</span><span class="s">)</span><span class="sc">;</span> | |
| 1120 1107 | |
| 1121 1108 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span> | |
| 1122 1109 | |
| 1123 1110 <span class="i">$Size</span> = <span class="i">$This</span>->{<span class="w">Size</span>}<span class="sc">;</span> | |
| 1124 1111 | |
| 1125 1112 <span class="i">$SkipBitPosCheck</span> = <span class="n">1</span><span class="sc">;</span> | |
| 1126 1113 <span class="i">$NumOfBitsToSetPerPath</span> = <span class="i">$This</span>->{<span class="w">NumOfBitsToSetPerPath</span>}<span class="sc">;</span> | |
| 1127 1114 | |
| 1128 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> | |
| 1129 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">$PathLength</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 1130 1117 <span class="i">$AtomPathHashCode</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$AtomPathString</span><span class="s">)</span><span class="sc">;</span> | |
| 1131 1118 | |
| 1132 1119 <span class="c"># Set random number seed...</span> | |
| 1133 1120 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1134 1121 <span class="i">CORE::</span><span class="k">srand</span><span class="s">(</span><span class="i">$AtomPathHashCode</span><span class="s">)</span><span class="sc">;</span> | |
| 1135 1122 <span class="s">}</span> | |
| 1136 1123 <span class="k">else</span> <span class="s">{</span> | |
| 1137 1124 <span class="i">MathUtil::srandom</span><span class="s">(</span><span class="i">$AtomPathHashCode</span><span class="s">)</span><span class="sc">;</span> | |
| 1138 1125 <span class="s">}</span> | |
| 1139 1126 | |
| 1140 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> | |
| 1141 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> | |
| 1142 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">$SkipBitPosCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 1143 1130 <span class="s">}</span> | |
| 1144 1131 <span class="s">}</span> | |
| 1145 1132 <span class="s">}</span> | |
| 1146 1133 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1147 1134 <span class="s">}</span> | |
| 1148 1135 | |
| 1149 1136 <span class="c"># Set final fingerprits vector...</span> | |
| 1150 1137 <span class="c">#</span> | |
| 1151 <a name="_SetFinalFingerprintsVector-"></a>1138 <span class="k">sub </span><span class="m">_SetFinalFingerprintsVector</span> <span class="s">{</span> | |
| 1152 1139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1153 1140 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomPathCount</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 1154 1141 | |
| 1155 1142 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1156 1143 <span class="i">@ValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1157 1144 | |
| 1158 1145 <span class="k">for</span> <span class="i">$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">$This</span>->{<span class="w">AtomPathsStrings</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 1159 1146 <span class="k">for</span> <span class="i">$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> | |
| 1160 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> | |
| 1161 1148 | |
| 1162 1149 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$AtomPathCount</span><span class="sc">;</span> | |
| 1163 1150 <span class="k">push</span> <span class="i">@ValueIDs</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="sc">;</span> | |
| 1164 1151 <span class="s">}</span> | |
| 1165 1152 <span class="s">}</span> | |
| 1166 1153 | |
| 1167 1154 <span class="c"># Add PathLengthIDs and values to fingerprint vector...</span> | |
| 1168 1155 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 1169 1156 <span class="i">$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> | |
| 1170 1157 | |
| 1171 1158 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1172 1159 <span class="s">}</span> | |
| 1173 1160 | |
| 1174 1161 <span class="c"># Cache appropriate molecule data...</span> | |
| 1175 1162 <span class="c">#</span> | |
| 1176 <a name="_SetupMoleculeDataCache-"></a>1163 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> | |
| 1177 1164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1178 1165 | |
| 1179 1166 <span class="c"># Get all atoms...</span> | |
| 1180 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> | |
| 1181 1168 | |
| 1182 1169 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1183 1170 <span class="s">}</span> | |
| 1184 1171 | |
| 1185 1172 <span class="c"># Clear cached molecule data...</span> | |
| 1186 1173 <span class="c">#</span> | |
| 1187 <a name="_ClearMoleculeDataCache-"></a>1174 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> | |
| 1188 1175 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1189 1176 | |
| 1190 1177 <span class="c"># Clear atoms...</span> | |
| 1191 1178 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1192 1179 | |
| 1193 1180 <span class="c"># Clear path atoms..</span> | |
| 1194 1181 <span class="i">$This</span>->{<span class="w">AtomPathsRef</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 1195 1182 | |
| 1196 1183 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1197 1184 <span class="s">}</span> | |
| 1198 1185 | |
| 1199 1186 <span class="c"># Set atomic invariants to use atom identifiers...</span> | |
| 1200 1187 <span class="c">#</span> | |
| 1201 <a name="SetAtomicInvariantsToUse-"></a>1188 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> | |
| 1202 1189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1203 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> | |
| 1204 1191 | |
| 1205 1192 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 1206 1193 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> | |
| 1207 1194 <span class="k">return</span><span class="sc">;</span> | |
| 1208 1195 <span class="s">}</span> | |
| 1209 1196 | |
| 1210 1197 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 1211 1198 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 1212 1199 | |
| 1213 1200 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1214 1201 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1215 1202 | |
| 1216 1203 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 1217 1204 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
| 1218 1205 <span class="s">}</span> | |
| 1219 1206 <span class="k">else</span> <span class="s">{</span> | |
| 1220 1207 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
| 1221 1208 <span class="s">}</span> | |
| 1222 1209 | |
| 1223 1210 <span class="c"># Make sure specified AtomicInvariants are valid...</span> | |
| 1224 1211 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> | |
| 1225 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> | |
| 1226 1213 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> | |
| 1227 1214 <span class="s">}</span> | |
| 1228 1215 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> | |
| 1229 1216 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> | |
| 1230 1217 <span class="s">}</span> | |
| 1231 1218 | |
| 1232 1219 <span class="c"># Set atomic invariants to use...</span> | |
| 1233 1220 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1234 1221 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> | |
| 1235 1222 | |
| 1236 1223 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1237 1224 <span class="s">}</span> | |
| 1238 1225 | |
| 1239 1226 <span class="c"># Set functional classes to use for atom identifiers...</span> | |
| 1240 1227 <span class="c">#</span> | |
| 1241 <a name="SetFunctionalClassesToUse-"></a>1228 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> | |
| 1242 1229 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1243 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> | |
| 1244 1231 | |
| 1245 1232 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 1246 1233 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> | |
| 1247 1234 <span class="k">return</span><span class="sc">;</span> | |
| 1248 1235 <span class="s">}</span> | |
| 1249 1236 | |
| 1250 1237 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1251 1238 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
| 1252 1239 <span class="k">return</span><span class="sc">;</span> | |
| 1253 1240 <span class="s">}</span> | |
| 1254 1241 | |
| 1255 1242 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 1256 1243 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 1257 1244 | |
| 1258 1245 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1259 1246 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1260 1247 | |
| 1261 1248 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 1262 1249 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
| 1263 1250 <span class="s">}</span> | |
| 1264 1251 <span class="k">else</span> <span class="s">{</span> | |
| 1265 1252 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
| 1266 1253 <span class="s">}</span> | |
| 1267 1254 | |
| 1268 1255 <span class="c"># Make sure specified FunctionalClasses are valid...</span> | |
| 1269 1256 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> | |
| 1270 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> | |
| 1271 1258 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> | |
| 1272 1259 <span class="s">}</span> | |
| 1273 1260 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> | |
| 1274 1261 <span class="s">}</span> | |
| 1275 1262 | |
| 1276 1263 <span class="c"># Set functional classes to use...</span> | |
| 1277 1264 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1278 1265 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> | |
| 1279 1266 | |
| 1280 1267 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1281 1268 <span class="s">}</span> | |
| 1282 1269 | |
| 1283 1270 <span class="c"># Initialize atom indentifier type information...</span> | |
| 1284 1271 <span class="c">#</span> | |
| 1285 1272 <span class="c"># Current supported values:</span> | |
| 1286 1273 <span class="c">#</span> | |
| 1287 1274 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span> | |
| 1288 1275 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> | |
| 1289 1276 <span class="c">#</span> | |
| 1290 <a name="_InitializeAtomIdentifierTypeInformation-"></a>1277 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> | |
| 1291 1278 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1292 1279 | |
| 1293 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> | |
| 1294 1281 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1295 1282 <span class="s">}</span> | |
| 1296 1283 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1297 1284 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1298 1285 <span class="s">}</span> | |
| 1299 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> | |
| 1300 1287 <span class="c"># Nothing to do for now...</span> | |
| 1301 1288 <span class="s">}</span> | |
| 1302 1289 <span class="k">else</span> <span class="s">{</span> | |
| 1303 1290 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
| 1304 1291 <span class="s">}</span> | |
| 1305 1292 | |
| 1306 1293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1307 1294 <span class="s">}</span> | |
| 1308 1295 | |
| 1309 1296 <span class="c"># Initialize atomic invariants atom types to use for generating atom identifiers...</span> | |
| 1310 1297 <span class="c">#</span> | |
| 1311 1298 <span class="c"># Let:</span> | |
| 1312 1299 <span class="c"># AS = Atom symbol corresponding to element symbol</span> | |
| 1313 1300 <span class="c">#</span> | |
| 1314 1301 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1315 1302 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1316 1303 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1317 1304 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1318 1305 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1319 1306 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1320 1307 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> | |
| 1321 1308 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> | |
| 1322 1309 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> | |
| 1323 1310 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> | |
| 1324 1311 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> | |
| 1325 1312 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> | |
| 1326 1313 <span class="c">#</span> | |
| 1327 1314 <span class="c"># Then:</span> | |
| 1328 1315 <span class="c">#</span> | |
| 1329 1316 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> | |
| 1330 1317 <span class="c">#</span> | |
| 1331 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> | |
| 1332 1319 <span class="c">#</span> | |
| 1333 1320 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> | |
| 1334 1321 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X<n>, BO<n>, H<n>, FC<+n/-n>.</span> | |
| 1335 1322 <span class="c"># AtomID specification doesn't include atomic invariants with zero or undefined values.</span> | |
| 1336 1323 <span class="c">#</span> | |
| 1337 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a>1324 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> | |
| 1338 1325 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1339 1326 | |
| 1340 1327 <span class="c"># Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC</span> | |
| 1341 1328 <span class="c">#</span> | |
| 1342 1329 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1343 1330 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> | |
| 1344 1331 | |
| 1345 1332 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1346 1333 <span class="s">}</span> | |
| 1347 1334 | |
| 1348 1335 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> | |
| 1349 1336 <span class="c"># class, to use for generating atom identifiers...</span> | |
| 1350 1337 <span class="c">#</span> | |
| 1351 1338 <span class="c"># Let:</span> | |
| 1352 1339 <span class="c"># HBD: HydrogenBondDonor</span> | |
| 1353 1340 <span class="c"># HBA: HydrogenBondAcceptor</span> | |
| 1354 1341 <span class="c"># PI : PositivelyIonizable</span> | |
| 1355 1342 <span class="c"># NI : NegativelyIonizable</span> | |
| 1356 1343 <span class="c"># Ar : Aromatic</span> | |
| 1357 1344 <span class="c"># Hal : Halogen</span> | |
| 1358 1345 <span class="c"># H : Hydrophobic</span> | |
| 1359 1346 <span class="c"># RA : RingAtom</span> | |
| 1360 1347 <span class="c"># CA : ChainAtom</span> | |
| 1361 1348 <span class="c">#</span> | |
| 1362 1349 <span class="c"># Then:</span> | |
| 1363 1350 <span class="c">#</span> | |
| 1364 1351 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> | |
| 1365 1352 <span class="c">#</span> | |
| 1366 1353 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> | |
| 1367 1354 <span class="c">#</span> | |
| 1368 1355 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> | |
| 1369 1356 <span class="c">#</span> | |
| 1370 1357 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> | |
| 1371 1358 <span class="c">#</span> | |
| 1372 1359 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> | |
| 1373 1360 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> | |
| 1374 1361 <span class="c"># PositivelyIonizable: +, NH2</span> | |
| 1375 1362 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> | |
| 1376 1363 <span class="c">#</span> | |
| 1377 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a>1364 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> | |
| 1378 1365 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1379 1366 | |
| 1380 1367 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span> | |
| 1381 1368 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span> | |
| 1382 1369 <span class="c">#</span> | |
| 1383 1370 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1384 1371 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> | |
| 1385 1372 | |
| 1386 1373 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1387 1374 <span class="s">}</span> | |
| 1388 1375 | |
| 1389 1376 <span class="c"># Return a string containg data for PathLengthFingerprints object...</span> | |
| 1390 1377 <span class="c">#</span> | |
| 1391 <a name="StringifyPathLengthFingerprints-"></a>1378 <span class="k">sub </span><span class="m">StringifyPathLengthFingerprints</span> <span class="s">{</span> | |
| 1392 1379 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1393 1380 <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthsFingerprintsString</span><span class="s">)</span><span class="sc">;</span> | |
| 1394 1381 | |
| 1395 1382 <span class="c"># Type of fingerprint...</span> | |
| 1396 1383 <span class="i">$PathLengthsFingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}"</span><span class="sc">;</span> | |
| 1397 1384 | |
| 1398 1385 <span class="c"># Path length...</span> | |
| 1399 1386 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; MinPathLength: $This->{MinLength}; MaxPathLength: $This->{MaxLength}"</span><span class="sc">;</span> | |
| 1400 1387 | |
| 1401 1388 <span class="c"># Fingerprint generation control...</span> | |
| 1402 1389 <span class="k">my</span><span class="s">(</span><span class="i">$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">$UseUniquePaths</span><span class="s">)</span><span class="sc">;</span> | |
| 1403 1390 | |
| 1404 1391 <span class="i">$AllowSharedBonds</span> = <span class="i">$This</span>->{<span class="w">AllowSharedBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> | |
| 1405 1392 <span class="i">$AllowRings</span> = <span class="i">$This</span>->{<span class="w">AllowRings</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> | |
| 1406 1393 <span class="i">$UseBondSymbols</span> = <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> | |
| 1407 1394 <span class="i">$UseUniquePaths</span> = <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> | |
| 1408 1395 | |
| 1409 1396 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; UseUniquePaths: $UseUniquePaths; AllowSharedBonds: $AllowSharedBonds; AllowRings: $AllowRings; UseBondSymbols: $UseBondSymbols"</span><span class="sc">;</span> | |
| 1410 1397 | |
| 1411 1398 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1412 1399 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1413 1400 | |
| 1414 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> | |
| 1415 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> | |
| 1416 1403 | |
| 1417 1404 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 1418 1405 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> | |
| 1419 1406 <span class="s">}</span> | |
| 1420 1407 | |
| 1421 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> | |
| 1422 1409 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 1423 1410 <span class="i">$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> | |
| 1424 1411 <span class="s">}</span> | |
| 1425 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> | |
| 1426 1413 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> | |
| 1427 1414 | |
| 1428 1415 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1429 1416 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1430 1417 | |
| 1431 1418 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 1432 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> | |
| 1433 1420 <span class="s">}</span> | |
| 1434 1421 | |
| 1435 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> | |
| 1436 1423 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 1437 1424 <span class="i">$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> | |
| 1438 1425 <span class="s">}</span> | |
| 1439 1426 | |
| 1440 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> | |
| 1441 1428 <span class="c"># Size...</span> | |
| 1442 1429 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; Size: $This->{Size}; MinSize: $This->{MinSize}; MaxSize: $This->{MaxSize}"</span><span class="sc">;</span> | |
| 1443 1430 | |
| 1444 1431 <span class="c"># NumOfBitsToSetPerPath...</span> | |
| 1445 1432 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; NumOfBitsToSetPerPath: $This->{NumOfBitsToSetPerPath}"</span><span class="sc">;</span> | |
| 1446 1433 | |
| 1447 1434 <span class="c"># Fingerprint bit density and num of bits set...</span> | |
| 1448 1435 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span> | |
| 1449 1436 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1450 1437 <span class="i">$BitDensity</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1451 1438 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity"</span><span class="sc">;</span> | |
| 1452 1439 | |
| 1453 1440 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; FingerprintsBitVector: < $This->{FingerprintsBitVector} >"</span><span class="sc">;</span> | |
| 1454 1441 <span class="s">}</span> | |
| 1455 1442 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1456 1443 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> | |
| 1457 1444 <span class="s">}</span> | |
| 1458 1445 | |
| 1459 1446 <span class="k">return</span> <span class="i">$PathLengthsFingerprintsString</span><span class="sc">;</span> | |
| 1460 1447 <span class="s">}</span> | |
| 1461 1448 | |
| 1462 <a name="EOF-"></a></pre> | |
| 1463 <p> </p> | |
| 1464 <br /> | |
| 1465 <center> | |
| 1466 <img src="../../../images/h2o2.png"> | |
| 1467 </center> | |
| 1468 </body> | |
| 1469 </html> |