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3 <title>MayaChemTools:Code:Fingerprints::ExtendedConnectivityFingerprints.pm</title>
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13 <pre>
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14 <a name="package-Fingerprints::ExtendedConnectivityFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span>
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: ExtendedConnectivityFingerprints.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
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18 5 <span class="c"># $Revision: 1.39 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span>
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54 41 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span>
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55 42 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span>
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56 43 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span>
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57 44 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span>
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58 45
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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>
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60 47
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61 48 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span>
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62 49 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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63 50 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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64 51
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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>
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66 53
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67 54 <span class="c"># Setup class variables...</span>
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68 55 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
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69 56 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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70 57
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71 58 <span class="c"># Overload Perl functions...</span>
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72 59 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyExtendedConnectivityFingerprints'</span><span class="sc">;</span>
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73 60
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74 61 <span class="c"># Class constructor...</span>
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75 <a name="new-"></a> 62 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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76 63 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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77 64
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78 65 <span class="c"># Initialize object...</span>
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79 66 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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80 67 <span class="k">bless</span> <span class="i">$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>
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81 68 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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82 69
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83 70 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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84 71
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85 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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86 73 <span class="s">}</span>
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87 74
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88 75 <span class="c"># Initialize object data...</span>
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89 76 <span class="c">#</span>
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90 <a name="_InitializeExtendedConnectivityFingerprints-"></a> 77 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprints</span> <span class="s">{</span>
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91 78 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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92 79
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93 80 <span class="c"># Type of fingerprint to generate:</span>
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94 81 <span class="c">#</span>
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95 82 <span class="c"># ExtendedConnectivity - Set of integer identifiers corresponding to structurally unique features</span>
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96 83 <span class="c"># ExtendedConnectivityCount - Set of integer identifiers corresponding to structurally unique features and their count</span>
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97 84 <span class="c"># ExtendedConnectivityBits - A bit vector indicating presence/absence of structurally unique features</span>
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98 85 <span class="c">#</span>
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99 86 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivity'</span><span class="sc">;</span>
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100 87
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101 88 <span class="c"># Atomic neighborhoods radius for extended connectivity...</span>
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102 89 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span>
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103 90
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104 91 <span class="c"># Size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span>
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105 92 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="n">1024</span><span class="sc">;</span>
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106 93
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107 94 <span class="c"># Min and max size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span>
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108 95 <span class="i">$This</span>->{<span class="w">MinSize</span>} = <span class="n">32</span><span class="sc">;</span>
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109 96 <span class="i">$This</span>->{<span class="w">MaxSize</span>} = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span>
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110 97
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111 98 <span class="c"># Type of atom attributes to use for initial identifier assignment to non-hydrogen atoms</span>
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112 99 <span class="c"># during the calculation of extended connectivity fingerprints [ Ref 48, Ref 52 ]...</span>
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113 100 <span class="c">#</span>
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114 101 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes,</span>
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115 102 <span class="c"># DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,</span>
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116 103 <span class="c"># TPSAAtomTypes, UFFAtomTypes</span>
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117 104 <span class="c">#</span>
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118 105 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span>
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119 106
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120 107 <span class="c"># Random number generator to use during generation of fingerprints bit-vector</span>
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121 108 <span class="c"># string: Perl CORE::rand or MayaChemTools MathUtil::random function.</span>
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122 109 <span class="c">#</span>
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123 110 <span class="c"># The random number generator implemented in MayaChemTools is a variant of</span>
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124 111 <span class="c"># linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].</span>
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125 112 <span class="c"># It is also referred to as Lehmer random number generator or Park-Miller</span>
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126 113 <span class="c"># random number generator.</span>
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127 114 <span class="c">#</span>
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128 115 <span class="c"># Unlike Perl's core random number generator function rand, the random number</span>
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129 116 <span class="c"># generator implemented in MayaChemTools, MathUtil::random, generates consistent</span>
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130 117 <span class="c"># random values across different platformsfor a specific random seed and leads</span>
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131 118 <span class="c"># to generation of portable fingerprints bit-vector strings.</span>
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132 119 <span class="c">#</span>
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133 120 <span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>} = <span class="n">1</span><span class="sc">;</span>
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134 121
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135 122 <span class="c"># Atom neighorhoods up to specified neighborhood radius...</span>
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136 123 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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137 124
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138 125 <span class="c"># Atom identifiers at different neighborhoods up to specified neighborhood radius...</span>
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139 126 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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140 127
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141 128 <span class="c"># Structurally unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span>
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142 129 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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143 130 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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144 131
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145 132 <span class="c"># Unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span>
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146 133 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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147 134 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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148 135
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149 136 <span class="c"># Structure feature information at different neighborhoods up to specified neighborhood</span>
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150 137 <span class="c"># radius used during removal of atom indentifiers which are structually equivalent...</span>
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151 138 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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152 139 <span class="s">}</span>
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153 140
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154 141 <span class="c"># Initialize class ...</span>
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155 <a name="_InitializeClass-"></a> 142 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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156 143 <span class="c">#Class name...</span>
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157 144 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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158 145 <span class="s">}</span>
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159 146
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160 147 <span class="c"># Initialize object properties....</span>
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161 <a name="_InitializeExtendedConnectivityFingerprintsProperties-"></a> 148 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsProperties</span> <span class="s">{</span>
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162 149 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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163 150
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164 151 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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165 152 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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166 153 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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167 154 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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168 155 <span class="s">}</span>
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169 156
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170 157 <span class="c"># Make sure molecule object was specified...</span>
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171 158 <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>
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172 159 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span>
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173 160 <span class="s">}</span>
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174 161
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175 162 <span class="c"># Make sure AtomIdentifierType was specified...</span>
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176 163 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
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177 164 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span>
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178 165 <span class="s">}</span>
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179 166
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180 167 <span class="c"># Make sure it's power of 2...</span>
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181 168 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span>
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182 169 <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>
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183 170 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Specified size value, $NamesAndValues{Size}, must be power of 2..."</span><span class="sc">;</span>
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184 171 <span class="s">}</span>
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185 172 <span class="s">}</span>
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186 173
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187 174 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span>
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188 175 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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189 176 <span class="s">}</span>
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190 177 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span>
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191 178 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityCountFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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192 179 <span class="s">}</span>
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193 180 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
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194 181 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityBitsFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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195 182 <span class="s">}</span>
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196 183 <span class="k">else</span> <span class="s">{</span>
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197 184 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeExtendedConnectivityFingerprintsProperties: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits..."</span><span class="sc">;</span>
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198 185 <span class="s">}</span>
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199 186
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200 187 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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201 188 <span class="s">}</span>
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202 189
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203 190 <span class="c"># Initialize extended connectivity fingerprints vector...</span>
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|
|
204 191 <span class="c">#</span>
|
|
|
205 <a name="_InitializeExtendedConnectivityFingerprintsVector-"></a> 192 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsVector</span> <span class="s">{</span>
|
|
|
206 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
207 194
|
|
|
208 195 <span class="c"># Type of vector...</span>
|
|
|
209 196 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span>
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|
|
210 197
|
|
|
211 198 <span class="c"># Type of FingerprintsVector...</span>
|
|
|
212 199 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'AlphaNumericalValues'</span><span class="sc">;</span>
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|
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213 200
|
|
|
214 201 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
|
215 202
|
|
|
216 203 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
217 204 <span class="s">}</span>
|
|
|
218 205
|
|
|
219 206 <span class="c"># Initialize extended connectivity count fingerprints vector...</span>
|
|
|
220 207 <span class="c">#</span>
|
|
|
221 <a name="_InitializeExtendedConnectivityCountFingerprintsVector-"></a> 208 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityCountFingerprintsVector</span> <span class="s">{</span>
|
|
|
222 209 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
223 210
|
|
|
224 211 <span class="c"># Type of vector...</span>
|
|
|
225 212 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span>
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226 213
|
|
|
227 214 <span class="c"># Type of FingerprintsVector...</span>
|
|
|
228 215 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span>
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|
|
229 216
|
|
|
230 217 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
231 218
|
|
|
232 219 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
233 220 <span class="s">}</span>
|
|
|
234 221
|
|
|
235 222 <span class="c"># Initialize extended connectivity bit fingerprints vector...</span>
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|
|
236 223 <span class="c">#</span>
|
|
|
237 <a name="_InitializeExtendedConnectivityBitsFingerprintsBitVector-"></a> 224 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityBitsFingerprintsBitVector</span> <span class="s">{</span>
|
|
|
238 225 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
239 226
|
|
|
240 227 <span class="c"># Type of vector...</span>
|
|
|
241 228 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span>
|
|
|
242 229
|
|
|
243 230 <span class="i">$This</span><span class="i">->_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
244 231
|
|
|
245 232 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
246 233 <span class="s">}</span>
|
|
|
247 234
|
|
|
248 235 <span class="c"># Set type...</span>
|
|
|
249 236 <span class="c">#</span>
|
|
|
250 <a name="SetType-"></a> 237 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span>
|
|
|
251 238 <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>
|
|
|
252 239
|
|
|
253 240 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
254 241 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivity'</span><span class="sc">;</span><span class="sc">;</span>
|
|
|
255 242 <span class="s">}</span>
|
|
|
256 243 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
257 244 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivityCount'</span><span class="sc">;</span><span class="sc">;</span>
|
|
|
258 245 <span class="s">}</span>
|
|
|
259 246 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
260 247 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivityBits'</span><span class="sc">;</span><span class="sc">;</span>
|
|
|
261 248 <span class="s">}</span>
|
|
|
262 249 <span class="k">else</span> <span class="s">{</span>
|
|
|
263 250 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits..."</span><span class="sc">;</span>
|
|
|
264 251 <span class="s">}</span>
|
|
|
265 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
266 253 <span class="s">}</span>
|
|
|
267 254
|
|
|
268 255 <span class="c"># Disable vector type change...</span>
|
|
|
269 256 <span class="c">#</span>
|
|
|
270 <a name="SetVectorType-"></a> 257 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span>
|
|
|
271 258 <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>
|
|
|
272 259
|
|
|
273 260 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Can't change vector type..."</span><span class="sc">;</span>
|
|
|
274 261
|
|
|
275 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
276 263 <span class="s">}</span>
|
|
|
277 264
|
|
|
278 265 <span class="c"># Disable vector type change...</span>
|
|
|
279 266 <span class="c">#</span>
|
|
|
280 <a name="SetFingerprintsVectorType-"></a> 267 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span>
|
|
|
281 268 <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>
|
|
|
282 269
|
|
|
283 270 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVectorType: Can't change fingerprints vector type..."</span><span class="sc">;</span>
|
|
|
284 271
|
|
|
285 272 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
286 273 <span class="s">}</span>
|
|
|
287 274
|
|
|
288 275 <span class="c"># Set intial atom identifier type..</span>
|
|
|
289 276 <span class="c">#</span>
|
|
|
290 <a name="SetAtomIdentifierType-"></a> 277 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
|
|
|
291 278 <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>
|
|
|
292 279
|
|
|
293 280 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
294 281 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span>
|
|
|
295 282 <span class="s">}</span>
|
|
|
296 283
|
|
|
297 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
298 285 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span>
|
|
|
299 286 <span class="s">}</span>
|
|
|
300 287
|
|
|
301 288 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
|
|
|
302 289
|
|
|
303 290 <span class="c"># Initialize identifier type information...</span>
|
|
|
304 291 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
305 292
|
|
|
306 293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
307 294 <span class="s">}</span>
|
|
|
308 295
|
|
|
309 296 <span class="c"># Set atom neighborhood radius...</span>
|
|
|
310 297 <span class="c">#</span>
|
|
|
311 <a name="SetNeighborhoodRadius-"></a> 298 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span>
|
|
|
312 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
313 300
|
|
|
314 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
315 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span>
|
|
|
316 303 <span class="s">}</span>
|
|
|
317 304
|
|
|
318 305 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
319 306 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span>
|
|
|
320 307 <span class="s">}</span>
|
|
|
321 308 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
322 309
|
|
|
323 310 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
324 311 <span class="s">}</span>
|
|
|
325 312
|
|
|
326 313 <span class="c"># Generate fingerprints description...</span>
|
|
|
327 314 <span class="c">#</span>
|
|
|
328 <a name="GetDescription-"></a> 315 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
|
|
|
329 316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
330 317
|
|
|
331 318 <span class="c"># Is description explicity set?</span>
|
|
|
332 319 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
333 320 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span>
|
|
|
334 321 <span class="s">}</span>
|
|
|
335 322
|
|
|
336 323 <span class="c"># Generate fingerprints description...</span>
|
|
|
337 324
|
|
|
338 325 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:Radius$This->{NeighborhoodRadius}"</span><span class="sc">;</span>
|
|
|
339 326 <span class="s">}</span>
|
|
|
340 327
|
|
|
341 328 <span class="c"># Generate fingerprints...</span>
|
|
|
342 329 <span class="c">#</span>
|
|
|
343 330 <span class="c"># Methodology:</span>
|
|
|
344 331 <span class="c"># . Assign initial atom identfiers to all non-hydrogen atoms in the molecule</span>
|
|
|
345 332 <span class="c">#</span>
|
|
|
346 333 <span class="c"># . Remove duplicates from the initial identifiers and add them to list corresponding</span>
|
|
|
347 334 <span class="c"># to molecule fingerprint</span>
|
|
|
348 335 <span class="c">#</span>
|
|
|
349 336 <span class="c"># . For NeighborhoodRadius value of 0, just return the molecule fingerprint list</span>
|
|
|
350 337 <span class="c">#</span>
|
|
|
351 338 <span class="c"># . For each NeighborhoodRadius level</span>
|
|
|
352 339 <span class="c"># . For each non-hydrogen CentralAtom at this NeighborhoodRadius level</span>
|
|
|
353 340 <span class="c"># . For each non-hydrogen SuccessorNeighborAtom</span>
|
|
|
354 341 <span class="c"># . Collect (BondOrder AtomIdentifier) pair of values corresponding to</span>
|
|
|
355 342 <span class="c"># (CentralAtom SuccessorNeighborAtom) and add it to a list</span>
|
|
|
356 343 <span class="c">#</span>
|
|
|
357 344 <span class="c"># . Sort list containing (BondOrder AtomIdentifier) pairs first by BondOrder followed</span>
|
|
|
358 345 <span class="c"># by AtomIdendifiers to make these values graph invariant</span>
|
|
|
359 346 <span class="c"># . Generate a hash code for the values in the list</span>
|
|
|
360 347 <span class="c"># . Assign hash code as new atom identifier at the current NeighborhoodRadius level</span>
|
|
|
361 348 <span class="c"># . Save all atoms and bonds corresponding to the substructure involved in</span>
|
|
|
362 349 <span class="c"># generating the hash code to be used for identifying structural duplicate hash code</span>
|
|
|
363 350 <span class="c">#</span>
|
|
|
364 351 <span class="c"># . Add the new identifier to the molecule fingerprint list making sure it's not a duplicate</span>
|
|
|
365 352 <span class="c"># identifier</span>
|
|
|
366 353 <span class="c">#</span>
|
|
|
367 354 <span class="c"># Hash code atom identifier deduplication:</span>
|
|
|
368 355 <span class="c"># . Track/remove the identifier generated at higher neighborhood radius level</span>
|
|
|
369 356 <span class="c">#</span>
|
|
|
370 357 <span class="c"># Structural atom identifier deduplication:</span>
|
|
|
371 358 <span class="c"># . For equivalent atoms and bonds corresponding to substructure at a NeighborhoodRadius level,</span>
|
|
|
372 359 <span class="c"># track/remove the atom identifier with largest value</span>
|
|
|
373 360 <span class="c">#</span>
|
|
|
374 361 <span class="c">#</span>
|
|
|
375 <a name="GenerateFingerprints-"></a> 362 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
|
|
|
376 363 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
377 364
|
|
|
378 365 <span class="c"># Cache appropriate molecule data...</span>
|
|
|
379 366 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
380 367
|
|
|
381 368 <span class="c"># Assign intial atom identifers...</span>
|
|
|
382 369 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignInitialAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
383 370 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span>
|
|
|
384 371 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
385 372 <span class="s">}</span>
|
|
|
386 373
|
|
|
387 374 <span class="c"># Identify atom neighborhoods up to specified radius...</span>
|
|
|
388 375 <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
389 376
|
|
|
390 377 <span class="c"># Assign atom identifiers to central atoms considering atom neighborhoods at each</span>
|
|
|
391 378 <span class="c"># radius level...</span>
|
|
|
392 379 <span class="i">$This</span><span class="i">->_AssignAtomIdentifiersToAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
393 380
|
|
|
394 381 <span class="c"># Remove duplicates identifiers...</span>
|
|
|
395 382 <span class="i">$This</span><span class="i">->_RemoveDuplicateAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
396 383
|
|
|
397 384 <span class="c"># Set final fingerprints...</span>
|
|
|
398 385 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
399 386
|
|
|
400 387 <span class="c"># Clear cached molecule data...</span>
|
|
|
401 388 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
402 389
|
|
|
403 390 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
404 391 <span class="s">}</span>
|
|
|
405 392
|
|
|
406 393 <span class="c"># Assign appropriate initial atom identifiers...</span>
|
|
|
407 394 <span class="c">#</span>
|
|
|
408 395 <span class="c"># Generation of initial identifier for a specific atom involves:</span>
|
|
|
409 396 <span class="c"># . Values of the specified atom attributes are appended in a specific order to</span>
|
|
|
410 397 <span class="c"># generate an initial atom identifier string</span>
|
|
|
411 398 <span class="c"># . A 32 bit unsigned integer hash key, using TextUtil::HashCode function, is</span>
|
|
|
412 399 <span class="c"># generated for the atom indentifier and assigned to the atom as initial</span>
|
|
|
413 400 <span class="c"># atom identifier.</span>
|
|
|
414 401 <span class="c">#</span>
|
|
|
415 <a name="_AssignInitialAtomIdentifiers-"></a> 402 <span class="k">sub </span><span class="m">_AssignInitialAtomIdentifiers</span> <span class="s">{</span>
|
|
|
416 403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
417 404 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$InitialAtomTypeString</span><span class="cm">,</span> <span class="i">$InitialAtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
|
|
|
418 405
|
|
|
419 406 <span class="c"># Initialize atom identifiers...</span>
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|
|
420 407 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
|
421 408
|
|
|
422 409 <span class="c"># Set up atom types...</span>
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|
|
423 410 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
424 411 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span>
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|
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425 412
|
|
|
426 413 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
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|
|
427 414 <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>
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|
|
428 415 <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>
|
|
|
429 416 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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|
|
430 417 <span class="s">}</span>
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431 418
|
|
|
432 419 <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>
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433 420 <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>
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|
434 421 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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|
435 422 <span class="s">}</span>
|
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|
436 423
|
|
|
437 424 <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>
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|
|
438 425 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
439 426 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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|
|
440 427 <span class="s">}</span>
|
|
|
441 428
|
|
|
442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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|
|
443 430 <span class="i">$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>
|
|
|
444 431 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
445 432 <span class="s">}</span>
|
|
|
446 433
|
|
|
447 434 <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>
|
|
|
448 435 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
449 436 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
450 437 <span class="s">}</span>
|
|
|
451 438
|
|
|
452 439 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
453 440 <span class="i">$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>
|
|
|
454 441 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
455 442 <span class="s">}</span>
|
|
|
456 443
|
|
|
457 444 <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>
|
|
|
458 445 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
459 446 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
460 447 <span class="s">}</span>
|
|
|
461 448
|
|
|
462 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
463 450 <span class="i">$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">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
464 451 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
465 452 <span class="s">}</span>
|
|
|
466 453
|
|
|
467 454 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
468 455 <span class="i">$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>
|
|
|
469 456 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
470 457 <span class="s">}</span>
|
|
|
471 458
|
|
|
472 459 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignInitialAtomIdentifiers: Couldn't assign intial atom identifiers: InitialAtomIdentifierType $This->{AtomIdentifierType} is not supported..."</span><span class="sc">;</span>
|
|
|
473 460 <span class="s">}</span>
|
|
|
474 461
|
|
|
475 462 <span class="c"># Assign atom types...</span>
|
|
|
476 463 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
477 464
|
|
|
478 465 <span class="c"># Make sure atom types assignment is successful...</span>
|
|
|
479 466 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
480 467 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
481 468 <span class="s">}</span>
|
|
|
482 469
|
|
|
483 470 <span class="c"># Assign atom identifiers at radius 0...</span>
|
|
|
484 471 <span class="i">$Radius</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
485 472 <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>
|
|
|
486 473 <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>
|
|
|
487 474
|
|
|
488 475 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
489 476 <span class="i">$InitialAtomTypeString</span> = <span class="i">$AtomType</span> ? <span class="i">$AtomType</span> <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span>
|
|
|
490 477
|
|
|
491 478 <span class="i">$InitialAtomIdentifier</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$InitialAtomTypeString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
492 479 <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$InitialAtomIdentifier</span><span class="sc">;</span>
|
|
|
493 480 <span class="s">}</span>
|
|
|
494 481
|
|
|
495 482 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
496 483 <span class="s">}</span>
|
|
|
497 484
|
|
|
498 485 <span class="c"># Initialize atom identifiers...</span>
|
|
|
499 486 <span class="c">#</span>
|
|
|
500 <a name="_InitializeAtomIdentifiers-"></a> 487 <span class="k">sub </span><span class="m">_InitializeAtomIdentifiers</span> <span class="s">{</span>
|
|
|
501 488 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
502 489 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="s">)</span><span class="sc">;</span>
|
|
|
503 490
|
|
|
504 491 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span>
|
|
|
505 492
|
|
|
506 493 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
507 494 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span>
|
|
|
508 495 <span class="c"># Atom idenfiers key and value correspond to AtomID and AtomIdentifier</span>
|
|
|
509 496 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
510 497
|
|
|
511 498 <span class="c"># Unique and strcuturally unique idenfiers key and value correspond to AtomIdentifier and AtomID</span>
|
|
|
512 499 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
513 500 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
514 501
|
|
|
515 502 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
516 503 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
517 504 <span class="s">}</span>
|
|
|
518 505
|
|
|
519 506 <span class="s">}</span>
|
|
|
520 507
|
|
|
521 508 <span class="c"># Collect atom neighborhoods upto specified neighborhood radius...</span>
|
|
|
522 509 <span class="c">#</span>
|
|
|
523 <a name="_GetAtomNeighborhoods-"></a> 510 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span>
|
|
|
524 511 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
525 512 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
526 513
|
|
|
527 514 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
528 515
|
|
|
529 516 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span>
|
|
|
530 517 <span class="k">if</span> <span class="s">(</span><span class="i">$Radius</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
531 518 <span class="c"># At radius level 0, it's just the atoms...</span>
|
|
|
532 519 <span class="k">return</span><span class="sc">;</span>
|
|
|
533 520 <span class="s">}</span>
|
|
|
534 521
|
|
|
535 522 <span class="c"># Initialize neighborhood at different radii...</span>
|
|
|
536 523 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span>
|
|
|
537 524 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
538 525 <span class="s">}</span>
|
|
|
539 526
|
|
|
540 527 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
541 528
|
|
|
542 529 <span class="c"># Collect available atom neighborhoods at different at different neighborhood level for each atom...</span>
|
|
|
543 530 <span class="k">my</span><span class="s">(</span><span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
544 531
|
|
|
545 532 <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>
|
|
|
546 533 <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>
|
|
|
547 534 <span class="i">$CurrentRadius</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
548 535 <span class="k">for</span> <span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
549 536 <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="sc">;</span>
|
|
|
550 537 <span class="i">$CurrentRadius</span>++<span class="sc">;</span>
|
|
|
551 538 <span class="s">}</span>
|
|
|
552 539 <span class="s">}</span>
|
|
|
553 540 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
554 541 <span class="s">}</span>
|
|
|
555 542
|
|
|
556 543 <span class="c"># Assign atom identifiers to central atom at each neighborhood radius level...</span>
|
|
|
557 544 <span class="c">#</span>
|
|
|
558 <a name="_AssignAtomIdentifiersToAtomNeighborhoods-"></a> 545 <span class="k">sub </span><span class="m">_AssignAtomIdentifiersToAtomNeighborhoods</span> <span class="s">{</span>
|
|
|
559 546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
560 547 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$NextRadius</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">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$SuccessorAtom</span><span class="cm">,</span> <span class="i">$SuccessorAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$SuccessorAtomCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
561 548
|
|
|
562 549 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} < <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
563 550 <span class="k">return</span><span class="sc">;</span>
|
|
|
564 551 <span class="s">}</span>
|
|
|
565 552
|
|
|
566 553 <span class="c"># Go over the atom neighborhoods at each radius upto specified radius and assign atom</span>
|
|
|
567 554 <span class="c"># indentifiers using their connected successor atoms and their identifiers.</span>
|
|
|
568 555 <span class="c">#</span>
|
|
|
569 556 <span class="c"># For a neighborhood atom at a specified radius, the successor connected atoms correpond</span>
|
|
|
570 557 <span class="c"># to next radius level and the last set of neighorhood atoms don't have any successor connected</span>
|
|
|
571 558 <span class="c"># atoms. Additionally, radius level 0 just correspond to initial atom identifiers.</span>
|
|
|
572 559 <span class="c">#</span>
|
|
|
573 560 <span class="c"># So in order to process atom neighborhood upto specified radius level, the last atom neighborhood</span>
|
|
|
574 561 <span class="c"># doesn't need to be processed: it gets processed at previous radius level as successor connected</span>
|
|
|
575 562 <span class="c"># atoms.</span>
|
|
|
576 563 <span class="c">#</span>
|
|
|
577 564 <span class="j">RADIUS:</span> <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
578 565 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
579 566 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
580 567
|
|
|
581 568 <span class="c"># Are there any available atom neighborhoods at this radius?</span>
|
|
|
582 569 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
583 570 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
584 571 <span class="s">}</span>
|
|
|
585 572 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span>
|
|
|
586 573
|
|
|
587 574 <span class="c"># Go over neighborhood atoms and their successor connected atoms at this radius and collect</span>
|
|
|
588 575 <span class="c"># (BondOrder AtomIdentifier) values for bonded atom pairs. Additionally, keep track of atom and bonds</span>
|
|
|
589 576 <span class="c"># for the neighorhoods to remove identifieres generated from structurally duplicate features.</span>
|
|
|
590 577 <span class="c">#</span>
|
|
|
591 578 <span class="k">my</span><span class="s">(</span><span class="i">%BondOrdersAndAtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
|
|
|
592 579
|
|
|
593 580 <span class="i">%BondOrdersAndAtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
594 581 <span class="i">$SuccessorAtomCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
595 582
|
|
|
596 583 <span class="j">NEIGHBORHOODS:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
597 584 <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span>}<span class="sc">;</span>
|
|
|
598 585
|
|
|
599 586 <span class="c"># Any connected successors for the NeighborhoodAtom?</span>
|
|
|
600 587 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
601 588 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span>
|
|
|
602 589 <span class="s">}</span>
|
|
|
603 590 <span class="j">SUCCESSORATOM:</span> <span class="k">for</span> <span class="i">$SuccessorAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
604 591 <span class="k">if</span> <span class="s">(</span><span class="i">$SuccessorAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
605 592 <span class="c"># Skip successor hydrogen atom...</span>
|
|
|
606 593 <span class="k">next</span> <span class="j">SUCCESSORATOM</span><span class="sc">;</span>
|
|
|
607 594 <span class="s">}</span>
|
|
|
608 595 <span class="i">$SuccessorAtomID</span> = <span class="i">$SuccessorAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
609 596 <span class="i">$SuccessorAtomCount</span>++<span class="sc">;</span>
|
|
|
610 597
|
|
|
611 598 <span class="i">$Bond</span> = <span class="i">$NeighborhoodAtom</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="i">$SuccessorAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
612 599 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"1.5"</span> <span class="co">:</span> <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
613 600
|
|
|
614 601 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
615 602 <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
616 603 <span class="s">}</span>
|
|
|
617 604 <span class="k">push</span> <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$SuccessorAtomID</span>}<span class="sc">;</span>
|
|
|
618 605 <span class="s">}</span>
|
|
|
619 606 <span class="s">}</span>
|
|
|
620 607 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SuccessorAtomCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
621 608 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
622 609 <span class="s">}</span>
|
|
|
623 610 <span class="c"># Assign a new atom identifier at the NextRadius level...</span>
|
|
|
624 611 <span class="i">$This</span><span class="i">->_AssignAtomIdentifierToAtomNeighborhood</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> \<span class="i">%BondOrdersAndAtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
|
|
|
625 612 <span class="s">}</span>
|
|
|
626 613 <span class="s">}</span>
|
|
|
627 614 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
628 615 <span class="s">}</span>
|
|
|
629 616
|
|
|
630 617 <span class="c"># Generate and assign atom indentifier for AtomID using atom neighborhood at next radius level...</span>
|
|
|
631 618 <span class="c">#</span>
|
|
|
632 <a name="_AssignAtomIdentifierToAtomNeighborhood-"></a> 619 <span class="k">sub </span><span class="m">_AssignAtomIdentifierToAtomNeighborhood</span> <span class="s">{</span>
|
|
|
633 620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$BondOrdersAndAtomIdentifiersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
634 621 <span class="k">my</span><span class="s">(</span><span class="i">$NextRadius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$SuccessorAtomIdentifier</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$AtomIdentifierString</span><span class="cm">,</span> <span class="i">@AtomIndentifiersInfo</span><span class="s">)</span><span class="sc">;</span>
|
|
|
635 622
|
|
|
636 623 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span>
|
|
|
637 624
|
|
|
638 625 <span class="i">@AtomIndentifiersInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
639 626
|
|
|
640 627 <span class="i">$AtomIdentifier</span> = <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
641 628 <span class="k">push</span> <span class="i">@AtomIndentifiersInfo</span><span class="cm">,</span> <span class="s">(</span><span class="i">$NextRadius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
|
|
|
642 629
|
|
|
643 630 <span class="c"># Sort out successor atom bond order and identifier pairs by bond order followed by atom identifiers</span>
|
|
|
644 631 <span class="c"># in order to make the final atom identifier graph invariant...</span>
|
|
|
645 632 <span class="c">#</span>
|
|
|
646 633 <span class="k">for</span> <span class="i">$BondOrder</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$BondOrdersAndAtomIdentifiersRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
647 634 <span class="k">for</span> <span class="i">$SuccessorAtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiersRef</span>->{<span class="i">$BondOrder</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
648 635 <span class="k">push</span> <span class="i">@AtomIndentifiersInfo</span><span class="cm">,</span> <span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$SuccessorAtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
|
|
|
649 636 <span class="s">}</span>
|
|
|
650 637 <span class="s">}</span>
|
|
|
651 638 <span class="i">$AtomIdentifierString</span> = <span class="k">join</span><span class="s">(</span><span class="q">""</span><span class="cm">,</span> <span class="i">@AtomIndentifiersInfo</span><span class="s">)</span><span class="sc">;</span>
|
|
|
652 639 <span class="i">$AtomIdentifier</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$AtomIdentifierString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
653 640
|
|
|
654 641 <span class="c"># Assign atom identifier to the atom at next radius level...</span>
|
|
|
655 642 <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$NextRadius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomIdentifier</span><span class="sc">;</span>
|
|
|
656 643
|
|
|
657 644 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
658 645 <span class="s">}</span>
|
|
|
659 646
|
|
|
660 647 <span class="c"># Remove duplicates atom identifiers...</span>
|
|
|
661 648 <span class="c">#</span>
|
|
|
662 <a name="_RemoveDuplicateAtomIdentifiers-"></a> 649 <span class="k">sub </span><span class="m">_RemoveDuplicateAtomIdentifiers</span> <span class="s">{</span>
|
|
|
663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
664 651
|
|
|
665 652 <span class="i">$This</span><span class="i">->_RemoveDuplicateIdentifiersByValue</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
666 653 <span class="i">$This</span><span class="i">->_RemoveStructurallyDuplicateIdenfiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
667 654
|
|
|
668 655 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
669 656 <span class="s">}</span>
|
|
|
670 657
|
|
|
671 658 <span class="c"># Remove duplicate identifiers at each radius level by just using their value...</span>
|
|
|
672 659 <span class="c">#</span>
|
|
|
673 <a name="_RemoveDuplicateIdentifiersByValue-"></a> 660 <span class="k">sub </span><span class="m">_RemoveDuplicateIdentifiersByValue</span> <span class="s">{</span>
|
|
|
674 661 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
675 662 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
|
|
|
676 663
|
|
|
677 664 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
678 665 <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>
|
|
|
679 666 <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>
|
|
|
680 667 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
681 668 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
682 669 <span class="s">}</span>
|
|
|
683 670 <span class="i">$AtomIdentifier</span> = <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
684 671 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
685 672 <span class="c"># It's a duplicate atom idenfier at this radius level...</span>
|
|
|
686 673 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
687 674 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
688 675 <span class="s">}</span>
|
|
|
689 676 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$AtomID</span><span class="sc">;</span>
|
|
|
690 677 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
691 678 <span class="s">}</span>
|
|
|
692 679 <span class="s">}</span>
|
|
|
693 680 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
694 681 <span class="s">}</span>
|
|
|
695 682
|
|
|
696 683 <span class="c"># Remove structurally duplicate identifiers at each radius level...</span>
|
|
|
697 684 <span class="c">#</span>
|
|
|
698 685 <span class="c"># Methodology:</span>
|
|
|
699 686 <span class="c"># . For unquie atom identifiers at each radius level, assign complete structure features</span>
|
|
|
700 687 <span class="c"># in terms all the bonds involved to generate that identifier</span>
|
|
|
701 688 <span class="c"># . Use the complete structure features to remover atom identifiers which are</span>
|
|
|
702 689 <span class="c"># structurally equivalent which can also be at earlier radii levels</span>
|
|
|
703 690 <span class="c">#</span>
|
|
|
704 691 <span class="c">#</span>
|
|
|
705 <a name="_RemoveStructurallyDuplicateIdenfiers-"></a> 692 <span class="k">sub </span><span class="m">_RemoveStructurallyDuplicateIdenfiers</span> <span class="s">{</span>
|
|
|
706 693 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
707 694 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifierRadius</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
|
|
|
708 695
|
|
|
709 696 <span class="c"># Setup structure features...</span>
|
|
|
710 697 <span class="i">$This</span><span class="i">->_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
711 698
|
|
|
712 699 <span class="c"># Identify structurally unqiue identifiers...</span>
|
|
|
713 700 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
714 701 <span class="j">ATOMIDENTIFIER:</span> <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$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">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
715 702 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
|
|
|
716 703
|
|
|
717 704 <span class="s">(</span><span class="i">$SimilarAtomIdentifierRadius</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifier</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_FindStructurallySimilarAtomIdentifier</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
|
|
|
718 705 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilarAtomIdentifier</span><span class="s">)</span> <span class="s">{</span>
|
|
|
719 706 <span class="c"># Current atom identifier is similar to an earlier structurally unique atom identifier...</span>
|
|
|
720 707 <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$SimilarAtomIdentifierRadius</span>}{<span class="i">$SimilarAtomIdentifier</span>} += <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
|
|
|
721 708 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span>
|
|
|
722 709 <span class="s">}</span>
|
|
|
723 710 <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$AtomID</span><span class="sc">;</span>
|
|
|
724 711
|
|
|
725 712 <span class="c"># Set structurally unique atom identifier count to the unique atom identifiers count...</span>
|
|
|
726 713 <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
|
|
|
727 714 <span class="s">}</span>
|
|
|
728 715 <span class="s">}</span>
|
|
|
729 716 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
730 717 <span class="s">}</span>
|
|
|
731 718
|
|
|
732 719 <span class="c"># Set final fingerpritns vector...</span>
|
|
|
733 720 <span class="c">#</span>
|
|
|
734 <a name="_SetFinalFingerprints-"></a> 721 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
|
|
|
735 722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
736 723
|
|
|
737 724 <span class="c"># Mark successful generation of fingerprints...</span>
|
|
|
738 725 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
739 726
|
|
|
740 727 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
741 728 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
742 729 <span class="s">}</span>
|
|
|
743 730 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
744 731 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityCountFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
745 732 <span class="s">}</span>
|
|
|
746 733 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
747 734 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityBitsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
748 735 <span class="s">}</span>
|
|
|
749 736
|
|
|
750 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
751 738 <span class="s">}</span>
|
|
|
752 739
|
|
|
753 740 <span class="c"># Set final extended connectivity fingerpritns vector...</span>
|
|
|
754 741 <span class="c">#</span>
|
|
|
755 <a name="_SetFinalExtendedConnectivityFingerprints-"></a> 742 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityFingerprints</span> <span class="s">{</span>
|
|
|
756 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
757 744 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
|
|
|
758 745
|
|
|
759 746 <span class="i">@AtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
760 747
|
|
|
761 748 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
762 749 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$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">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
763 750 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span>
|
|
|
764 751 <span class="s">}</span>
|
|
|
765 752 <span class="s">}</span>
|
|
|
766 753 <span class="c"># Add atom identifiers to fingerprint vector...</span>
|
|
|
767 754 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
|
|
|
768 755
|
|
|
769 756 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
770 757 <span class="s">}</span>
|
|
|
771 758
|
|
|
772 759 <span class="c"># Set final extended connectivity count fingerpritns vector...</span>
|
|
|
773 760 <span class="c">#</span>
|
|
|
774 <a name="_SetFinalExtendedConnectivityCountFingerprints-"></a> 761 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityCountFingerprints</span> <span class="s">{</span>
|
|
|
775 762 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
776 763 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$AtomIdentifierCount</span><span class="cm">,</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">@AtomIdentifiersCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
777 764
|
|
|
778 765 <span class="i">@AtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIdentifiersCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
779 766
|
|
|
780 767 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
781 768 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$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">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
782 769 <span class="i">$AtomIdentifierCount</span> = <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
|
|
|
783 770 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span>
|
|
|
784 771 <span class="k">push</span> <span class="i">@AtomIdentifiersCount</span><span class="cm">,</span> <span class="i">$AtomIdentifierCount</span><span class="sc">;</span>
|
|
|
785 772 <span class="s">}</span>
|
|
|
786 773 <span class="s">}</span>
|
|
|
787 774 <span class="c"># Add atom identifiers to fingerprint vector as value IDs...</span>
|
|
|
788 775 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
|
|
|
789 776
|
|
|
790 777 <span class="c"># Add atom identifiers to count to fingerprint vector as values...</span>
|
|
|
791 778 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiersCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
792 779
|
|
|
793 780 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
794 781 <span class="s">}</span>
|
|
|
795 782
|
|
|
796 783 <span class="c"># Set final extended connectivity bits fingerpritns vector...</span>
|
|
|
797 784 <span class="c">#</span>
|
|
|
798 <a name="_SetFinalExtendedConnectivityBitsFingerprints-"></a> 785 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityBitsFingerprints</span> <span class="s">{</span>
|
|
|
799 786 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
800 787 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="cm">,</span> <span class="i">$Size</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="cm">,</span> <span class="i">$AtomIdentifierBitPos</span><span class="cm">,</span> <span class="i">$SetBitNum</span><span class="s">)</span><span class="sc">;</span>
|
|
|
801 788
|
|
|
802 789 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span>
|
|
|
803 790
|
|
|
804 791 <span class="i">$Size</span> = <span class="i">$This</span>->{<span class="w">Size</span>}<span class="sc">;</span>
|
|
|
805 792
|
|
|
806 793 <span class="i">$SkipBitPosCheck</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
807 794
|
|
|
808 795 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
809 796 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
810 797 <span class="c"># Set random number seed...</span>
|
|
|
811 798 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
812 799 <span class="i">CORE::</span><span class="k">srand</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
|
|
|
813 800 <span class="s">}</span>
|
|
|
814 801 <span class="k">else</span> <span class="s">{</span>
|
|
|
815 802 <span class="i">MathUtil::srandom</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
|
|
|
816 803 <span class="s">}</span>
|
|
|
817 804
|
|
|
818 805 <span class="c"># Set bit position...</span>
|
|
|
819 806 <span class="i">$AtomIdentifierBitPos</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">$Size</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
820 807 <span class="i">$FingerprintsBitVector</span><span class="i">->SetBit</span><span class="s">(</span><span class="i">$AtomIdentifierBitPos</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
821 808 <span class="s">}</span>
|
|
|
822 809 <span class="s">}</span>
|
|
|
823 810 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
824 811 <span class="s">}</span>
|
|
|
825 812
|
|
|
826 813
|
|
|
827 814 <span class="c"># Identify structurally unique identifiers by comparing structure features involved in</span>
|
|
|
828 815 <span class="c"># generating identifiear by comparing it agains all the previous structurally unique</span>
|
|
|
829 816 <span class="c"># identifiers...</span>
|
|
|
830 817 <span class="c">#</span>
|
|
|
831 <a name="_FindStructurallySimilarAtomIdentifier-"></a> 818 <span class="k">sub </span><span class="m">_FindStructurallySimilarAtomIdentifier</span> <span class="s">{</span>
|
|
|
832 819 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$SpecifiedRadius</span><span class="cm">,</span> <span class="i">$SpecifiedAtomID</span><span class="cm">,</span> <span class="i">$SpecifiedAtomIdentifier</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
833 820 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$FeatureAtomCount</span><span class="cm">,</span> <span class="i">$FeatureAtomIDsRef</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomID</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomCount</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomIDsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
834 821
|
|
|
835 822 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedRadius</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
836 823 <span class="c"># After duplicate removal by value, all identifier at radius level 0 would be structurally unique...</span>
|
|
|
837 824 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
838 825 <span class="s">}</span>
|
|
|
839 826
|
|
|
840 827 <span class="i">$SpecifiedFeatureAtomCount</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$SpecifiedRadius</span>}{<span class="i">$SpecifiedAtomID</span>}<span class="sc">;</span>
|
|
|
841 828 <span class="i">$SpecifiedFeatureAtomIDsRef</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$SpecifiedRadius</span>}{<span class="i">$SpecifiedAtomID</span>}<span class="sc">;</span>
|
|
|
842 829
|
|
|
843 830 <span class="c"># No need to compare features at radius 0...</span>
|
|
|
844 831 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$SpecifiedRadius</span><span class="s">)</span> <span class="s">{</span>
|
|
|
845 832 <span class="j">ATOMIDENTIFIER:</span> <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
846 833 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
|
|
|
847 834
|
|
|
848 835 <span class="i">$FeatureAtomCount</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
849 836 <span class="i">$FeatureAtomIDsRef</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
850 837
|
|
|
851 838 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedFeatureAtomCount</span> != <span class="i">$FeatureAtomCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
852 839 <span class="c"># Couldn't be structurally equivalent...</span>
|
|
|
853 840 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span>
|
|
|
854 841 <span class="s">}</span>
|
|
|
855 842 <span class="k">for</span> <span class="i">$SpecifiedFeatureAtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span> {<span class="i">$SpecifiedFeatureAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
856 843 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$FeatureAtomIDsRef</span>->{<span class="i">$SpecifiedFeatureAtomID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
857 844 <span class="c"># For structural equivalency, all atom in specified feature must also be present in a previously</span>
|
|
|
858 845 <span class="c"># identified structurally unique structure feature...</span>
|
|
|
859 846 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span>
|
|
|
860 847 <span class="s">}</span>
|
|
|
861 848 <span class="s">}</span>
|
|
|
862 849 <span class="c"># Found structurally equivalent feature...</span>
|
|
|
863 850 <span class="k">return</span> <span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
|
|
|
864 851 <span class="s">}</span>
|
|
|
865 852 <span class="s">}</span>
|
|
|
866 853 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
867 854 <span class="s">}</span>
|
|
|
868 855
|
|
|
869 856 <span class="c"># Setup structure features for atom IDs involved in unique atom identifiers at all</span>
|
|
|
870 857 <span class="c"># radii level...</span>
|
|
|
871 858 <span class="c">#</span>
|
|
|
872 <a name="_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers-"></a> 859 <span class="k">sub </span><span class="m">_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span> <span class="s">{</span>
|
|
|
873 860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
874 861 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$PreviousRadius</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">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">%AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
875 862
|
|
|
876 863 <span class="i">$This</span><span class="i">->_InitializeStructureFeatures</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
877 864
|
|
|
878 865 <span class="c"># Collect atom IDs involved in unique atom identifiers...</span>
|
|
|
879 866 <span class="i">%AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
880 867 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
881 868 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
882 869 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
|
|
|
883 870 <span class="i">$AtomIDs</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomID</span><span class="sc">;</span>
|
|
|
884 871 <span class="s">}</span>
|
|
|
885 872 <span class="s">}</span>
|
|
|
886 873
|
|
|
887 874 <span class="c"># Setup structure features...</span>
|
|
|
888 875 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
889 876 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AtomIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
890 877 <span class="k">my</span><span class="s">(</span><span class="i">$StructureFeatureAtomCount</span><span class="cm">,</span> <span class="i">%StructureFeatureAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
891 878
|
|
|
892 879 <span class="i">$StructureFeatureAtomCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
893 880 <span class="i">%StructureFeatureAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
894 881
|
|
|
895 882 <span class="c"># Get partial structure features for the atom at previous radius level...</span>
|
|
|
896 883 <span class="i">$PreviousRadius</span> = <span class="i">$Radius</span> - <span class="n">1</span><span class="sc">;</span>
|
|
|
897 884 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRadius</span> >= <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
898 885 <span class="i">$StructureFeatureAtomCount</span> += <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$PreviousRadius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
899 886 <span class="i">%StructureFeatureAtomIDs</span> = <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$PreviousRadius</span>}{<span class="i">$AtomID</span>}}<span class="sc">;</span>
|
|
|
900 887 <span class="s">}</span>
|
|
|
901 888
|
|
|
902 889 <span class="c"># Get all neighborhood atom at this radius level...</span>
|
|
|
903 890 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}<span class="s">)</span> && <span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
904 891 <span class="j">NEIGHBORHOODS:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
905 892 <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span>}<span class="sc">;</span>
|
|
|
906 893 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
907 894 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span>
|
|
|
908 895 <span class="s">}</span>
|
|
|
909 896 <span class="i">$NeighborhoodAtomID</span> = <span class="i">$NeighborhoodAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
910 897 <span class="i">$StructureFeatureAtomCount</span>++<span class="sc">;</span>
|
|
|
911 898 <span class="i">$StructureFeatureAtomIDs</span>{<span class="i">$NeighborhoodAtomID</span>} = <span class="i">$NeighborhoodAtomID</span><span class="sc">;</span>
|
|
|
912 899 <span class="s">}</span>
|
|
|
913 900 <span class="s">}</span>
|
|
|
914 901
|
|
|
915 902 <span class="c"># Assign structure features to atom at this radius level...</span>
|
|
|
916 903 <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$StructureFeatureAtomCount</span><span class="sc">;</span>
|
|
|
917 904 <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = \<span class="i">%StructureFeatureAtomIDs</span><span class="sc">;</span>
|
|
|
918 905 <span class="s">}</span>
|
|
|
919 906 <span class="s">}</span>
|
|
|
920 907 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
921 908 <span class="s">}</span>
|
|
|
922 909
|
|
|
923 910 <span class="c"># Intialize structure features at each radius level...</span>
|
|
|
924 911 <span class="c">#</span>
|
|
|
925 <a name="_InitializeStructureFeatures-"></a> 912 <span class="k">sub </span><span class="m">_InitializeStructureFeatures</span> <span class="s">{</span>
|
|
|
926 913 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
927 914 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
928 915
|
|
|
929 916 <span class="c"># Initialize all structure features...</span>
|
|
|
930 917
|
|
|
931 918 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
932 919 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
933 920 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
934 921
|
|
|
935 922 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span>
|
|
|
936 923 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span>
|
|
|
937 924 <span class="c"># Structure features for at specific radii accessed using atom IDs...</span>
|
|
|
938 925 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
939 926 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
940 927 <span class="s">}</span>
|
|
|
941 928 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
942 929 <span class="s">}</span>
|
|
|
943 930
|
|
|
944 931 <span class="c"># Cache appropriate molecule data...</span>
|
|
|
945 932 <span class="c">#</span>
|
|
|
946 <a name="_SetupMoleculeDataCache-"></a> 933 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
|
|
|
947 934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
948 935
|
|
|
949 936 <span class="c"># Get all non-hydrogen atoms...</span>
|
|
|
950 937 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
|
|
|
951 938 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
952 939 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="q">"IsHydrogen"</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
|
|
|
953 940
|
|
|
954 941 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
955 942 <span class="s">}</span>
|
|
|
956 943
|
|
|
957 944 <span class="c"># Clear cached molecule data...</span>
|
|
|
958 945 <span class="c">#</span>
|
|
|
959 <a name="_ClearMoleculeDataCache-"></a> 946 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
|
|
|
960 947 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
961 948
|
|
|
962 949 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
963 950
|
|
|
964 951 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
965 952 <span class="s">}</span>
|
|
|
966 953
|
|
|
967 954 <span class="c"># Initialize atom indentifier type information...</span>
|
|
|
968 955 <span class="c">#</span>
|
|
|
969 956 <span class="c"># Current supported values:</span>
|
|
|
970 957 <span class="c">#</span>
|
|
|
971 958 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span>
|
|
|
972 959 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
|
|
|
973 960 <span class="c">#</span>
|
|
|
974 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 961 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
|
|
|
975 962 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
976 963
|
|
|
977 964 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
|
|
|
978 965 <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>
|
|
|
979 966 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
980 967 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
981 968 <span class="s">}</span>
|
|
|
982 969 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
983 970 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
984 971 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
985 972 <span class="s">}</span>
|
|
|
986 973 <span class="k">if</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>
|
|
|
987 974 <span class="c"># Nothing to do for now...</span>
|
|
|
988 975 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
989 976 <span class="s">}</span>
|
|
|
990 977 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
|
|
|
991 978 <span class="s">}</span>
|
|
|
992 979 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
993 980 <span class="s">}</span>
|
|
|
994 981
|
|
|
995 982 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span>
|
|
|
996 983 <span class="c"># class, to use for generating initial atom identifiers...</span>
|
|
|
997 984 <span class="c">#</span>
|
|
|
998 985 <span class="c"># Let:</span>
|
|
|
999 986 <span class="c"># AS = Atom symbol corresponding to element symbol</span>
|
|
|
1000 987 <span class="c">#</span>
|
|
|
1001 988 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
1002 989 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
1003 990 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
1004 991 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
1005 992 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
1006 993 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
1007 994 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span>
|
|
|
1008 995 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
|
|
|
1009 996 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span>
|
|
|
1010 997 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span>
|
|
|
1011 998 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span>
|
|
|
1012 999 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
|
|
|
1013 1000 <span class="c">#</span>
|
|
|
1014 1001 <span class="c"># Then:</span>
|
|
|
1015 1002 <span class="c">#</span>
|
|
|
1016 1003 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
|
|
|
1017 1004 <span class="c">#</span>
|
|
|
1018 1005 <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>
|
|
|
1019 1006 <span class="c">#</span>
|
|
|
1020 1007 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span>
|
|
|
1021 1008 <span class="c"># optional.</span>
|
|
|
1022 1009 <span class="c">#</span>
|
|
|
1023 1010 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span>
|
|
|
1024 1011 <span class="c">#</span>
|
|
|
1025 1012 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span>
|
|
|
1026 1013 <span class="c">#</span>
|
|
|
1027 1014 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span>
|
|
|
1028 1015 <span class="c"># are also allowed:</span>
|
|
|
1029 1016 <span class="c">#</span>
|
|
|
1030 1017 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span>
|
|
|
1031 1018 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span>
|
|
|
1032 1019 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span>
|
|
|
1033 1020 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span>
|
|
|
1034 1021 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span>
|
|
|
1035 1022 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span>
|
|
|
1036 1023 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span>
|
|
|
1037 1024 <span class="c"># Ar : Aromatic</span>
|
|
|
1038 1025 <span class="c"># RA : RingAtom</span>
|
|
|
1039 1026 <span class="c"># FC : FormalCharge</span>
|
|
|
1040 1027 <span class="c"># MN : MassNumber</span>
|
|
|
1041 1028 <span class="c"># SM : SpinMultiplicity</span>
|
|
|
1042 1029 <span class="c">#</span>
|
|
|
1043 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a>1030 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
|
|
|
1044 1031 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1045 1032
|
|
|
1046 1033 <span class="c"># Default atomic invariants to use for generating initial atom identifiers are: AS, X, BO, LBO, H, FC</span>
|
|
|
1047 1034 <span class="c">#</span>
|
|
|
1048 1035 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1049 1036 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="cm">,</span> <span class="q">'MN'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1050 1037
|
|
|
1051 1038 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1052 1039 <span class="s">}</span>
|
|
|
1053 1040
|
|
|
1054 1041 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
|
|
|
1055 1042 <span class="c"># class, to use for generating initial atom identifiers...</span>
|
|
|
1056 1043 <span class="c">#</span>
|
|
|
1057 1044 <span class="c"># Let:</span>
|
|
|
1058 1045 <span class="c"># HBD: HydrogenBondDonor</span>
|
|
|
1059 1046 <span class="c"># HBA: HydrogenBondAcceptor</span>
|
|
|
1060 1047 <span class="c"># PI : PositivelyIonizable</span>
|
|
|
1061 1048 <span class="c"># NI : NegativelyIonizable</span>
|
|
|
1062 1049 <span class="c"># Ar : Aromatic</span>
|
|
|
1063 1050 <span class="c"># Hal : Halogen</span>
|
|
|
1064 1051 <span class="c"># H : Hydrophobic</span>
|
|
|
1065 1052 <span class="c"># RA : RingAtom</span>
|
|
|
1066 1053 <span class="c"># CA : ChainAtom</span>
|
|
|
1067 1054 <span class="c">#</span>
|
|
|
1068 1055 <span class="c"># Then:</span>
|
|
|
1069 1056 <span class="c">#</span>
|
|
|
1070 1057 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span>
|
|
|
1071 1058 <span class="c">#</span>
|
|
|
1072 1059 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
|
|
|
1073 1060 <span class="c">#</span>
|
|
|
1074 1061 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
|
|
|
1075 1062 <span class="c">#</span>
|
|
|
1076 1063 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
|
|
|
1077 1064 <span class="c">#</span>
|
|
|
1078 1065 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span>
|
|
|
1079 1066 <span class="c"># HydrogenBondAcceptor: N[!H], O</span>
|
|
|
1080 1067 <span class="c"># PositivelyIonizable: +, NH2</span>
|
|
|
1081 1068 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
|
|
|
1082 1069 <span class="c">#</span>
|
|
|
1083 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a>1070 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
|
|
|
1084 1071 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1085 1072
|
|
|
1086 1073 <span class="c"># Default functional class atom typess to use for generating initial atom identifiers</span>
|
|
|
1087 1074 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span>
|
|
|
1088 1075 <span class="c">#</span>
|
|
|
1089 1076 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1090 1077 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1091 1078
|
|
|
1092 1079 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1093 1080 <span class="s">}</span>
|
|
|
1094 1081
|
|
|
1095 1082 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span>
|
|
|
1096 1083 <span class="c">#</span>
|
|
|
1097 <a name="SetAtomicInvariantsToUse-"></a>1084 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
|
|
|
1098 1085 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1099 1086 <span class="k">my</span><span class="s">(</span><span class="i">$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">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1100 1087
|
|
|
1101 1088 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1102 1089 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span>
|
|
|
1103 1090 <span class="k">return</span><span class="sc">;</span>
|
|
|
1104 1091 <span class="s">}</span>
|
|
|
1105 1092
|
|
|
1106 1093 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1107 1094 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalAtomTypesToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
|
|
|
1108 1095 <span class="k">return</span><span class="sc">;</span>
|
|
|
1109 1096 <span class="s">}</span>
|
|
|
1110 1097
|
|
|
1111 1098 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
1112 1099 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
1113 1100
|
|
|
1114 1101 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1115 1102 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1116 1103
|
|
|
1117 1104 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1118 1105 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
|
|
|
1119 1106 <span class="s">}</span>
|
|
|
1120 1107 <span class="k">else</span> <span class="s">{</span>
|
|
|
1121 1108 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
|
|
|
1122 1109 <span class="s">}</span>
|
|
|
1123 1110
|
|
|
1124 1111 <span class="c"># Make sure specified AtomicInvariants are valid...</span>
|
|
|
1125 1112 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1126 1113 <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>
|
|
|
1127 1114 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span>
|
|
|
1128 1115 <span class="s">}</span>
|
|
|
1129 1116 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
|
|
|
1130 1117 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
|
|
|
1131 1118 <span class="s">}</span>
|
|
|
1132 1119
|
|
|
1133 1120 <span class="c"># Set atomic invariants to use...</span>
|
|
|
1134 1121 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1135 1122 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
|
|
|
1136 1123
|
|
|
1137 1124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1138 1125 <span class="s">}</span>
|
|
|
1139 1126
|
|
|
1140 1127 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span>
|
|
|
1141 1128 <span class="c">#</span>
|
|
|
1142 <a name="SetFunctionalClassesToUse-"></a>1129 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
|
|
|
1143 1130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1144 1131 <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>
|
|
|
1145 1132
|
|
|
1146 1133 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1147 1134 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span>
|
|
|
1148 1135 <span class="k">return</span><span class="sc">;</span>
|
|
|
1149 1136 <span class="s">}</span>
|
|
|
1150 1137
|
|
|
1151 1138 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1152 1139 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
|
|
|
1153 1140 <span class="k">return</span><span class="sc">;</span>
|
|
|
1154 1141 <span class="s">}</span>
|
|
|
1155 1142
|
|
|
1156 1143 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
1157 1144 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
1158 1145
|
|
|
1159 1146 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1160 1147 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1161 1148
|
|
|
1162 1149 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1163 1150 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
|
|
|
1164 1151 <span class="s">}</span>
|
|
|
1165 1152 <span class="k">else</span> <span class="s">{</span>
|
|
|
1166 1153 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
|
|
|
1167 1154 <span class="s">}</span>
|
|
|
1168 1155
|
|
|
1169 1156 <span class="c"># Make sure specified FunctionalClasses are valid...</span>
|
|
|
1170 1157 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1171 1158 <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>
|
|
|
1172 1159 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span>
|
|
|
1173 1160 <span class="s">}</span>
|
|
|
1174 1161 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
|
|
|
1175 1162 <span class="s">}</span>
|
|
|
1176 1163
|
|
|
1177 1164 <span class="c"># Set functional classes to use...</span>
|
|
|
1178 1165 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1179 1166 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
|
|
|
1180 1167
|
|
|
1181 1168 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1182 1169 <span class="s">}</span>
|
|
|
1183 1170
|
|
|
1184 1171 <span class="c"># Return a string containg data for ExtendedConnectivityFingerprints object...</span>
|
|
|
1185 <a name="StringifyExtendedConnectivityFingerprints-"></a>1172 <span class="k">sub </span><span class="m">StringifyExtendedConnectivityFingerprints</span> <span class="s">{</span>
|
|
|
1186 1173 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1187 1174 <span class="k">my</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprintsString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1188 1175
|
|
|
1189 1176 <span class="i">$ExtendedConnectivityFingerprintsString</span> = <span class="q">"InitialAtomIdentifierType: $This->{AtomIdentifierType}; NeighborhoodRadius: $This->{NeighborhoodRadius}"</span><span class="sc">;</span>
|
|
|
1190 1177
|
|
|
1191 1178 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1192 1179 <span class="k">my</span><span class="s">(</span><span class="i">$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>
|
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1193 1180
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1194 1181 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1195 1182 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1196 1183
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1197 1184 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
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1198 1185 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span>
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1199 1186 <span class="s">}</span>
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1200 1187
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1201 1188 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
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1202 1189 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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1203 1190 <span class="i">$ExtendedConnectivityFingerprintsString</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>
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1204 1191 <span class="s">}</span>
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1205 1192 <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>
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1206 1193 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
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1207 1194
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1208 1195 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1209 1196 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1210 1197
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1211 1198 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
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1212 1199 <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>
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1213 1200 <span class="s">}</span>
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1214 1201
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1215 1202 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
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|
1216 1203 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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|
1217 1204 <span class="i">$ExtendedConnectivityFingerprintsString</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>
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1218 1205 <span class="s">}</span>
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1219 1206
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|
1220 1207 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
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1221 1208 <span class="c"># Size...</span>
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1222 1209 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; Size: $This->{Size}; MinSize: $This->{MinSize}; MaxSize: $This->{MaxSize}"</span><span class="sc">;</span>
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1223 1210
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1224 1211 <span class="c"># Fingerprint bit density and num of bits set...</span>
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|
1225 1212 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span>
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|
1226 1213 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
1227 1214 <span class="i">$BitDensity</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1228 1215 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity"</span><span class="sc">;</span>
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1229 1216
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|
1230 1217 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FingerprintsBitVector: < $This->{FingerprintsBitVector} >"</span><span class="sc">;</span>
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|
1231 1218 <span class="s">}</span>
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|
1232 1219 <span class="k">else</span> <span class="s">{</span>
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|
1233 1220 <span class="c"># Number of identifiers...</span>
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|
1234 1221 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; NumOfIdentifiers: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
1235 1222
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1236 1223 <span class="c"># FingerprintsVector...</span>
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|
1237 1224 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span>
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|
1238 1225 <span class="s">}</span>
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|
1239 1226
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|
1240 1227 <span class="k">return</span> <span class="i">$ExtendedConnectivityFingerprintsString</span><span class="sc">;</span>
|
|
|
1241 1228 <span class="s">}</span>
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1242 1229
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1243 <a name="EOF-"></a></pre>
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1244 <p> </p>
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1245 <br />
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1246 <center>
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1247 <img src="../../../images/h2o2.png">
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1248 </center>
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1249 </body>
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1250 </html>
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