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14 <a name="package-Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</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: TopologicalPharmacophoreAtomPairsFingerprints.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: 1.34 $</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">Fingerprints::Fingerprints</span><span class="sc">;</span>
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46 33 <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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47 34 <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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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::FunctionalClassAtomTypes</span><span class="sc">;</span>
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50 37
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51 38 <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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52 39
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53 40 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span>
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54 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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55 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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56 43
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57 44 <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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58 45
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59 46 <span class="c"># Setup class variables...</span>
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60 47 <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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61 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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62 49
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63 50 <span class="c"># Overload Perl functions...</span>
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64 51 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTopologicalPharmacophoreAtomPairsFingerprints'</span><span class="sc">;</span>
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65 52
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66 53 <span class="c"># Class constructor...</span>
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67 <a name="new-"></a> 54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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68 55 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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69 56
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70 57 <span class="c"># Initialize object...</span>
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71 58 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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72 59 <span class="k">bless</span> <span class="i">$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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73 60 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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74 61
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75 62 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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76 63
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77 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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78 65 <span class="s">}</span>
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79 66
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80 67 <span class="c"># Initialize object data...</span>
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81 68 <span class="c">#</span>
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82 <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprints-"></a> 69 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span>
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83 70 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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84 71
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85 72 <span class="c"># Type of fingerprint...</span>
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86 73 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalPharmacophoreAtomPairs'</span><span class="sc">;</span>
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87 74
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88 75 <span class="c"># Type of vector...</span>
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89 76 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span>
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90 77
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91 78 <span class="c"># AtomPairsSetSizeToUse...</span>
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92 79 <span class="c">#</span>
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93 80 <span class="c"># ArbitrarySize - Corrresponds to atom pairs with non-zero count</span>
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94 81 <span class="c"># FixedSize - Corresponds to all atom pairs with zero and non-zero count</span>
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95 82 <span class="c">#</span>
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96 83 <span class="c"># Possible values: ArbitrarySize or FixedSize. Default: ArbitrarySize</span>
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97 84 <span class="c">#</span>
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98 85 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">''</span><span class="sc">;</span>
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99 86
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100 87 <span class="c"># Type of FingerprintsVector...</span>
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101 88 <span class="c">#</span>
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102 89 <span class="c"># OrderedNumericalValues - For ArbitrarySize value of AtomPairsSetSizeToUse</span>
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103 90 <span class="c"># NumericalValues - For FixedSize value of AtomPairsSetSizeToUse</span>
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104 91 <span class="c">#</span>
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105 92 <span class="c"># Possible values: OrderedNumericalValues or NumericalValues. Default: NumericalValues</span>
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106 93 <span class="c">#</span>
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107 94 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</span><span class="sc">;</span>
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108 95
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109 96 <span class="c"># Vector values precision for real values which might be generated after</span>
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110 97 <span class="c"># normalization and fuzzification...</span>
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111 98 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="n">2</span><span class="sc">;</span>
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112 99
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113 100 <span class="c"># Minimum and maximum bond distance between pharmacophore atom paris...</span>
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114 101 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span>
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115 102 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span>
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116 103
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117 104 <span class="c"># Initialize atom types and weight information...</span>
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118 105 <span class="i">$This</span><span class="i">->_InitializePharmacophoreAtomTypesAndWeightInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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119 106
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120 107 <span class="c"># Normalization methodology to use for scaling the occurance count of pharmacophore atom</span>
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121 108 <span class="c"># pairs at various distances.</span>
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122 109 <span class="c">#</span>
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123 110 <span class="c"># Possible values: None, ByHeavyAtomsCount, ByAtomTypesCount. Default: None</span>
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124 111 <span class="c">#</span>
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125 112 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span>
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126 113
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127 114 <span class="c"># Initialize fuzzification parameters...</span>
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128 115 <span class="c">#</span>
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129 116 <span class="i">$This</span><span class="i">->_InitializeFuzzificationInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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130 117
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131 118 <span class="c"># Pharmacophore types assigned to each heavy atom...</span>
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132 119 <span class="c">#</span>
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133 120 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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134 121
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135 122 <span class="c"># Assigned Atom types count of each type in the molecule...</span>
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136 123 <span class="c">#</span>
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137 124 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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138 125
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139 126 <span class="c"># All pharmacophore atom pairs between minimum and maximum distance...</span>
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140 127 <span class="c">#</span>
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141 128 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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142 129 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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143 130 <span class="s">}</span>
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144 131
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145 132 <span class="c"># Inialize pharmacophore atom types and weight information...</span>
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146 133 <span class="c">#</span>
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147 <a name="_InitializePharmacophoreAtomTypesAndWeightInformation-"></a> 134 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomTypesAndWeightInformation</span> <span class="s">{</span>
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148 135 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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149 136
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150 137 <span class="c"># Default pharmacophore atom types to use for atom pairs fingerprint generation</span>
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151 138 <span class="c"># are: HBD, HBA, PI, NI, H</span>
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152 139 <span class="c">#</span>
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153 140 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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154 141 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="k">sort</span> <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="s">)</span><span class="sc">;</span>
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155 142
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156 143 <span class="c"># Weight of the various pharmacophore atom types to use for their contribution to atom</span>
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157 144 <span class="c"># pair interaction. It allows to increase the importance of specific pharmacophore atom</span>
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158 145 <span class="c"># types in the generted fingerprints.</span>
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159 146 <span class="c">#</span>
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160 147 <span class="c"># A value of 0 eliminates the contribution by a particular pharmacophore atom</span>
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161 148 <span class="c"># type and 2 doubles its contribution.</span>
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162 149 <span class="c">#</span>
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163 150 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span>
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164 151
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165 152 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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166 153
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167 154 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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168 155 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span> <span class="s">{</span>
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169 156 <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>} = <span class="n">1</span><span class="sc">;</span>
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170 157 <span class="s">}</span>
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171 158 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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172 159 <span class="s">}</span>
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173 160
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174 161 <span class="c"># Initialize fuzzification information...</span>
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175 162 <span class="c">#</span>
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176 <a name="_InitializeFuzzificationInformation-"></a> 163 <span class="k">sub </span><span class="m">_InitializeFuzzificationInformation</span> <span class="s">{</span>
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177 164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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178 165
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179 166 <span class="c"># To fuzz or not to fuzz atom pairs count. Default: No fuzzication</span>
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180 167 <span class="c">#</span>
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181 168 <span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} = <span class="n">0</span><span class="sc">;</span>
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182 169
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183 170 <span class="c"># When to fuzz atom pair count...</span>
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184 171 <span class="c">#</span>
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185 172 <span class="c"># Possible values: BeforeNormalization or AfterNormalization. Default: AfterNormalization</span>
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186 173 <span class="c">#</span>
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187 174 <span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} = <span class="q">'AfterNormalization'</span><span class="sc">;</span>
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188 175
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189 176 <span class="c"># How to fuzz atom pair count...</span>
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190 177 <span class="c">#</span>
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191 178 <span class="c"># Possible values: FuzzyBinning or FuzzyBinSmoothing. Default: FuzzyBinning</span>
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192 179 <span class="c">#</span>
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193 180 <span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} = <span class="q">'FuzzyBinning'</span><span class="sc">;</span>
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194 181
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195 182 <span class="c"># By how much to fuzz atom pairs count...</span>
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196 183 <span class="c">#</span>
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197 184 <span class="i">$This</span>->{<span class="w">FuzzFactor</span>} = <span class="n">0.15</span><span class="sc">;</span>
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198 185
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199 186 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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200 187 <span class="s">}</span>
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201 188
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202 189 <span class="c"># Initialize class ...</span>
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203 <a name="_InitializeClass-"></a> 190 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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204 191 <span class="c">#Class name...</span>
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205 192 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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206 193 <span class="s">}</span>
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207 194
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208 195 <span class="c"># Initialize object properties....</span>
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209 <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties-"></a> 196 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties</span> <span class="s">{</span>
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210 197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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211 198
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212 199 <span class="k">my</span><span class="s">(</span><span class="i">$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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213 200 <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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214 201 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
|
|
|
215 202 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
216 203 <span class="s">}</span>
|
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|
217 204
|
|
|
218 205 <span class="c"># Make sure molecule object was specified...</span>
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|
|
219 206 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
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|
220 207 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span>
|
|
|
221 208 <span class="s">}</span>
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|
222 209
|
|
|
223 210 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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224 211
|
|
|
225 212 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
226 213 <span class="s">}</span>
|
|
|
227 214
|
|
|
228 215 <span class="c"># Initialize fingerprints vector...</span>
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|
229 216 <span class="c">#</span>
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|
230 <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector-"></a> 217 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector</span> <span class="s">{</span>
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|
|
231 218 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
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|
232 219
|
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|
233 220 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
234 221 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span>
|
|
|
235 222 <span class="s">}</span>
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236 223
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|
237 224 <span class="c"># Vector type and type of values...</span>
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|
238 225 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span>
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|
239 226
|
|
|
240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
241 228 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</span><span class="sc">;</span>
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|
242 229 <span class="s">}</span>
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|
243 230 <span class="k">else</span> <span class="s">{</span>
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|
|
244 231 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span>
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|
245 232 <span class="s">}</span>
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246 233
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|
|
247 234 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
248 235 <span class="s">}</span>
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249 236
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250 237 <span class="c"># Set atom parits set size to use...</span>
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251 238 <span class="c">#</span>
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|
252 <a name="SetAtomPairsSetSizeToUse-"></a> 239 <span class="k">sub </span><span class="m">SetAtomPairsSetSizeToUse</span> <span class="s">{</span>
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|
253 240 <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>
|
|
|
254 241
|
|
|
255 242 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
256 243 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomPairsSetSizeToUse: Can't change size: It's already set..."</span><span class="sc">;</span>
|
|
|
257 244 <span class="s">}</span>
|
|
|
258 245
|
|
|
259 246 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
260 247 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomPairsSetSizeToUse: Unknown AtomPairsSetSizeToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span>
|
|
|
261 248 <span class="s">}</span>
|
|
|
262 249
|
|
|
263 250 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
264 251
|
|
|
265 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
266 253 <span class="s">}</span>
|
|
|
267 254
|
|
|
268 255 <span class="c"># Disable change of AvailableAtomTypes...</span>
|
|
|
269 256 <span class="c">#</span>
|
|
|
270 <a name="SetAvailableAtomTypes-"></a> 257 <span class="k">sub </span><span class="m">SetAvailableAtomTypes</span> <span class="s">{</span>
|
|
|
271 258 <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>
|
|
|
272 259
|
|
|
273 260 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAvailableAtomTypes: AvailableAtomTypes value can't be set..."</span><span class="sc">;</span>
|
|
|
274 261
|
|
|
275 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
276 263 <span class="s">}</span>
|
|
|
277 264
|
|
|
278 265 <span class="c"># Set atom types to use for atom pairs...</span>
|
|
|
279 266 <span class="c">#</span>
|
|
|
280 <a name="SetAtomTypesToUse-"></a> 267 <span class="k">sub </span><span class="m">SetAtomTypesToUse</span> <span class="s">{</span>
|
|
|
281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
282 269 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$SpecifiedAtomType</span><span class="cm">,</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@AtomTypesToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
283 270
|
|
|
284 271 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
285 272 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomTypesToUse: No values specified..."</span><span class="sc">;</span>
|
|
|
286 273 <span class="k">return</span><span class="sc">;</span>
|
|
|
287 274 <span class="s">}</span>
|
|
|
288 275
|
|
|
289 276 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
290 277 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
291 278
|
|
|
292 279 <span class="i">@SpecifiedAtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
293 280 <span class="i">@AtomTypesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
294 281
|
|
|
295 282 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
296 283 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
|
|
|
297 284 <span class="s">}</span>
|
|
|
298 285 <span class="k">else</span> <span class="s">{</span>
|
|
|
299 286 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
|
|
|
300 287 <span class="s">}</span>
|
|
|
301 288
|
|
|
302 289 <span class="c"># Make sure specified AtomTypes are valid...</span>
|
|
|
303 290 <span class="k">for</span> <span class="i">$SpecifiedAtomType</span> <span class="s">(</span><span class="i">@SpecifiedAtomTypes</span><span class="s">)</span> <span class="s">{</span>
|
|
|
304 291 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
305 292 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesToUse: Specified atom type, $SpecifiedAtomType, is not supported...\n "</span><span class="sc">;</span>
|
|
|
306 293 <span class="s">}</span>
|
|
|
307 294 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomType</span><span class="sc">;</span>
|
|
|
308 295 <span class="k">push</span> <span class="i">@AtomTypesToUse</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span>
|
|
|
309 296 <span class="s">}</span>
|
|
|
310 297
|
|
|
311 298 <span class="c"># Set atom types to use...</span>
|
|
|
312 299 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
313 300 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="k">sort</span> <span class="i">@AtomTypesToUse</span><span class="sc">;</span>
|
|
|
314 301
|
|
|
315 302 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
316 303 <span class="s">}</span>
|
|
|
317 304
|
|
|
318 305 <span class="c"># Set vector values precision for real values which might be generated after</span>
|
|
|
319 306 <span class="c"># normalization and fuzzification...</span>
|
|
|
320 307 <span class="c">#</span>
|
|
|
321 <a name="SetValuesPrecision-"></a> 308 <span class="k">sub </span><span class="m">SetValuesPrecision</span> <span class="s">{</span>
|
|
|
322 309 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
323 310
|
|
|
324 311 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
325 312 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValuesPrecision: ValuesPrecision value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
326 313 <span class="s">}</span>
|
|
|
327 314 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
328 315
|
|
|
329 316 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
330 317 <span class="s">}</span>
|
|
|
331 318
|
|
|
332 319 <span class="c"># Set minimum distance for pharmacophore atom pairs...</span>
|
|
|
333 320 <span class="c">#</span>
|
|
|
334 <a name="SetMinDistance-"></a> 321 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span>
|
|
|
335 322 <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>
|
|
|
336 323
|
|
|
337 324 <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>
|
|
|
338 325 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span>
|
|
|
339 326 <span class="s">}</span>
|
|
|
340 327 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
341 328
|
|
|
342 329 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
343 330 <span class="s">}</span>
|
|
|
344 331
|
|
|
345 332 <span class="c"># Set maximum distance for pharmacophore atom pairs...</span>
|
|
|
346 333 <span class="c">#</span>
|
|
|
347 <a name="SetMaxDistance-"></a> 334 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span>
|
|
|
348 335 <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>
|
|
|
349 336
|
|
|
350 337 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
351 338 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
352 339 <span class="s">}</span>
|
|
|
353 340 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
354 341
|
|
|
355 342 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
356 343 <span class="s">}</span>
|
|
|
357 344
|
|
|
358 345 <span class="c"># Set normalization methodology to use for scaling the occurance count of pharmacophore atom</span>
|
|
|
359 346 <span class="c"># pairs over distance range beween minimum and maximum distance.</span>
|
|
|
360 347 <span class="c">#</span>
|
|
|
361 <a name="SetNormalizationMethodology-"></a> 348 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span>
|
|
|
362 349 <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>
|
|
|
363 350
|
|
|
364 351 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|ByAtomTypesCount|None)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
365 352 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByAtomTypesCount..."</span><span class="sc">;</span>
|
|
|
366 353 <span class="s">}</span>
|
|
|
367 354
|
|
|
368 355 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
369 356
|
|
|
370 357 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
371 358 <span class="s">}</span>
|
|
|
372 359
|
|
|
373 360 <span class="c"># Set weight of the various pharmacophore atom types to use for their contribution to atom</span>
|
|
|
374 361 <span class="c"># pair interaction using atom types label and value hash.</span>
|
|
|
375 362 <span class="c">#</span>
|
|
|
376 363 <span class="c"># It allows to increase the importance of specific pharmacophore atom</span>
|
|
|
377 364 <span class="c"># types in the generted fingerprints.</span>
|
|
|
378 365 <span class="c">#</span>
|
|
|
379 366 <span class="c"># A value of 0 eliminates the contribution by a particular pharmacophore atom</span>
|
|
|
380 367 <span class="c"># type and 2 doubles its contribution.</span>
|
|
|
381 368 <span class="c">#</span>
|
|
|
382 <a name="SetAtomTypesWeight-"></a> 369 <span class="k">sub </span><span class="m">SetAtomTypesWeight</span> <span class="s">{</span>
|
|
|
383 370 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%AtomTypesWeight</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
384 371 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span><span class="sc">;</span>
|
|
|
385 372
|
|
|
386 373 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%AtomTypesWeight</span><span class="s">)</span> <span class="s">{</span>
|
|
|
387 374 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
388 375 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesWeight: AtomTypeWeight for $AtomType couldn't be set: Unknown atom type..."</span><span class="sc">;</span>
|
|
|
389 376 <span class="s">}</span>
|
|
|
390 377 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Weight</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Weight</span> >= <span class="n">0</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
391 378 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesWeight: Specified weight value, $Weight, for AtomType, $AtomType, muts be >= 0..."</span><span class="sc">;</span>
|
|
|
392 379 <span class="s">}</span>
|
|
|
393 380 <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>} = <span class="i">$Weight</span><span class="sc">;</span>
|
|
|
394 381 <span class="s">}</span>
|
|
|
395 382 <span class="s">}</span>
|
|
|
396 383
|
|
|
397 384 <span class="c"># Set fuzzification methodology to use for fuzzifying atom pairs count...</span>
|
|
|
398 385 <span class="c">#</span>
|
|
|
399 <a name="SetFuzzificationMethodology-"></a> 386 <span class="k">sub </span><span class="m">SetFuzzificationMethodology</span> <span class="s">{</span>
|
|
|
400 387 <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>
|
|
|
401 388
|
|
|
402 389 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(FuzzyBinning|FuzzyBinSmoothing)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
403 390 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzificationMethodology: FuzzificationMethodology value, $Value, is not valid. Supported values: FuzzyBinning or FuzzyBinSmoothing..."</span><span class="sc">;</span>
|
|
|
404 391 <span class="s">}</span>
|
|
|
405 392
|
|
|
406 393 <span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
407 394
|
|
|
408 395 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
409 396 <span class="s">}</span>
|
|
|
410 397
|
|
|
411 398 <span class="c"># Set fuzzification mode for fuzzifying atom pairs count...</span>
|
|
|
412 399 <span class="c">#</span>
|
|
|
413 <a name="SetFuzzificationMode-"></a> 400 <span class="k">sub </span><span class="m">SetFuzzificationMode</span> <span class="s">{</span>
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|
|
414 401 <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>
|
|
|
415 402
|
|
|
416 403 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(BeforeNormalization|AfterNormalization)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
417 404 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzificationMode: FuzzificationMode value, $Value, is not valid. Supported values: BeforeNormalization or AfterNormalization..."</span><span class="sc">;</span>
|
|
|
418 405 <span class="s">}</span>
|
|
|
419 406
|
|
|
420 407 <span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
421 408
|
|
|
422 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
423 410 <span class="s">}</span>
|
|
|
424 411
|
|
|
425 412 <span class="c"># Set fuzz factor values used for fuzzifying atom pairs count...</span>
|
|
|
426 413 <span class="c">#</span>
|
|
|
427 <a name="SetFuzzFactor-"></a> 414 <span class="k">sub </span><span class="m">SetFuzzFactor</span> <span class="s">{</span>
|
|
|
428 415 <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>
|
|
|
429 416
|
|
|
430 417 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinning$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
431 418 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$Value</span> >=<span class="n">0</span> && <span class="i">$Value</span> <= <span class="n">1.0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
432 419 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzFactor: Specified fuzz factor value, $Value, must be >= 0 and <= 1..."</span><span class="sc">;</span>
|
|
|
433 420 <span class="s">}</span>
|
|
|
434 421 <span class="s">}</span>
|
|
|
435 422 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinSmoothing$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
436 423 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$Value</span> >=<span class="n">0</span> && <span class="i">$Value</span> <= <span class="n">0.5</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
437 424 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzFactor: Specified fuzz factor value, $Value, must be >= 0 and <= 0.5..."</span><span class="sc">;</span>
|
|
|
438 425 <span class="s">}</span>
|
|
|
439 426 <span class="s">}</span>
|
|
|
440 427 <span class="k">else</span> <span class="s">{</span>
|
|
|
441 428 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzFactor: Fuzz factor value can't be changed: Uknown FuzzificationMethodology: $This->{FuzzificationMethodology}..."</span><span class="sc">;</span>
|
|
|
442 429 <span class="s">}</span>
|
|
|
443 430
|
|
|
444 431 <span class="i">$This</span>->{<span class="w">FuzzFactor</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
445 432
|
|
|
446 433 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
447 434 <span class="s">}</span>
|
|
|
448 435
|
|
|
449 436 <span class="c"># Generate fingerprints description...</span>
|
|
|
450 437 <span class="c">#</span>
|
|
|
451 <a name="GetDescription-"></a> 438 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
|
|
|
452 439 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
453 440
|
|
|
454 441 <span class="c"># Is description explicity set?</span>
|
|
|
455 442 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
456 443 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span>
|
|
|
457 444 <span class="s">}</span>
|
|
|
458 445
|
|
|
459 446 <span class="c"># Generate fingerprints description...</span>
|
|
|
460 447
|
|
|
461 448 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomPairsSetSizeToUse}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span>
|
|
|
462 449 <span class="s">}</span>
|
|
|
463 450
|
|
|
464 451 <span class="c"># Generate topological pharmacophore atom pairs [ Ref 60-62, Ref 65, Ref 68 ] fingerprints...</span>
|
|
|
465 452 <span class="c">#</span>
|
|
|
466 453 <span class="c"># Methodology:</span>
|
|
|
467 454 <span class="c"># . Generate a distance matrix.</span>
|
|
|
468 455 <span class="c"># . Assign pharmacophore atom types to all the atoms.</span>
|
|
|
469 456 <span class="c"># . Initialize pharmacophore atom pairs basis set for all unique pairs between</span>
|
|
|
470 457 <span class="c"># minimum and maximum distance.</span>
|
|
|
471 458 <span class="c"># . Using distance matrix and pharmacophore atom types, count occurance of</span>
|
|
|
472 459 <span class="c"># unique atom pairs between specified distance range - It corresponds to the</span>
|
|
|
473 460 <span class="c"># correlation-vector for the atom pairs.</span>
|
|
|
474 461 <span class="c"># . Weigh contribution of each atom type to atom pair interaction by its specified</span>
|
|
|
475 462 <span class="c"># weight during occurance count.</span>
|
|
|
476 463 <span class="c"># . Assign count to appropriate distance bin for a specific atom pair</span>
|
|
|
477 464 <span class="c">#</span>
|
|
|
478 465 <span class="c"># . Normalize occurance count of pharmacophore atom pairs by heavy atom count</span>
|
|
|
479 466 <span class="c"># or sum of AtomTypeCounts of each pharmacophore atom type in the atom pair</span>
|
|
|
480 467 <span class="c"># at a specific distance.</span>
|
|
|
481 468 <span class="c">#</span>
|
|
|
482 469 <span class="c"># . Fuzzify occurance count of pharmacophore atom pairs using FuzzyBinning or</span>
|
|
|
483 470 <span class="c"># FuzzySmothing methodology.</span>
|
|
|
484 471 <span class="c">#</span>
|
|
|
485 472 <span class="c"># Notes:</span>
|
|
|
486 473 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span>
|
|
|
487 474 <span class="c">#</span>
|
|
|
488 <a name="GenerateFingerprints-"></a> 475 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
|
|
|
489 476 <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>
|
|
|
490 477
|
|
|
491 478 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
492 479 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalPharmacophoreAtomPairsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span>
|
|
|
493 480 <span class="s">}</span>
|
|
|
494 481
|
|
|
495 482 <span class="c"># Cache appropriate molecule data...</span>
|
|
|
496 483 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
497 484
|
|
|
498 485 <span class="c"># Generate distance matrix...</span>
|
|
|
499 486 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_SetupDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
500 487 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: Fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span>
|
|
|
501 488 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
502 489 <span class="s">}</span>
|
|
|
503 490
|
|
|
504 491 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span>
|
|
|
505 492 <span class="i">$This</span><span class="i">->_AssignPharmacophoreAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
506 493
|
|
|
507 494 <span class="c"># Initialize values of all possible pharmacohore atom pairs...</span>
|
|
|
508 495 <span class="i">$This</span><span class="i">->_InitializePharmacophoreAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
509 496
|
|
|
510 497 <span class="c"># Count atom pairs...</span>
|
|
|
511 498 <span class="i">$This</span><span class="i">->_CountPharmacohoreAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
512 499
|
|
|
513 500 <span class="c"># Fuzzify atom pairs count...</span>
|
|
|
514 501 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} =~ <span class="q">/^BeforeNormalization$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
515 502 <span class="i">$This</span><span class="i">->_FuzzifyPharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
516 503 <span class="s">}</span>
|
|
|
517 504
|
|
|
518 505 <span class="c"># Normalize atom pairs count...</span>
|
|
|
519 506 <span class="i">$This</span><span class="i">->_NormalizePharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
520 507
|
|
|
521 508 <span class="c"># Fuzzify atom pairs count...</span>
|
|
|
522 509 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} =~ <span class="q">/^AfterNormalization$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
523 510 <span class="i">$This</span><span class="i">->_FuzzifyPharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
524 511 <span class="s">}</span>
|
|
|
525 512
|
|
|
526 513 <span class="c"># Set final fingerprints...</span>
|
|
|
527 514 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
528 515
|
|
|
529 516 <span class="c"># Clear cached molecule data...</span>
|
|
|
530 517 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
531 518
|
|
|
532 519 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
533 520 <span class="s">}</span>
|
|
|
534 521
|
|
|
535 522 <span class="c"># Setup distance matrix...</span>
|
|
|
536 523 <span class="c">#</span>
|
|
|
537 <a name="_SetupDistanceMatrix-"></a> 524 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span>
|
|
|
538 525 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
539 526
|
|
|
540 527 <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
541 528
|
|
|
542 529 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
543 530 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
544 531 <span class="s">}</span>
|
|
|
545 532
|
|
|
546 533 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
547 534 <span class="s">}</span>
|
|
|
548 535
|
|
|
549 536 <span class="c"># Assign pharmacohore atom types to all heavy atoms and count each atom</span>
|
|
|
550 537 <span class="c"># types assigned...</span>
|
|
|
551 538 <span class="c">#</span>
|
|
|
552 <a name="_AssignPharmacophoreAtomTypes-"></a> 539 <span class="k">sub </span><span class="m">_AssignPharmacophoreAtomTypes</span> <span class="s">{</span>
|
|
|
553 540 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
554 541 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$AssignedAtomType</span><span class="cm">,</span> <span class="i">$FunctionalClassAtomTypes</span><span class="s">)</span><span class="sc">;</span>
|
|
|
555 542
|
|
|
556 543 <span class="c"># Assign topological pharmacophore atom types...</span>
|
|
|
557 544 <span class="i">$FunctionalClassAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
558 545 <span class="i">$FunctionalClassAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
559 546
|
|
|
560 547 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
561 548
|
|
|
562 549 <span class="c"># Initialize assigned atom types count...</span>
|
|
|
563 550 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
564 551 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
565 552 <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
566 553 <span class="s">}</span>
|
|
|
567 554
|
|
|
568 555 <span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
569 556
|
|
|
570 557 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
571 558 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
572 559 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
573 560 <span class="s">}</span>
|
|
|
574 561 <span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
575 562
|
|
|
576 563 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
577 564
|
|
|
578 565 <span class="c"># Collect all possible pharmacophore atom types which could be assigned to atom...</span>
|
|
|
579 566 <span class="k">my</span><span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span><span class="sc">;</span>
|
|
|
580 567
|
|
|
581 568 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
582 569 <span class="i">$AssignedAtomType</span> = <span class="i">$FunctionalClassAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
583 570 <span class="k">if</span> <span class="s">(</span><span class="i">$AssignedAtomType</span> && <span class="i">$AssignedAtomType</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
584 571 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AssignedAtomType</span><span class="sc">;</span>
|
|
|
585 572 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span> <span class="s">{</span>
|
|
|
586 573 <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
587 574 <span class="s">}</span>
|
|
|
588 575 <span class="s">}</span>
|
|
|
589 576
|
|
|
590 577 <span class="c"># Assign phramacophore types to atom...</span>
|
|
|
591 578 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
592 579 <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = \<span class="i">@AtomTypes</span><span class="sc">;</span>
|
|
|
593 580 <span class="s">}</span>
|
|
|
594 581 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
595 582 <span class="s">}</span>
|
|
|
596 583
|
|
|
597 584 <span class="c"># Initialize values of all possible pharmacohore atom pairs...</span>
|
|
|
598 585 <span class="c">#</span>
|
|
|
599 586 <span class="c"># Let:</span>
|
|
|
600 587 <span class="c"># Dmin = Minimum distance correspoding to number of bonds between two atoms</span>
|
|
|
601 588 <span class="c"># Dmax = Maximum distance correspoding to number of bonds between two atoms</span>
|
|
|
602 589 <span class="c"># D = Distance correspoding to number of bonds between two atoms</span>
|
|
|
603 590 <span class="c">#</span>
|
|
|
604 591 <span class="c"># P = Number of pharmacophore atom types to consider</span>
|
|
|
605 592 <span class="c"># PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn</span>
|
|
|
606 593 <span class="c">#</span>
|
|
|
607 594 <span class="c"># PPT = Total number of possible pharmacophore atom pairs at all distances between Dmin and Dmax</span>
|
|
|
608 595 <span class="c">#</span>
|
|
|
609 596 <span class="c"># Then:</span>
|
|
|
610 597 <span class="c">#</span>
|
|
|
611 598 <span class="c"># PPD = (P * (P - 1))/2 + P</span>
|
|
|
612 599 <span class="c">#</span>
|
|
|
613 600 <span class="c"># PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)</span>
|
|
|
614 601 <span class="c"># = ((Dmax - Dmin) + 1) * PPD</span>
|
|
|
615 602 <span class="c">#</span>
|
|
|
616 603 <span class="c">#</span>
|
|
|
617 604 <span class="c"># So for default values of Dmin = 1, Dmax = 10 and P = 5,</span>
|
|
|
618 605 <span class="c">#</span>
|
|
|
619 606 <span class="c"># PPD = (5 * (5 - 1))/2 + 5 = 15</span>
|
|
|
620 607 <span class="c"># PPT = ((10 - 1) + 1) * 15 = 150</span>
|
|
|
621 608 <span class="c">#</span>
|
|
|
622 609 <span class="c"># the pharmacophore atom pairs bais set includes 150 values.</span>
|
|
|
623 610 <span class="c">#</span>
|
|
|
624 <a name="_InitializePharmacophoreAtomPairs-"></a> 611 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomPairs</span> <span class="s">{</span>
|
|
|
625 612 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
626 613 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
627 614
|
|
|
628 615 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
629 616
|
|
|
630 617 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
631 618 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
632 619
|
|
|
633 620 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
634 621 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span>
|
|
|
635 622 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
636 623
|
|
|
637 624 <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
638 625 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span>
|
|
|
639 626 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
640 627 <span class="s">}</span>
|
|
|
641 628 <span class="s">}</span>
|
|
|
642 629 <span class="s">}</span>
|
|
|
643 630 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
644 631 <span class="s">}</span>
|
|
|
645 632
|
|
|
646 633 <span class="c"># Count pharmacophore atom pairs between mininum and maximum distance at each</span>
|
|
|
647 634 <span class="c"># distance using distance matrix and pharmacophore atom types assiged to each heavy</span>
|
|
|
648 635 <span class="c"># atom.</span>
|
|
|
649 636 <span class="c">#</span>
|
|
|
650 637 <span class="c"># Let:</span>
|
|
|
651 638 <span class="c"># Px = Pharmacophore atom type x</span>
|
|
|
652 639 <span class="c"># Py = Pharmacophore atom type y</span>
|
|
|
653 640 <span class="c"># Dn = Distance between Px and Py in specified distance range</span>
|
|
|
654 641 <span class="c">#</span>
|
|
|
655 642 <span class="c"># Then:</span>
|
|
|
656 643 <span class="c"># Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn</span>
|
|
|
657 644 <span class="c">#</span>
|
|
|
658 645 <span class="c"># For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on</span>
|
|
|
659 646 <span class="c">#</span>
|
|
|
660 647 <span class="c"># Notes:</span>
|
|
|
661 648 <span class="c"># . The row and column indices of distance matrix correspond to atom indices.</span>
|
|
|
662 649 <span class="c"># . Distance value of BigNumber implies the atom is not connected to any other atom.</span>
|
|
|
663 650 <span class="c"># . Due to symmetric nature of distance matrix, only upper or lower triangular matrix</span>
|
|
|
664 651 <span class="c"># needs to be processed during identification and count of pharmacophore atom pairs.</span>
|
|
|
665 652 <span class="c">#</span>
|
|
|
666 <a name="_CountPharmacohoreAtomPairs-"></a> 653 <span class="k">sub </span><span class="m">_CountPharmacohoreAtomPairs</span> <span class="s">{</span>
|
|
|
667 654 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
668 655 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$CountIncrement</span><span class="s">)</span><span class="sc">;</span>
|
|
|
669 656
|
|
|
670 657 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span>
|
|
|
671 658 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
672 659 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
673 660
|
|
|
674 661 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
675 662 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span>
|
|
|
676 663 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span> && <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
677 664 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span>
|
|
|
678 665 <span class="s">}</span>
|
|
|
679 666
|
|
|
680 667 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="i">$RowIndex</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
681 668 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span>
|
|
|
682 669 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span> && <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
683 670 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
|
|
|
684 671 <span class="s">}</span>
|
|
|
685 672
|
|
|
686 673 <span class="i">$Distance</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
687 674 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> < <span class="i">$This</span>->{<span class="w">MinDistance</span>} || <span class="i">$Distance</span> > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
688 675 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
|
|
|
689 676 <span class="s">}</span>
|
|
|
690 677
|
|
|
691 678 <span class="j">ATOMTYPE1:</span> <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
692 679 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType1</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
693 680 <span class="k">next</span> <span class="j">ATOMTYPE1</span><span class="sc">;</span>
|
|
|
694 681 <span class="s">}</span>
|
|
|
695 682 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
696 683 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
697 684 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span>
|
|
|
698 685 <span class="s">}</span>
|
|
|
699 686 <span class="i">$CountIncrement</span> = <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType1</span>} * <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
|
|
|
700 687 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType1</span> <span class="k">le</span> <span class="i">$AtomType2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
701 688 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="i">$CountIncrement</span><span class="sc">;</span>
|
|
|
702 689 <span class="s">}</span>
|
|
|
703 690 <span class="k">else</span> <span class="s">{</span>
|
|
|
704 691 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType2</span>}{<span class="i">$AtomType1</span>} += <span class="i">$CountIncrement</span><span class="sc">;</span>
|
|
|
705 692 <span class="s">}</span>
|
|
|
706 693 <span class="s">}</span>
|
|
|
707 694 <span class="s">}</span>
|
|
|
708 695 <span class="s">}</span>
|
|
|
709 696 <span class="s">}</span>
|
|
|
710 697 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
711 698 <span class="s">}</span>
|
|
|
712 699
|
|
|
713 700 <span class="c"># Normalize the occurance count of pharmacophore atom pairs over the specified distance</span>
|
|
|
714 701 <span class="c"># range...</span>
|
|
|
715 702 <span class="c">#</span>
|
|
|
716 <a name="_NormalizePharmacohoreAtomPairsCount-"></a> 703 <span class="k">sub </span><span class="m">_NormalizePharmacohoreAtomPairsCount</span> <span class="s">{</span>
|
|
|
717 704 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
718 705
|
|
|
719 706 <span class="j">METHODOLOGY:</span> <span class="s">{</span>
|
|
|
720 707 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
721 708 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span>
|
|
|
722 709 <span class="s">}</span>
|
|
|
723 710 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByHeavyAtomsCount$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
724 711 <span class="i">$This</span><span class="i">->_NormalizeAtomPairsCountByHeavyAtomsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
725 712 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span>
|
|
|
726 713 <span class="s">}</span>
|
|
|
727 714 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByAtomTypesCount$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
728 715 <span class="i">$This</span><span class="i">->_NormalizeAtomPairsCountByAtomTypesCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
729 716 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span>
|
|
|
730 717 <span class="s">}</span>
|
|
|
731 718 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_NormalizePharmacohoreAtomPairsCount: Unknown NormalizationMethodology: $This->{NormalizationMethodology}..."</span><span class="sc">;</span>
|
|
|
732 719 <span class="s">}</span>
|
|
|
733 720 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
734 721 <span class="s">}</span>
|
|
|
735 722
|
|
|
736 723
|
|
|
737 724 <span class="c"># Normalize the occurance count of pharmacophore atom pairs at various distances by</span>
|
|
|
738 725 <span class="c"># heavy atom count...</span>
|
|
|
739 726 <span class="c">#</span>
|
|
|
740 <a name="_NormalizeAtomPairsCountByHeavyAtomsCount-"></a> 727 <span class="k">sub </span><span class="m">_NormalizeAtomPairsCountByHeavyAtomsCount</span> <span class="s">{</span>
|
|
|
741 728 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
742 729 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
743 730
|
|
|
744 731 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
745 732 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
746 733 <span class="s">}</span>
|
|
|
747 734
|
|
|
748 735 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} <span class="s">)</span> <span class="s">{</span>
|
|
|
749 736 <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span>
|
|
|
750 737 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span>
|
|
|
751 738 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
752 739 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span>
|
|
|
753 740 <span class="s">}</span>
|
|
|
754 741 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} /= <span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>}<span class="sc">;</span>
|
|
|
755 742 <span class="s">}</span>
|
|
|
756 743 <span class="s">}</span>
|
|
|
757 744 <span class="s">}</span>
|
|
|
758 745 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
759 746 <span class="s">}</span>
|
|
|
760 747
|
|
|
761 748 <span class="c"># Normalize the occurance count of pharmacophore atom pairs at various distances by</span>
|
|
|
762 749 <span class="c"># dividing it using sum of the count of each pharmacophore atom type present in the</span>
|
|
|
763 750 <span class="c"># molecule for the corresponding atom pair.</span>
|
|
|
764 751 <span class="c">#</span>
|
|
|
765 <a name="_NormalizeAtomPairsCountByAtomTypesCount-"></a> 752 <span class="k">sub </span><span class="m">_NormalizeAtomPairsCountByAtomTypesCount</span> <span class="s">{</span>
|
|
|
766 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
767 754 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType1Count</span><span class="cm">,</span> <span class="i">$AtomType2Count</span><span class="cm">,</span> <span class="i">$NormalizationFactor</span><span class="s">)</span><span class="sc">;</span>
|
|
|
768 755
|
|
|
769 756 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} <span class="s">)</span> <span class="s">{</span>
|
|
|
770 757 <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span>
|
|
|
771 758 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span>
|
|
|
772 759 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
773 760 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span>
|
|
|
774 761 <span class="s">}</span>
|
|
|
775 762 <span class="i">$NormalizationFactor</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType1</span>} + <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
|
|
|
776 763 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} /= <span class="i">$NormalizationFactor</span><span class="sc">;</span>
|
|
|
777 764 <span class="s">}</span>
|
|
|
778 765 <span class="s">}</span>
|
|
|
779 766 <span class="s">}</span>
|
|
|
780 767 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
781 768 <span class="s">}</span>
|
|
|
782 769
|
|
|
783 770 <span class="c"># Fuzzify pharmacophore atom pairs count...</span>
|
|
|
784 771 <span class="c">#</span>
|
|
|
785 772 <span class="c"># Let:</span>
|
|
|
786 773 <span class="c"># Px = Pharmacophore atom type x</span>
|
|
|
787 774 <span class="c"># Py = Pharmacophore atom type y</span>
|
|
|
788 775 <span class="c">#</span>
|
|
|
789 776 <span class="c"># PPxy = Pharmacophore atom pair between atom type Px and Py</span>
|
|
|
790 777 <span class="c">#</span>
|
|
|
791 778 <span class="c"># PPxyDn = Pharmacophore atom pairs count between atom type Px and Py at distance Dn</span>
|
|
|
792 779 <span class="c"># PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py at distance Dn - 1</span>
|
|
|
793 780 <span class="c"># PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py at distance Dn + 1</span>
|
|
|
794 781 <span class="c">#</span>
|
|
|
795 782 <span class="c"># FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing</span>
|
|
|
796 783 <span class="c">#</span>
|
|
|
797 784 <span class="c"># Then:</span>
|
|
|
798 785 <span class="c">#</span>
|
|
|
799 786 <span class="c"># For FuzzyBinning:</span>
|
|
|
800 787 <span class="c">#</span>
|
|
|
801 788 <span class="c"># PPxyDn = PPxyDn (Unchanged)</span>
|
|
|
802 789 <span class="c">#</span>
|
|
|
803 790 <span class="c"># PPxyDn-1 = PPxyDn-1 + PPxyDn * FF</span>
|
|
|
804 791 <span class="c"># PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</span>
|
|
|
805 792 <span class="c">#</span>
|
|
|
806 793 <span class="c"># For FuzzyBinSmoothing:</span>
|
|
|
807 794 <span class="c">#</span>
|
|
|
808 795 <span class="c"># PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax</span>
|
|
|
809 796 <span class="c"># PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax</span>
|
|
|
810 797 <span class="c">#</span>
|
|
|
811 798 <span class="c"># PPxyDn-1 = PPxyDn-1 + PPxyDn * FF</span>
|
|
|
812 799 <span class="c"># PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</span>
|
|
|
813 800 <span class="c">#</span>
|
|
|
814 801 <span class="c"># In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurance counts.</span>
|
|
|
815 802 <span class="c"># A value of 1 during FuzzyBinning corresponds to maximum fuzzification of occurance counts;</span>
|
|
|
816 803 <span class="c"># however, a value of 1 during FuzzyBinSmoothing ends up completely distributing the value over</span>
|
|
|
817 804 <span class="c"># the previous and next distance bins.</span>
|
|
|
818 805 <span class="c">#</span>
|
|
|
819 806 <span class="c"># So for default value of FuzzFactor (FF) 0.15, the occurance count of pharmacohore atom pairs</span>
|
|
|
820 807 <span class="c"># at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1</span>
|
|
|
821 808 <span class="c"># are incremened by PPxyDn * 0.15.</span>
|
|
|
822 809 <span class="c">#</span>
|
|
|
823 810 <span class="c"># And during FuzzyBinSmoothing the occurance counts at Distance Dn is scaled back using multiplicate</span>
|
|
|
824 811 <span class="c"># factor of (1 - 2*0.15) and the occurance counts at distances Dn -1 and Dn + 1 are incremened by</span>
|
|
|
825 812 <span class="c"># PPxyDn * 0.15. In otherwords, occurance bin count is smoothed out by distributing it over the</span>
|
|
|
826 813 <span class="c"># previous and next distance value.</span>
|
|
|
827 814 <span class="c">#</span>
|
|
|
828 <a name="_FuzzifyPharmacohoreAtomPairsCount-"></a> 815 <span class="k">sub </span><span class="m">_FuzzifyPharmacohoreAtomPairsCount</span> <span class="s">{</span>
|
|
|
829 816 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
830 817 <span class="k">my</span><span class="s">(</span><span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$CurrentDistance</span><span class="cm">,</span> <span class="i">$CurrentCount</span><span class="cm">,</span> <span class="i">$NextDistance</span><span class="cm">,</span> <span class="i">$NextCount</span><span class="cm">,</span> <span class="i">$PreviousDistance</span><span class="cm">,</span> <span class="i">$ModifyCurrentCount</span><span class="cm">,</span> <span class="i">$ChangeInCountValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
831 818
|
|
|
832 819 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} && <span class="i">$This</span>->{<span class="w">FuzzFactor</span>} > <span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
833 820 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
834 821 <span class="s">}</span>
|
|
|
835 822
|
|
|
836 823 <span class="i">$ModifyCurrentCount</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinSmoothing$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
837 824
|
|
|
838 825 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
839 826 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span>
|
|
|
840 827 <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
841 828 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span>
|
|
|
842 829
|
|
|
843 830 <span class="i">$CurrentCount</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NextCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
844 831
|
|
|
845 832 <span class="i">$NextDistance</span> = <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span>
|
|
|
846 833 <span class="i">$NextCount</span> = <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$NextDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
|
|
|
847 834
|
|
|
848 835 <span class="j">DISTANCE:</span> <span class="k">for</span> <span class="i">$CurrentDistance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
849 836 <span class="i">$NextDistance</span> = <span class="i">$CurrentDistance</span> + <span class="n">1</span><span class="sc">;</span>
|
|
|
850 837 <span class="i">$PreviousDistance</span> = <span class="i">$CurrentDistance</span> - <span class="n">1</span><span class="sc">;</span>
|
|
|
851 838
|
|
|
852 839 <span class="i">$CurrentCount</span> = <span class="i">$NextCount</span><span class="sc">;</span>
|
|
|
853 840 <span class="i">$NextCount</span> = <span class="s">(</span><span class="i">$CurrentDistance</span> < <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> ? <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$NextDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
854 841
|
|
|
855 842 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentCount</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
856 843 <span class="c"># No contribution to fuzzy binning from this distance...</span>
|
|
|
857 844 <span class="k">next</span> <span class="j">DISTANCE</span><span class="sc">;</span>
|
|
|
858 845 <span class="s">}</span>
|
|
|
859 846
|
|
|
860 847 <span class="i">$ChangeInCountValue</span> = <span class="i">$CurrentCount</span> * <span class="i">$This</span>->{<span class="w">FuzzFactor</span>}<span class="sc">;</span>
|
|
|
861 848
|
|
|
862 849 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentDistance</span> > <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
863 850 <span class="c"># Increment count at previous distance...</span>
|
|
|
864 851 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$PreviousDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="i">$ChangeInCountValue</span><span class="sc">;</span>
|
|
|
865 852 <span class="s">}</span>
|
|
|
866 853
|
|
|
867 854 <span class="k">if</span> <span class="s">(</span><span class="i">$ModifyCurrentCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
868 855 <span class="c"># Decrement count at current distance for FuzzyBinSmoothing...</span>
|
|
|
869 856 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentDistance</span> > <span class="i">$This</span>->{<span class="w">MinDistance</span>} && <span class="i">$CurrentDistance</span> < <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
870 857 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$CurrentDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} -= <span class="n">2</span> * <span class="i">$ChangeInCountValue</span><span class="sc">;</span>
|
|
|
871 858 <span class="s">}</span>
|
|
|
872 859 <span class="k">else</span> <span class="s">{</span>
|
|
|
873 860 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$CurrentDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} -= <span class="i">$ChangeInCountValue</span><span class="sc">;</span>
|
|
|
874 861 <span class="s">}</span>
|
|
|
875 862 <span class="s">}</span>
|
|
|
876 863
|
|
|
877 864 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentDistance</span> < <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
878 865 <span class="c"># Increment count at next distance...</span>
|
|
|
879 866 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$NextDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="i">$ChangeInCountValue</span><span class="sc">;</span>
|
|
|
880 867 <span class="s">}</span>
|
|
|
881 868 <span class="s">}</span>
|
|
|
882 869 <span class="s">}</span>
|
|
|
883 870 <span class="s">}</span>
|
|
|
884 871 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
885 872 <span class="s">}</span>
|
|
|
886 873
|
|
|
887 874 <span class="c"># Set final fingerpritns vector...</span>
|
|
|
888 875 <span class="c">#</span>
|
|
|
889 <a name="_SetFinalFingerprints-"></a> 876 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
|
|
|
890 877 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
891 878 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$RoundOffValues</span><span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="cm">,</span> <span class="i">$UseArbitrarySetSize</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
892 879
|
|
|
893 880 <span class="c"># Mark successful generation of fingerprints...</span>
|
|
|
894 881 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
895 882
|
|
|
896 883 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
897 884 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
898 885
|
|
|
899 886 <span class="c"># Do values need to be rounded off?</span>
|
|
|
900 887 <span class="i">$RoundOffValues</span> = <span class="s">(</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> || <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>}<span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
901 888 <span class="i">$ValuesPrecision</span> = <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>}<span class="sc">;</span>
|
|
|
902 889
|
|
|
903 890 <span class="c"># Is it an ArbitraySize atom pairs set size?</span>
|
|
|
904 891 <span class="i">$UseArbitrarySetSize</span> = <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
905 892
|
|
|
906 893 <span class="c"># Collect all atom paris count values...</span>
|
|
|
907 894 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
908 895 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
909 896 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span>
|
|
|
910 897 <span class="j">INDEX2:</span> <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
911 898 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span>
|
|
|
912 899
|
|
|
913 900 <span class="c"># Atom pair count...</span>
|
|
|
914 901 <span class="i">$Value</span> = <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
|
|
|
915 902 <span class="k">if</span> <span class="s">(</span><span class="i">$RoundOffValues</span><span class="s">)</span> <span class="s">{</span>
|
|
|
916 903 <span class="i">$Value</span> = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$Value</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>}<span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
|
|
|
917 904 <span class="s">}</span>
|
|
|
918 905
|
|
|
919 906 <span class="c"># Ignore or not to ignore...</span>
|
|
|
920 907 <span class="k">if</span> <span class="s">(</span><span class="i">$UseArbitrarySetSize</span> && <span class="i">$Value</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
921 908 <span class="k">next</span> <span class="j">INDEX2</span><span class="sc">;</span>
|
|
|
922 909 <span class="s">}</span>
|
|
|
923 910
|
|
|
924 911 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="cm">,</span> <span class="q">"${AtomType1}-D${Distance}-${AtomType2}"</span><span class="sc">;</span>
|
|
|
925 912 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span>
|
|
|
926 913 <span class="s">}</span>
|
|
|
927 914 <span class="s">}</span>
|
|
|
928 915 <span class="s">}</span>
|
|
|
929 916
|
|
|
930 917 <span class="c"># Add AtomPairsIDs and count values to fingerprint vector...</span>
|
|
|
931 918 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
932 919 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
933 920
|
|
|
934 921 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
935 922 <span class="s">}</span>
|
|
|
936 923
|
|
|
937 924 <span class="c"># Get pharmacophore atom pair IDs corresponding to atom pairs count values in</span>
|
|
|
938 925 <span class="c"># fingerprint vector as an array or reference to an array...</span>
|
|
|
939 926 <span class="c">#</span>
|
|
|
940 927 <span class="c"># AtomPairIDs list is generated during finalization of fingerprints and the fingerprint</span>
|
|
|
941 928 <span class="c"># vector containing count values matches the atom pairs array.</span>
|
|
|
942 929 <span class="c">#</span>
|
|
|
943 930 <span class="c">#</span>
|
|
|
944 <a name="GetAtomPairIDs-"></a> 931 <span class="k">sub </span><span class="m">GetAtomPairIDs</span> <span class="s">{</span>
|
|
|
945 932 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
946 933
|
|
|
947 934 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="sc">;</span>
|
|
|
948 935 <span class="s">}</span>
|
|
|
949 936
|
|
|
950 937 <span class="c"># Cache appropriate molecule data...</span>
|
|
|
951 938 <span class="c">#</span>
|
|
|
952 <a name="_SetupMoleculeDataCache-"></a> 939 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
|
|
|
953 940 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
954 941
|
|
|
955 942 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span>
|
|
|
956 943 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span>
|
|
|
957 944 <span class="c">#</span>
|
|
|
958 945 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
959 946
|
|
|
960 947 <span class="c"># Get all atom IDs...</span>
|
|
|
961 948 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
962 949 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
963 950 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span>
|
|
|
964 951
|
|
|
965 952 <span class="c"># Set AtomIndex to AtomID hash...</span>
|
|
|
966 953 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
967 954 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span>
|
|
|
968 955
|
|
|
969 956 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
970 957 <span class="s">}</span>
|
|
|
971 958
|
|
|
972 959 <span class="c"># Clear cached molecule data...</span>
|
|
|
973 960 <span class="c">#</span>
|
|
|
974 <a name="_ClearMoleculeDataCache-"></a> 961 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
|
|
|
975 962 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
976 963
|
|
|
977 964 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
978 965
|
|
|
979 966 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
980 967 <span class="s">}</span>
|
|
|
981 968
|
|
|
982 969
|
|
|
983 970 <span class="c"># Return a string containg data for TopologicalPharmacophoreAtomPairsFingerprints object...</span>
|
|
|
984 <a name="StringifyTopologicalPharmacophoreAtomPairsFingerprints-"></a> 971 <span class="k">sub </span><span class="m">StringifyTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span>
|
|
|
985 972 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
986 973 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
987 974
|
|
|
988 975 <span class="c"># Type of fingerprint...</span>
|
|
|
989 976 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomPairsSetSizeToUse: $This->{AtomPairsSetSizeToUse}"</span><span class="sc">;</span>
|
|
|
990 977
|
|
|
991 978 <span class="c"># Min and max distance...</span>
|
|
|
992 979 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}"</span><span class="sc">;</span>
|
|
|
993 980
|
|
|
994 981 <span class="c"># Pharmacophore type labels and description...</span>
|
|
|
995 982 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span>
|
|
|
996 983
|
|
|
997 984 <span class="i">@AtomTypesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
998 985 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
999 986
|
|
|
1000 987 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1001 988 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesOrder</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1002 989 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="q">"$AtomType: $AvailableAtomTypes{$AtomType}"</span><span class="sc">;</span>
|
|
|
1003 990 <span class="s">}</span>
|
|
|
1004 991
|
|
|
1005 992 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</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>
|
|
|
1006 993 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
|
|
|
1007 994 <span class="i">$FingerprintsString</span> .= <span class="q">"; AvailableAtomTypes: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypes</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>
|
|
|
1008 995
|
|
|
1009 996 <span class="c"># Normalization method...</span>
|
|
|
1010 997 <span class="i">$FingerprintsString</span> .= <span class="q">"; NormalizationMethodology: $This->{NormalizationMethodology}"</span><span class="sc">;</span>
|
|
|
1011 998
|
|
|
1012 999 <span class="c"># Weights...</span>
|
|
|
1013 1000 <span class="k">my</span><span class="s">(</span><span class="i">$FirstLabel</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1014 1001
|
|
|
1015 1002 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesWeight <Labels: Weight>: <"</span><span class="sc">;</span>
|
|
|
1016 1003 <span class="i">$FirstLabel</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
1017 1004 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1018 1005 <span class="i">$Weight</span> = <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$Label</span>}<span class="sc">;</span>
|
|
|
1019 1006 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstLabel</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1020 1007 <span class="i">$FirstLabel</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1021 1008 <span class="i">$FingerprintsString</span> .= <span class="q">" ${Label}: ${Weight}"</span><span class="sc">;</span>
|
|
|
1022 1009 <span class="s">}</span>
|
|
|
1023 1010 <span class="k">else</span> <span class="s">{</span>
|
|
|
1024 1011 <span class="i">$FingerprintsString</span> .= <span class="q">"; ${Label}: ${Weight}"</span><span class="sc">;</span>
|
|
|
1025 1012 <span class="s">}</span>
|
|
|
1026 1013 <span class="s">}</span>
|
|
|
1027 1014 <span class="i">$FingerprintsString</span> .= <span class="q">">"</span><span class="sc">;</span>
|
|
|
1028 1015
|
|
|
1029 1016 <span class="c"># Fuzzification of count...</span>
|
|
|
1030 1017 <span class="k">my</span><span class="s">(</span><span class="i">$FuzzifyFlag</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1031 1018 <span class="i">$FuzzifyFlag</span> = <span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span>
|
|
|
1032 1019 <span class="i">$FingerprintsString</span> .= <span class="q">"; FuzzifyAtomPairsCount: $FuzzifyFlag; FuzzificationMode: $This->{FuzzificationMode}; FuzzificationMethodology: $This->{FuzzificationMethodology}; FuzzFactor: $This->{FuzzFactor}"</span><span class="sc">;</span>
|
|
|
1033 1020
|
|
|
1034 1021 <span class="c"># Total number of pharmacophore atom pairs...</span>
|
|
|
1035 1022 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomPairs: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1036 1023
|
|
|
1037 1024 <span class="c"># FingerprintsVector...</span>
|
|
|
1038 1025 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span>
|
|
|
1039 1026
|
|
|
1040 1027 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span>
|
|
|
1041 1028 <span class="s">}</span>
|
|
|
1042 1029
|
|
|
1043 <a name="EOF-"></a></pre>
|
|
|
1044 <p> </p>
|
|
|
1045 <br />
|
|
|
1046 <center>
|
|
|
1047 <img src="../../../images/h2o2.png">
|
|
|
1048 </center>
|
|
|
1049 </body>
|
|
|
1050 </html>
|
