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14 <a name="package-Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</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: TopologicalPharmacophoreAtomTripletsFingerprints.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: 1.30 $</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">'StringifyTopologicalPharmacophoreAtomTripletsFingerprints'</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">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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74 61
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75 62 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsProperties</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">$This</span><span class="sc">;</span>
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78 65 <span class="s">}</span>
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79 66
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80 67 <span class="c"># Initialize object data...</span>
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81 68 <span class="c">#</span>
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82 <a name="_InitializeTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 69 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span>
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83 70 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalPharmacophoreAtomTriplets'</span><span class="sc">;</span>
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87 74
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88 75 <span class="c"># Type of vector...</span>
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89 76 <span class="i">$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"># AtomTripletsSetSizeToUse...</span>
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92 79 <span class="c">#</span>
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93 80 <span class="c"># ArbitrarySize - Corrresponds to atom triplets with non-zero count</span>
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94 81 <span class="c"># FixedSize - Corresponds to all atom triplets 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">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="q">''</span><span class="sc">;</span>
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99 86
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100 87 <span class="c">#</span>
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101 88 <span class="c"># OrderedNumericalValues - For ArbitrarySize value of AtomTripletsSetSizeToUse</span>
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102 89 <span class="c"># NumericalValues - For FixedSize value of AtomTripletsSetSizeToUse</span>
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103 90 <span class="c">#</span>
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104 91 <span class="c"># Possible values: OrderedNumericalValues or NumericalValues. Default: NumericalValues</span>
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105 92 <span class="c">#</span>
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106 93 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</span><span class="sc">;</span>
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107 94
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108 95 <span class="c"># Minimum and maximum bond distance between pharmacophore atom pairs corresponding to</span>
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109 96 <span class="c"># atom triplets and distance bin size used for binning distances.</span>
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110 97 <span class="c">#</span>
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111 98 <span class="c"># In order to distribute distance bins of equal size, the last bin is allowed to go past the</span>
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112 99 <span class="c"># maximum distance specified by upto distance bin size.</span>
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113 100 <span class="c">#</span>
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114 101 <span class="c"># The default MinDistance and MaxDistance values of 1 and 10 with DistanceBinSize of</span>
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115 102 <span class="c"># 2 [ Ref 70 ] generates the following 5 distance bins: [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</span>
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116 103 <span class="c">#</span>
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117 104 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span>
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118 105 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span>
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119 106
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120 107 <span class="c"># Distance bin size used for binning distances...</span>
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121 108 <span class="c">#</span>
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122 109 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="n">2</span><span class="sc">;</span>
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123 110
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124 111 <span class="c"># Determines whether to apply triangle inequality to distances triplets during basis set generation...</span>
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125 112 <span class="c">#</span>
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126 113 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="n">1</span><span class="sc">;</span>
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127 114
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128 115 <span class="c"># Initialize pharmacophore atom types information...</span>
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129 116 <span class="i">$This</span><span class="i">->_InitializeToplogicalPharmacophoreAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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130 117
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131 118 <span class="c"># Pharmacophore types assigned to each heavy atom...</span>
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132 119 <span class="c">#</span>
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133 120 <span class="i">%</span>{<span class="i">$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"># All pharmacophore atom triplets between minimum and maximum distance...</span>
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136 123 <span class="c">#</span>
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137 124 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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138 125 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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139 126 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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140 127 <span class="s">}</span>
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141 128
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142 129 <span class="c"># Initialize class ...</span>
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143 <a name="_InitializeClass-"></a> 130 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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144 131 <span class="c">#Class name...</span>
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145 132 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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146 133 <span class="s">}</span>
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147 134
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148 135 <span class="c"># Initialize object properties....</span>
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149 <a name="_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsProperties-"></a> 136 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsProperties</span> <span class="s">{</span>
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150 137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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151 138
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152 139 <span class="k">my</span><span class="s">(</span><span class="i">$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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153 140 <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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154 141 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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155 142 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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156 143 <span class="s">}</span>
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157 144
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158 145 <span class="c"># Make sure molecule object was specified...</span>
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159 146 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
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160 147 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span>
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161 148 <span class="s">}</span>
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162 149 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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163 150
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164 151 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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165 152 <span class="s">}</span>
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166 153
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167 154 <span class="c"># Initialize fingerprints vector...</span>
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168 155 <span class="c">#</span>
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169 <a name="_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsVector-"></a> 156 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsVector</span> <span class="s">{</span>
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170 157 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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171 158
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172 159 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span>
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173 160 <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span>
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174 161 <span class="s">}</span>
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175 162
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176 163 <span class="c"># Vector type and type of values...</span>
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177 164 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span>
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178 165
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179 166 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span>
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180 167 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</span><span class="sc">;</span>
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181 168 <span class="s">}</span>
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182 169 <span class="k">else</span> <span class="s">{</span>
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183 170 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span>
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184 171 <span class="s">}</span>
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185 172
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186 173 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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187 174 <span class="s">}</span>
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188 175
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189 176 <span class="c"># Set atom parits set size to use...</span>
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190 177 <span class="c">#</span>
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191 <a name="SetAtomTripletsSetSizeToUse-"></a> 178 <span class="k">sub </span><span class="m">SetAtomTripletsSetSizeToUse</span> <span class="s">{</span>
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192 179 <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>
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193 180
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194 181 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span>
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195 182 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTripletsSetSizeToUse: Can't change size: It's already set..."</span><span class="sc">;</span>
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196 183 <span class="s">}</span>
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197 184
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198 185 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span>
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199 186 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTripletsSetSizeToUse: Unknown AtomTripletsSetSizeToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span>
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200 187 <span class="s">}</span>
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201 188
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202 189 <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="i">$Value</span><span class="sc">;</span>
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203 190
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204 191 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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205 192 <span class="s">}</span>
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206 193
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207 194 <span class="c"># Initialize topological atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
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208 195 <span class="c"># class, to use for atom triplets fingerprint generation...</span>
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209 196 <span class="c">#</span>
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210 197 <span class="c"># Let:</span>
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211 198 <span class="c"># HBD: HydrogenBondDonor</span>
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|
212 199 <span class="c"># HBA: HydrogenBondAcceptor</span>
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|
213 200 <span class="c"># PI : PositivelyIonizable</span>
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|
214 201 <span class="c"># NI : NegativelyIonizable</span>
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215 202 <span class="c"># Ar : Aromatic</span>
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216 203 <span class="c"># Hal : Halogen</span>
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|
217 204 <span class="c"># H : Hydrophobic</span>
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218 205 <span class="c"># RA : RingAtom</span>
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|
219 206 <span class="c"># CA : ChainAtom</span>
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|
220 207 <span class="c">#</span>
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|
221 208 <span class="c"># Then:</span>
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|
222 209 <span class="c">#</span>
|
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|
223 210 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span>
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224 211 <span class="c">#</span>
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|
225 212 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
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|
226 213 <span class="c">#</span>
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227 214 <span class="c"># Default pharmacophore atom types [ Ref 71 ] to use for atom triplets fingerprint generation</span>
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228 215 <span class="c"># are: HBD, HBA, PI, NI, H, Ar</span>
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229 216 <span class="c">#</span>
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230 217 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
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231 218 <span class="c">#</span>
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232 219 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span>
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233 220 <span class="c"># HydrogenBondAcceptor: N[!H], O</span>
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234 221 <span class="c"># PositivelyIonizable: +, NH2</span>
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235 222 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
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236 223 <span class="c">#</span>
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237 <a name="_InitializeToplogicalPharmacophoreAtomTypesInformation-"></a> 224 <span class="k">sub </span><span class="m">_InitializeToplogicalPharmacophoreAtomTypesInformation</span> <span class="s">{</span>
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238 225 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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239 226
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240 227 <span class="c"># Default pharmacophore atom types to use for atom triplets fingerprint generation</span>
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|
241 228 <span class="c"># are: HBD, HBA, PI, NI, H, Ar</span>
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|
242 229 <span class="c">#</span>
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243 230 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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244 231 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="k">sort</span> <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="s">)</span><span class="sc">;</span>
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245 232
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246 233 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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|
247 234 <span class="s">}</span>
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248 235
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249 236 <span class="c"># Set atom types to use for atom triplets...</span>
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250 237 <span class="c">#</span>
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251 <a name="SetAtomTypesToUse-"></a> 238 <span class="k">sub </span><span class="m">SetAtomTypesToUse</span> <span class="s">{</span>
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252 239 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
|
253 240 <span class="k">my</span><span class="s">(</span><span class="i">$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>
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|
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254 241
|
|
|
255 242 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
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|
|
256 243 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomTypesToUse: No values specified..."</span><span class="sc">;</span>
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|
257 244 <span class="k">return</span><span class="sc">;</span>
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|
|
258 245 <span class="s">}</span>
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|
|
259 246
|
|
|
260 247 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
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|
|
261 248 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
262 249
|
|
|
263 250 <span class="i">@SpecifiedAtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
264 251 <span class="i">@AtomTypesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
265 252
|
|
|
266 253 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
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|
|
267 254 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
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|
|
268 255 <span class="s">}</span>
|
|
|
269 256 <span class="k">else</span> <span class="s">{</span>
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|
270 257 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
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|
271 258 <span class="s">}</span>
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|
272 259
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|
273 260 <span class="c"># Make sure specified AtomTypes are valid...</span>
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|
|
274 261 <span class="k">for</span> <span class="i">$SpecifiedAtomType</span> <span class="s">(</span><span class="i">@SpecifiedAtomTypes</span><span class="s">)</span> <span class="s">{</span>
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|
|
275 262 <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>
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|
|
276 263 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesToUse: Specified atom type, $SpecifiedAtomType, is not supported...\n "</span><span class="sc">;</span>
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|
|
277 264 <span class="s">}</span>
|
|
|
278 265 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomType</span><span class="sc">;</span>
|
|
|
279 266 <span class="k">push</span> <span class="i">@AtomTypesToUse</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span>
|
|
|
280 267 <span class="s">}</span>
|
|
|
281 268
|
|
|
282 269 <span class="c"># Set atom types to use...</span>
|
|
|
283 270 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
284 271 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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>
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|
|
285 272
|
|
|
286 273 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
287 274 <span class="s">}</span>
|
|
|
288 275
|
|
|
289 276 <span class="c"># Set minimum distance for pharmacophore atom pairs in atom triplets...</span>
|
|
|
290 277 <span class="c">#</span>
|
|
|
291 <a name="SetMinDistance-"></a> 278 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span>
|
|
|
292 279 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
293 280
|
|
|
294 281 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
295 282 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
296 283 <span class="s">}</span>
|
|
|
297 284 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
298 285
|
|
|
299 286 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
300 287 <span class="s">}</span>
|
|
|
301 288
|
|
|
302 289 <span class="c"># Set maximum distance for pharmacophore atom pairs in atom triplets...</span>
|
|
|
303 290 <span class="c">#</span>
|
|
|
304 <a name="SetMaxDistance-"></a> 291 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span>
|
|
|
305 292 <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>
|
|
|
306 293
|
|
|
307 294 <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>
|
|
|
308 295 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
309 296 <span class="s">}</span>
|
|
|
310 297 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
311 298
|
|
|
312 299 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
313 300 <span class="s">}</span>
|
|
|
314 301
|
|
|
315 302 <span class="c"># Set distance bin size for binning pharmacophore atom pair distances in atom triplets...</span>
|
|
|
316 303 <span class="c">#</span>
|
|
|
317 <a name="SetDistanceBinSize-"></a> 304 <span class="k">sub </span><span class="m">SetDistanceBinSize</span> <span class="s">{</span>
|
|
|
318 305 <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>
|
|
|
319 306
|
|
|
320 307 <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>
|
|
|
321 308 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDistanceBinSize: DistanceBinSize value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
322 309 <span class="s">}</span>
|
|
|
323 310 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
324 311
|
|
|
325 312 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
326 313 <span class="s">}</span>
|
|
|
327 314
|
|
|
328 315 <span class="c"># Generate fingerprints description...</span>
|
|
|
329 316 <span class="c">#</span>
|
|
|
330 <a name="GetDescription-"></a> 317 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
|
|
|
331 318 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
332 319
|
|
|
333 320 <span class="c"># Is description explicity set?</span>
|
|
|
334 321 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
335 322 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span>
|
|
|
336 323 <span class="s">}</span>
|
|
|
337 324
|
|
|
338 325 <span class="c"># Generate fingerprints description...</span>
|
|
|
339 326
|
|
|
340 327 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomTripletsSetSizeToUse}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span>
|
|
|
341 328 <span class="s">}</span>
|
|
|
342 329
|
|
|
343 330 <span class="c"># Generate topological pharmacophore atom triplets [ Ref 66, Ref 68-71 ] fingerprints...</span>
|
|
|
344 331 <span class="c">#</span>
|
|
|
345 332 <span class="c"># Let:</span>
|
|
|
346 333 <span class="c">#</span>
|
|
|
347 334 <span class="c"># P = Any of the supported pharmacophore atom types</span>
|
|
|
348 335 <span class="c">#</span>
|
|
|
349 336 <span class="c"># Px = Pharmacophore atom x</span>
|
|
|
350 337 <span class="c"># Py = Pharmacophore atom y</span>
|
|
|
351 338 <span class="c"># Pz = Pharmacophore atom z</span>
|
|
|
352 339 <span class="c">#</span>
|
|
|
353 340 <span class="c"># Dxy = Distance or lower bound of binned distance between Px and Py</span>
|
|
|
354 341 <span class="c"># Dxz = Distance or lower bound of binned distance between Px and Pz</span>
|
|
|
355 342 <span class="c"># Dyz = Distance or lower bound of binned distance between Py and Pz</span>
|
|
|
356 343 <span class="c">#</span>
|
|
|
357 344 <span class="c"># Then:</span>
|
|
|
358 345 <span class="c"># PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet ID for atoms Px, Py and Pz</span>
|
|
|
359 346 <span class="c">#</span>
|
|
|
360 347 <span class="c"># For example: H1-H1-H1, H2-HBA-H2 and so on</span>
|
|
|
361 348 <span class="c">#</span>
|
|
|
362 349 <span class="c"># Methodology:</span>
|
|
|
363 350 <span class="c"># . Generate a distance matrix.</span>
|
|
|
364 351 <span class="c"># . Using specified minimum, maximum and distance bin size, generate a binned distance</span>
|
|
|
365 352 <span class="c"># matrix from distance matrix. The lower distance bound on the distance bin is used</span>
|
|
|
366 353 <span class="c"># in the binned distance matrix and atom triplet IDs.</span>
|
|
|
367 354 <span class="c"># . Assign pharmacophore atom types to all the atoms.</span>
|
|
|
368 355 <span class="c"># . Initialize pharmacophore atom triplets basis set for all unique triplets constituting</span>
|
|
|
369 356 <span class="c"># atom pairs binned distances between minimum and maximum distance.</span>
|
|
|
370 357 <span class="c"># . Optionally, trinagle inequality is also implied which means:</span>
|
|
|
371 358 <span class="c"># . Distance or binned distance between any two pairs in a triplet must be less than the</span>
|
|
|
372 359 <span class="c"># sum of distances or binned distances between other two pairs and greater than the</span>
|
|
|
373 360 <span class="c"># difference of distances between other pairs.</span>
|
|
|
374 361 <span class="c"># . Using binned distance matrix and pharmacophore atom types, count occurance of</span>
|
|
|
375 362 <span class="c"># unique atom triplets.</span>
|
|
|
376 363 <span class="c">#</span>
|
|
|
377 364 <span class="c"># Notes:</span>
|
|
|
378 365 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span>
|
|
|
379 366 <span class="c">#</span>
|
|
|
380 <a name="GenerateFingerprints-"></a> 367 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
|
|
|
381 368 <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>
|
|
|
382 369
|
|
|
383 370 <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>
|
|
|
384 371 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalPharmacophoreAtomTripletsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span>
|
|
|
385 372 <span class="s">}</span>
|
|
|
386 373
|
|
|
387 374 <span class="c"># Cache appropriate molecule data...</span>
|
|
|
388 375 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
389 376
|
|
|
390 377 <span class="c"># Generate distance matrix...</span>
|
|
|
391 378 <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>
|
|
|
392 379 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: Fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span>
|
|
|
393 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
394 381 <span class="s">}</span>
|
|
|
395 382
|
|
|
396 383 <span class="c"># Generate binned distance matrix...</span>
|
|
|
397 384 <span class="i">$This</span><span class="i">->_GenerateBinnedDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
398 385
|
|
|
399 386 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span>
|
|
|
400 387 <span class="i">$This</span><span class="i">->_AssignPharmacophoreAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
401 388
|
|
|
402 389 <span class="c"># Initialize values of all possible pharmacohore atom triplets...</span>
|
|
|
403 390 <span class="i">$This</span><span class="i">->_InitializePharmacophoreAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
404 391
|
|
|
405 392 <span class="c"># Count atom triplets...</span>
|
|
|
406 393 <span class="i">$This</span><span class="i">->_CountPharmacohoreAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
407 394
|
|
|
408 395 <span class="c"># Set final fingerprints...</span>
|
|
|
409 396 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
410 397
|
|
|
411 398 <span class="c"># Clear cached molecule data...</span>
|
|
|
412 399 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
413 400
|
|
|
414 401 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
415 402 <span class="s">}</span>
|
|
|
416 403
|
|
|
417 404 <span class="c"># Setup distance matrix...</span>
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|
|
418 405 <span class="c">#</span>
|
|
|
419 <a name="_SetupDistanceMatrix-"></a> 406 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span>
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|
|
420 407 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
421 408
|
|
|
422 409 <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>
|
|
|
423 410
|
|
|
424 411 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
425 412 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
426 413 <span class="s">}</span>
|
|
|
427 414
|
|
|
428 415 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
429 416 <span class="s">}</span>
|
|
|
430 417
|
|
|
431 418 <span class="c"># Generate binned distance matrix for distances with in the specified distance ranges...</span>
|
|
|
432 419 <span class="c">#</span>
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|
433 <a name="_GenerateBinnedDistanceMatrix-"></a> 420 <span class="k">sub </span><span class="m">_GenerateBinnedDistanceMatrix</span> <span class="s">{</span>
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|
|
434 421 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
|
435 422 <span class="k">my</span><span class="s">(</span><span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$BinnedDistanceMatrix</span><span class="cm">,</span> <span class="i">$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">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
|
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|
436 423
|
|
|
437 424 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span>
|
|
|
438 425 <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">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
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439 426
|
|
|
440 427 <span class="c"># Initialize binned distance matrix...</span>
|
|
|
441 428 <span class="i">$BinnedDistanceMatrix</span> = <span class="i">new</span> <span class="i">Matrix</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span><span class="sc">;</span>
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|
|
442 429
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|
443 430 <span class="c"># Setup distance to binned distance map...</span>
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|
444 431 <span class="k">my</span><span class="s">(</span><span class="i">$BinnedDistance</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">%DistanceToBinnedDistance</span><span class="s">)</span><span class="sc">;</span>
|
|
|
445 432 <span class="i">%DistanceToBinnedDistance</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
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|
446 433 <span class="k">for</span> <span class="s">(</span><span class="i">$BinnedDistance</span> = <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance</span> <= <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance</span> += <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
447 434 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$BinnedDistance</span> .. <span class="s">(</span><span class="i">$BinnedDistance</span> + <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
448 435 <span class="i">$DistanceToBinnedDistance</span>{<span class="i">$Distance</span>} = <span class="i">$BinnedDistance</span><span class="sc">;</span>
|
|
|
449 436 <span class="s">}</span>
|
|
|
450 437 <span class="s">}</span>
|
|
|
451 438
|
|
|
452 439 <span class="c"># Generate binned distance matrix...</span>
|
|
|
453 440 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
454 441 <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>
|
|
|
455 442 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$RowIndex</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
456 443 <span class="i">$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>
|
|
|
457 444 <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>
|
|
|
458 445 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
|
|
|
459 446 <span class="s">}</span>
|
|
|
460 447 <span class="i">$BinnedDistance</span> = <span class="i">$DistanceToBinnedDistance</span>{<span class="i">$Distance</span>}<span class="sc">;</span>
|
|
|
461 448 <span class="i">$BinnedDistanceMatrix</span><span class="i">->SetValue</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">$BinnedDistance</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
462 449 <span class="i">$BinnedDistanceMatrix</span><span class="i">->SetValue</span><span class="s">(</span><span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$BinnedDistance</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
463 450 <span class="s">}</span>
|
|
|
464 451 <span class="s">}</span>
|
|
|
465 452
|
|
|
466 453 <span class="i">$This</span>->{<span class="w">BinnedDistanceMatrix</span>} = <span class="i">$BinnedDistanceMatrix</span><span class="sc">;</span>
|
|
|
467 454
|
|
|
468 455 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
469 456 <span class="s">}</span>
|
|
|
470 457
|
|
|
471 458 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span>
|
|
|
472 459 <span class="c">#</span>
|
|
|
473 <a name="_AssignPharmacophoreAtomTypes-"></a> 460 <span class="k">sub </span><span class="m">_AssignPharmacophoreAtomTypes</span> <span class="s">{</span>
|
|
|
474 461 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
475 462 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FunctionalClassAtomTypes</span><span class="s">)</span><span class="sc">;</span>
|
|
|
476 463
|
|
|
477 464 <span class="c"># Assign topological pharmacophore atom types...</span>
|
|
|
478 465 <span class="i">$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>
|
|
|
479 466 <span class="i">$FunctionalClassAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
480 467
|
|
|
481 468 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
482 469
|
|
|
483 470 <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>
|
|
|
484 471 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
485 472 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
486 473 <span class="s">}</span>
|
|
|
487 474 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
488 475
|
|
|
489 476 <span class="k">my</span><span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span><span class="sc">;</span>
|
|
|
490 477 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
491 478
|
|
|
492 479 <span class="i">$AtomType</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>
|
|
|
493 480 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> && <span class="i">$AtomType</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
494 481 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span>
|
|
|
495 482 <span class="s">}</span>
|
|
|
496 483 <span class="c"># Assign phramacophore types list to atom...</span>
|
|
|
497 484 <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = \<span class="i">@AtomTypes</span><span class="sc">;</span>
|
|
|
498 485 <span class="s">}</span>
|
|
|
499 486 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
500 487 <span class="s">}</span>
|
|
|
501 488
|
|
|
502 489 <span class="c"># Initialize pharmacophore atom triplets basis set for all unique triplets constituting atom pairs</span>
|
|
|
503 490 <span class="c"># binned distances between minimum and maximum distance and optionally applying triangle</span>
|
|
|
504 491 <span class="c"># inequality. The DistanceBinSize determines the size of the distance bins. The lower distance</span>
|
|
|
505 492 <span class="c"># bound, along with specified pharmacophore types, is used during generation of atom triplet</span>
|
|
|
506 493 <span class="c"># IDs.</span>
|
|
|
507 494 <span class="c">#</span>
|
|
|
508 495 <span class="c">#</span>
|
|
|
509 <a name="_InitializePharmacophoreAtomTriplets-"></a> 496 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomTriplets</span> <span class="s">{</span>
|
|
|
510 497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
511 498 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$BinnedDistance12</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
512 499
|
|
|
513 500 <span class="c"># Initialize atom triplets information...</span>
|
|
|
514 501 <span class="k">for</span> <span class="s">(</span><span class="i">$BinnedDistance12</span> = <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance12</span> <= <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance12</span> += <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
515 502 <span class="k">for</span> <span class="s">(</span><span class="i">$BinnedDistance13</span> = <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance13</span> <= <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance13</span> += <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
516 503 <span class="j">DISTANCE23:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$BinnedDistance23</span> = <span class="i">$BinnedDistance12</span><span class="sc">;</span> <span class="i">$BinnedDistance23</span> <= <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance23</span> += <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
517 504 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} && !<span class="i">$This</span><span class="i">->_DoDistancesSatisfyTriangleInequality</span><span class="s">(</span><span class="i">$BinnedDistance12</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
518 505 <span class="k">next</span> <span class="j">DISTANCE23</span><span class="sc">;</span>
|
|
|
519 506 <span class="s">}</span>
|
|
|
520 507 <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">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
521 508 <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">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
522 509 <span class="j">ATOMTYPE3:</span> <span class="k">for</span> <span class="i">$AtomType3</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
523 510 <span class="i">$AtomTripletID</span> = <span class="i">$This</span><span class="i">->_GetAtomTripletID</span><span class="s">(</span><span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$BinnedDistance12</span><span class="s">)</span><span class="sc">;</span>
|
|
|
524 511 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$AtomTripletID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
525 512 <span class="k">next</span> <span class="j">ATOMTYPE3</span><span class="sc">;</span>
|
|
|
526 513 <span class="s">}</span>
|
|
|
527 514 <span class="c"># Unique atom triplets information...</span>
|
|
|
528 515 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="sc">;</span>
|
|
|
529 516 <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$AtomTripletID</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
530 517 <span class="s">}</span>
|
|
|
531 518 <span class="s">}</span>
|
|
|
532 519 <span class="s">}</span>
|
|
|
533 520 <span class="s">}</span>
|
|
|
534 521 <span class="s">}</span>
|
|
|
535 522 <span class="s">}</span>
|
|
|
536 523 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
537 524 <span class="s">}</span>
|
|
|
538 525
|
|
|
539 526 <span class="c"># Check triangle inequality...</span>
|
|
|
540 527 <span class="c">#</span>
|
|
|
541 <a name="_DoDistancesSatisfyTriangleInequality-"></a> 528 <span class="k">sub </span><span class="m">_DoDistancesSatisfyTriangleInequality</span> <span class="s">{</span>
|
|
|
542 529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Distance1</span><span class="cm">,</span> <span class="i">$Distance2</span><span class="cm">,</span> <span class="i">$Distance3</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
543 530
|
|
|
544 531 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$Distance1</span> > <span class="k">abs</span><span class="s">(</span><span class="i">$Distance2</span> - <span class="i">$Distance3</span><span class="s">)</span> && <span class="i">$Distance1</span> < <span class="s">(</span><span class="i">$Distance2</span> + <span class="i">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
545 532 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
546 533 <span class="s">}</span>
|
|
|
547 534 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$Distance2</span> > <span class="k">abs</span><span class="s">(</span><span class="i">$Distance1</span> - <span class="i">$Distance3</span><span class="s">)</span> && <span class="i">$Distance2</span> < <span class="s">(</span><span class="i">$Distance1</span> + <span class="i">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
548 535 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
549 536 <span class="s">}</span>
|
|
|
550 537 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$Distance3</span> > <span class="k">abs</span><span class="s">(</span><span class="i">$Distance1</span> - <span class="i">$Distance2</span><span class="s">)</span> && <span class="i">$Distance3</span> < <span class="s">(</span><span class="i">$Distance1</span> + <span class="i">$Distance2</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
551 538 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
552 539 <span class="s">}</span>
|
|
|
553 540 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
554 541 <span class="s">}</span>
|
|
|
555 542
|
|
|
556 543 <span class="c"># Count pharmacophore atom triplets...</span>
|
|
|
557 544 <span class="c">#</span>
|
|
|
558 <a name="_CountPharmacohoreAtomTriplets-"></a> 545 <span class="k">sub </span><span class="m">_CountPharmacohoreAtomTriplets</span> <span class="s">{</span>
|
|
|
559 546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
560 547 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfAtoms</span><span class="cm">,</span> <span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomIndex3</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">$AtomID3</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$BinnedDistance12</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$BinnedDistanceMatrix</span><span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
561 548
|
|
|
562 549 <span class="i">$NumOfAtoms</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span>
|
|
|
563 550 <span class="i">$BinnedDistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">BinnedDistanceMatrix</span>}<span class="sc">;</span>
|
|
|
564 551 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
565 552
|
|
|
566 553 <span class="j">ATOMINDEX1:</span> <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
567 554 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex1</span>}<span class="sc">;</span>
|
|
|
568 555 <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>
|
|
|
569 556 <span class="k">next</span> <span class="j">ATOMINDEX1</span><span class="sc">;</span>
|
|
|
570 557 <span class="s">}</span>
|
|
|
571 558
|
|
|
572 559 <span class="j">ATOMINDEX2:</span> <span class="k">for</span> <span class="i">$AtomIndex2</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
573 560 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex2</span>}<span class="sc">;</span>
|
|
|
574 561 <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>
|
|
|
575 562 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span>
|
|
|
576 563 <span class="s">}</span>
|
|
|
577 564 <span class="i">$BinnedDistance12</span> = <span class="i">$BinnedDistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
578 565 <span class="k">if</span> <span class="s">(</span><span class="i">$BinnedDistance12</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
579 566 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span>
|
|
|
580 567 <span class="s">}</span>
|
|
|
581 568
|
|
|
582 569 <span class="j">ATOMINDEX3:</span> <span class="k">for</span> <span class="i">$AtomIndex3</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomIndex2</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
583 570 <span class="i">$AtomID3</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex3</span>}<span class="sc">;</span>
|
|
|
584 571 <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">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID3</span>}<span class="s">)</span> && <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID3</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
585 572 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span>
|
|
|
586 573 <span class="s">}</span>
|
|
|
587 574 <span class="i">$BinnedDistance13</span> = <span class="i">$BinnedDistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex3</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
588 575 <span class="i">$BinnedDistance23</span> = <span class="i">$BinnedDistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomIndex3</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
589 576 <span class="k">if</span> <span class="s">(</span><span class="i">$BinnedDistance13</span> == <span class="n">0</span> || <span class="i">$BinnedDistance23</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
590 577 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span>
|
|
|
591 578 <span class="s">}</span>
|
|
|
592 579 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} && !<span class="i">$This</span><span class="i">->_DoDistancesSatisfyTriangleInequality</span><span class="s">(</span><span class="i">$BinnedDistance12</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
593 580 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span>
|
|
|
594 581 <span class="s">}</span>
|
|
|
595 582
|
|
|
596 583 <span class="c"># Go over possible pharmacohore triplets for the three pharmacophore atoms using the</span>
|
|
|
597 584 <span class="c"># binned distances...</span>
|
|
|
598 585 <span class="k">for</span> <span class="i">$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>
|
|
|
599 586 <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">$AtomID2</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
600 587 <span class="k">for</span> <span class="i">$AtomType3</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID3</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
601 588 <span class="i">$AtomTripletID</span> = <span class="i">$This</span><span class="i">->_GetAtomTripletID</span><span class="s">(</span><span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$BinnedDistance12</span><span class="s">)</span><span class="sc">;</span>
|
|
|
602 589 <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$AtomTripletID</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
603 590 <span class="s">}</span>
|
|
|
604 591 <span class="s">}</span>
|
|
|
605 592 <span class="s">}</span>
|
|
|
606 593 <span class="s">}</span>
|
|
|
607 594 <span class="s">}</span>
|
|
|
608 595 <span class="s">}</span>
|
|
|
609 596 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
610 597 <span class="s">}</span>
|
|
|
611 598
|
|
|
612 599 <span class="c"># Set final fingerpritns vector...</span>
|
|
|
613 600 <span class="c">#</span>
|
|
|
614 <a name="_SetFinalFingerprints-"></a> 601 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
|
|
|
615 602 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
616 603 <span class="k">my</span><span class="s">(</span><span class="i">$UseArbitrarySetSize</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
617 604
|
|
|
618 605 <span class="c"># Mark successful generation of fingerprints...</span>
|
|
|
619 606 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
620 607
|
|
|
621 608 <span class="c"># Is it an ArbitraySize atom triplets set size?</span>
|
|
|
622 609 <span class="i">$UseArbitrarySetSize</span> = <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
623 610
|
|
|
624 611 <span class="c"># Set atom triplet count values...</span>
|
|
|
625 612 <span class="i">@IDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
626 613
|
|
|
627 614 <span class="k">if</span> <span class="s">(</span><span class="i">$UseArbitrarySetSize</span><span class="s">)</span> <span class="s">{</span>
|
|
|
628 615 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
629 616 <span class="i">$Value</span> = <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
|
|
|
630 617 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
631 618 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
|
|
|
632 619 <span class="s">}</span>
|
|
|
633 620 <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span>
|
|
|
634 621 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span>
|
|
|
635 622 <span class="s">}</span>
|
|
|
636 623 <span class="s">}</span>
|
|
|
637 624 <span class="k">else</span> <span class="s">{</span>
|
|
|
638 625 <span class="i">@Values</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$_</span>} <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="sc">;</span>
|
|
|
639 626 <span class="s">}</span>
|
|
|
640 627
|
|
|
641 628 <span class="c"># Set atom triplet IDs for fingerprint vector...</span>
|
|
|
642 629 <span class="k">if</span> <span class="s">(</span><span class="i">$UseArbitrarySetSize</span><span class="s">)</span> <span class="s">{</span>
|
|
|
643 630 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
644 631 <span class="s">}</span>
|
|
|
645 632 <span class="k">else</span> <span class="s">{</span>
|
|
|
646 633 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
647 634 <span class="s">}</span>
|
|
|
648 635
|
|
|
649 636 <span class="c"># Set atom triplets count values for fingerprint vector...</span>
|
|
|
650 637 <span class="i">$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>
|
|
|
651 638
|
|
|
652 639 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
653 640 <span class="s">}</span>
|
|
|
654 641
|
|
|
655 642 <span class="c"># Return an array or reference to an array containing atom triplet IDs...</span>
|
|
|
656 643 <span class="c">#</span>
|
|
|
657 <a name="GetAtomTripletIDs-"></a> 644 <span class="k">sub </span><span class="m">GetAtomTripletIDs</span> <span class="s">{</span>
|
|
|
658 645 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
659 646
|
|
|
660 647 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="sc">;</span>
|
|
|
661 648 <span class="s">}</span>
|
|
|
662 649
|
|
|
663 650 <span class="c"># Get pharmacophore atom triplet ID corresponding to atom types and distances</span>
|
|
|
664 651 <span class="c"># corresponding to atom triplet...</span>
|
|
|
665 652 <span class="c">#</span>
|
|
|
666 <a name="_GetAtomTripletID-"></a> 653 <span class="k">sub </span><span class="m">_GetAtomTripletID</span> <span class="s">{</span>
|
|
|
667 654 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Px</span><span class="cm">,</span> <span class="i">$Dyz</span><span class="cm">,</span> <span class="i">$Py</span><span class="cm">,</span> <span class="i">$Dxz</span><span class="cm">,</span> <span class="i">$Pz</span><span class="cm">,</span> <span class="i">$Dxy</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
668 655 <span class="k">my</span><span class="s">(</span><span class="i">$AtomTripletID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
669 656
|
|
|
670 657 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
671 658
|
|
|
672 659 <span class="i">@AtomIDs</span> = <span class="k">sort</span><span class="s">(</span><span class="q">"${Px}${Dyz}"</span><span class="cm">,</span> <span class="q">"${Py}${Dxz}"</span><span class="cm">,</span> <span class="q">"${Pz}${Dxy}"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
673 660 <span class="i">$AtomTripletID</span> = <span class="k">join</span> <span class="q">"-"</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="sc">;</span>
|
|
|
674 661
|
|
|
675 662 <span class="k">return</span> <span class="i">$AtomTripletID</span><span class="sc">;</span>
|
|
|
676 663 <span class="s">}</span>
|
|
|
677 664
|
|
|
678 665 <span class="c"># Cache appropriate molecule data...</span>
|
|
|
679 666 <span class="c">#</span>
|
|
|
680 <a name="_SetupMoleculeDataCache-"></a> 667 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
|
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|
681 668 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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682 669
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683 670 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span>
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684 671 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span>
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685 672 <span class="c">#</span>
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686 673 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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687 674
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688 675 <span class="c"># Get all atom IDs...</span>
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689 676 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
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690 677 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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691 678 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</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">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span>
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692 679
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693 680 <span class="c"># Set AtomIndex to AtomID hash...</span>
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694 681 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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695 682 <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>
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696 683
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697 684 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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698 685 <span class="s">}</span>
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699 686
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700 687 <span class="c"># Clear cached molecule data...</span>
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701 688 <span class="c">#</span>
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702 <a name="_ClearMoleculeDataCache-"></a> 689 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
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703 690 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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704 691
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705 692 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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706 693
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707 694 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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708 695 <span class="s">}</span>
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709 696
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710 697
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711 698 <span class="c"># Return a string containg data for TopologicalPharmacophoreAtomTripletsFingerprints object...</span>
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712 699 <span class="c">#</span>
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713 <a name="StringifyTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 700 <span class="k">sub </span><span class="m">StringifyTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span>
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714 701 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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715 702 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="cm">,</span> <span class="i">$UseTriangleInequality</span><span class="s">)</span><span class="sc">;</span>
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716 703
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717 704 <span class="c"># Type of fingerprint...</span>
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718 705 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomTripletsSetSizeToUse: $This->{AtomTripletsSetSizeToUse}"</span><span class="sc">;</span>
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719 706
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720 707 <span class="c"># Distances information...</span>
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721 708 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}; DistanceBinSize: $This->{DistanceBinSize}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span>
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722 709
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723 710 <span class="c"># Pharmacophore atom type labels and description...</span>
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724 711 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span>
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725 712
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726 713 <span class="i">@AtomTypesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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727 714 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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728 715
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729 716 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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730 717 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesOrder</span><span class="s">)</span> <span class="s">{</span>
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731 718 <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>
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732 719 <span class="s">}</span>
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733 720
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734 721 <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>
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735 722 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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736 723 <span class="i">$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>
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737 724
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738 725 <span class="c"># Total number of pharmacophore atom triplets...</span>
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739 726 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomTriplets: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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740 727
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741 728 <span class="c"># FingerprintsVector...</span>
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742 729 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span>
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743 730
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744 731 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span>
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745 732 <span class="s">}</span>
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746 733
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747 <a name="EOF-"></a></pre>
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748 <p> </p>
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749 <br />
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750 <center>
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751 <img src="../../../images/h2o2.png">
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752 </center>
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753 </body>
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754 </html>
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