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14 <a name="package-MolecularDescriptors::MolecularComplexityDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularComplexityDescriptors</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: MolecularComplexityDescriptors.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span>
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18 5 <span class="c"># $Revision: 1.15 $</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">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">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">Atom</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">Fingerprints::AtomTypesFingerprints</span><span class="sc">;</span>
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54 41 <span class="k">use</span> <span class="w">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span>
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55 42 <span class="k">use</span> <span class="w">Fingerprints::MACCSKeys</span><span class="sc">;</span>
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56 43 <span class="k">use</span> <span class="w">Fingerprints::PathLengthFingerprints</span><span class="sc">;</span>
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57 44 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="sc">;</span>
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58 45 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="sc">;</span>
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59 46 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="sc">;</span>
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60 47 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span>
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61 48 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span>
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62 49
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63 50 <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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64 51
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65 52 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span>
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66 53 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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67 54 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames GetMolecularComplexityTypeAbbreviation)</span><span class="sc">;</span>
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68 55
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69 56 <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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70 57
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71 58 <span class="c"># Setup class variables...</span>
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72 59 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
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73 60 <span class="i">_InitializeClass</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="c"># Overload Perl functions...</span>
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76 63 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecularComplexityDescriptors'</span><span class="sc">;</span>
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77 64
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78 65 <span class="c"># Class constructor...</span>
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79 <a name="new-"></a> 66 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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80 67 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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81 68
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82 69 <span class="c"># Initialize object...</span>
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83 70 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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84 71 <span class="k">bless</span> <span class="i">$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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85 72 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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86 73
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87 74 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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88 75
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89 76 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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90 77 <span class="s">}</span>
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91 78
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92 79 <span class="c"># Initialize class ...</span>
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93 <a name="_InitializeClass-"></a> 80 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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94 81 <span class="c">#Class name...</span>
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95 82 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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96 83
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97 84 <span class="c"># Descriptor names...</span>
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98 85 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'MolecularComplexity'</span><span class="s">)</span><span class="sc">;</span>
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99 86
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100 87 <span class="s">}</span>
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101 88
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102 89 <span class="c"># Get descriptor names as an array.</span>
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103 90 <span class="c">#</span>
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104 91 <span class="c"># This functionality can be either invoked as a class function or an</span>
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105 92 <span class="c"># object method.</span>
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106 93 <span class="c">#</span>
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107 <a name="GetDescriptorNames-"></a> 94 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
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108 95 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
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109 96 <span class="s">}</span>
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110 97
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111 98 <span class="c"># Initialize object data...</span>
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112 99 <span class="c">#</span>
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113 <a name="_InitializeMolecularComplexityDescriptors-"></a> 100 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptors</span> <span class="s">{</span>
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114 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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115 102
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116 103 <span class="c"># Type of MolecularDescriptor...</span>
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117 104 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'MolecularComplexity'</span><span class="sc">;</span>
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118 105
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119 106 <span class="c">#</span>
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120 107 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span>
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121 108 <span class="c"># corresponding to number of bits-set or unique keys [ Ref 117-119 ] in molecular</span>
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122 109 <span class="c"># fingerprints. The following types of fingerprints based molecular complexity measures</span>
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123 110 <span class="c"># are supported:</span>
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124 111 <span class="c">#</span>
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125 112 <span class="c"># AtomTypesFingerprints</span>
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126 113 <span class="c"># ExtendedConnectivityFingerprints</span>
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127 114 <span class="c"># MACCSKeys</span>
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128 115 <span class="c"># PathLengthFingerprints</span>
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129 116 <span class="c"># TopologicalAtomPairsFingerprints</span>
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130 117 <span class="c"># TopologicalAtomTripletsFingerprints</span>
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131 118 <span class="c"># TopologicalAtomTorsionsFingerprints</span>
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132 119 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span>
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133 120 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span>
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134 121 <span class="c">#</span>
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135 122 <span class="c"># Default: MACCSKeys</span>
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136 123 <span class="c">#</span>
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137 124 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">''</span><span class="sc">;</span>
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138 125
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139 126 <span class="c"># Atom types to use for generating fingerprints...</span>
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140 127 <span class="c">#</span>
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141 128 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span>
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142 129 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span>
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143 130 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
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144 131 <span class="c">#</span>
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145 132 <span class="c"># Notes:</span>
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146 133 <span class="c"># . AtomicInvariantsAtomTypes for all supported MolecularComplexityType except for</span>
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147 134 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints and TopologicalPharmacophoreAtomTripletsFingerprints</span>
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148 135 <span class="c"># . This value is not used for MACCSKeys</span>
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149 136 <span class="c"># . FunctionalClassAtomTypes is the only valid value during topological pharmacophore fingerprints.</span>
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150 137 <span class="c">#</span>
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151 138 <span class="c"># . Default values for AtomicInvariantsToUse and FunctionalClassesToUse are set appropriately</span>
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152 139 <span class="c"># for different types of fingerprints as shown below.</span>
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153 140 <span class="c">#</span>
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154 141 <span class="c"># MolecularComplexityType AtomicInvariantsToUse</span>
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155 142 <span class="c">#</span>
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156 143 <span class="c"># AtomTypesFingerprints AS, X, BO, H, FC</span>
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157 144 <span class="c"># TopologicalAtomPairsFingerprints AS, X, BO, H, FC</span>
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158 145 <span class="c"># TopologicalAtomTripletsFingerprints AS, X, BO, H, FC</span>
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159 146 <span class="c"># TopologicalAtomTorsionsFingerprints AS, X, BO, H, FC</span>
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160 147 <span class="c">#</span>
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161 148 <span class="c"># ExtendedConnectivityFingerprints AS, X, BO, H, FC, MN</span>
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162 149 <span class="c"># PathLengthFingerprints AS</span>
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163 150 <span class="c">#</span>
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164 151 <span class="c"># Default for FunctionalClassesToUse for all fingerprints is set to:</span>
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165 152 <span class="c">#</span>
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166 153 <span class="c"># HBD, HBA, PI, NI, Ar, Hal</span>
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167 154 <span class="c">#</span>
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168 155 <span class="c"># except for the following two MolecularComplexityType fingerprints:</span>
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169 156 <span class="c">#</span>
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170 157 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints HBD, HBA, PI, NI, H</span>
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171 158 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints HBD, HBA, PI, NI, H, Ar</span>
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172 159 <span class="c">#</span>
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173 160 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span>
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174 161
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175 162 <span class="c"># Size of MACCS key set: 166 or 322...</span>
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176 163 <span class="c">#</span>
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177 164 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="n">166</span><span class="sc">;</span>
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178 165
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179 166 <span class="c"># Atomic neighborhoods radius for extended connectivity fingerprints...</span>
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180 167 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span>
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181 168
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182 169 <span class="c"># Minimum and maximum path lengths to use for path length fingerprints...</span>
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183 170 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="n">1</span><span class="sc">;</span>
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184 171 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="n">8</span><span class="sc">;</span>
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185 172
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186 173 <span class="c"># By default bond symbols are included in atom path strings used to generate path length</span>
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187 174 <span class="c"># fingerprints... ...</span>
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188 175 <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} = <span class="n">1</span><span class="sc">;</span>
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189 176
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190 177 <span class="c"># Minimum and maximum bond distance between atom pairs during topological</span>
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191 178 <span class="c"># atom pairs/triplets fingerprints...</span>
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192 179 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span>
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193 180 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span>
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194 181
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195 182 <span class="c"># Determines whether to apply triangle inequality to distance triplets...</span>
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196 183 <span class="c">#</span>
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197 184 <span class="c"># Default for TopologicalAtomTripletsFingerprints: 0</span>
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198 185 <span class="c"># Default for TopologicalPharmacophoreAtomTripletsFingerprints: 1</span>
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199 186 <span class="c">#</span>
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200 187 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="q">''</span><span class="sc">;</span>
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201 188
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202 189 <span class="c"># Distance bin size used for binning distances during generation of</span>
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203 190 <span class="c"># topological pharmacophore atom triplets fingerprints...</span>
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204 191 <span class="c">#</span>
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205 192 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="n">2</span><span class="sc">;</span>
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206 193
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207 194 <span class="c"># Normalization methodology to use for scaling the number of bits-set or unique keys</span>
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208 195 <span class="c"># for:</span>
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209 196 <span class="c">#</span>
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210 197 <span class="c"># ExtendedConnectivityFingerprints</span>
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211 198 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span>
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212 199 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span>
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213 200 <span class="c">#</span>
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214 201 <span class="c"># This option is gnored for all other types of fingerprints.</span>
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215 202 <span class="c">#</span>
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216 203 <span class="c"># Possible values during extended connectivity fingerprints: None or ByHeavyAtomsCount. Default:</span>
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217 204 <span class="c"># None.</span>
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218 205 <span class="c">#</span>
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219 206 <span class="c"># Possible values during topological pharmacophore atom pairs and tripletes fingerprints: None,</span>
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220 207 <span class="c"># or ByPossibleKeysCount. Default: None. ByPossibleKeysCount corresponds to total number of</span>
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221 208 <span class="c"># possible topological pharmacophore atom pairs or triplets in a molecule.</span>
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222 209 <span class="c">#</span>
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223 210 <span class="c">#</span>
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224 211 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span>
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225 212
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226 213 <span class="c"># Intialize descriptor names and values...</span>
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227 214 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
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228 215
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229 216 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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230 217 <span class="s">}</span>
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231 218
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232 219 <span class="c"># Initialize object properties...</span>
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233 220 <span class="c">#</span>
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234 <a name="_InitializeMolecularComplexityDescriptorsProperties-"></a> 221 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptorsProperties</span> <span class="s">{</span>
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235 222 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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236 223
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237 224 <span class="k">my</span><span class="s">(</span><span class="i">$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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238 225 <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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|
|
239 226 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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|
240 227 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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241 228 <span class="s">}</span>
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242 229
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243 230 <span class="c"># Make sure MolecularComplexityType is set...</span>
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244 231 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span>
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|
245 232 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">'MACCSKeys'</span><span class="sc">;</span>
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246 233 <span class="s">}</span>
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247 234
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248 235 <span class="c"># Make sure AtomIdentifierType is set...</span>
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|
249 236 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span>
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250 237 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
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|
251 238 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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252 239 <span class="s">}</span>
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|
253 240 <span class="s">}</span>
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254 241
|
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|
255 242 <span class="c"># Make sure UseTriangleInequality is set...</span>
|
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|
256 243 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalAtomTripletsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
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|
|
257 244 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">UseTriangleInequality</span>}<span class="s">)</span> <span class="s">{</span>
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|
|
258 245 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
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|
259 246 <span class="s">}</span>
|
|
|
260 247 <span class="s">}</span>
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|
|
261 248
|
|
|
262 249 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
263 250 <span class="s">}</span>
|
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|
264 251
|
|
|
265 252 <span class="c"># Initialize atom identifer type...</span>
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|
266 253 <span class="c">#</span>
|
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|
267 <a name="_InitializeAtomIdentifierType-"></a> 254 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierType</span> <span class="s">{</span>
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|
268 255 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
269 256 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
270 257
|
|
|
271 258 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
272 259 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
273 260 <span class="s">}</span>
|
|
|
274 261
|
|
|
275 262 <span class="i">$AtomIdentifierType</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> ? <span class="q">'FunctionalClassAtomTypes'</span> <span class="co">:</span> <span class="q">'AtomicInvariantsAtomTypes'</span><span class="sc">;</span>
|
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|
276 263
|
|
|
277 264 <span class="i">$This</span><span class="i">->SetAtomIdentifierType</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
278 265
|
|
|
279 266 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
280 267 <span class="s">}</span>
|
|
|
281 268
|
|
|
282 269 <span class="c"># Get abbreviation for specified molecular complexity type or using descriptors object...</span>
|
|
|
283 270 <span class="c">#</span>
|
|
|
284 271 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
285 272 <span class="c"># object method.</span>
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|
|
286 273 <span class="c">#</span>
|
|
|
287 <a name="GetMolecularComplexityTypeAbbreviation-"></a> 274 <span class="k">sub </span><span class="m">GetMolecularComplexityTypeAbbreviation</span> <span class="s">{</span>
|
|
|
288 275 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
289 276 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ComplexityType</span><span class="cm">,</span> <span class="i">%ComplexityTypeToAbbrev</span><span class="s">)</span><span class="sc">;</span>
|
|
|
290 277
|
|
|
291 278 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecularComplexityDescriptors</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
292 279 <span class="i">$This</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
|
|
|
293 280 <span class="i">$ComplexityType</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span>
|
|
|
294 281 <span class="s">}</span>
|
|
|
295 282 <span class="k">else</span> <span class="s">{</span>
|
|
|
296 283 <span class="i">$ComplexityType</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
|
|
|
297 284 <span class="s">}</span>
|
|
|
298 285
|
|
|
299 286 <span class="i">%ComplexityTypeToAbbrev</span> = <span class="s">(</span><span class="k">lc</span> <span class="q">'AtomTypesFingerprints'</span> <span class="cm">=></span> <span class="q">'ATFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'ExtendedConnectivityFingerprints'</span> <span class="cm">=></span> <span class="q">'ECFP'</span><span class="cm">,</span>
|
|
|
300 287 <span class="k">lc</span> <span class="q">'MACCSKeys'</span> <span class="cm">=></span> <span class="q">'MACCSKeys'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'PathLengthFingerprints'</span> <span class="cm">=></span> <span class="q">'PLFP'</span><span class="cm">,</span>
|
|
|
301 288 <span class="k">lc</span> <span class="q">'TopologicalAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TAPFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'TopologicalAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span>
|
|
|
302 289 <span class="k">lc</span> <span class="q">'TopologicalAtomTorsionsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span>
|
|
|
303 290 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPAPFP'</span><span class="cm">,</span>
|
|
|
304 291 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPATFP'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
305 292
|
|
|
306 293 <span class="k">return</span> <span class="k">exists</span> <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} ? <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
307 294 <span class="s">}</span>
|
|
|
308 295
|
|
|
309 296 <span class="c"># Set MACCS key set size...</span>
|
|
|
310 297 <span class="c">#</span>
|
|
|
311 <a name="SetMACCSKeysSize-"></a> 298 <span class="k">sub </span><span class="m">SetMACCSKeysSize</span> <span class="s">{</span>
|
|
|
312 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
313 300
|
|
|
314 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
315 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: Size value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
316 303 <span class="s">}</span>
|
|
|
317 304 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(166|322)/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
318 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: The current release of MayaChemTools doesn't support MDL MACCS $Value keys..."</span><span class="sc">;</span>
|
|
|
319 306 <span class="s">}</span>
|
|
|
320 307 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
321 308
|
|
|
322 309 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
323 310 <span class="s">}</span>
|
|
|
324 311
|
|
|
325 312 <span class="c"># Set minimum path length...</span>
|
|
|
326 313 <span class="c">#</span>
|
|
|
327 <a name="SetMinPathLength-"></a> 314 <span class="k">sub </span><span class="m">SetMinPathLength</span> <span class="s">{</span>
|
|
|
328 315 <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>
|
|
|
329 316
|
|
|
330 317 <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>
|
|
|
331 318 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinPathLength: MinPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
332 319 <span class="s">}</span>
|
|
|
333 320 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
334 321
|
|
|
335 322 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
336 323 <span class="s">}</span>
|
|
|
337 324
|
|
|
338 325 <span class="c"># Set maximum path length...</span>
|
|
|
339 326 <span class="c">#</span>
|
|
|
340 <a name="SetMaxPathLength-"></a> 327 <span class="k">sub </span><span class="m">SetMaxPathLength</span> <span class="s">{</span>
|
|
|
341 328 <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>
|
|
|
342 329
|
|
|
343 330 <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>
|
|
|
344 331 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxPathLength: MaxPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
345 332 <span class="s">}</span>
|
|
|
346 333 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
347 334
|
|
|
348 335 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
349 336 <span class="s">}</span>
|
|
|
350 337
|
|
|
351 338 <span class="c"># Set minimum bond distance between atom pairs during topological and topological</span>
|
|
|
352 339 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span>
|
|
|
353 340 <span class="c">#</span>
|
|
|
354 <a name="SetMinDistance-"></a> 341 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span>
|
|
|
355 342 <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>
|
|
|
356 343
|
|
|
357 344 <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>
|
|
|
358 345 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
359 346 <span class="s">}</span>
|
|
|
360 347 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
361 348
|
|
|
362 349 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
363 350 <span class="s">}</span>
|
|
|
364 351
|
|
|
365 352 <span class="c"># Set maximum bond distance between atom pairs during topological and topological</span>
|
|
|
366 353 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span>
|
|
|
367 354 <span class="c">#</span>
|
|
|
368 <a name="SetMaxDistance-"></a> 355 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span>
|
|
|
369 356 <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>
|
|
|
370 357
|
|
|
371 358 <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>
|
|
|
372 359 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
373 360 <span class="s">}</span>
|
|
|
374 361 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
375 362
|
|
|
376 363 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
377 364 <span class="s">}</span>
|
|
|
378 365
|
|
|
379 366 <span class="c"># Set atom neighborhood radius...</span>
|
|
|
380 367 <span class="c">#</span>
|
|
|
381 <a name="SetNeighborhoodRadius-"></a> 368 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span>
|
|
|
382 369 <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>
|
|
|
383 370
|
|
|
384 371 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
385 372 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span>
|
|
|
386 373 <span class="s">}</span>
|
|
|
387 374
|
|
|
388 375 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
389 376 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span>
|
|
|
390 377 <span class="s">}</span>
|
|
|
391 378 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
392 379
|
|
|
393 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
394 381 <span class="s">}</span>
|
|
|
395 382
|
|
|
396 383 <span class="c"># Set molecular complexity type...</span>
|
|
|
397 384 <span class="c">#</span>
|
|
|
398 <a name="SetMolecularComplexityType-"></a> 385 <span class="k">sub </span><span class="m">SetMolecularComplexityType</span> <span class="s">{</span>
|
|
|
399 386 <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>
|
|
|
400 387
|
|
|
401 388 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|MACCSKeys|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
402 389 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecularComplexityType: MolecularComplexityType value, $Value, is not valid. Supported values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..."</span><span class="sc">;</span>
|
|
|
403 390 <span class="s">}</span>
|
|
|
404 391
|
|
|
405 392 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
406 393
|
|
|
407 394 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
408 395 <span class="s">}</span>
|
|
|
409 396
|
|
|
410 397 <span class="c"># Set distance bin size for binning pharmacophore atom pair distances in atom triplets...</span>
|
|
|
411 398 <span class="c">#</span>
|
|
|
412 <a name="SetDistanceBinSize-"></a> 399 <span class="k">sub </span><span class="m">SetDistanceBinSize</span> <span class="s">{</span>
|
|
|
413 400 <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>
|
|
|
414 401
|
|
|
415 402 <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>
|
|
|
416 403 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDistanceBinSize: DistanceBinSize value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
|
|
|
417 404 <span class="s">}</span>
|
|
|
418 405 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
419 406
|
|
|
420 407 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
421 408 <span class="s">}</span>
|
|
|
422 409
|
|
|
423 410 <span class="c"># Set normalization methodology to use for scaling the number of bits-set or unique keys</span>
|
|
|
424 411 <span class="c"># in fingerprints...</span>
|
|
|
425 412 <span class="c">#</span>
|
|
|
426 <a name="SetNormalizationMethodology-"></a> 413 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span>
|
|
|
427 414 <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>
|
|
|
428 415
|
|
|
429 416 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|ByPossibleKeysCount|None)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
430 417 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span>
|
|
|
431 418 <span class="s">}</span>
|
|
|
432 419
|
|
|
433 420 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
434 421 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^(ExtendedConnectivityFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
435 422 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: Normalization is not supported for MolecularComplexityType: $This->{MolecularComplexityType}. Valid MolecularComplexityType values: ExtendedConnectivityFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints...\n"</span><span class="sc">;</span>
|
|
|
436 423 <span class="s">}</span>
|
|
|
437 424
|
|
|
438 425 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|None)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
439 426 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByHeavyAtomsCount..."</span><span class="sc">;</span>
|
|
|
440 427 <span class="s">}</span>
|
|
|
441 428
|
|
|
442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByPossibleKeysCount|None)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
443 430 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByPossibleKeysCount..."</span><span class="sc">;</span>
|
|
|
444 431 <span class="s">}</span>
|
|
|
445 432 <span class="s">}</span>
|
|
|
446 433
|
|
|
447 434 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
448 435
|
|
|
449 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
450 437 <span class="s">}</span>
|
|
|
451 438
|
|
|
452 439 <span class="c"># Set intial atom identifier type..</span>
|
|
|
453 440 <span class="c">#</span>
|
|
|
454 <a name="SetAtomIdentifierType-"></a> 441 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
|
|
|
455 442 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
456 443
|
|
|
457 444 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
458 445 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span>
|
|
|
459 446 <span class="s">}</span>
|
|
|
460 447
|
|
|
461 448 <span class="c"># FunctionalClassAtomTypes is the only valid atom identifier type for pharmacophore fingerprints...</span>
|
|
|
462 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
463 450 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
464 451 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported type for $This->{MolecularComplexityType} complexity type: FunctionalClassAtomTypes."</span><span class="sc">;</span>
|
|
|
465 452 <span class="s">}</span>
|
|
|
466 453 <span class="s">}</span>
|
|
|
467 454
|
|
|
468 455 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
469 456 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span>
|
|
|
470 457 <span class="s">}</span>
|
|
|
471 458
|
|
|
472 459 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
|
|
|
473 460
|
|
|
474 461 <span class="c"># Initialize identifier type information...</span>
|
|
|
475 462 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
476 463
|
|
|
477 464 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
478 465 <span class="s">}</span>
|
|
|
479 466
|
|
|
480 467 <span class="c"># Calculate molecular complexity [ Ref 117-119 ] of a molecule using its fingerprints.</span>
|
|
|
481 468 <span class="c">#</span>
|
|
|
482 469 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span>
|
|
|
483 470 <span class="c"># corresponding to the number of bits-set or unique keys in molecular fingerprints. The</span>
|
|
|
484 471 <span class="c"># following types of fingerprints based molecular complexity measures are supported:</span>
|
|
|
485 472 <span class="c">#</span>
|
|
|
486 473 <span class="c"># AtomTypesFingerprints</span>
|
|
|
487 474 <span class="c"># ExtendedConnectivityFingerprints</span>
|
|
|
488 475 <span class="c"># MACCSKeys</span>
|
|
|
489 476 <span class="c"># PathLengthFingerprints</span>
|
|
|
490 477 <span class="c"># TopologicalAtomPairsFingerprints</span>
|
|
|
491 478 <span class="c"># TopologicalAtomTripletsFingerprints</span>
|
|
|
492 479 <span class="c"># TopologicalAtomTorsionsFingerprints</span>
|
|
|
493 480 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span>
|
|
|
494 481 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span>
|
|
|
495 482 <span class="c">#</span>
|
|
|
496 483 <span class="c"># After the molecular complexity value has been calculated, it can also be normalized by</span>
|
|
|
497 484 <span class="c"># by scaling the number of bits-set or unique keys for following types of fingerprints:</span>
|
|
|
498 485 <span class="c">#</span>
|
|
|
499 486 <span class="c"># ExtendedConnectivityFingerprints</span>
|
|
|
500 487 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span>
|
|
|
501 488 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span>
|
|
|
502 489 <span class="c">#</span>
|
|
|
503 490 <span class="c"># Two types of normalization methodologies are supported: by heavy atoms count for</span>
|
|
|
504 491 <span class="c"># extended connectivity fingerprints; by possible keys count for topological pharmacophore</span>
|
|
|
505 492 <span class="c"># atom pairs and triplets fingerprints.</span>
|
|
|
506 493 <span class="c">#</span>
|
|
|
507 <a name="GenerateDescriptors-"></a> 494 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
|
|
|
508 495 <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>
|
|
|
509 496
|
|
|
510 497 <span class="c"># Initialize descriptor values...</span>
|
|
|
511 498 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
512 499
|
|
|
513 500 <span class="c"># Check availability of molecule...</span>
|
|
|
514 501 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
515 502 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span>
|
|
|
516 503 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
517 504 <span class="s">}</span>
|
|
|
518 505
|
|
|
519 506 <span class="c"># Calculate descriptor values...</span>
|
|
|
520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
521 508 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate MolecularComplexity values corresponding to assigned MolecularComplexity atom types..."</span><span class="sc">;</span>
|
|
|
522 509 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
523 510 <span class="s">}</span>
|
|
|
524 511
|
|
|
525 512 <span class="c"># Set final descriptor values...</span>
|
|
|
526 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
527 514
|
|
|
528 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
529 516 <span class="s">}</span>
|
|
|
530 517
|
|
|
531 518 <span class="c"># Calculate molecular complexity value...</span>
|
|
|
532 519 <span class="c">#</span>
|
|
|
533 <a name="_CalculateDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
|
|
|
534 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
535 522 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
536 523
|
|
|
537 524 <span class="c"># Setup fingerprints object and generate fingerprints...</span>
|
|
|
538 525 <span class="i">$MethodName</span> = <span class="q">"_Setup"</span> . <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span>
|
|
|
539 526 <span class="i">$FingerprintsObject</span> = <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
540 527
|
|
|
541 528 <span class="i">$FingerprintsObject</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
542 529
|
|
|
543 530 <span class="c"># Make sure atom types fingerprints generation is successful...</span>
|
|
|
544 531 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsObject</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
545 532 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
546 533 <span class="s">}</span>
|
|
|
547 534
|
|
|
548 535 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
549 536 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
550 537 <span class="s">}</span>
|
|
|
551 538
|
|
|
552 539 <span class="c"># Normalize molecular complexity...</span>
|
|
|
553 540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
554 541 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_NormalizeMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
555 542 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
556 543 <span class="s">}</span>
|
|
|
557 544 <span class="s">}</span>
|
|
|
558 545
|
|
|
559 546 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
560 547 <span class="s">}</span>
|
|
|
561 548
|
|
|
562 549 <span class="c"># Setup atom types fingerprints...</span>
|
|
|
563 550 <span class="c">#</span>
|
|
|
564 <a name="_SetupAtomTypesFingerprints-"></a> 551 <span class="k">sub </span><span class="m">_SetupAtomTypesFingerprints</span> <span class="s">{</span>
|
|
|
565 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
566 553 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
567 554
|
|
|
568 555 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::AtomTypesFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'AtomTypesCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
569 556 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
570 557
|
|
|
571 558 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
572 559 <span class="s">}</span>
|
|
|
573 560
|
|
|
574 561 <span class="c"># Setup extended connectivity fingerprints...</span>
|
|
|
575 562 <span class="c">#</span>
|
|
|
576 <a name="_SetupExtendedConnectivityFingerprints-"></a> 563 <span class="k">sub </span><span class="m">_SetupExtendedConnectivityFingerprints</span> <span class="s">{</span>
|
|
|
577 564 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
578 565 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
579 566
|
|
|
580 567 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'ExtendedConnectivity'</span><span class="cm">,</span> <span class="q">'NeighborhoodRadius'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
581 568 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
582 569
|
|
|
583 570 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
584 571 <span class="s">}</span>
|
|
|
585 572
|
|
|
586 573 <span class="c"># Setup MACCS keys...</span>
|
|
|
587 574 <span class="c">#</span>
|
|
|
588 <a name="_SetupMACCSKeys-"></a> 575 <span class="k">sub </span><span class="m">_SetupMACCSKeys</span> <span class="s">{</span>
|
|
|
589 576 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
590 577 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
591 578
|
|
|
592 579 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::MACCSKeys</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'MACCSKeyBits'</span><span class="cm">,</span> <span class="q">'Size'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
593 580
|
|
|
594 581 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
595 582 <span class="s">}</span>
|
|
|
596 583
|
|
|
597 584 <span class="c"># Set up path length fingerprints...</span>
|
|
|
598 585 <span class="c">#</span>
|
|
|
599 <a name="_SetupPathLengthFingerprints-"></a> 586 <span class="k">sub </span><span class="m">_SetupPathLengthFingerprints</span> <span class="s">{</span>
|
|
|
600 587 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
601 588 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
602 589
|
|
|
603 590 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::PathLengthFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'PathLengthCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'MinLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinPathLength</span>}<span class="cm">,</span> <span class="q">'MaxLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxPathLength</span>}<span class="cm">,</span> <span class="q">'AllowRings'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'AllowSharedBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'UseBondSymbols'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">'UseUniquePaths'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
604 591 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
605 592
|
|
|
606 593 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
607 594 <span class="s">}</span>
|
|
|
608 595
|
|
|
609 596 <span class="c"># Setup topological atom pairs fingerprints...</span>
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|
|
610 597 <span class="c">#</span>
|
|
|
611 <a name="_SetupTopologicalAtomPairsFingerprints-"></a> 598 <span class="k">sub </span><span class="m">_SetupTopologicalAtomPairsFingerprints</span> <span class="s">{</span>
|
|
|
612 599 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
613 600 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
614 601
|
|
|
615 602 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
616 603 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
617 604
|
|
|
618 605 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
619 606 <span class="s">}</span>
|
|
|
620 607
|
|
|
621 608 <span class="c"># Setup topological atom triplets fingerprints...</span>
|
|
|
622 609 <span class="c">#</span>
|
|
|
623 <a name="_SetupTopologicalAtomTripletsFingerprints-"></a> 610 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTripletsFingerprints</span> <span class="s">{</span>
|
|
|
624 611 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
625 612 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
626 613
|
|
|
627 614 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
628 615 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
629 616
|
|
|
630 617 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
631 618 <span class="s">}</span>
|
|
|
632 619
|
|
|
633 620 <span class="c"># Setup topological atom torsions fingerprints...</span>
|
|
|
634 621 <span class="c">#</span>
|
|
|
635 <a name="_SetupTopologicalAtomTorsionsFingerprints-"></a> 622 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTorsionsFingerprints</span> <span class="s">{</span>
|
|
|
636 623 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
637 624 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
638 625
|
|
|
639 626 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
640 627
|
|
|
641 628 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
642 629
|
|
|
643 630 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
644 631 <span class="s">}</span>
|
|
|
645 632
|
|
|
646 633 <span class="c"># Setup TopologicalPharmacophoreAtomPairsFingerprints...</span>
|
|
|
647 634 <span class="c">#</span>
|
|
|
648 <a name="_SetupTopologicalPharmacophoreAtomPairsFingerprints-"></a> 635 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span>
|
|
|
649 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
650 637 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomPairsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
651 638
|
|
|
652 639 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span>
|
|
|
653 640 <span class="i">$AtomPairsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span>
|
|
|
654 641
|
|
|
655 642 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomPairsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomPairsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="q">'None'</span><span class="cm">,</span> <span class="q">'ValuesPrecision'</span> <span class="cm">=></span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
656 643
|
|
|
657 644 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
658 645 <span class="s">}</span>
|
|
|
659 646
|
|
|
660 647 <span class="c"># Setup TopologicalPharmacophoreAtomTripletsFingerprints...</span>
|
|
|
661 648 <span class="c">#</span>
|
|
|
662 <a name="_SetupTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 649 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span>
|
|
|
663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
664 651 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
665 652
|
|
|
666 653 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span>
|
|
|
667 654 <span class="i">$AtomTripletsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span>
|
|
|
668 655
|
|
|
669 656 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomTripletsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'DistanceBinSize'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
670 657
|
|
|
671 658 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
672 659 <span class="s">}</span>
|
|
|
673 660
|
|
|
674 661 <span class="c"># Normalize molecular complexity value...</span>
|
|
|
675 662 <span class="c">#</span>
|
|
|
676 <a name="_NormalizeMolecularComplexity-"></a> 663 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexity</span> <span class="s">{</span>
|
|
|
677 664 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
678 665
|
|
|
679 666 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByHeavyAtomsCount$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
680 667 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByHeavyAtomsCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
681 668 <span class="s">}</span>
|
|
|
682 669 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
683 670 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByPossibleKeysCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
684 671 <span class="s">}</span>
|
|
|
685 672 <span class="k">else</span> <span class="s">{</span>
|
|
|
686 673 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_NormalizeMolecularComplexity: NormalizationMethodology value, $This->{NormalizationMethodology}, is not valid. Supported values: ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span>
|
|
|
687 674 <span class="s">}</span>
|
|
|
688 675 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
689 676 <span class="s">}</span>
|
|
|
690 677
|
|
|
691 678 <span class="c"># Normalize molecular complexity value by heavy atom count...</span>
|
|
|
692 679 <span class="c">#</span>
|
|
|
693 <a name="_NormalizeMolecularComplexityByHeavyAtomsCount-"></a> 680 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByHeavyAtomsCount</span> <span class="s">{</span>
|
|
|
694 681 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
695 682 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfHeavyAtoms</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
696 683
|
|
|
697 684 <span class="i">$NumOfHeavyAtoms</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetNumOfHeavyAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
698 685 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfHeavyAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
699 686 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
700 687 <span class="s">}</span>
|
|
|
701 688
|
|
|
702 689 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfHeavyAtoms</span><span class="sc">;</span>
|
|
|
703 690 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
|
|
|
704 691
|
|
|
705 692 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
706 693 <span class="s">}</span>
|
|
|
707 694
|
|
|
708 695 <span class="c"># Normalize molecular complexity value by possible keys count...</span>
|
|
|
709 696 <span class="c">#</span>
|
|
|
710 <a name="_NormalizeMolecularComplexityByPossibleKeysCount-"></a> 697 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByPossibleKeysCount</span> <span class="s">{</span>
|
|
|
711 698 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
712 699 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPossibleKeys</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
713 700
|
|
|
714 701 <span class="i">$NumOfPossibleKeys</span> = <span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
715 702 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfPossibleKeys</span><span class="s">)</span> <span class="s">{</span>
|
|
|
716 703 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
717 704 <span class="s">}</span>
|
|
|
718 705
|
|
|
719 706 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfPossibleKeys</span><span class="sc">;</span>
|
|
|
720 707 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
|
|
|
721 708
|
|
|
722 709 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
723 710 <span class="s">}</span>
|
|
|
724 711
|
|
|
725 712 <span class="c"># Calculate molecular complexity value using fingerprints objects...</span>
|
|
|
726 713 <span class="c">#</span>
|
|
|
727 <a name="_CalculateMolecularComplexity-"></a> 714 <span class="k">sub </span><span class="m">_CalculateMolecularComplexity</span> <span class="s">{</span>
|
|
|
728 715 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
729 716
|
|
|
730 717 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
731 718 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsBitVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
732 719 <span class="s">}</span>
|
|
|
733 720 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
734 721 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
735 722 <span class="s">}</span>
|
|
|
736 723 <span class="k">else</span> <span class="s">{</span>
|
|
|
737 724 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_CalculateMolecularComplexity: Fingerprints vector type is not valid. Supported values: FingerprintsBitVector or FingerprintsVector..."</span><span class="sc">;</span>
|
|
|
738 725 <span class="s">}</span>
|
|
|
739 726
|
|
|
740 727 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
741 728 <span class="s">}</span>
|
|
|
742 729
|
|
|
743 730 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span>
|
|
|
744 731 <span class="c">#</span>
|
|
|
745 <a name="_CalculateMolecularComplexityUsingFingerprintsVector-"></a> 732 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsVector</span> <span class="s">{</span>
|
|
|
746 733 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
747 734
|
|
|
748 735 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="s">(</span><span class="i">$FingerprintsVector</span><span class="i">->GetType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^(OrderedNumericalValues|NumericalValues)$/i</span><span class="s">)</span> ? <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfNonZeroValues</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
749 736
|
|
|
750 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
751 738 <span class="s">}</span>
|
|
|
752 739
|
|
|
753 740 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span>
|
|
|
754 741 <span class="c">#</span>
|
|
|
755 <a name="_CalculateMolecularComplexityUsingFingerprintsBitVector-"></a> 742 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsBitVector</span> <span class="s">{</span>
|
|
|
756 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
757 744
|
|
|
758 745 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">$FingerprintsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
759 746
|
|
|
760 747 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
761 748 <span class="s">}</span>
|
|
|
762 749
|
|
|
763 750 <span class="c"># Setup final descriptor values...</span>
|
|
|
764 751 <span class="c">#</span>
|
|
|
765 <a name="_SetFinalDescriptorValues-"></a> 752 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
|
|
|
766 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
767 754
|
|
|
768 755 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
769 756
|
|
|
770 757 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexity</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
771 758
|
|
|
772 759 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
773 760 <span class="s">}</span>
|
|
|
774 761
|
|
|
775 762 <span class="c"># Set atom identifier type to use for generating fingerprints...</span>
|
|
|
776 763 <span class="c">#</span>
|
|
|
777 <a name="_SetAtomIdentifierTypeValuesToUse-"></a> 764 <span class="k">sub </span><span class="m">_SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span>
|
|
|
778 765 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
779 766
|
|
|
780 767 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
781 768 <span class="i">$FingerprintsObject</span><span class="i">->SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
782 769 <span class="s">}</span>
|
|
|
783 770 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
784 771 <span class="i">$FingerprintsObject</span><span class="i">->SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
785 772 <span class="s">}</span>
|
|
|
786 773 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
787 774 <span class="c"># Nothing to do for now...</span>
|
|
|
788 775 <span class="s">}</span>
|
|
|
789 776 <span class="k">else</span> <span class="s">{</span>
|
|
|
790 777 <span class="w">croak</span> <span class="q">"Error: The value specified, $This->{AtomIdentifierType}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span>
|
|
|
791 778 <span class="s">}</span>
|
|
|
792 779 <span class="s">}</span>
|
|
|
793 780
|
|
|
794 781 <span class="c"># Initialize atom indentifier type information...</span>
|
|
|
795 782 <span class="c">#</span>
|
|
|
796 783 <span class="c"># Current supported values:</span>
|
|
|
797 784 <span class="c">#</span>
|
|
|
798 785 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span>
|
|
|
799 786 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
|
|
|
800 787 <span class="c">#</span>
|
|
|
801 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 788 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
|
|
|
802 789 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
803 790
|
|
|
804 791 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
|
|
|
805 792 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
806 793 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
807 794 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
808 795 <span class="s">}</span>
|
|
|
809 796 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
810 797 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
811 798 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
812 799 <span class="s">}</span>
|
|
|
813 800 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
814 801 <span class="c"># Nothing to do for now...</span>
|
|
|
815 802 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
816 803 <span class="s">}</span>
|
|
|
817 804 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
|
|
|
818 805 <span class="s">}</span>
|
|
|
819 806 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
820 807 <span class="s">}</span>
|
|
|
821 808
|
|
|
822 809 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span>
|
|
|
823 810 <span class="c"># class, to use for generating initial atom identifiers...</span>
|
|
|
824 811 <span class="c">#</span>
|
|
|
825 812 <span class="c"># Let:</span>
|
|
|
826 813 <span class="c"># AS = Atom symbol corresponding to element symbol</span>
|
|
|
827 814 <span class="c">#</span>
|
|
|
828 815 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
829 816 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
830 817 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
831 818 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
832 819 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
833 820 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
834 821 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span>
|
|
|
835 822 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
|
|
|
836 823 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span>
|
|
|
837 824 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span>
|
|
|
838 825 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span>
|
|
|
839 826 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
|
|
|
840 827 <span class="c">#</span>
|
|
|
841 828 <span class="c"># Then:</span>
|
|
|
842 829 <span class="c">#</span>
|
|
|
843 830 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
|
|
|
844 831 <span class="c">#</span>
|
|
|
845 832 <span class="c"># AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></span>
|
|
|
846 833 <span class="c">#</span>
|
|
|
847 834 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span>
|
|
|
848 835 <span class="c"># optional.</span>
|
|
|
849 836 <span class="c">#</span>
|
|
|
850 837 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span>
|
|
|
851 838 <span class="c">#</span>
|
|
|
852 839 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span>
|
|
|
853 840 <span class="c">#</span>
|
|
|
854 841 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span>
|
|
|
855 842 <span class="c"># are also allowed:</span>
|
|
|
856 843 <span class="c">#</span>
|
|
|
857 844 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span>
|
|
|
858 845 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span>
|
|
|
859 846 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span>
|
|
|
860 847 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span>
|
|
|
861 848 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span>
|
|
|
862 849 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span>
|
|
|
863 850 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span>
|
|
|
864 851 <span class="c"># Ar : Aromatic</span>
|
|
|
865 852 <span class="c"># RA : RingAtom</span>
|
|
|
866 853 <span class="c"># FC : FormalCharge</span>
|
|
|
867 854 <span class="c"># MN : MassNumber</span>
|
|
|
868 855 <span class="c"># SM : SpinMultiplicity</span>
|
|
|
869 856 <span class="c">#</span>
|
|
|
870 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 857 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
|
|
|
871 858 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
872 859
|
|
|
873 860 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
874 861
|
|
|
875 862 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
876 863 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
877 864 <span class="s">}</span>
|
|
|
878 865 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
879 866 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="cm">,</span> <span class="q">'MN'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
880 867 <span class="s">}</span>
|
|
|
881 868 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
882 869 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
883 870 <span class="s">}</span>
|
|
|
884 871
|
|
|
885 872 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
886 873 <span class="s">}</span>
|
|
|
887 874
|
|
|
888 875 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
|
|
|
889 876 <span class="c"># class, to use for generating initial atom identifiers...</span>
|
|
|
890 877 <span class="c">#</span>
|
|
|
891 878 <span class="c"># Let:</span>
|
|
|
892 879 <span class="c"># HBD: HydrogenBondDonor</span>
|
|
|
893 880 <span class="c"># HBA: HydrogenBondAcceptor</span>
|
|
|
894 881 <span class="c"># PI : PositivelyIonizable</span>
|
|
|
895 882 <span class="c"># NI : NegativelyIonizable</span>
|
|
|
896 883 <span class="c"># Ar : Aromatic</span>
|
|
|
897 884 <span class="c"># Hal : Halogen</span>
|
|
|
898 885 <span class="c"># H : Hydrophobic</span>
|
|
|
899 886 <span class="c"># RA : RingAtom</span>
|
|
|
900 887 <span class="c"># CA : ChainAtom</span>
|
|
|
901 888 <span class="c">#</span>
|
|
|
902 889 <span class="c"># Then:</span>
|
|
|
903 890 <span class="c">#</span>
|
|
|
904 891 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span>
|
|
|
905 892 <span class="c">#</span>
|
|
|
906 893 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
|
|
|
907 894 <span class="c">#</span>
|
|
|
908 895 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
|
|
|
909 896 <span class="c">#</span>
|
|
|
910 897 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
|
|
|
911 898 <span class="c">#</span>
|
|
|
912 899 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span>
|
|
|
913 900 <span class="c"># HydrogenBondAcceptor: N[!H], O</span>
|
|
|
914 901 <span class="c"># PositivelyIonizable: +, NH2</span>
|
|
|
915 902 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
|
|
|
916 903 <span class="c">#</span>
|
|
|
917 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 904 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
|
|
|
918 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
919 906
|
|
|
920 907 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
921 908
|
|
|
922 909 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
923 910 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
924 911 <span class="s">}</span>
|
|
|
925 912 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
926 913 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
927 914 <span class="s">}</span>
|
|
|
928 915 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
929 916 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
930 917 <span class="s">}</span>
|
|
|
931 918
|
|
|
932 919 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
933 920 <span class="s">}</span>
|
|
|
934 921
|
|
|
935 922 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span>
|
|
|
936 923 <span class="c">#</span>
|
|
|
937 <a name="SetAtomicInvariantsToUse-"></a> 924 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
|
|
|
938 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
939 926 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
940 927
|
|
|
941 928 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
942 929 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span>
|
|
|
943 930 <span class="k">return</span><span class="sc">;</span>
|
|
|
944 931 <span class="s">}</span>
|
|
|
945 932
|
|
|
946 933 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
947 934 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
|
|
|
948 935 <span class="k">return</span><span class="sc">;</span>
|
|
|
949 936 <span class="s">}</span>
|
|
|
950 937
|
|
|
951 938 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
952 939 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
953 940
|
|
|
954 941 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
955 942 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
956 943
|
|
|
957 944 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
958 945 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
|
|
|
959 946 <span class="s">}</span>
|
|
|
960 947 <span class="k">else</span> <span class="s">{</span>
|
|
|
961 948 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
|
|
|
962 949 <span class="s">}</span>
|
|
|
963 950
|
|
|
964 951 <span class="c"># Make sure specified AtomicInvariants are valid...</span>
|
|
|
965 952 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
|
|
|
966 953 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
967 954 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span>
|
|
|
968 955 <span class="s">}</span>
|
|
|
969 956 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
|
|
|
970 957 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
|
|
|
971 958 <span class="s">}</span>
|
|
|
972 959
|
|
|
973 960 <span class="c"># Set atomic invariants to use...</span>
|
|
|
974 961 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
975 962 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
|
|
|
976 963
|
|
|
977 964 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
978 965 <span class="s">}</span>
|
|
|
979 966
|
|
|
980 967 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span>
|
|
|
981 968 <span class="c">#</span>
|
|
|
982 <a name="SetFunctionalClassesToUse-"></a> 969 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
|
|
|
983 970 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
984 971 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="cm">,</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
985 972
|
|
|
986 973 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
987 974 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span>
|
|
|
988 975 <span class="k">return</span><span class="sc">;</span>
|
|
|
989 976 <span class="s">}</span>
|
|
|
990 977
|
|
|
991 978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
992 979 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
|
|
|
993 980 <span class="k">return</span><span class="sc">;</span>
|
|
|
994 981 <span class="s">}</span>
|
|
|
995 982
|
|
|
996 983 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
997 984 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
998 985
|
|
|
999 986 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1000 987 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1001 988
|
|
|
1002 989 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1003 990 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
|
|
|
1004 991 <span class="s">}</span>
|
|
|
1005 992 <span class="k">else</span> <span class="s">{</span>
|
|
|
1006 993 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
|
|
|
1007 994 <span class="s">}</span>
|
|
|
1008 995
|
|
|
1009 996 <span class="c"># Make sure specified FunctionalClasses are valid...</span>
|
|
|
1010 997 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1011 998 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedFunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1012 999 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span>
|
|
|
1013 1000 <span class="s">}</span>
|
|
|
1014 1001 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
|
|
|
1015 1002 <span class="s">}</span>
|
|
|
1016 1003
|
|
|
1017 1004 <span class="c"># Set functional classes to use...</span>
|
|
|
1018 1005 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1019 1006 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
|
|
|
1020 1007
|
|
|
1021 1008 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1022 1009 <span class="s">}</span>
|
|
|
1023 1010
|
|
|
1024 1011 <span class="c"># Return a string containg data for MolecularComplexityDescriptors object...</span>
|
|
|
1025 1012 <span class="c">#</span>
|
|
|
1026 <a name="StringifyMolecularComplexityDescriptors-"></a>1013 <span class="k">sub </span><span class="m">StringifyMolecularComplexityDescriptors</span> <span class="s">{</span>
|
|
|
1027 1014 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1028 1015 <span class="k">my</span><span class="s">(</span><span class="i">$ComplexityDescriptorsString</span><span class="cm">,</span> <span class="i">$Nothing</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1029 1016
|
|
|
1030 1017 <span class="i">$ComplexityDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; MolecularComplexityType: $This->{MolecularComplexityType}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1031 1018
|
|
|
1032 1019 <span class="c"># Setup fingerprints specific information...</span>
|
|
|
1033 1020 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1034 1021 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MACCSKeysSize = $This->{MACCSKeysSize}"</span><span class="sc">;</span>
|
|
|
1035 1022 <span class="s">}</span>
|
|
|
1036 1023 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
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1037 1024 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; NeighborhoodRadius = $This->{NeighborhoodRadius}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span>
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1038 1025 <span class="s">}</span>
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1039 1026 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
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1040 1027 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinPathLength = $This->{MinPathLength}; MaxPathLength = $This->{MaxPathLength}; UseBondSymbols: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span>
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1041 1028 <span class="s">}</span>
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|
1042 1029 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
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1043 1030 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span>
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1044 1031 <span class="s">}</span>
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|
1045 1032 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
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1046 1033 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$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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1047 1034 <span class="s">}</span>
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|
|
1048 1035 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTorsionsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
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|
1049 1036 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span>
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|
|
1050 1037 <span class="s">}</span>
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|
1051 1038 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
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|
|
1052 1039 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span>
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|
1053 1040 <span class="s">}</span>
|
|
|
1054 1041 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
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|
|
1055 1042 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}; 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>
|
|
|
1056 1043 <span class="s">}</span>
|
|
|
1057 1044
|
|
|
1058 1045 <span class="c"># Setup atom identifier information...</span>
|
|
|
1059 1046 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
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|
1060 1047 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomIdentifierType = $This->{AtomIdentifierType}"</span><span class="sc">;</span>
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|
1061 1048
|
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|
1062 1049 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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|
|
1063 1050 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1064 1051
|
|
|
1065 1052 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1066 1053 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
|
1067 1054
|
|
|
1068 1055 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1069 1056 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span>
|
|
|
1070 1057 <span class="s">}</span>
|
|
|
1071 1058
|
|
|
1072 1059 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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|
1073 1060 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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|
1074 1061 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableAtomicInvariants: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
|
|
|
1075 1062 <span class="s">}</span>
|
|
|
1076 1063 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1077 1064 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1078 1065
|
|
|
1079 1066 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1080 1067 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
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1081 1068
|
|
|
1082 1069 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1083 1070 <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">"$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}"</span><span class="sc">;</span>
|
|
|
1084 1071 <span class="s">}</span>
|
|
|
1085 1072
|
|
|
1086 1073 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
|
|
|
1087 1074 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
|
|
|
1088 1075 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableFunctionalClasses: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
|
|
|
1089 1076 <span class="s">}</span>
|
|
|
1090 1077 <span class="s">}</span>
|
|
|
1091 1078 <span class="k">return</span> <span class="i">$ComplexityDescriptorsString</span><span class="sc">;</span>
|
|
|
1092 1079 <span class="s">}</span>
|
|
|
1093 1080
|
|
|
1094 1081 <span class="c"># Is it a MolecularComplexityDescriptors object?</span>
|
|
|
1095 <a name="_IsMolecularComplexityDescriptors-"></a>1082 <span class="k">sub </span><span class="m">_IsMolecularComplexityDescriptors</span> <span class="s">{</span>
|
|
|
1096 1083 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1097 1084
|
|
|
1098 1085 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1099 1086 <span class="s">}</span>
|
|
|
1100 1087
|
|
|
1101 <a name="EOF-"></a></pre>
|
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1102 <p> </p>
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1103 <br />
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1104 <center>
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1105 <img src="../../../images/h2o2.png">
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1106 </center>
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1107 </body>
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1108 </html>
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