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1 package Fingerprints::ExtendedConnectivityFingerprints;
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2 #
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3 # $RCSfile: ExtendedConnectivityFingerprints.pm,v $
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4 # $Date: 2015/02/28 20:48:54 $
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5 # $Revision: 1.39 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use Carp;
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31 use Exporter;
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32 use TextUtil ();
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33 use MathUtil ();
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34 use Fingerprints::Fingerprints;
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35 use Molecule;
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36 use AtomTypes::AtomicInvariantsAtomTypes;
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37 use AtomTypes::FunctionalClassAtomTypes;
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38 use AtomTypes::DREIDINGAtomTypes;
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39 use AtomTypes::EStateAtomTypes;
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40 use AtomTypes::MMFF94AtomTypes;
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41 use AtomTypes::SLogPAtomTypes;
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42 use AtomTypes::SYBYLAtomTypes;
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43 use AtomTypes::TPSAAtomTypes;
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44 use AtomTypes::UFFAtomTypes;
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45
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46 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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47
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48 @ISA = qw(Fingerprints::Fingerprints Exporter);
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49 @EXPORT = qw();
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50 @EXPORT_OK = qw();
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51
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52 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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53
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54 # Setup class variables...
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55 my($ClassName);
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56 _InitializeClass();
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57
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58 # Overload Perl functions...
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59 use overload '""' => 'StringifyExtendedConnectivityFingerprints';
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60
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61 # Class constructor...
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62 sub new {
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63 my($Class, %NamesAndValues) = @_;
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64
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65 # Initialize object...
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66 my $This = $Class->SUPER::new();
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67 bless $This, ref($Class) || $Class;
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68 $This->_InitializeExtendedConnectivityFingerprints();
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69
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70 $This->_InitializeExtendedConnectivityFingerprintsProperties(%NamesAndValues);
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71
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72 return $This;
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73 }
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74
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75 # Initialize object data...
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76 #
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77 sub _InitializeExtendedConnectivityFingerprints {
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78 my($This) = @_;
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79
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80 # Type of fingerprint to generate:
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81 #
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82 # ExtendedConnectivity - Set of integer identifiers corresponding to structurally unique features
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83 # ExtendedConnectivityCount - Set of integer identifiers corresponding to structurally unique features and their count
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84 # ExtendedConnectivityBits - A bit vector indicating presence/absence of structurally unique features
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85 #
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86 $This->{Type} = 'ExtendedConnectivity';
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87
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88 # Atomic neighborhoods radius for extended connectivity...
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89 $This->{NeighborhoodRadius} = 2;
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90
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91 # Size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...
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92 $This->{Size} = 1024;
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93
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94 # Min and max size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...
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95 $This->{MinSize} = 32;
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96 $This->{MaxSize} = 2**32;
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97
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98 # Type of atom attributes to use for initial identifier assignment to non-hydrogen atoms
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99 # during the calculation of extended connectivity fingerprints [ Ref 48, Ref 52 ]...
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100 #
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101 # Currently supported values are: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes,
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102 # DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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103 # TPSAAtomTypes, UFFAtomTypes
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104 #
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105 $This->{AtomIdentifierType} = '';
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106
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107 # Random number generator to use during generation of fingerprints bit-vector
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108 # string: Perl CORE::rand or MayaChemTools MathUtil::random function.
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109 #
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110 # The random number generator implemented in MayaChemTools is a variant of
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111 # linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].
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112 # It is also referred to as Lehmer random number generator or Park-Miller
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113 # random number generator.
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114 #
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115 # Unlike Perl's core random number generator function rand, the random number
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116 # generator implemented in MayaChemTools, MathUtil::random, generates consistent
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117 # random values across different platformsfor a specific random seed and leads
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118 # to generation of portable fingerprints bit-vector strings.
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119 #
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120 $This->{UsePerlCoreRandom} = 1;
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121
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122 # Atom neighorhoods up to specified neighborhood radius...
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123 %{$This->{AtomNeighborhoods}} = ();
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124
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125 # Atom identifiers at different neighborhoods up to specified neighborhood radius...
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126 %{$This->{AtomIdentifiers}} = ();
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127
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128 # Structurally unique atom identifiers at different neighborhoods up to specified neighborhood radius...
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129 %{$This->{UniqueAtomIdentifiers}} = ();
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130 %{$This->{UniqueAtomIdentifiersCount}} = ();
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131
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132 # Unique atom identifiers at different neighborhoods up to specified neighborhood radius...
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133 %{$This->{StructurallyUniqueAtomIdentifiers}} = ();
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134 %{$This->{StructurallyUniqueAtomIdentifiersCount}} = ();
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135
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136 # Structure feature information at different neighborhoods up to specified neighborhood
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137 # radius used during removal of atom indentifiers which are structually equivalent...
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138 %{$This->{StructureFeatures}} = ();
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139 }
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140
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141 # Initialize class ...
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142 sub _InitializeClass {
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143 #Class name...
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144 $ClassName = __PACKAGE__;
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145 }
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146
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147 # Initialize object properties....
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148 sub _InitializeExtendedConnectivityFingerprintsProperties {
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149 my($This, %NamesAndValues) = @_;
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150
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151 my($Name, $Value, $MethodName);
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152 while (($Name, $Value) = each %NamesAndValues) {
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153 $MethodName = "Set${Name}";
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154 $This->$MethodName($Value);
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155 }
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156
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157 # Make sure molecule object was specified...
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158 if (!exists $NamesAndValues{Molecule}) {
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159 croak "Error: ${ClassName}->New: Object can't be instantiated without specifying molecule...";
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160 }
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161
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162 # Make sure AtomIdentifierType was specified...
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163 if (!exists $NamesAndValues{AtomIdentifierType}) {
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164 croak "Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType...";
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165 }
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166
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167 # Make sure it's power of 2...
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168 if (exists $NamesAndValues{Size}) {
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169 if (!TextUtil::IsNumberPowerOfNumber($NamesAndValues{Size}, 2)) {
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170 croak "Error: ${ClassName}->New: Specified size value, $NamesAndValues{Size}, must be power of 2...";
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171 }
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172 }
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173
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174 if ($This->{Type} =~ /^ExtendedConnectivity$/i) {
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175 $This->_InitializeExtendedConnectivityFingerprintsVector();
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176 }
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177 elsif ($This->{Type} =~ /^ExtendedConnectivityCount$/i) {
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178 $This->_InitializeExtendedConnectivityCountFingerprintsVector();
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179 }
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180 elsif ($This->{Type} =~ /^ExtendedConnectivityBits$/i) {
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181 $This->_InitializeExtendedConnectivityBitsFingerprintsBitVector();
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182 }
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183 else {
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184 croak "Error: ${ClassName}->_InitializeExtendedConnectivityFingerprintsProperties: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits...";
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185 }
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186
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187 return $This;
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188 }
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189
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190 # Initialize extended connectivity fingerprints vector...
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191 #
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192 sub _InitializeExtendedConnectivityFingerprintsVector {
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193 my($This) = @_;
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194
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195 # Type of vector...
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196 $This->{VectorType} = 'FingerprintsVector';
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197
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198 # Type of FingerprintsVector...
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199 $This->{FingerprintsVectorType} = 'AlphaNumericalValues';
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200
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201 $This->_InitializeFingerprintsVector();
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202
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203 return $This;
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204 }
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205
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206 # Initialize extended connectivity count fingerprints vector...
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207 #
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208 sub _InitializeExtendedConnectivityCountFingerprintsVector {
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209 my($This) = @_;
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210
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211 # Type of vector...
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212 $This->{VectorType} = 'FingerprintsVector';
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213
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214 # Type of FingerprintsVector...
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215 $This->{FingerprintsVectorType} = 'NumericalValues';
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216
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217 $This->_InitializeFingerprintsVector();
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218
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219 return $This;
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220 }
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221
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222 # Initialize extended connectivity bit fingerprints vector...
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223 #
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224 sub _InitializeExtendedConnectivityBitsFingerprintsBitVector {
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225 my($This) = @_;
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226
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227 # Type of vector...
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228 $This->{VectorType} = 'FingerprintsBitVector';
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229
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230 $This->_InitializeFingerprintsBitVector();
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231
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232 return $This;
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233 }
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234
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235 # Set type...
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236 #
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237 sub SetType {
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238 my($This, $Type) = @_;
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239
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240 if ($Type =~ /^ExtendedConnectivity$/i) {
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241 $This->{Type} = 'ExtendedConnectivity';;
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242 }
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243 elsif ($Type =~ /^ExtendedConnectivityCount$/i) {
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244 $This->{Type} = 'ExtendedConnectivityCount';;
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245 }
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246 elsif ($Type =~ /^ExtendedConnectivityBits$/i) {
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247 $This->{Type} = 'ExtendedConnectivityBits';;
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248 }
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249 else {
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250 croak "Error: ${ClassName}->SetType: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits...";
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251 }
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252 return $This;
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253 }
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254
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255 # Disable vector type change...
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256 #
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257 sub SetVectorType {
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258 my($This, $Type) = @_;
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259
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260 croak "Error: ${ClassName}->SetVectorType: Can't change vector type...";
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261
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262 return $This;
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263 }
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264
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265 # Disable vector type change...
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266 #
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267 sub SetFingerprintsVectorType {
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268 my($This, $Type) = @_;
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269
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270 croak "Error: ${ClassName}->SetFingerprintsVectorType: Can't change fingerprints vector type...";
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271
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272 return $This;
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273 }
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274
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275 # Set intial atom identifier type..
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276 #
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277 sub SetAtomIdentifierType {
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278 my($This, $IdentifierType) = @_;
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279
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280 if ($IdentifierType !~ /^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
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281 croak "Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes.";
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282 }
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283
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284 if ($This->{AtomIdentifierType}) {
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285 croak "Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set...";
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286 }
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287
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288 $This->{AtomIdentifierType} = $IdentifierType;
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289
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290 # Initialize identifier type information...
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291 $This->_InitializeAtomIdentifierTypeInformation();
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292
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293 return $This;
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294 }
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295
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296 # Set atom neighborhood radius...
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297 #
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298 sub SetNeighborhoodRadius {
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299 my($This, $Value) = @_;
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300
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301 if (!TextUtil::IsInteger($Value)) {
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302 croak "Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer...";
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303 }
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304
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305 if ($Value < 0 ) {
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306 croak "Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0...";
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307 }
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308 $This->{NeighborhoodRadius} = $Value;
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309
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310 return $This;
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311 }
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312
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313 # Generate fingerprints description...
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314 #
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315 sub GetDescription {
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316 my($This) = @_;
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317
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318 # Is description explicity set?
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319 if (exists $This->{Description}) {
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320 return $This->{Description};
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321 }
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322
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323 # Generate fingerprints description...
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324
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325 return "$This->{Type}:$This->{AtomIdentifierType}:Radius$This->{NeighborhoodRadius}";
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326 }
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327
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328 # Generate fingerprints...
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329 #
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330 # Methodology:
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331 # . Assign initial atom identfiers to all non-hydrogen atoms in the molecule
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332 #
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333 # . Remove duplicates from the initial identifiers and add them to list corresponding
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334 # to molecule fingerprint
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335 #
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336 # . For NeighborhoodRadius value of 0, just return the molecule fingerprint list
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337 #
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338 # . For each NeighborhoodRadius level
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339 # . For each non-hydrogen CentralAtom at this NeighborhoodRadius level
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340 # . For each non-hydrogen SuccessorNeighborAtom
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341 # . Collect (BondOrder AtomIdentifier) pair of values corresponding to
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342 # (CentralAtom SuccessorNeighborAtom) and add it to a list
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343 #
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344 # . Sort list containing (BondOrder AtomIdentifier) pairs first by BondOrder followed
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345 # by AtomIdendifiers to make these values graph invariant
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346 # . Generate a hash code for the values in the list
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347 # . Assign hash code as new atom identifier at the current NeighborhoodRadius level
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348 # . Save all atoms and bonds corresponding to the substructure involved in
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349 # generating the hash code to be used for identifying structural duplicate hash code
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350 #
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351 # . Add the new identifier to the molecule fingerprint list making sure it's not a duplicate
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352 # identifier
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353 #
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354 # Hash code atom identifier deduplication:
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355 # . Track/remove the identifier generated at higher neighborhood radius level
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356 #
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357 # Structural atom identifier deduplication:
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358 # . For equivalent atoms and bonds corresponding to substructure at a NeighborhoodRadius level,
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359 # track/remove the atom identifier with largest value
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360 #
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361 #
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362 sub GenerateFingerprints {
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363 my($This) = @_;
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364
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365 # Cache appropriate molecule data...
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366 $This->_SetupMoleculeDataCache();
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367
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368 # Assign intial atom identifers...
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369 if (!$This->_AssignInitialAtomIdentifiers()) {
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370 carp "Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms...";
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371 return $This;
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372 }
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373
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374 # Identify atom neighborhoods up to specified radius...
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375 $This->_GetAtomNeighborhoods();
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376
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377 # Assign atom identifiers to central atoms considering atom neighborhoods at each
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378 # radius level...
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379 $This->_AssignAtomIdentifiersToAtomNeighborhoods();
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380
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381 # Remove duplicates identifiers...
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382 $This->_RemoveDuplicateAtomIdentifiers();
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383
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384 # Set final fingerprints...
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385 $This->_SetFinalFingerprints();
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386
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387 # Clear cached molecule data...
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388 $This->_ClearMoleculeDataCache();
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389
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390 return $This;
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391 }
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392
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393 # Assign appropriate initial atom identifiers...
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394 #
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395 # Generation of initial identifier for a specific atom involves:
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396 # . Values of the specified atom attributes are appended in a specific order to
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397 # generate an initial atom identifier string
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398 # . A 32 bit unsigned integer hash key, using TextUtil::HashCode function, is
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399 # generated for the atom indentifier and assigned to the atom as initial
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400 # atom identifier.
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401 #
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402 sub _AssignInitialAtomIdentifiers {
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403 my($This) = @_;
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404 my($Atom, $AtomID, $Radius, $SpecifiedAtomTypes, $IgnoreHydrogens, $AtomType, $InitialAtomTypeString, $InitialAtomIdentifier);
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405
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406 # Initialize atom identifiers...
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407 $This->_InitializeAtomIdentifiers();
|
|
|
408
|
|
|
409 # Set up atom types...
|
|
|
410 $IgnoreHydrogens = 1;
|
|
|
411 $SpecifiedAtomTypes = undef;
|
|
|
412
|
|
|
413 IDENTIFIERTYPE: {
|
|
|
414 if ($This->{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
415 $SpecifiedAtomTypes = new AtomTypes::AtomicInvariantsAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens, 'AtomicInvariantsToUse' => $This->{AtomicInvariantsToUse});
|
|
|
416 last IDENTIFIERTYPE;
|
|
|
417 }
|
|
|
418
|
|
|
419 if ($This->{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
420 $SpecifiedAtomTypes = new AtomTypes::FunctionalClassAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens, 'FunctionalClassesToUse' => $This->{FunctionalClassesToUse});
|
|
|
421 last IDENTIFIERTYPE;
|
|
|
422 }
|
|
|
423
|
|
|
424 if ($This->{AtomIdentifierType} =~ /^DREIDINGAtomTypes$/i) {
|
|
|
425 $SpecifiedAtomTypes = new AtomTypes::DREIDINGAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
|
|
|
426 last IDENTIFIERTYPE;
|
|
|
427 }
|
|
|
428
|
|
|
429 if ($This->{AtomIdentifierType} =~ /^EStateAtomTypes$/i) {
|
|
|
430 $SpecifiedAtomTypes = new AtomTypes::EStateAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
|
|
|
431 last IDENTIFIERTYPE;
|
|
|
432 }
|
|
|
433
|
|
|
434 if ($This->{AtomIdentifierType} =~ /^MMFF94AtomTypes$/i) {
|
|
|
435 $SpecifiedAtomTypes = new AtomTypes::MMFF94AtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
|
|
|
436 last IDENTIFIERTYPE;
|
|
|
437 }
|
|
|
438
|
|
|
439 if ($This->{AtomIdentifierType} =~ /^SLogPAtomTypes$/i) {
|
|
|
440 $SpecifiedAtomTypes = new AtomTypes::SLogPAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
|
|
|
441 last IDENTIFIERTYPE;
|
|
|
442 }
|
|
|
443
|
|
|
444 if ($This->{AtomIdentifierType} =~ /^SYBYLAtomTypes$/i) {
|
|
|
445 $SpecifiedAtomTypes = new AtomTypes::SYBYLAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
|
|
|
446 last IDENTIFIERTYPE;
|
|
|
447 }
|
|
|
448
|
|
|
449 if ($This->{AtomIdentifierType} =~ /^TPSAAtomTypes$/i) {
|
|
|
450 $SpecifiedAtomTypes = new AtomTypes::TPSAAtomTypes('Molecule' => $This->{Molecule}, 'IgnorePhosphorus' => 0, 'IgnoreSulfur' => 0);
|
|
|
451 last IDENTIFIERTYPE;
|
|
|
452 }
|
|
|
453
|
|
|
454 if ($This->{AtomIdentifierType} =~ /^UFFAtomTypes$/i) {
|
|
|
455 $SpecifiedAtomTypes = new AtomTypes::UFFAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
|
|
|
456 last IDENTIFIERTYPE;
|
|
|
457 }
|
|
|
458
|
|
|
459 croak "Error: ${ClassName}->_AssignInitialAtomIdentifiers: Couldn't assign intial atom identifiers: InitialAtomIdentifierType $This->{AtomIdentifierType} is not supported...";
|
|
|
460 }
|
|
|
461
|
|
|
462 # Assign atom types...
|
|
|
463 $SpecifiedAtomTypes->AssignAtomTypes();
|
|
|
464
|
|
|
465 # Make sure atom types assignment is successful...
|
|
|
466 if (!$SpecifiedAtomTypes->IsAtomTypesAssignmentSuccessful()) {
|
|
|
467 return undef;
|
|
|
468 }
|
|
|
469
|
|
|
470 # Assign atom identifiers at radius 0...
|
|
|
471 $Radius = 0;
|
|
|
472 for $Atom (@{$This->{Atoms}}) {
|
|
|
473 $AtomID = $Atom->GetID();
|
|
|
474
|
|
|
475 $AtomType = $SpecifiedAtomTypes->GetAtomType($Atom);
|
|
|
476 $InitialAtomTypeString = $AtomType ? $AtomType : 'None';
|
|
|
477
|
|
|
478 $InitialAtomIdentifier = TextUtil::HashCode($InitialAtomTypeString);
|
|
|
479 $This->{AtomIdentifiers}{$Radius}{$AtomID} = $InitialAtomIdentifier;
|
|
|
480 }
|
|
|
481
|
|
|
482 return $This;
|
|
|
483 }
|
|
|
484
|
|
|
485 # Initialize atom identifiers...
|
|
|
486 #
|
|
|
487 sub _InitializeAtomIdentifiers {
|
|
|
488 my($This) = @_;
|
|
|
489 my($Radius, $CurrentRadius);
|
|
|
490
|
|
|
491 $Radius = $This->{NeighborhoodRadius};
|
|
|
492
|
|
|
493 %{$This->{AtomIdentifiers}} = ();
|
|
|
494 for $CurrentRadius (0 .. $Radius) {
|
|
|
495 # Atom idenfiers key and value correspond to AtomID and AtomIdentifier
|
|
|
496 %{$This->{AtomIdentifiers}{$CurrentRadius}} = ();
|
|
|
497
|
|
|
498 # Unique and strcuturally unique idenfiers key and value correspond to AtomIdentifier and AtomID
|
|
|
499 %{$This->{UniqueAtomIdentifiers}{$CurrentRadius}} = ();
|
|
|
500 %{$This->{UniqueAtomIdentifiersCount}{$CurrentRadius}} = ();
|
|
|
501
|
|
|
502 %{$This->{StructurallyUniqueAtomIdentifiers}{$CurrentRadius}} = ();
|
|
|
503 %{$This->{StructurallyUniqueAtomIdentifiersCount}{$CurrentRadius}} = ();
|
|
|
504 }
|
|
|
505
|
|
|
506 }
|
|
|
507
|
|
|
508 # Collect atom neighborhoods upto specified neighborhood radius...
|
|
|
509 #
|
|
|
510 sub _GetAtomNeighborhoods {
|
|
|
511 my($This) = @_;
|
|
|
512 my($Atom, $AtomID, $Radius, $CurrentRadius, $Molecule);
|
|
|
513
|
|
|
514 %{$This->{AtomNeighborhoods}} = ();
|
|
|
515
|
|
|
516 $Radius = $This->{NeighborhoodRadius};
|
|
|
517 if ($Radius < 1) {
|
|
|
518 # At radius level 0, it's just the atoms...
|
|
|
519 return;
|
|
|
520 }
|
|
|
521
|
|
|
522 # Initialize neighborhood at different radii...
|
|
|
523 for $CurrentRadius (0 .. $Radius) {
|
|
|
524 %{$This->{AtomNeighborhoods}{$CurrentRadius}} = ();
|
|
|
525 }
|
|
|
526
|
|
|
527 $Molecule = $This->GetMolecule();
|
|
|
528
|
|
|
529 # Collect available atom neighborhoods at different at different neighborhood level for each atom...
|
|
|
530 my($AtomsNeighborhoodWithSuccessorAtomsRef);
|
|
|
531
|
|
|
532 for $Atom (@{$This->{Atoms}}) {
|
|
|
533 $AtomID = $Atom->GetID();
|
|
|
534 $CurrentRadius = 0;
|
|
|
535 for $AtomsNeighborhoodWithSuccessorAtomsRef ($Molecule->GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto($Atom, $Radius)) {
|
|
|
536 $This->{AtomNeighborhoods}{$CurrentRadius}{$AtomID} = $AtomsNeighborhoodWithSuccessorAtomsRef;
|
|
|
537 $CurrentRadius++;
|
|
|
538 }
|
|
|
539 }
|
|
|
540 return $This;
|
|
|
541 }
|
|
|
542
|
|
|
543 # Assign atom identifiers to central atom at each neighborhood radius level...
|
|
|
544 #
|
|
|
545 sub _AssignAtomIdentifiersToAtomNeighborhoods {
|
|
|
546 my($This) = @_;
|
|
|
547 my($Radius, $NextRadius, $Atom, $AtomID, $NeighborhoodAtom, $SuccessorAtom, $SuccessorAtomID, $NeighborhoodAtomSuccessorAtomsRef, $NeighborhoodAtomsWithSuccessorAtomsRef, $Bond, $BondOrder, $SuccessorAtomCount);
|
|
|
548
|
|
|
549 if ($This->{NeighborhoodRadius} < 1) {
|
|
|
550 return;
|
|
|
551 }
|
|
|
552
|
|
|
553 # Go over the atom neighborhoods at each radius upto specified radius and assign atom
|
|
|
554 # indentifiers using their connected successor atoms and their identifiers.
|
|
|
555 #
|
|
|
556 # For a neighborhood atom at a specified radius, the successor connected atoms correpond
|
|
|
557 # to next radius level and the last set of neighorhood atoms don't have any successor connected
|
|
|
558 # atoms. Additionally, radius level 0 just correspond to initial atom identifiers.
|
|
|
559 #
|
|
|
560 # So in order to process atom neighborhood upto specified radius level, the last atom neighborhood
|
|
|
561 # doesn't need to be processed: it gets processed at previous radius level as successor connected
|
|
|
562 # atoms.
|
|
|
563 #
|
|
|
564 RADIUS: for $Radius (0 .. ($This->{NeighborhoodRadius} - 1)) {
|
|
|
565 ATOM: for $Atom (@{$This->{Atoms}}) {
|
|
|
566 $AtomID = $Atom->GetID();
|
|
|
567
|
|
|
568 # Are there any available atom neighborhoods at this radius?
|
|
|
569 if (!exists $This->{AtomNeighborhoods}{$Radius}{$AtomID}) {
|
|
|
570 next ATOM;
|
|
|
571 }
|
|
|
572 $NextRadius = $Radius + 1;
|
|
|
573
|
|
|
574 # Go over neighborhood atoms and their successor connected atoms at this radius and collect
|
|
|
575 # (BondOrder AtomIdentifier) values for bonded atom pairs. Additionally, keep track of atom and bonds
|
|
|
576 # for the neighorhoods to remove identifieres generated from structurally duplicate features.
|
|
|
577 #
|
|
|
578 my(%BondOrdersAndAtomIdentifiers);
|
|
|
579
|
|
|
580 %BondOrdersAndAtomIdentifiers = ();
|
|
|
581 $SuccessorAtomCount = 0;
|
|
|
582
|
|
|
583 NEIGHBORHOODS: for $NeighborhoodAtomsWithSuccessorAtomsRef (@{$This->{AtomNeighborhoods}{$Radius}{$AtomID}}) {
|
|
|
584 ($NeighborhoodAtom, $NeighborhoodAtomSuccessorAtomsRef) = @{$NeighborhoodAtomsWithSuccessorAtomsRef};
|
|
|
585
|
|
|
586 # Any connected successors for the NeighborhoodAtom?
|
|
|
587 if (!@{$NeighborhoodAtomSuccessorAtomsRef}) {
|
|
|
588 next NEIGHBORHOODS;
|
|
|
589 }
|
|
|
590 SUCCESSORATOM: for $SuccessorAtom (@{$NeighborhoodAtomSuccessorAtomsRef}) {
|
|
|
591 if ($SuccessorAtom->IsHydrogen()) {
|
|
|
592 # Skip successor hydrogen atom...
|
|
|
593 next SUCCESSORATOM;
|
|
|
594 }
|
|
|
595 $SuccessorAtomID = $SuccessorAtom->GetID();
|
|
|
596 $SuccessorAtomCount++;
|
|
|
597
|
|
|
598 $Bond = $NeighborhoodAtom->GetBondToAtom($SuccessorAtom);
|
|
|
599 $BondOrder = $Bond->IsAromatic() ? "1.5" : $Bond->GetBondOrder();
|
|
|
600
|
|
|
601 if (!exists $BondOrdersAndAtomIdentifiers{$BondOrder}) {
|
|
|
602 @{$BondOrdersAndAtomIdentifiers{$BondOrder}} = ();
|
|
|
603 }
|
|
|
604 push @{$BondOrdersAndAtomIdentifiers{$BondOrder}}, $This->{AtomIdentifiers}{$Radius}{$SuccessorAtomID};
|
|
|
605 }
|
|
|
606 }
|
|
|
607 if (!$SuccessorAtomCount) {
|
|
|
608 next ATOM;
|
|
|
609 }
|
|
|
610 # Assign a new atom identifier at the NextRadius level...
|
|
|
611 $This->_AssignAtomIdentifierToAtomNeighborhood($AtomID, $Radius, \%BondOrdersAndAtomIdentifiers);
|
|
|
612 }
|
|
|
613 }
|
|
|
614 return $This;
|
|
|
615 }
|
|
|
616
|
|
|
617 # Generate and assign atom indentifier for AtomID using atom neighborhood at next radius level...
|
|
|
618 #
|
|
|
619 sub _AssignAtomIdentifierToAtomNeighborhood {
|
|
|
620 my($This, $AtomID, $Radius, $BondOrdersAndAtomIdentifiersRef) = @_;
|
|
|
621 my($NextRadius, $AtomIdentifier, $SuccessorAtomIdentifier, $BondOrder, $AtomIdentifierString, @AtomIndentifiersInfo);
|
|
|
622
|
|
|
623 $NextRadius = $Radius + 1;
|
|
|
624
|
|
|
625 @AtomIndentifiersInfo = ();
|
|
|
626
|
|
|
627 $AtomIdentifier = $This->{AtomIdentifiers}{$Radius}{$AtomID};
|
|
|
628 push @AtomIndentifiersInfo, ($NextRadius, $AtomIdentifier);
|
|
|
629
|
|
|
630 # Sort out successor atom bond order and identifier pairs by bond order followed by atom identifiers
|
|
|
631 # in order to make the final atom identifier graph invariant...
|
|
|
632 #
|
|
|
633 for $BondOrder (sort { $a <=> $b } keys %{$BondOrdersAndAtomIdentifiersRef}) {
|
|
|
634 for $SuccessorAtomIdentifier (sort { $a <=> $b } @{$BondOrdersAndAtomIdentifiersRef->{$BondOrder}}) {
|
|
|
635 push @AtomIndentifiersInfo, ($BondOrder, $SuccessorAtomIdentifier);
|
|
|
636 }
|
|
|
637 }
|
|
|
638 $AtomIdentifierString = join("", @AtomIndentifiersInfo);
|
|
|
639 $AtomIdentifier = TextUtil::HashCode($AtomIdentifierString);
|
|
|
640
|
|
|
641 # Assign atom identifier to the atom at next radius level...
|
|
|
642 $This->{AtomIdentifiers}{$NextRadius}{$AtomID} = $AtomIdentifier;
|
|
|
643
|
|
|
644 return $This;
|
|
|
645 }
|
|
|
646
|
|
|
647 # Remove duplicates atom identifiers...
|
|
|
648 #
|
|
|
649 sub _RemoveDuplicateAtomIdentifiers {
|
|
|
650 my($This) = @_;
|
|
|
651
|
|
|
652 $This->_RemoveDuplicateIdentifiersByValue();
|
|
|
653 $This->_RemoveStructurallyDuplicateIdenfiers();
|
|
|
654
|
|
|
655 return $This;
|
|
|
656 }
|
|
|
657
|
|
|
658 # Remove duplicate identifiers at each radius level by just using their value...
|
|
|
659 #
|
|
|
660 sub _RemoveDuplicateIdentifiersByValue {
|
|
|
661 my($This) = @_;
|
|
|
662 my($Radius, $Atom, $AtomID, $AtomIdentifier);
|
|
|
663
|
|
|
664 for $Radius (0 .. $This->{NeighborhoodRadius}) {
|
|
|
665 ATOM: for $Atom (@{$This->{Atoms}}) {
|
|
|
666 $AtomID = $Atom->GetID();
|
|
|
667 if (!exists $This->{AtomIdentifiers}{$Radius}{$AtomID}) {
|
|
|
668 next ATOM;
|
|
|
669 }
|
|
|
670 $AtomIdentifier = $This->{AtomIdentifiers}{$Radius}{$AtomID};
|
|
|
671 if (exists $This->{UniqueAtomIdentifiers}{$Radius}{$AtomIdentifier}) {
|
|
|
672 # It's a duplicate atom idenfier at this radius level...
|
|
|
673 $This->{UniqueAtomIdentifiersCount}{$Radius}{$AtomIdentifier} += 1;
|
|
|
674 next ATOM;
|
|
|
675 }
|
|
|
676 $This->{UniqueAtomIdentifiers}{$Radius}{$AtomIdentifier} = $AtomID;
|
|
|
677 $This->{UniqueAtomIdentifiersCount}{$Radius}{$AtomIdentifier} = 1;
|
|
|
678 }
|
|
|
679 }
|
|
|
680 return $This;
|
|
|
681 }
|
|
|
682
|
|
|
683 # Remove structurally duplicate identifiers at each radius level...
|
|
|
684 #
|
|
|
685 # Methodology:
|
|
|
686 # . For unquie atom identifiers at each radius level, assign complete structure features
|
|
|
687 # in terms all the bonds involved to generate that identifier
|
|
|
688 # . Use the complete structure features to remover atom identifiers which are
|
|
|
689 # structurally equivalent which can also be at earlier radii levels
|
|
|
690 #
|
|
|
691 #
|
|
|
692 sub _RemoveStructurallyDuplicateIdenfiers {
|
|
|
693 my($This) = @_;
|
|
|
694 my($Radius, $AtomID, $AtomIdentifier, $SimilarAtomIdentifierRadius, $SimilarAtomIdentifier);
|
|
|
695
|
|
|
696 # Setup structure features...
|
|
|
697 $This->_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers();
|
|
|
698
|
|
|
699 # Identify structurally unqiue identifiers...
|
|
|
700 for $Radius (0 .. $This->{NeighborhoodRadius}) {
|
|
|
701 ATOMIDENTIFIER: for $AtomIdentifier (sort { $a <=> $b } keys %{$This->{UniqueAtomIdentifiers}{$Radius}}) {
|
|
|
702 $AtomID = $This->{UniqueAtomIdentifiers}{$Radius}{$AtomIdentifier};
|
|
|
703
|
|
|
704 ($SimilarAtomIdentifierRadius, $SimilarAtomIdentifier) = $This->_FindStructurallySimilarAtomIdentifier($Radius, $AtomID, $AtomIdentifier);
|
|
|
705 if ($SimilarAtomIdentifier) {
|
|
|
706 # Current atom identifier is similar to an earlier structurally unique atom identifier...
|
|
|
707 $This->{StructurallyUniqueAtomIdentifiersCount}{$SimilarAtomIdentifierRadius}{$SimilarAtomIdentifier} += $This->{UniqueAtomIdentifiersCount}{$Radius}{$AtomIdentifier};
|
|
|
708 next ATOMIDENTIFIER;
|
|
|
709 }
|
|
|
710 $This->{StructurallyUniqueAtomIdentifiers}{$Radius}{$AtomIdentifier} = $AtomID;
|
|
|
711
|
|
|
712 # Set structurally unique atom identifier count to the unique atom identifiers count...
|
|
|
713 $This->{StructurallyUniqueAtomIdentifiersCount}{$Radius}{$AtomIdentifier} = $This->{UniqueAtomIdentifiersCount}{$Radius}{$AtomIdentifier};
|
|
|
714 }
|
|
|
715 }
|
|
|
716 return $This;
|
|
|
717 }
|
|
|
718
|
|
|
719 # Set final fingerpritns vector...
|
|
|
720 #
|
|
|
721 sub _SetFinalFingerprints {
|
|
|
722 my($This) = @_;
|
|
|
723
|
|
|
724 # Mark successful generation of fingerprints...
|
|
|
725 $This->{FingerprintsGenerated} = 1;
|
|
|
726
|
|
|
727 if ($This->{Type} =~ /^ExtendedConnectivity$/i) {
|
|
|
728 $This->_SetFinalExtendedConnectivityFingerprints();
|
|
|
729 }
|
|
|
730 elsif ($This->{Type} =~ /^ExtendedConnectivityCount$/i) {
|
|
|
731 $This->_SetFinalExtendedConnectivityCountFingerprints();
|
|
|
732 }
|
|
|
733 elsif ($This->{Type} =~ /^ExtendedConnectivityBits$/i) {
|
|
|
734 $This->_SetFinalExtendedConnectivityBitsFingerprints();
|
|
|
735 }
|
|
|
736
|
|
|
737 return $This;
|
|
|
738 }
|
|
|
739
|
|
|
740 # Set final extended connectivity fingerpritns vector...
|
|
|
741 #
|
|
|
742 sub _SetFinalExtendedConnectivityFingerprints {
|
|
|
743 my($This) = @_;
|
|
|
744 my($Radius, $AtomIdentifier, @AtomIdentifiers);
|
|
|
745
|
|
|
746 @AtomIdentifiers = ();
|
|
|
747
|
|
|
748 for $Radius (0 .. $This->{NeighborhoodRadius}) {
|
|
|
749 for $AtomIdentifier (sort { $a <=> $b } keys %{$This->{StructurallyUniqueAtomIdentifiers}{$Radius}}) {
|
|
|
750 push @AtomIdentifiers, $AtomIdentifier;
|
|
|
751 }
|
|
|
752 }
|
|
|
753 # Add atom identifiers to fingerprint vector...
|
|
|
754 $This->{FingerprintsVector}->AddValues(\@AtomIdentifiers);
|
|
|
755
|
|
|
756 return $This;
|
|
|
757 }
|
|
|
758
|
|
|
759 # Set final extended connectivity count fingerpritns vector...
|
|
|
760 #
|
|
|
761 sub _SetFinalExtendedConnectivityCountFingerprints {
|
|
|
762 my($This) = @_;
|
|
|
763 my($Radius, $AtomIdentifier, $AtomIdentifierCount, @AtomIdentifiers, @AtomIdentifiersCount);
|
|
|
764
|
|
|
765 @AtomIdentifiers = (); @AtomIdentifiersCount = ();
|
|
|
766
|
|
|
767 for $Radius (0 .. $This->{NeighborhoodRadius}) {
|
|
|
768 for $AtomIdentifier (sort { $a <=> $b } keys %{$This->{StructurallyUniqueAtomIdentifiers}{$Radius}}) {
|
|
|
769 $AtomIdentifierCount = $This->{StructurallyUniqueAtomIdentifiersCount}{$Radius}{$AtomIdentifier};
|
|
|
770 push @AtomIdentifiers, $AtomIdentifier;
|
|
|
771 push @AtomIdentifiersCount, $AtomIdentifierCount;
|
|
|
772 }
|
|
|
773 }
|
|
|
774 # Add atom identifiers to fingerprint vector as value IDs...
|
|
|
775 $This->{FingerprintsVector}->AddValueIDs(\@AtomIdentifiers);
|
|
|
776
|
|
|
777 # Add atom identifiers to count to fingerprint vector as values...
|
|
|
778 $This->{FingerprintsVector}->AddValues(\@AtomIdentifiersCount);
|
|
|
779
|
|
|
780 return $This;
|
|
|
781 }
|
|
|
782
|
|
|
783 # Set final extended connectivity bits fingerpritns vector...
|
|
|
784 #
|
|
|
785 sub _SetFinalExtendedConnectivityBitsFingerprints {
|
|
|
786 my($This) = @_;
|
|
|
787 my($Radius, $AtomIdentifier, $FingerprintsBitVector, $Size, $SkipBitPosCheck, $AtomIdentifierBitPos, $SetBitNum);
|
|
|
788
|
|
|
789 $FingerprintsBitVector = $This->{FingerprintsBitVector};
|
|
|
790
|
|
|
791 $Size = $This->{Size};
|
|
|
792
|
|
|
793 $SkipBitPosCheck = 1;
|
|
|
794
|
|
|
795 for $Radius (0 .. $This->{NeighborhoodRadius}) {
|
|
|
796 for $AtomIdentifier (keys %{$This->{StructurallyUniqueAtomIdentifiers}{$Radius}}) {
|
|
|
797 # Set random number seed...
|
|
|
798 if ($This->{UsePerlCoreRandom}) {
|
|
|
799 CORE::srand($AtomIdentifier);
|
|
|
800 }
|
|
|
801 else {
|
|
|
802 MathUtil::srandom($AtomIdentifier);
|
|
|
803 }
|
|
|
804
|
|
|
805 # Set bit position...
|
|
|
806 $AtomIdentifierBitPos = $This->{UsePerlCoreRandom} ? int(CORE::rand($Size)) : int(MathUtil::random($Size));
|
|
|
807 $FingerprintsBitVector->SetBit($AtomIdentifierBitPos, $SkipBitPosCheck);
|
|
|
808 }
|
|
|
809 }
|
|
|
810 return $This;
|
|
|
811 }
|
|
|
812
|
|
|
813
|
|
|
814 # Identify structurally unique identifiers by comparing structure features involved in
|
|
|
815 # generating identifiear by comparing it agains all the previous structurally unique
|
|
|
816 # identifiers...
|
|
|
817 #
|
|
|
818 sub _FindStructurallySimilarAtomIdentifier {
|
|
|
819 my($This, $SpecifiedRadius, $SpecifiedAtomID, $SpecifiedAtomIdentifier) = @_;
|
|
|
820 my($Radius, $AtomID, $AtomIdentifier, $FeatureAtomCount, $FeatureAtomIDsRef, $SpecifiedFeatureAtomID, $SpecifiedFeatureAtomCount, $SpecifiedFeatureAtomIDsRef);
|
|
|
821
|
|
|
822 if ($SpecifiedRadius == 0) {
|
|
|
823 # After duplicate removal by value, all identifier at radius level 0 would be structurally unique...
|
|
|
824 return (undef, undef);
|
|
|
825 }
|
|
|
826
|
|
|
827 $SpecifiedFeatureAtomCount = $This->{StructureFeatures}{AtomCount}{$SpecifiedRadius}{$SpecifiedAtomID};
|
|
|
828 $SpecifiedFeatureAtomIDsRef = $This->{StructureFeatures}{AtomIDs}{$SpecifiedRadius}{$SpecifiedAtomID};
|
|
|
829
|
|
|
830 # No need to compare features at radius 0...
|
|
|
831 for $Radius (1 .. $SpecifiedRadius) {
|
|
|
832 ATOMIDENTIFIER: for $AtomIdentifier (keys %{$This->{StructurallyUniqueAtomIdentifiers}{$Radius}}) {
|
|
|
833 $AtomID = $This->{StructurallyUniqueAtomIdentifiers}{$Radius}{$AtomIdentifier};
|
|
|
834
|
|
|
835 $FeatureAtomCount = $This->{StructureFeatures}{AtomCount}{$Radius}{$AtomID};
|
|
|
836 $FeatureAtomIDsRef = $This->{StructureFeatures}{AtomIDs}{$Radius}{$AtomID};
|
|
|
837
|
|
|
838 if ($SpecifiedFeatureAtomCount != $FeatureAtomCount) {
|
|
|
839 # Couldn't be structurally equivalent...
|
|
|
840 next ATOMIDENTIFIER;
|
|
|
841 }
|
|
|
842 for $SpecifiedFeatureAtomID (keys % {$SpecifiedFeatureAtomIDsRef}) {
|
|
|
843 if (! exists $FeatureAtomIDsRef->{$SpecifiedFeatureAtomID}) {
|
|
|
844 # For structural equivalency, all atom in specified feature must also be present in a previously
|
|
|
845 # identified structurally unique structure feature...
|
|
|
846 next ATOMIDENTIFIER;
|
|
|
847 }
|
|
|
848 }
|
|
|
849 # Found structurally equivalent feature...
|
|
|
850 return ($Radius, $AtomIdentifier);
|
|
|
851 }
|
|
|
852 }
|
|
|
853 return (undef, undef);
|
|
|
854 }
|
|
|
855
|
|
|
856 # Setup structure features for atom IDs involved in unique atom identifiers at all
|
|
|
857 # radii level...
|
|
|
858 #
|
|
|
859 sub _SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers {
|
|
|
860 my($This) = @_;
|
|
|
861 my($Radius, $PreviousRadius, $Atom, $AtomID, $AtomIdentifier, $NeighborhoodAtomID, $NeighborhoodAtomsWithSuccessorAtomsRef, $NeighborhoodAtom, $NeighborhoodAtomSuccessorAtomsRef, %AtomIDs);
|
|
|
862
|
|
|
863 $This->_InitializeStructureFeatures();
|
|
|
864
|
|
|
865 # Collect atom IDs involved in unique atom identifiers...
|
|
|
866 %AtomIDs = ();
|
|
|
867 for $Radius (0 .. $This->{NeighborhoodRadius}) {
|
|
|
868 for $AtomIdentifier (keys %{$This->{UniqueAtomIdentifiers}{$Radius}}) {
|
|
|
869 $AtomID = $This->{UniqueAtomIdentifiers}{$Radius}{$AtomIdentifier};
|
|
|
870 $AtomIDs{$AtomID} = $AtomID;
|
|
|
871 }
|
|
|
872 }
|
|
|
873
|
|
|
874 # Setup structure features...
|
|
|
875 for $Radius (0 .. $This->{NeighborhoodRadius}) {
|
|
|
876 for $AtomID (keys %AtomIDs) {
|
|
|
877 my($StructureFeatureAtomCount, %StructureFeatureAtomIDs);
|
|
|
878
|
|
|
879 $StructureFeatureAtomCount = 0;
|
|
|
880 %StructureFeatureAtomIDs = ();
|
|
|
881
|
|
|
882 # Get partial structure features for the atom at previous radius level...
|
|
|
883 $PreviousRadius = $Radius - 1;
|
|
|
884 if ($PreviousRadius >= 0) {
|
|
|
885 $StructureFeatureAtomCount += $This->{StructureFeatures}{AtomCount}{$PreviousRadius}{$AtomID};
|
|
|
886 %StructureFeatureAtomIDs = %{$This->{StructureFeatures}{AtomIDs}{$PreviousRadius}{$AtomID}};
|
|
|
887 }
|
|
|
888
|
|
|
889 # Get all neighborhood atom at this radius level...
|
|
|
890 if (exists($This->{AtomNeighborhoods}{$Radius}) && exists($This->{AtomNeighborhoods}{$Radius}{$AtomID})) {
|
|
|
891 NEIGHBORHOODS: for $NeighborhoodAtomsWithSuccessorAtomsRef (@{$This->{AtomNeighborhoods}{$Radius}{$AtomID}}) {
|
|
|
892 ($NeighborhoodAtom, $NeighborhoodAtomSuccessorAtomsRef) = @{$NeighborhoodAtomsWithSuccessorAtomsRef};
|
|
|
893 if ($NeighborhoodAtom->IsHydrogen()) {
|
|
|
894 next NEIGHBORHOODS;
|
|
|
895 }
|
|
|
896 $NeighborhoodAtomID = $NeighborhoodAtom->GetID();
|
|
|
897 $StructureFeatureAtomCount++;
|
|
|
898 $StructureFeatureAtomIDs{$NeighborhoodAtomID} = $NeighborhoodAtomID;
|
|
|
899 }
|
|
|
900 }
|
|
|
901
|
|
|
902 # Assign structure features to atom at this radius level...
|
|
|
903 $This->{StructureFeatures}{AtomCount}{$Radius}{$AtomID} = $StructureFeatureAtomCount;
|
|
|
904 $This->{StructureFeatures}{AtomIDs}{$Radius}{$AtomID} = \%StructureFeatureAtomIDs;
|
|
|
905 }
|
|
|
906 }
|
|
|
907 return $This;
|
|
|
908 }
|
|
|
909
|
|
|
910 # Intialize structure features at each radius level...
|
|
|
911 #
|
|
|
912 sub _InitializeStructureFeatures {
|
|
|
913 my($This) = @_;
|
|
|
914 my($Radius, $CurrentRadius, $Atom, $AtomID);
|
|
|
915
|
|
|
916 # Initialize all structure features...
|
|
|
917
|
|
|
918 %{$This->{StructureFeatures}} = ();
|
|
|
919 %{$This->{StructureFeatures}{AtomCount}} = ();
|
|
|
920 %{$This->{StructureFeatures}{AtomIDs}} = ();
|
|
|
921
|
|
|
922 $Radius = $This->{NeighborhoodRadius};
|
|
|
923 for $CurrentRadius (0 .. $Radius) {
|
|
|
924 # Structure features for at specific radii accessed using atom IDs...
|
|
|
925 %{$This->{StructureFeatures}{AtomCount}{$CurrentRadius}} = ();
|
|
|
926 %{$This->{StructureFeatures}{AtomIDs}{$CurrentRadius}} = ();
|
|
|
927 }
|
|
|
928 return $This;
|
|
|
929 }
|
|
|
930
|
|
|
931 # Cache appropriate molecule data...
|
|
|
932 #
|
|
|
933 sub _SetupMoleculeDataCache {
|
|
|
934 my($This) = @_;
|
|
|
935
|
|
|
936 # Get all non-hydrogen atoms...
|
|
|
937 my($NegateAtomCheckMethod);
|
|
|
938 $NegateAtomCheckMethod = 1;
|
|
|
939 @{$This->{Atoms}} = $This->GetMolecule()->GetAtoms("IsHydrogen", $NegateAtomCheckMethod);
|
|
|
940
|
|
|
941 return $This;
|
|
|
942 }
|
|
|
943
|
|
|
944 # Clear cached molecule data...
|
|
|
945 #
|
|
|
946 sub _ClearMoleculeDataCache {
|
|
|
947 my($This) = @_;
|
|
|
948
|
|
|
949 @{$This->{Atoms}} = ();
|
|
|
950
|
|
|
951 return $This;
|
|
|
952 }
|
|
|
953
|
|
|
954 # Initialize atom indentifier type information...
|
|
|
955 #
|
|
|
956 # Current supported values:
|
|
|
957 #
|
|
|
958 # AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
959 # MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
960 #
|
|
|
961 sub _InitializeAtomIdentifierTypeInformation {
|
|
|
962 my($This) = @_;
|
|
|
963
|
|
|
964 IDENTIFIERTYPE: {
|
|
|
965 if ($This->{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
966 $This->_InitializeAtomicInvariantsAtomTypesInformation();
|
|
|
967 last IDENTIFIERTYPE;
|
|
|
968 }
|
|
|
969 if ($This->{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
970 $This->_InitializeFunctionalClassAtomTypesInformation();
|
|
|
971 last IDENTIFIERTYPE;
|
|
|
972 }
|
|
|
973 if ($This->{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
974 # Nothing to do for now...
|
|
|
975 last IDENTIFIERTYPE;
|
|
|
976 }
|
|
|
977 carp "Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}...";
|
|
|
978 }
|
|
|
979 return $This;
|
|
|
980 }
|
|
|
981
|
|
|
982 # Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes
|
|
|
983 # class, to use for generating initial atom identifiers...
|
|
|
984 #
|
|
|
985 # Let:
|
|
|
986 # AS = Atom symbol corresponding to element symbol
|
|
|
987 #
|
|
|
988 # X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
989 # BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
990 # LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
991 # SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
992 # DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
993 # TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
994 # H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
995 # Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
996 # RA = Ring atom annotation indicating whether atom is a ring
|
|
|
997 # FC<+n/-n> = Formal charge assigned to atom
|
|
|
998 # MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
999 # SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)
|
|
|
1000 #
|
|
|
1001 # Then:
|
|
|
1002 #
|
|
|
1003 # Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
1004 #
|
|
|
1005 # AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
1006 #
|
|
|
1007 # Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
1008 # optional.
|
|
|
1009 #
|
|
|
1010 # Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:
|
|
|
1011 #
|
|
|
1012 # AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n>
|
|
|
1013 #
|
|
|
1014 # In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
1015 # are also allowed:
|
|
|
1016 #
|
|
|
1017 # X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
1018 # BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
1019 # LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
1020 # SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
1021 # DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
1022 # TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
1023 # H : NumOfImplicitAndExplicitHydrogens
|
|
|
1024 # Ar : Aromatic
|
|
|
1025 # RA : RingAtom
|
|
|
1026 # FC : FormalCharge
|
|
|
1027 # MN : MassNumber
|
|
|
1028 # SM : SpinMultiplicity
|
|
|
1029 #
|
|
|
1030 sub _InitializeAtomicInvariantsAtomTypesInformation {
|
|
|
1031 my($This) = @_;
|
|
|
1032
|
|
|
1033 # Default atomic invariants to use for generating initial atom identifiers are: AS, X, BO, LBO, H, FC
|
|
|
1034 #
|
|
|
1035 @{$This->{AtomicInvariantsToUse}} = ();
|
|
|
1036 @{$This->{AtomicInvariantsToUse}} = ('AS', 'X', 'BO', 'H', 'FC', 'MN');
|
|
|
1037
|
|
|
1038 return $This;
|
|
|
1039 }
|
|
|
1040
|
|
|
1041 # Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes
|
|
|
1042 # class, to use for generating initial atom identifiers...
|
|
|
1043 #
|
|
|
1044 # Let:
|
|
|
1045 # HBD: HydrogenBondDonor
|
|
|
1046 # HBA: HydrogenBondAcceptor
|
|
|
1047 # PI : PositivelyIonizable
|
|
|
1048 # NI : NegativelyIonizable
|
|
|
1049 # Ar : Aromatic
|
|
|
1050 # Hal : Halogen
|
|
|
1051 # H : Hydrophobic
|
|
|
1052 # RA : RingAtom
|
|
|
1053 # CA : ChainAtom
|
|
|
1054 #
|
|
|
1055 # Then:
|
|
|
1056 #
|
|
|
1057 # Functiononal class atom type specification for an atom corresponds to:
|
|
|
1058 #
|
|
|
1059 # Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
1060 #
|
|
|
1061 # Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal
|
|
|
1062 #
|
|
|
1063 # FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
1064 #
|
|
|
1065 # HydrogenBondDonor: NH, NH2, OH
|
|
|
1066 # HydrogenBondAcceptor: N[!H], O
|
|
|
1067 # PositivelyIonizable: +, NH2
|
|
|
1068 # NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1069 #
|
|
|
1070 sub _InitializeFunctionalClassAtomTypesInformation {
|
|
|
1071 my($This) = @_;
|
|
|
1072
|
|
|
1073 # Default functional class atom typess to use for generating initial atom identifiers
|
|
|
1074 # are: HBD, HBA, PI, NI, Ar, Hal
|
|
|
1075 #
|
|
|
1076 @{$This->{FunctionalClassesToUse}} = ();
|
|
|
1077 @{$This->{FunctionalClassesToUse}} = ('HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal');
|
|
|
1078
|
|
|
1079 return $This;
|
|
|
1080 }
|
|
|
1081
|
|
|
1082 # Set atomic invariants to use for generation of intial atom indentifiers...
|
|
|
1083 #
|
|
|
1084 sub SetAtomicInvariantsToUse {
|
|
|
1085 my($This, @Values) = @_;
|
|
|
1086 my($FirstValue, $TypeOfFirstValue, $AtomicInvariant, $SpecifiedAtomicInvariant, @SpecifiedAtomicInvariants, @AtomicInvariantsToUse);
|
|
|
1087
|
|
|
1088 if (!@Values) {
|
|
|
1089 carp "Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified...";
|
|
|
1090 return;
|
|
|
1091 }
|
|
|
1092
|
|
|
1093 if ($This->{AtomIdentifierType} !~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
1094 carp "Warning: ${ClassName}->SetFunctionalAtomTypesToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}...";
|
|
|
1095 return;
|
|
|
1096 }
|
|
|
1097
|
|
|
1098 $FirstValue = $Values[0];
|
|
|
1099 $TypeOfFirstValue = ref $FirstValue;
|
|
|
1100
|
|
|
1101 @SpecifiedAtomicInvariants = ();
|
|
|
1102 @AtomicInvariantsToUse = ();
|
|
|
1103
|
|
|
1104 if ($TypeOfFirstValue =~ /^ARRAY/) {
|
|
|
1105 push @SpecifiedAtomicInvariants, @{$FirstValue};
|
|
|
1106 }
|
|
|
1107 else {
|
|
|
1108 push @SpecifiedAtomicInvariants, @Values;
|
|
|
1109 }
|
|
|
1110
|
|
|
1111 # Make sure specified AtomicInvariants are valid...
|
|
|
1112 for $SpecifiedAtomicInvariant (@SpecifiedAtomicInvariants) {
|
|
|
1113 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($SpecifiedAtomicInvariant)) {
|
|
|
1114 croak "Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n ";
|
|
|
1115 }
|
|
|
1116 $AtomicInvariant = $SpecifiedAtomicInvariant;
|
|
|
1117 push @AtomicInvariantsToUse, $AtomicInvariant;
|
|
|
1118 }
|
|
|
1119
|
|
|
1120 # Set atomic invariants to use...
|
|
|
1121 @{$This->{AtomicInvariantsToUse}} = ();
|
|
|
1122 push @{$This->{AtomicInvariantsToUse}}, @AtomicInvariantsToUse;
|
|
|
1123
|
|
|
1124 return $This;
|
|
|
1125 }
|
|
|
1126
|
|
|
1127 # Set functional classes to use for generation of intial atom indentifiers...
|
|
|
1128 #
|
|
|
1129 sub SetFunctionalClassesToUse {
|
|
|
1130 my($This, @Values) = @_;
|
|
|
1131 my($FirstValue, $TypeOfFirstValue, $FunctionalClass, $SpecifiedFunctionalClass, @SpecifiedFunctionalClasses, @FunctionalClassesToUse);
|
|
|
1132
|
|
|
1133 if (!@Values) {
|
|
|
1134 carp "Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified...";
|
|
|
1135 return;
|
|
|
1136 }
|
|
|
1137
|
|
|
1138 if ($This->{AtomIdentifierType} !~ /^FunctionalClassAtomTypes$/i) {
|
|
|
1139 carp "Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}...";
|
|
|
1140 return;
|
|
|
1141 }
|
|
|
1142
|
|
|
1143 $FirstValue = $Values[0];
|
|
|
1144 $TypeOfFirstValue = ref $FirstValue;
|
|
|
1145
|
|
|
1146 @SpecifiedFunctionalClasses = ();
|
|
|
1147 @FunctionalClassesToUse = ();
|
|
|
1148
|
|
|
1149 if ($TypeOfFirstValue =~ /^ARRAY/) {
|
|
|
1150 push @SpecifiedFunctionalClasses, @{$FirstValue};
|
|
|
1151 }
|
|
|
1152 else {
|
|
|
1153 push @SpecifiedFunctionalClasses, @Values;
|
|
|
1154 }
|
|
|
1155
|
|
|
1156 # Make sure specified FunctionalClasses are valid...
|
|
|
1157 for $SpecifiedFunctionalClass (@SpecifiedFunctionalClasses) {
|
|
|
1158 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($SpecifiedFunctionalClass)) {
|
|
|
1159 croak "Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n ";
|
|
|
1160 }
|
|
|
1161 push @FunctionalClassesToUse, $SpecifiedFunctionalClass;
|
|
|
1162 }
|
|
|
1163
|
|
|
1164 # Set functional classes to use...
|
|
|
1165 @{$This->{FunctionalClassesToUse}} = ();
|
|
|
1166 push @{$This->{FunctionalClassesToUse}}, @FunctionalClassesToUse;
|
|
|
1167
|
|
|
1168 return $This;
|
|
|
1169 }
|
|
|
1170
|
|
|
1171 # Return a string containg data for ExtendedConnectivityFingerprints object...
|
|
|
1172 sub StringifyExtendedConnectivityFingerprints {
|
|
|
1173 my($This) = @_;
|
|
|
1174 my($ExtendedConnectivityFingerprintsString);
|
|
|
1175
|
|
|
1176 $ExtendedConnectivityFingerprintsString = "InitialAtomIdentifierType: $This->{AtomIdentifierType}; NeighborhoodRadius: $This->{NeighborhoodRadius}";
|
|
|
1177
|
|
|
1178 if ($This->{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
1179 my($AtomicInvariant, @AtomicInvariants, @AtomicInvariantsOrder, %AvailableAtomicInvariants);
|
|
|
1180
|
|
|
1181 @AtomicInvariantsOrder = AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder();
|
|
|
1182 %AvailableAtomicInvariants = AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants();
|
|
|
1183
|
|
|
1184 for $AtomicInvariant (@AtomicInvariantsOrder) {
|
|
|
1185 push @AtomicInvariants, "$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}";
|
|
|
1186 }
|
|
|
1187
|
|
|
1188 $ExtendedConnectivityFingerprintsString .= "; AtomicInvariantsToUse: <" . TextUtil::JoinWords(\@{$This->{AtomicInvariantsToUse}}, ", ", 0) . ">";
|
|
|
1189 $ExtendedConnectivityFingerprintsString .= "; AtomicInvariantsOrder: <" . TextUtil::JoinWords(\@AtomicInvariantsOrder, ", ", 0) . ">";
|
|
|
1190 $ExtendedConnectivityFingerprintsString .= "; AvailableAtomicInvariants: <" . TextUtil::JoinWords(\@AtomicInvariants, ", ", 0) . ">";
|
|
|
1191 }
|
|
|
1192 elsif ($This->{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
1193 my($FunctionalClass, @FunctionalClasses, @FunctionalClassesOrder, %AvailableFunctionalClasses);
|
|
|
1194
|
|
|
1195 @FunctionalClassesOrder = AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder();
|
|
|
1196 %AvailableFunctionalClasses = AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses();
|
|
|
1197
|
|
|
1198 for $FunctionalClass (@FunctionalClassesOrder) {
|
|
|
1199 push @FunctionalClasses, "$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}";
|
|
|
1200 }
|
|
|
1201
|
|
|
1202 $ExtendedConnectivityFingerprintsString .= "; FunctionalClassesToUse: <" . TextUtil::JoinWords(\@{$This->{FunctionalClassesToUse}}, ", ", 0) . ">";
|
|
|
1203 $ExtendedConnectivityFingerprintsString .= "; FunctionalClassesOrder: <" . TextUtil::JoinWords(\@FunctionalClassesOrder, ", ", 0) . ">";
|
|
|
1204 $ExtendedConnectivityFingerprintsString .= "; AvailableFunctionalClasses: <" . TextUtil::JoinWords(\@FunctionalClasses, ", ", 0) . ">";
|
|
|
1205 }
|
|
|
1206
|
|
|
1207 if ($This->{Type} =~ /^ExtendedConnectivityBits$/i) {
|
|
|
1208 # Size...
|
|
|
1209 $ExtendedConnectivityFingerprintsString .= "; Size: $This->{Size}; MinSize: $This->{MinSize}; MaxSize: $This->{MaxSize}";
|
|
|
1210
|
|
|
1211 # Fingerprint bit density and num of bits set...
|
|
|
1212 my($NumOfSetBits, $BitDensity);
|
|
|
1213 $NumOfSetBits = $This->{FingerprintsBitVector}->GetNumOfSetBits();
|
|
|
1214 $BitDensity = $This->{FingerprintsBitVector}->GetFingerprintsBitDensity();
|
|
|
1215 $ExtendedConnectivityFingerprintsString .= "; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity";
|
|
|
1216
|
|
|
1217 $ExtendedConnectivityFingerprintsString .= "; FingerprintsBitVector: < $This->{FingerprintsBitVector} >";
|
|
|
1218 }
|
|
|
1219 else {
|
|
|
1220 # Number of identifiers...
|
|
|
1221 $ExtendedConnectivityFingerprintsString .= "; NumOfIdentifiers: " . $This->{FingerprintsVector}->GetNumOfValues();
|
|
|
1222
|
|
|
1223 # FingerprintsVector...
|
|
|
1224 $ExtendedConnectivityFingerprintsString .= "; FingerprintsVector: < $This->{FingerprintsVector} >";
|
|
|
1225 }
|
|
|
1226
|
|
|
1227 return $ExtendedConnectivityFingerprintsString;
|
|
|
1228 }
|
|
|
1229
|
|
|
1230 1;
|
|
|
1231
|
|
|
1232 __END__
|
|
|
1233
|
|
|
1234 =head1 NAME
|
|
|
1235
|
|
|
1236 ExtendedConnectivityFingerprints
|
|
|
1237
|
|
|
1238 =head1 SYNOPSIS
|
|
|
1239
|
|
|
1240 use Fingerprints::ExtendedConnectivityFingerprints;
|
|
|
1241
|
|
|
1242 use Fingerprints::ExtendedConnectivityFingerprints qw(:all);
|
|
|
1243
|
|
|
1244 =head1 DESCRIPTION
|
|
|
1245
|
|
|
1246 ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] class provides the following methods:
|
|
|
1247
|
|
|
1248 new, GenerateFingerprints, GetDescription, SetAtomIdentifierType,
|
|
|
1249 SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetNeighborhoodRadius,
|
|
|
1250 StringifyExtendedConnectivityFingerprints
|
|
|
1251
|
|
|
1252 B<ExtendedConnectivityFingerprints> is derived from B<Fingerprints> class which in turn
|
|
|
1253 is derived from B<ObjectProperty> base class that provides methods not explicitly defined
|
|
|
1254 in B<ExtendedConnectivityFingerprints>, B<Fingerprints> or B<ObjectProperty> classes using Perl's
|
|
|
1255 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:
|
|
|
1256
|
|
|
1257 Set<PropertyName>(<PropertyValue>);
|
|
|
1258 $PropertyValue = Get<PropertyName>();
|
|
|
1259 Delete<PropertyName>();
|
|
|
1260
|
|
|
1261 The current release of MayaChemTools supports generation of B<ExtendedConnectivityFingerprints>
|
|
|
1262 corresponding to following B<AtomtomIdentifierTypes>:
|
|
|
1263
|
|
|
1264 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
1265 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
1266 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
1267
|
|
|
1268 Based on the values specified for B<AtomIdentifierType>, B<AtomicInvariantsToUse>
|
|
|
1269 and B<FunctionalClassesToUse>, initial atom types are assigned to all non-hydrogen atoms in
|
|
|
1270 a molecule and these atom types strings are converted into initial atom identifier integers using
|
|
|
1271 B<TextUtil::HashCode> function. The duplicate atom identifiers are removed.
|
|
|
1272
|
|
|
1273 For B<NeighborhoodRadius> value of I<0>, the initial set of unique atom identifiers comprises
|
|
|
1274 the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen
|
|
|
1275 atom up-to specified B<NeighborhoodRadius> value. For each non-hydrogen central atom
|
|
|
1276 at a specific radius, its neighbors at next radius level along with their bond orders and previously
|
|
|
1277 calculated atom identifiers are collected which in turn are used to generate a new integer
|
|
|
1278 atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order
|
|
|
1279 followed by atom identifiers to make these values graph invariant.
|
|
|
1280
|
|
|
1281 After integer atom identifiers have been generated for all non-hydrogen atoms at all specified
|
|
|
1282 neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code
|
|
|
1283 value generated using B<TextUtil::HashCode> are tracked by keeping the atom identifiers at
|
|
|
1284 lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified
|
|
|
1285 radius are also tracked by identifying equivalent atom and bonds corresponding to substructures
|
|
|
1286 used for generating atom identifier and keeping integer atom identifier with lowest value.
|
|
|
1287
|
|
|
1288 For I<ExtendedConnnectivity> value of fingerprints B<Type>, the duplicate identifiers are
|
|
|
1289 removed from the list and the unique atom identifiers constitute the extended connectivity
|
|
|
1290 fingerprints of a molecule.
|
|
|
1291
|
|
|
1292 For I<ExtendedConnnectivityCount> value of fingerprints B<Type>, the occurrence of each
|
|
|
1293 unique atom identifiers appears is counted and the unique atom identifiers along with their
|
|
|
1294 count constitute the extended connectivity fingerprints of a molecule.
|
|
|
1295
|
|
|
1296 For I<ExtendedConnectivityBits> value of fingerprints B<-m, --mode>, the unique atom identifiers
|
|
|
1297 are used as a random number seed to generate a random integer value between 0 and B<--Size> which
|
|
|
1298 in turn is used to set corresponding bits in the fingerprint bit-vector string.
|
|
|
1299
|
|
|
1300 The current release of MayaChemTools generates the following types of extended connectivity
|
|
|
1301 fingerprints vector strings:
|
|
|
1302
|
|
|
1303 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
|
|
|
1304 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
|
|
|
1305 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
|
|
|
1306 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
|
|
|
1307 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
|
|
|
1308 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
|
|
|
1309
|
|
|
1310 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
|
|
|
1311 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
|
|
|
1312 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
|
|
|
1313 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
|
|
|
1314 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
|
|
|
1315 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
|
|
|
1316
|
|
|
1317 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
1318 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
|
|
|
1319 0000000001010000000110000011000000000000100000000000000000000000100001
|
|
|
1320 1000000110000000000000000000000000010011000000000000000000000000010000
|
|
|
1321 0000000000000000000000000010000000000000000001000000000000000000000000
|
|
|
1322 0000000000010000100001000000000000101000000000000000100000000000000...
|
|
|
1323
|
|
|
1324 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
1325 es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
|
|
|
1326 0300000091000004000000020000100000000124008200020000000040020000000000
|
|
|
1327 2080000000820040010020000000008040000000000080001000000000400000000000
|
|
|
1328 4040000090000061010000000800200000000000001400000000020080000000000020
|
|
|
1329 00008020200000408000
|
|
|
1330
|
|
|
1331 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
|
|
|
1332 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
|
|
|
1333 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
|
|
|
1334 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
|
|
|
1335 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
|
|
|
1336 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
|
|
|
1337
|
|
|
1338 FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
|
|
|
1339 Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
|
|
|
1340 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
|
|
|
1341 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
|
|
|
1342 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
|
|
|
1343 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1
|
|
|
1344
|
|
|
1345 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
|
|
|
1346 s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
|
|
|
1347 0000000001000100000000001000000000000000000000000000000000101000000010
|
|
|
1348 0000001000000000010000000000000000000000000000000000000000000000000100
|
|
|
1349 0000000000001000000000000001000000000001001000000000000000000000000000
|
|
|
1350 0000000000000000100000000000001000000000000000000000000000000000000...
|
|
|
1351
|
|
|
1352 FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
|
|
|
1353 lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
|
|
|
1354 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
|
|
|
1355 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
|
|
|
1356 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
|
|
|
1357 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...
|
|
|
1358
|
|
|
1359 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
|
|
|
1360 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
|
|
|
1361 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
|
|
|
1362 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
|
|
|
1363 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
|
|
|
1364 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
|
|
|
1365
|
|
|
1366 FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
|
|
|
1367 haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
|
|
|
1368 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
|
|
|
1369 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
|
|
|
1370 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
|
|
|
1371 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...
|
|
|
1372
|
|
|
1373 FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
|
|
|
1374 aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
|
|
|
1375 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
|
|
|
1376 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
|
|
|
1377 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
|
|
|
1378 41915747 679881756 721736571 794256218 908276640 992898760 10987549...
|
|
|
1379
|
|
|
1380 FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
|
|
|
1381 aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
|
|
|
1382 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
|
|
|
1383 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
|
|
|
1384 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
|
|
|
1385 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...
|
|
|
1386
|
|
|
1387 FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
|
|
|
1388 NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
|
|
|
1389 700688206 265614156 363161397 681332588 810600886 885767127 950172500
|
|
|
1390 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
|
|
|
1391 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
|
|
|
1392 654 256360355 279492740 291251259 317592700 333763396 972105960 101...
|
|
|
1393
|
|
|
1394 FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
|
|
|
1395 umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
|
|
|
1396 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
|
|
|
1397 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
|
|
|
1398 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
|
|
|
1399 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...
|
|
|
1400
|
|
|
1401 =head2 METHODS
|
|
|
1402
|
|
|
1403 =over 4
|
|
|
1404
|
|
|
1405 =item B<new>
|
|
|
1406
|
|
|
1407 $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1408 %NamesAndValues);
|
|
|
1409
|
|
|
1410 Using specified I<ExtendedConnectivityFingerprints> property names and values hash, B<new>
|
|
|
1411 method creates a new object and returns a reference to newly created B<ExtendedConnectivityFingerprints>
|
|
|
1412 object. By default, the following properties are initialized:
|
|
|
1413
|
|
|
1414 Molecule = ''
|
|
|
1415 Type = 'ExtendedConnectivity'
|
|
|
1416 NeighborhoodRadius = 2
|
|
|
1417 AtomIdentifierType = ''
|
|
|
1418 AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
|
|
|
1419 FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']
|
|
|
1420
|
|
|
1421 Examples:
|
|
|
1422
|
|
|
1423 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1424 'Molecule' => $Molecule,
|
|
|
1425 'AtomIdentifierType' =>
|
|
|
1426 'AtomicInvariantsAtomTypes');
|
|
|
1427
|
|
|
1428 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1429 'Type' => 'ExtendedConnectivityCount',
|
|
|
1430 'Molecule' => $Molecule,
|
|
|
1431 'AtomIdentifierType' =>
|
|
|
1432 'AtomicInvariantsAtomTypes');
|
|
|
1433
|
|
|
1434 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1435 'Type' => 'ExtendedConnectivityBits',
|
|
|
1436 'Molecule' => $Molecule,
|
|
|
1437 'Size' => 1024,
|
|
|
1438 'AtomIdentifierType' =>
|
|
|
1439 'AtomicInvariantsAtomTypes');
|
|
|
1440
|
|
|
1441 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1442 'Type' => 'ExtendedConnectivity',
|
|
|
1443 'Molecule' => $Molecule,
|
|
|
1444 'NeighborhoodRadius' => 2,
|
|
|
1445 'AtomIdentifierType' =>
|
|
|
1446 'AtomicInvariantsAtomTypes',
|
|
|
1447 'AtomicInvariantsToUse' =>
|
|
|
1448 ['AS', 'X', 'BO', 'H', 'FC', 'MN'] );
|
|
|
1449
|
|
|
1450 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1451 'Type' => 'ExtendedConnectivity',
|
|
|
1452 'Molecule' => $Molecule,
|
|
|
1453 'NeighborhoodRadius' => 2,
|
|
|
1454 'AtomIdentifierType' =>
|
|
|
1455 'FunctionalClassAtomTypes',
|
|
|
1456 'FunctionalClassesToUse' =>
|
|
|
1457 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );
|
|
|
1458
|
|
|
1459 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1460 'Type' => 'ExtendedConnectivity',
|
|
|
1461 'Molecule' => $Molecule,;
|
|
|
1462 'AtomIdentifierType' =>
|
|
|
1463 'MMFF94AtomTypes');
|
|
|
1464
|
|
|
1465 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1466 'Type' => 'ExtendedConnectivityCount',
|
|
|
1467 'Molecule' => $Molecule,;
|
|
|
1468 'AtomIdentifierType' =>
|
|
|
1469 'MMFF94AtomTypes');
|
|
|
1470
|
|
|
1471 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1472 'Type' => 'ExtendedConnectivityCount',
|
|
|
1473 'Molecule' => $Molecule,;
|
|
|
1474 'AtomIdentifierType' =>
|
|
|
1475 'SLogPAtomTypes');
|
|
|
1476
|
|
|
1477 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1478 'Type' => 'ExtendedConnectivity',
|
|
|
1479 'Molecule' => $Molecule,;
|
|
|
1480 'AtomIdentifierType' =>
|
|
|
1481 'SLogPAtomTypes');
|
|
|
1482
|
|
|
1483 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
1484 'Type' => 'ExtendedConnectivity',
|
|
|
1485 'Molecule' => $Molecule,;
|
|
|
1486 'AtomIdentifierType' =>
|
|
|
1487 'SYBYLAtomTypes');
|
|
|
1488
|
|
|
1489 $ExtendedConnectivityFingerprints->GenerateFingerprints();
|
|
|
1490 print "$ExtendedConnectivityFingerprints\n";
|
|
|
1491
|
|
|
1492 =item B<GenerateFingerprints>
|
|
|
1493
|
|
|
1494 $ExtendedConnectivityFingerprints->GenerateFingerprints();
|
|
|
1495
|
|
|
1496 Generates extended connectivity fingerprints and returns I<ExtendedConnectivityFingerprints>.
|
|
|
1497
|
|
|
1498 =item B<GetDescription>
|
|
|
1499
|
|
|
1500 $Description = $ExtendedConnectivityFingerprints->GetDescription();
|
|
|
1501
|
|
|
1502 Returns a string containing description of extended connectivity fingerprints
|
|
|
1503 fingerprints.
|
|
|
1504
|
|
|
1505 =item B<SetAtomIdentifierType>
|
|
|
1506
|
|
|
1507 $ExtendedConnectivityFingerprints->SetAtomIdentifierType($IdentifierType);
|
|
|
1508
|
|
|
1509 Sets atom I<IdentifierType> to use during extended connectivity fingerprints generation and
|
|
|
1510 returns I<ExtendedConnectivityFingerprints>.
|
|
|
1511
|
|
|
1512 Possible values: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
1513 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
1514 TPSAAtomTypes, UFFAtomTypes>.
|
|
|
1515
|
|
|
1516 =item B<SetAtomicInvariantsToUse>
|
|
|
1517
|
|
|
1518 $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse($ValuesRef);
|
|
|
1519 $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse(@Values);
|
|
|
1520
|
|
|
1521 Sets atomic invariants to use during I<AtomicInvariantsAtomTypes> value of I<AtomIdentifierType>
|
|
|
1522 for extended connectivity fingerprints generation and returns I<ExtendedConnectivityFingerprints>.
|
|
|
1523
|
|
|
1524 Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB,
|
|
|
1525 H, Ar, RA, FC, MN, SM>. Default value [ Ref 24 ]: I<AS,X,BO,H,FC,MN>.
|
|
|
1526
|
|
|
1527 The atomic invariants abbreviations correspond to:
|
|
|
1528
|
|
|
1529 AS = Atom symbol corresponding to element symbol
|
|
|
1530
|
|
|
1531 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
1532 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
1533 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
1534 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1535 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1536 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1537 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
1538 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
1539 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
1540 FC<+n/-n> = Formal charge assigned to atom
|
|
|
1541 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
1542 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
1543 3 (triplet)
|
|
|
1544
|
|
|
1545 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
1546
|
|
|
1547 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
1548
|
|
|
1549 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
1550 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
1551
|
|
|
1552 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
1553 are also allowed:
|
|
|
1554
|
|
|
1555 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
1556 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
1557 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
1558 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
1559 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
1560 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
1561 H : NumOfImplicitAndExplicitHydrogens
|
|
|
1562 Ar : Aromatic
|
|
|
1563 RA : RingAtom
|
|
|
1564 FC : FormalCharge
|
|
|
1565 MN : MassNumber
|
|
|
1566 SM : SpinMultiplicity
|
|
|
1567
|
|
|
1568 I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant
|
|
|
1569 atom types.
|
|
|
1570
|
|
|
1571 =item B<SetFunctionalClassesToUse>
|
|
|
1572
|
|
|
1573 $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse($ValuesRef);
|
|
|
1574 $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse(@Values);
|
|
|
1575
|
|
|
1576 Sets functional classes invariants to use during I<FunctionalClassAtomTypes> value of I<AtomIdentifierType>
|
|
|
1577 for extended connectivity fingerprints generation and returns I<ExtendedConnectivityFingerprints>.
|
|
|
1578
|
|
|
1579 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
|
|
|
1580 Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>.
|
|
|
1581
|
|
|
1582 The functional class abbreviations correspond to:
|
|
|
1583
|
|
|
1584 HBD: HydrogenBondDonor
|
|
|
1585 HBA: HydrogenBondAcceptor
|
|
|
1586 PI : PositivelyIonizable
|
|
|
1587 NI : NegativelyIonizable
|
|
|
1588 Ar : Aromatic
|
|
|
1589 Hal : Halogen
|
|
|
1590 H : Hydrophobic
|
|
|
1591 RA : RingAtom
|
|
|
1592 CA : ChainAtom
|
|
|
1593
|
|
|
1594 Functional class atom type specification for an atom corresponds to:
|
|
|
1595
|
|
|
1596 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
|
|
|
1597
|
|
|
1598 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
|
|
|
1599 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
1600
|
|
|
1601 HydrogenBondDonor: NH, NH2, OH
|
|
|
1602 HydrogenBondAcceptor: N[!H], O
|
|
|
1603 PositivelyIonizable: +, NH2
|
|
|
1604 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1605
|
|
|
1606 =item B<SetNeighborhoodRadius>
|
|
|
1607
|
|
|
1608 $ExtendedConnectivityFingerprints->SetNeighborhoodRadius($Radius);
|
|
|
1609
|
|
|
1610 Sets neighborhood radius to use during extended connectivity fingerprints generation and
|
|
|
1611 returns I<ExtendedConnectivityFingerprints>.
|
|
|
1612
|
|
|
1613 =item B<StringifyExtendedConnectivityFingerprints>
|
|
|
1614
|
|
|
1615 $String = $Fingerprints->StringifyExtendedConnectivityFingerprints();
|
|
|
1616
|
|
|
1617 Returns a string containing information about I<ExtendedConnectivityFingerprints> object.
|
|
|
1618
|
|
|
1619 =back
|
|
|
1620
|
|
|
1621 =head1 AUTHOR
|
|
|
1622
|
|
|
1623 Manish Sud <msud@san.rr.com>
|
|
|
1624
|
|
|
1625 =head1 SEE ALSO
|
|
|
1626
|
|
|
1627 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
|
|
|
1628 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, MACCSKeys.pm,
|
|
|
1629 PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
|
|
|
1630 TopologicalAtomTripletsFingerprints.pm, TopologicalAtomTorsionsFingerprints.pm,
|
|
|
1631 TopologicalPharmacophoreAtomPairsFingerprints.pm,
|
|
|
1632 TopologicalPharmacophoreAtomTripletsFingerprints.pm
|
|
|
1633
|
|
|
1634
|
|
|
1635 =head1 COPYRIGHT
|
|
|
1636
|
|
|
1637 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
1638
|
|
|
1639 This file is part of MayaChemTools.
|
|
|
1640
|
|
|
1641 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1642 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1643 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1644 any later version.
|
|
|
1645
|
|
|
1646 =cut
|
