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1 package Fingerprints::AtomNeighborhoodsFingerprints;
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2 #
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3 # $RCSfile: AtomNeighborhoodsFingerprints.pm,v $
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4 # $Date: 2015/02/28 20:48:53 $
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5 # $Revision: 1.27 $
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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 Fingerprints::Fingerprints;
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33 use TextUtil ();
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34 use Molecule;
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35 use AtomTypes::AtomicInvariantsAtomTypes;
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36 use AtomTypes::DREIDINGAtomTypes;
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37 use AtomTypes::EStateAtomTypes;
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38 use AtomTypes::FunctionalClassAtomTypes;
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39 use AtomTypes::MMFF94AtomTypes;
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40 use AtomTypes::SLogPAtomTypes;
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41 use AtomTypes::SYBYLAtomTypes;
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42 use AtomTypes::TPSAAtomTypes;
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43 use AtomTypes::UFFAtomTypes;
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44
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45 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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46
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47 @ISA = qw(Fingerprints::Fingerprints Exporter);
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48 @EXPORT = qw();
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49 @EXPORT_OK = qw();
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50
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51 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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52
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53 # Setup class variables...
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54 my($ClassName);
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55 _InitializeClass();
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56
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57 # Overload Perl functions...
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58 use overload '""' => 'StringifyAtomNeighborhoodsFingerprints';
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59
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60 # Class constructor...
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61 sub new {
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62 my($Class, %NamesAndValues) = @_;
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63
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64 # Initialize object...
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65 my $This = $Class->SUPER::new();
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66 bless $This, ref($Class) || $Class;
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67 $This->_InitializeAtomNeighborhoodsFingerprints();
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68
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69 $This->_InitializeAtomNeighborhoodsFingerprintsProperties(%NamesAndValues);
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70
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71 return $This;
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72 }
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73
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74 # Initialize object data...
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75 #
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76 sub _InitializeAtomNeighborhoodsFingerprints {
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77 my($This) = @_;
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78
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79 # Type of fingerprint...
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80 $This->{Type} = 'AtomNeighborhoods';
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81
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82 # Type of vector...
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83 $This->{VectorType} = 'FingerprintsVector';
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84
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85 # Type of FingerprintsVector...
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86 $This->{FingerprintsVectorType} = 'AlphaNumericalValues';
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87
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88 # Minimum and maximum atomic neighborhoods radii...
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89 $This->{MinNeighborhoodRadius} = 0;
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90 $This->{MaxNeighborhoodRadius} = 2;
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91
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92 # Atom identifier type to use for atom IDs in atom neighborhood atoms...
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93 #
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94 # Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
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95 # EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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96 # SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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97 #
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98 $This->{AtomIdentifierType} = '';
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99
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100 # Atom types assigned to each heavy atom...
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101 %{$This->{AssignedAtomTypes}} = ();
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102
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103 # Atom neighorhoods with in specified atom radii..
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104 %{$This->{AtomNeighborhoods}} = ();
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105
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106 # Atom neighborhoods atom types count at different neighborhoods...
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107 %{$This->{NeighborhoodAtomTypesCount}} = ();
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108
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109 # Atom neighborhood identifiers using specified atom identifier types methodology...
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110 @{$This->{AtomNeighborhoodsIdentifiers}} = ();
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111 }
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112
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113 # Initialize class ...
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114 sub _InitializeClass {
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115 #Class name...
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116 $ClassName = __PACKAGE__;
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117 }
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118
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119 # Initialize object properties....
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120 sub _InitializeAtomNeighborhoodsFingerprintsProperties {
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121 my($This, %NamesAndValues) = @_;
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122
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123 my($Name, $Value, $MethodName);
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124 while (($Name, $Value) = each %NamesAndValues) {
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125 $MethodName = "Set${Name}";
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126 $This->$MethodName($Value);
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127 }
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128
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129 # Make sure molecule object was specified...
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130 if (!exists $NamesAndValues{Molecule}) {
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131 croak "Error: ${ClassName}->New: Object can't be instantiated without specifying molecule...";
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132 }
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133 if (exists $NamesAndValues{Size}) {
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134 croak "Error: ${ClassName}->New: Object can't be instantiated with a user specified size: It's an arbitrary length vector...";
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135 }
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136 if (!exists $NamesAndValues{AtomIdentifierType}) {
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137 croak "Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType...";
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138 }
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139
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140 $This->_InitializeFingerprintsVector();
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141
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142 return $This;
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143 }
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144
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145 # Set atom identifier type..
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146 #
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147 sub SetAtomIdentifierType {
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148 my($This, $IdentifierType) = @_;
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149
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150 if ($IdentifierType !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
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151 croak "Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes.";
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152 }
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153
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154 if ($This->{AtomIdentifierType}) {
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155 croak "Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set...";
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156 }
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157
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158 $This->{AtomIdentifierType} = $IdentifierType;
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159
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160 # Initialize atom identifier type information...
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161 $This->_InitializeAtomIdentifierTypeInformation();
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162
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163 return $This;
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164 }
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165
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166 # Set minimum atom neighborhood radius...
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167 #
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168 sub SetMinNeighborhoodRadius {
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169 my($This, $Value) = @_;
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170
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171 if (!TextUtil::IsInteger($Value)) {
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172 croak "Error: ${ClassName}->SetMinNeighborhoodRadius: MinNeighborhoodRadius value, $Value, is not valid: It must be an integer...";
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173 }
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174
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175 if ($Value < 0 ) {
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176 croak "Error: ${ClassName}->SetMinNeighborhoodRadius: MinNeighborhoodRadius value, $Value, is not valid: It must be >= 0...";
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177 }
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178 $This->{MinNeighborhoodRadius} = $Value;
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179
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180 return $This;
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181 }
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182
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183 # Set maximum atom neighborhood radius...
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184 #
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185 sub SetMaxNeighborhoodRadius {
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186 my($This, $Value) = @_;
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187
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188 if (!TextUtil::IsInteger($Value)) {
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189 croak "Error: ${ClassName}->SetMaxNeighborhoodRadius: MaxNeighborhoodRadius value, $Value, is not valid: It must be an integer...";
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190 }
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191
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192 if ($Value < 0 ) {
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193 croak "Error: ${ClassName}->SetMaxNeighborhoodRadius: MaxNeighborhoodRadius value, $Value, is not valid: It must be >= 0...";
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194 }
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195 $This->{MaxNeighborhoodRadius} = $Value;
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196
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197 return $This;
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198 }
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199
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200 # Generate fingerprints description...
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201 #
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202 sub GetDescription {
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203 my($This) = @_;
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204
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205 # Is description explicity set?
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206 if (exists $This->{Description}) {
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207 return $This->{Description};
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208 }
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209
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210 # Generate fingerprints description...
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211
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212 return "$This->{Type}:$This->{AtomIdentifierType}:MinRadius$This->{MinNeighborhoodRadius}:MaxRadius$This->{MaxNeighborhoodRadius}";
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213 }
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214
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215 # Generate atom neighborhood [ Ref 53-56, Ref 73 ] fingerprints...
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216 #
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217 # Methodology:
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218 # . Assign atom types to all non-hydrogen atoms in the molecule
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219 # . Get atom neighborhoods up to MaxNeighborhoodRadis
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220 # . Count unqiue atom types at each neighborhood radii for all heavy atoms
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221 # . Generate neighborhood identifiers for all neighborhoods around central
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222 # heavy atom
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223 # . Atom neighborhood identifier for a specific radii is generated using neighborhood
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224 # radius, assigned atom type and its count as follows:
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225 #
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226 # NR<n>-<AtomType>-ATC<n>
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227 #
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228 # . Atom neighborhood identifier for a central atom at all specified radii is generated
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229 # by concatenating neighborhood identifiers at each radii by colon:
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230 #
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231 # NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:
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232 #
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233 # . Set final fingerprints as list of neighborhood atom indentifiers
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234 #
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235 sub GenerateFingerprints {
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236 my($This) = @_;
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237
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238 if ($This->{MinNeighborhoodRadius} > $This->{MaxNeighborhoodRadius}) {
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239 croak "Error: ${ClassName}->GenerateFingerprints: No fingerpritns generated: MinLength, $This->{MinNeighborhoodRadius}, must be less than MaxLength, $This->{MaxNeighborhoodRadius}...";
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240 }
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241
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242 # Cache appropriate molecule data...
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243 $This->_SetupMoleculeDataCache();
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244
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245 # Assign atom types to all heavy atoms...
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246 if (!$This->_AssignAtomTypes()) {
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247 carp "Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms...";
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248 return $This;
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249 }
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250
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251 # Intialize atom neighborhoods information...
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252 $This->_InitializeAtomNeighborhoods();
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253
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254 # Identify atom neighborhoods with in specified radii...
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255 $This->_GetAtomNeighborhoods();
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256
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257 # Count atom neighborhoods atom types...
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258 $This->_CountAtomNeighborhoodsAtomTypes();
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259
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260 # Genenerate atom neighborhood identifiers...
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261 $This->_GenerateAtomNeighborhoodIdentifiers();
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262
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263 # Set final fingerprints...
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264 $This->_SetFinalFingerprints();
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265
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266 # Clear cached molecule data...
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267 $This->_ClearMoleculeDataCache();
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268
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269 return $This;
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270 }
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271
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272 # Assign appropriate atom types to all heavy atoms...
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273 #
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274 sub _AssignAtomTypes {
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275 my($This) = @_;
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276 my($SpecifiedAtomTypes, $Atom, $AtomID, $IgnoreHydrogens);
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277
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278 %{$This->{AssignedAtomTypes}} = ();
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279 $IgnoreHydrogens = 1;
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280
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281 $SpecifiedAtomTypes = undef;
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282
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283 IDENTIFIERTYPE: {
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284 if ($This->{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
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285 $SpecifiedAtomTypes = new AtomTypes::AtomicInvariantsAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens, 'AtomicInvariantsToUse' => $This->{AtomicInvariantsToUse});
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286 last IDENTIFIERTYPE;
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287 }
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288
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289 if ($This->{AtomIdentifierType} =~ /^DREIDINGAtomTypes$/i) {
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290 $SpecifiedAtomTypes = new AtomTypes::DREIDINGAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
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291 last IDENTIFIERTYPE;
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292 }
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293
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294 if ($This->{AtomIdentifierType} =~ /^EStateAtomTypes$/i) {
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295 $SpecifiedAtomTypes = new AtomTypes::EStateAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
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296 last IDENTIFIERTYPE;
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297 }
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298
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299 if ($This->{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
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300 $SpecifiedAtomTypes = new AtomTypes::FunctionalClassAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens, 'FunctionalClassesToUse' => $This->{FunctionalClassesToUse});
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301 last IDENTIFIERTYPE;
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302 }
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303
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304 if ($This->{AtomIdentifierType} =~ /^MMFF94AtomTypes$/i) {
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305 $SpecifiedAtomTypes = new AtomTypes::MMFF94AtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
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306 last IDENTIFIERTYPE;
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307 }
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308
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309 if ($This->{AtomIdentifierType} =~ /^SLogPAtomTypes$/i) {
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310 $SpecifiedAtomTypes = new AtomTypes::SLogPAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
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311 last IDENTIFIERTYPE;
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312 }
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313 if ($This->{AtomIdentifierType} =~ /^SYBYLAtomTypes$/i) {
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314 $SpecifiedAtomTypes = new AtomTypes::SYBYLAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
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315 last IDENTIFIERTYPE;
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316 }
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317
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318 if ($This->{AtomIdentifierType} =~ /^TPSAAtomTypes$/i) {
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319 $SpecifiedAtomTypes = new AtomTypes::TPSAAtomTypes('Molecule' => $This->{Molecule}, 'IgnorePhosphorus' => 0, 'IgnoreSulfur' => 0);
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320 last IDENTIFIERTYPE;
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321 }
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322
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323 if ($This->{AtomIdentifierType} =~ /^UFFAtomTypes$/i) {
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324 $SpecifiedAtomTypes = new AtomTypes::UFFAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens);
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325 last IDENTIFIERTYPE;
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326 }
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327
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328 croak "Error: ${ClassName}->_AssignAtomTypes: Unknown atom indentifier type $This->{AtomIdentifierType}...";
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329 }
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330
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331 # Assign atom types...
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332 $SpecifiedAtomTypes->AssignAtomTypes();
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333
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334 # Make sure atom types assignment is successful...
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335 if (!$SpecifiedAtomTypes->IsAtomTypesAssignmentSuccessful()) {
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336 return undef;
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337 }
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338
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339 # Collect assigned atom types...
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340 ATOM: for $Atom (@{$This->{Atoms}}) {
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341 if ($Atom->IsHydrogen()) {
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342 next ATOM;
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343 }
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344 $AtomID = $Atom->GetID();
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345 $This->{AssignedAtomTypes}{$AtomID} = $SpecifiedAtomTypes->GetAtomType($Atom);
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346 }
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347
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348 return $This;
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349 }
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350
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351 # Initialize topological atom pairs between specified distance range...
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352 #
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353 sub _InitializeAtomNeighborhoods {
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354 my($This) = @_;
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355 my($Radius);
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356
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357 # Initialize atom neighborhood count information between specified radii...
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358 %{$This->{NeighborhoodAtomTypesCount}} = ();
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359
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360 for $Radius ($This->{MinNeighborhoodRadius} .. $This->{MaxNeighborhoodRadius}) {
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361 %{$This->{NeighborhoodAtomTypesCount}{$Radius}} = ();
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362 }
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363
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364 # Initialize atom neighborhoods atoms information at all specified radii...
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365 #
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366 %{$This->{AtomNeighborhoods}} = ();
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367
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368 for $Radius (0 .. $This->{MaxNeighborhoodRadius}) {
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369 %{$This->{AtomNeighborhoods}{$Radius}} = ();
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370 }
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371
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372 return $This;
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373 }
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374
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375 # Collect atom neighborhoods upto maximum neighborhood radius...
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376 #
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377 # Notes:
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378 # . Fingerprints are only generated for neighborhoods between specified minimum
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379 # and maximum neighborhood radii.
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380 #
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381 sub _GetAtomNeighborhoods {
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382 my($This) = @_;
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383 my($Atom, $AtomID, $MaxRadius, $Radius, $Molecule);
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384
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385 $MaxRadius = $This->{MaxNeighborhoodRadius};
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386 $Molecule = $This->GetMolecule();
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387
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388 # Collect atom neighborhoods...
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389
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390 ATOM: for $Atom (@{$This->{Atoms}}) {
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|
|
391 $AtomID = $Atom->GetID();
|
|
|
392 $Radius = 0;
|
|
|
393
|
|
|
394 if ($MaxRadius == 0) {
|
|
|
395 # Atom is its own neighborhood at 0 radius...
|
|
|
396 my(@AtomNeighborhoodsAtoms);
|
|
|
397
|
|
|
398 @AtomNeighborhoodsAtoms = ($Atom);
|
|
|
399 $This->{AtomNeighborhoods}{$Radius}{$AtomID} = \@AtomNeighborhoodsAtoms;
|
|
|
400
|
|
|
401 next ATOM;
|
|
|
402 }
|
|
|
403
|
|
|
404 # Collect available atom neighborhoods at different neighborhood radii levels...
|
|
|
405 my($AtomNeighborhoodAtomsRef);
|
|
|
406
|
|
|
407 for $AtomNeighborhoodAtomsRef ($Molecule->GetAtomNeighborhoodsWithRadiusUpto($Atom, $MaxRadius)) {
|
|
|
408 $This->{AtomNeighborhoods}{$Radius}{$AtomID} = $AtomNeighborhoodAtomsRef;
|
|
|
409 $Radius++;
|
|
|
410 }
|
|
|
411 }
|
|
|
412 return $This;
|
|
|
413 }
|
|
|
414
|
|
|
415 # Count atom neighborhoods atom types for each non-hydrogen central atoms with
|
|
|
416 # neighborhoods in specified radii range...
|
|
|
417 #
|
|
|
418 sub _CountAtomNeighborhoodsAtomTypes {
|
|
|
419 my($This) = @_;
|
|
|
420 my($AtomID, $NeighborhoodAtomID, $Radius, $NeighborhoodAtom, $NeighborhoodAtomType, $AtomNeighborhoodAtomsRef);
|
|
|
421
|
|
|
422 RADIUS: for $Radius (sort { $a <=> $b } keys %{$This->{AtomNeighborhoods}} ) {
|
|
|
423 if ($Radius < $This->{MinNeighborhoodRadius} || $Radius > $This->{MaxNeighborhoodRadius}) {
|
|
|
424 next RADIUS;
|
|
|
425 }
|
|
|
426 # Go over the neighborhoods of each atom at the current radius...
|
|
|
427 for $AtomID (keys %{$This->{AtomNeighborhoods}{$Radius}}) {
|
|
|
428 $AtomNeighborhoodAtomsRef = $This->{AtomNeighborhoods}{$Radius}{$AtomID};
|
|
|
429 NEIGHBORHOODATOM: for $NeighborhoodAtom (@{$AtomNeighborhoodAtomsRef}) {
|
|
|
430 if ($NeighborhoodAtom->IsHydrogen()) {
|
|
|
431 next NEIGHBORHOODATOM;
|
|
|
432 }
|
|
|
433 $NeighborhoodAtomID = $NeighborhoodAtom->GetID();
|
|
|
434 $NeighborhoodAtomType = $This->{AssignedAtomTypes}{$NeighborhoodAtomID};
|
|
|
435
|
|
|
436 # Count neighbothood atom types for each atom at different radii...
|
|
|
437 if (!exists $This->{NeighborhoodAtomTypesCount}{$Radius}{$AtomID}) {
|
|
|
438 %{$This->{NeighborhoodAtomTypesCount}{$Radius}{$AtomID}} = ();
|
|
|
439 }
|
|
|
440 if (exists $This->{NeighborhoodAtomTypesCount}{$Radius}{$AtomID}{$NeighborhoodAtomType}) {
|
|
|
441 $This->{NeighborhoodAtomTypesCount}{$Radius}{$AtomID}{$NeighborhoodAtomType} += 1;
|
|
|
442 }
|
|
|
443 else {
|
|
|
444 $This->{NeighborhoodAtomTypesCount}{$Radius}{$AtomID}{$NeighborhoodAtomType} = 1;
|
|
|
445 }
|
|
|
446 }
|
|
|
447 }
|
|
|
448 }
|
|
|
449 return $This;
|
|
|
450 }
|
|
|
451
|
|
|
452 # Generate atom neighborhood identifiers for each non-hydrogen atom using atom
|
|
|
453 # neighborhood atom types and their count information...
|
|
|
454 #
|
|
|
455 # Let:
|
|
|
456 # NR<n> = Neighborhood radius
|
|
|
457 # AtomType = Assigned atom type
|
|
|
458 # ATC<n> = AtomType count
|
|
|
459 #
|
|
|
460 # Then:
|
|
|
461 #
|
|
|
462 # AtomNeighborhoodAtomIdentifier for a neighborhood atom generated for
|
|
|
463 # AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
464 #
|
|
|
465 # NR<n>-<AtomType>-ATC<n>
|
|
|
466 #
|
|
|
467 # AtomNeighborhoodsIdentifier for all specified atom neighbothoods of an atom generated for
|
|
|
468 # AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
469 #
|
|
|
470 # NR<n>-<AtomType>-ATC<n>;NR<n>-<AtomType>-ATC<n>;...
|
|
|
471 #
|
|
|
472 sub _GenerateAtomNeighborhoodIdentifiers {
|
|
|
473 my($This) = @_;
|
|
|
474 my($Atom, $AtomID, $Radius, $AtomType, $AtomTypeCount, $AtomNeighborhoodIdentifier, @AtomNeighborhoodIdentifiers);
|
|
|
475
|
|
|
476 @{$This->{AtomNeighborhoodsIdentifiers}} = ();
|
|
|
477
|
|
|
478 for $Atom (@{$This->{Atoms}}) {
|
|
|
479 $AtomID = $Atom->GetID();
|
|
|
480 @AtomNeighborhoodIdentifiers = ();
|
|
|
481 RADIUS: for $Radius ($This->{MinNeighborhoodRadius} .. $This->{MaxNeighborhoodRadius}) {
|
|
|
482 if (!exists $This->{NeighborhoodAtomTypesCount}{$Radius}{$AtomID}) {
|
|
|
483 next RADIUS;
|
|
|
484 }
|
|
|
485 for $AtomType (sort keys %{$This->{NeighborhoodAtomTypesCount}{$Radius}{$AtomID}}) {
|
|
|
486 $AtomTypeCount = $This->{NeighborhoodAtomTypesCount}{$Radius}{$AtomID}{$AtomType};
|
|
|
487 push @AtomNeighborhoodIdentifiers, "NR${Radius}-${AtomType}-ATC${AtomTypeCount}";
|
|
|
488 }
|
|
|
489 }
|
|
|
490 $AtomNeighborhoodIdentifier = join(":", @AtomNeighborhoodIdentifiers);
|
|
|
491 push @{$This->{AtomNeighborhoodsIdentifiers}}, $AtomNeighborhoodIdentifier;
|
|
|
492 }
|
|
|
493
|
|
|
494 return $This;
|
|
|
495 }
|
|
|
496
|
|
|
497 # Set final fingerprits vector...
|
|
|
498 #
|
|
|
499 sub _SetFinalFingerprints {
|
|
|
500 my($This) = @_;
|
|
|
501
|
|
|
502 # Mark successful generation of fingerprints...
|
|
|
503 $This->{FingerprintsGenerated} = 1;
|
|
|
504
|
|
|
505 # Sort AtomNeighborhoodsIdentifiers..
|
|
|
506 #
|
|
|
507 @{$This->{AtomNeighborhoodsIdentifiers}} = sort @{$This->{AtomNeighborhoodsIdentifiers}};
|
|
|
508
|
|
|
509 # Add sorted atom neighborhood identifiers to FingerprintsVector which is already defined
|
|
|
510 # during initialization containing AlphaNumericalValues...
|
|
|
511 #
|
|
|
512 $This->{FingerprintsVector}->AddValues(\@{$This->{AtomNeighborhoodsIdentifiers}});
|
|
|
513
|
|
|
514 return $This;
|
|
|
515 }
|
|
|
516
|
|
|
517 # Cache appropriate molecule data...
|
|
|
518 #
|
|
|
519 sub _SetupMoleculeDataCache {
|
|
|
520 my($This) = @_;
|
|
|
521
|
|
|
522 # Get all non-hydrogen atoms...
|
|
|
523 my($NegateAtomCheckMethod);
|
|
|
524 $NegateAtomCheckMethod = 1;
|
|
|
525 @{$This->{Atoms}} = $This->GetMolecule()->GetAtoms("IsHydrogen", $NegateAtomCheckMethod);
|
|
|
526
|
|
|
527 return $This;
|
|
|
528 }
|
|
|
529
|
|
|
530 # Clear cached molecule data...
|
|
|
531 #
|
|
|
532 sub _ClearMoleculeDataCache {
|
|
|
533 my($This) = @_;
|
|
|
534
|
|
|
535 @{$This->{Atoms}} = ();
|
|
|
536
|
|
|
537 return $This;
|
|
|
538 }
|
|
|
539
|
|
|
540 # Set atomic invariants to use for atom identifiers...
|
|
|
541 #
|
|
|
542 sub SetAtomicInvariantsToUse {
|
|
|
543 my($This, @Values) = @_;
|
|
|
544 my($FirstValue, $TypeOfFirstValue, $AtomicInvariant, $SpecifiedAtomicInvariant, $AtomicInvariantValue, @SpecifiedAtomicInvariants, @AtomicInvariantsToUse);
|
|
|
545
|
|
|
546 if (!@Values) {
|
|
|
547 carp "Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified...";
|
|
|
548 return;
|
|
|
549 }
|
|
|
550
|
|
|
551 $FirstValue = $Values[0];
|
|
|
552 $TypeOfFirstValue = ref $FirstValue;
|
|
|
553
|
|
|
554 @SpecifiedAtomicInvariants = ();
|
|
|
555 @AtomicInvariantsToUse = ();
|
|
|
556
|
|
|
557 if ($TypeOfFirstValue =~ /^ARRAY/) {
|
|
|
558 push @SpecifiedAtomicInvariants, @{$FirstValue};
|
|
|
559 }
|
|
|
560 else {
|
|
|
561 push @SpecifiedAtomicInvariants, @Values;
|
|
|
562 }
|
|
|
563
|
|
|
564 # Make sure specified AtomicInvariants are valid...
|
|
|
565 for $SpecifiedAtomicInvariant (@SpecifiedAtomicInvariants) {
|
|
|
566 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($SpecifiedAtomicInvariant)) {
|
|
|
567 croak "Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n ";
|
|
|
568 }
|
|
|
569 $AtomicInvariant = $SpecifiedAtomicInvariant;
|
|
|
570 push @AtomicInvariantsToUse, $AtomicInvariant;
|
|
|
571 }
|
|
|
572
|
|
|
573 # Set atomic invariants to use...
|
|
|
574 @{$This->{AtomicInvariantsToUse}} = ();
|
|
|
575 push @{$This->{AtomicInvariantsToUse}}, @AtomicInvariantsToUse;
|
|
|
576
|
|
|
577 return $This;
|
|
|
578 }
|
|
|
579
|
|
|
580 # Set functional classes to use for atom identifiers...
|
|
|
581 #
|
|
|
582 sub SetFunctionalClassesToUse {
|
|
|
583 my($This, @Values) = @_;
|
|
|
584 my($FirstValue, $TypeOfFirstValue, $FunctionalClass, $SpecifiedFunctionalClass, @SpecifiedFunctionalClasses, @FunctionalClassesToUse);
|
|
|
585
|
|
|
586 if (!@Values) {
|
|
|
587 carp "Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified...";
|
|
|
588 return;
|
|
|
589 }
|
|
|
590
|
|
|
591 if ($This->{AtomIdentifierType} !~ /^FunctionalClassAtomTypes$/i) {
|
|
|
592 carp "Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}...";
|
|
|
593 return;
|
|
|
594 }
|
|
|
595
|
|
|
596 $FirstValue = $Values[0];
|
|
|
597 $TypeOfFirstValue = ref $FirstValue;
|
|
|
598
|
|
|
599 @SpecifiedFunctionalClasses = ();
|
|
|
600 @FunctionalClassesToUse = ();
|
|
|
601
|
|
|
602 if ($TypeOfFirstValue =~ /^ARRAY/) {
|
|
|
603 push @SpecifiedFunctionalClasses, @{$FirstValue};
|
|
|
604 }
|
|
|
605 else {
|
|
|
606 push @SpecifiedFunctionalClasses, @Values;
|
|
|
607 }
|
|
|
608
|
|
|
609 # Make sure specified FunctionalClasses are valid...
|
|
|
610 for $SpecifiedFunctionalClass (@SpecifiedFunctionalClasses) {
|
|
|
611 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($SpecifiedFunctionalClass)) {
|
|
|
612 croak "Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n ";
|
|
|
613 }
|
|
|
614 push @FunctionalClassesToUse, $SpecifiedFunctionalClass;
|
|
|
615 }
|
|
|
616
|
|
|
617 # Set functional classes to use...
|
|
|
618 @{$This->{FunctionalClassesToUse}} = ();
|
|
|
619 push @{$This->{FunctionalClassesToUse}}, @FunctionalClassesToUse;
|
|
|
620
|
|
|
621 return $This;
|
|
|
622 }
|
|
|
623
|
|
|
624 # Initialize atom indentifier type information...
|
|
|
625 #
|
|
|
626 # Current supported values:
|
|
|
627 #
|
|
|
628 # AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,
|
|
|
629 # MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
630 #
|
|
|
631 sub _InitializeAtomIdentifierTypeInformation {
|
|
|
632 my($This) = @_;
|
|
|
633
|
|
|
634 if ($This->{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
635 $This->_InitializeAtomicInvariantsAtomTypesInformation();
|
|
|
636 }
|
|
|
637 elsif ($This->{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
638 $This->_InitializeFunctionalClassAtomTypesInformation();
|
|
|
639 }
|
|
|
640 elsif ($This->{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
641 # Nothing to do for now...
|
|
|
642 }
|
|
|
643 else {
|
|
|
644 croak "Error: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}...";
|
|
|
645 }
|
|
|
646
|
|
|
647 return $This;
|
|
|
648 }
|
|
|
649
|
|
|
650 # Initialize atomic invariants atom types to use for generating atom identifiers...
|
|
|
651 #
|
|
|
652 # Let:
|
|
|
653 # AS = Atom symbol corresponding to element symbol
|
|
|
654 #
|
|
|
655 # X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
656 # BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
657 # LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
658 # SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
659 # DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
660 # TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom
|
|
|
661 # H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
662 # Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
663 # RA = Ring atom annotation indicating whether atom is a ring
|
|
|
664 # FC<+n/-n> = Formal charge assigned to atom
|
|
|
665 # MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
666 # SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)
|
|
|
667 #
|
|
|
668 # Then:
|
|
|
669 #
|
|
|
670 # Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
671 #
|
|
|
672 # AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
673 #
|
|
|
674 # Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
675 # optional. Default atomic invariants used for AtomID are: AS, X<n>, BO<n>, H<n>, FC<+n/-n>.
|
|
|
676 # AtomID specification doesn't include atomic invariants with zero or undefined values.
|
|
|
677 #
|
|
|
678 sub _InitializeAtomicInvariantsAtomTypesInformation {
|
|
|
679 my($This) = @_;
|
|
|
680
|
|
|
681 # Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC
|
|
|
682 #
|
|
|
683 @{$This->{AtomicInvariantsToUse}} = ();
|
|
|
684 @{$This->{AtomicInvariantsToUse}} = ('AS', 'X', 'BO', 'H', 'FC');
|
|
|
685
|
|
|
686 return $This;
|
|
|
687 }
|
|
|
688
|
|
|
689 # Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes
|
|
|
690 # class, to use for generating atom identifiers...
|
|
|
691 #
|
|
|
692 # Let:
|
|
|
693 # HBD: HydrogenBondDonor
|
|
|
694 # HBA: HydrogenBondAcceptor
|
|
|
695 # PI : PositivelyIonizable
|
|
|
696 # NI : NegativelyIonizable
|
|
|
697 # Ar : Aromatic
|
|
|
698 # Hal : Halogen
|
|
|
699 # H : Hydrophobic
|
|
|
700 # RA : RingAtom
|
|
|
701 # CA : ChainAtom
|
|
|
702 #
|
|
|
703 # Then:
|
|
|
704 #
|
|
|
705 # Functiononal class atom type specification for an atom corresponds to:
|
|
|
706 #
|
|
|
707 # Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
708 #
|
|
|
709 # Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal
|
|
|
710 #
|
|
|
711 # FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
712 #
|
|
|
713 # HydrogenBondDonor: NH, NH2, OH
|
|
|
714 # HydrogenBondAcceptor: N[!H], O
|
|
|
715 # PositivelyIonizable: +, NH2
|
|
|
716 # NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
717 #
|
|
|
718 sub _InitializeFunctionalClassAtomTypesInformation {
|
|
|
719 my($This) = @_;
|
|
|
720
|
|
|
721 # Default functional class atom typess to use for generating atom identifiers
|
|
|
722 # are: HBD, HBA, PI, NI, Ar, Hal
|
|
|
723 #
|
|
|
724 @{$This->{FunctionalClassesToUse}} = ();
|
|
|
725 @{$This->{FunctionalClassesToUse}} = ('HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal');
|
|
|
726
|
|
|
727 return $This;
|
|
|
728 }
|
|
|
729
|
|
|
730 # Return a string containg data for AtomNeighborhoodsFingerprints object...
|
|
|
731 #
|
|
|
732 sub StringifyAtomNeighborhoodsFingerprints {
|
|
|
733 my($This) = @_;
|
|
|
734 my($FingerprintsString);
|
|
|
735
|
|
|
736 # Type of fingerprint...
|
|
|
737 $FingerprintsString = "Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}; MinNeighborhoodRadius: $This->{MinNeighborhoodRadius}; MaxNeighborhoodRadius: $This->{MaxNeighborhoodRadius}";
|
|
|
738
|
|
|
739 if ($This->{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
740 my($AtomicInvariant, @AtomicInvariants, @AtomicInvariantsOrder, %AvailableAtomicInvariants);
|
|
|
741
|
|
|
742 @AtomicInvariantsOrder = AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder();
|
|
|
743 %AvailableAtomicInvariants = AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants();
|
|
|
744
|
|
|
745 for $AtomicInvariant (@AtomicInvariantsOrder) {
|
|
|
746 push @AtomicInvariants, "$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}";
|
|
|
747 }
|
|
|
748
|
|
|
749 $FingerprintsString .= "; AtomicInvariantsToUse: <" . TextUtil::JoinWords(\@{$This->{AtomicInvariantsToUse}}, ", ", 0) . ">";
|
|
|
750 $FingerprintsString .= "; AtomicInvariantsOrder: <" . TextUtil::JoinWords(\@AtomicInvariantsOrder, ", ", 0) . ">";
|
|
|
751 $FingerprintsString .= "; AvailableAtomicInvariants: <" . TextUtil::JoinWords(\@AtomicInvariants, ", ", 0) . ">";
|
|
|
752 }
|
|
|
753 elsif ($This->{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
754 my($FunctionalClass, @FunctionalClasses, @FunctionalClassesOrder, %AvailableFunctionalClasses);
|
|
|
755
|
|
|
756 @FunctionalClassesOrder = AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder();
|
|
|
757 %AvailableFunctionalClasses = AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses();
|
|
|
758
|
|
|
759 for $FunctionalClass (@FunctionalClassesOrder) {
|
|
|
760 push @FunctionalClasses, "$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}";
|
|
|
761 }
|
|
|
762
|
|
|
763 $FingerprintsString .= "; FunctionalClassesToUse: <" . TextUtil::JoinWords(\@{$This->{FunctionalClassesToUse}}, ", ", 0) . ">";
|
|
|
764 $FingerprintsString .= "; FunctionalClassesOrder: <" . TextUtil::JoinWords(\@FunctionalClassesOrder, ", ", 0) . ">";
|
|
|
765 $FingerprintsString .= "; AvailableFunctionalClasses: <" . TextUtil::JoinWords(\@FunctionalClasses, ", ", 0) . ">";
|
|
|
766 }
|
|
|
767
|
|
|
768 # Total number of atom neighborhood atom IDs...
|
|
|
769 $FingerprintsString .= "; NumOfAtomNeighborhoodAtomIdentifiers: " . $This->{FingerprintsVector}->GetNumOfValues();
|
|
|
770
|
|
|
771 # FingerprintsVector...
|
|
|
772 $FingerprintsString .= "; FingerprintsVector: < $This->{FingerprintsVector} >";
|
|
|
773
|
|
|
774 return $FingerprintsString;
|
|
|
775 }
|
|
|
776
|
|
|
777 1;
|
|
|
778
|
|
|
779 __END__
|
|
|
780
|
|
|
781 =head1 NAME
|
|
|
782
|
|
|
783 AtomNeighborhoodsFingerprints
|
|
|
784
|
|
|
785 =head1 SYNOPSIS
|
|
|
786
|
|
|
787 use Fingerprints::AtomNeighborhoodsFingerprints;
|
|
|
788
|
|
|
789 use Fingerprints::AtomNeighborhoodsFingerprints qw(:all);
|
|
|
790
|
|
|
791 =head1 DESCRIPTION
|
|
|
792
|
|
|
793 B<AtomNeighborhoodsFingerprints> [ Ref 53-56, Ref 73 ] class provides the following methods:
|
|
|
794
|
|
|
795 new, GenerateFingerprints, GetDescription, SetAtomIdentifierType,
|
|
|
796 SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetMaxNeighborhoodRadius,
|
|
|
797 SetMinNeighborhoodRadius, StringifyAtomNeighborhoodsFingerprints
|
|
|
798
|
|
|
799 B<AtomNeighborhoodsFingerprints> is derived from B<Fingerprints> class which in turn
|
|
|
800 is derived from B<ObjectProperty> base class that provides methods not explicitly defined
|
|
|
801 in B<AtomNeighborhoodsFingerprints>, B<Fingerprints> or B<ObjectProperty> classes using Perl's
|
|
|
802 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:
|
|
|
803
|
|
|
804 Set<PropertyName>(<PropertyValue>);
|
|
|
805 $PropertyValue = Get<PropertyName>();
|
|
|
806 Delete<PropertyName>();
|
|
|
807
|
|
|
808 The current release of MayaChemTools supports generation of B<AtomNeighborhoodsFingerprints>
|
|
|
809 corresponding to following B<AtomIdentifierTypes>:
|
|
|
810
|
|
|
811 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
812 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
813 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
814
|
|
|
815 Based on the values specified for B<AtomIdentifierType> along with other specified
|
|
|
816 sucb as B<AtomicInvariantsToUse> and B<FunctionalClassesToUse>, initial atom types are
|
|
|
817 assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods
|
|
|
818 around each non-hydrogen central atom corresponding to radii between specified values
|
|
|
819 B<MinNeighborhoodRadius> and B<MaxNeighborhoodRadius>, unique atom types at each radii
|
|
|
820 level are counted and an atom neighborhood identifier is generated.
|
|
|
821
|
|
|
822 The format of an atom neighborhood identifier around a central non-hydrogen atom at a
|
|
|
823 specific radius is:
|
|
|
824
|
|
|
825 NR<n>-<AtomType>-ATC<n>
|
|
|
826
|
|
|
827 NR: Neighborhood radius
|
|
|
828 AtomType: Assigned atom type
|
|
|
829 ATC: Atom type count
|
|
|
830
|
|
|
831 The atom neighborhood identifier for non-hydrogen central atom corresponding to all specified radii
|
|
|
832 is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:
|
|
|
833
|
|
|
834 NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...
|
|
|
835
|
|
|
836 The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are
|
|
|
837 concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.
|
|
|
838
|
|
|
839 The current release of MayaChemTools generates the following types of atom neighborhoods
|
|
|
840 fingerprints vector strings:
|
|
|
841
|
|
|
842 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
|
|
|
843 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
|
|
|
844 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
|
|
|
845 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
|
|
|
846 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
|
|
|
847 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
|
|
|
848
|
|
|
849 FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
|
|
|
850 adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
|
|
|
851 NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
|
|
|
852 _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
|
|
|
853 C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
|
|
|
854 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...
|
|
|
855
|
|
|
856 FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
|
|
|
857 ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
|
|
|
858 NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
|
|
|
859 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
|
|
|
860 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
|
|
|
861 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...
|
|
|
862
|
|
|
863 FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
|
|
|
864 s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
|
|
|
865 ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
|
|
|
866 C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
|
|
|
867 R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
|
|
|
868 TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...
|
|
|
869
|
|
|
870 FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
|
|
|
871 ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
|
|
|
872 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
|
|
|
873 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
|
|
|
874 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
|
|
|
875 C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...
|
|
|
876
|
|
|
877 FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
|
|
|
878 us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
|
|
|
879 CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
|
|
|
880 NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
|
|
|
881 ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
|
|
|
882 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...
|
|
|
883
|
|
|
884 FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
|
|
|
885 us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
|
|
|
886 -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
|
|
|
887 O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
|
|
|
888 ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
|
|
|
889 C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...
|
|
|
890
|
|
|
891 FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
|
|
|
892 s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
|
|
|
893 -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
|
|
|
894 e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
|
|
|
895 ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
|
|
|
896 TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...
|
|
|
897
|
|
|
898 FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
|
|
|
899 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
|
|
|
900 _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
|
|
|
901 C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
|
|
|
902 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
|
|
|
903 -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...
|
|
|
904
|
|
|
905 =head2 METHODS
|
|
|
906
|
|
|
907 =over 4
|
|
|
908
|
|
|
909 =item B<new>
|
|
|
910
|
|
|
911 $NewAtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
|
|
|
912 %NamesAndValues);
|
|
|
913
|
|
|
914 Using specified I<AtomNeighborhoodsFingerprints> property names and values hash, B<new>
|
|
|
915 method creates a new object and returns a reference to newly created B<AtomNeighborhoodsFingerprints>
|
|
|
916 object. By default, the following properties are initialized:
|
|
|
917
|
|
|
918 Molecule = ''
|
|
|
919 Type = 'AtomNeighborhoods'
|
|
|
920 MinNeighborhoodRadius = 0
|
|
|
921 MaxNeighborhoodRadius = 2
|
|
|
922 AtomIdentifierType = ''
|
|
|
923 AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
|
|
|
924 FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']
|
|
|
925
|
|
|
926 Examples:
|
|
|
927
|
|
|
928 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
|
|
|
929 'Molecule' => $Molecule,
|
|
|
930 'AtomIdentifierType' =>
|
|
|
931 "AtomicInvariantsAtomTypes");
|
|
|
932
|
|
|
933 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
|
|
|
934 'Molecule' => $Molecule,
|
|
|
935 'MinNeighborhoodRadius' => 0,
|
|
|
936 'MaxNeighborhoodRadius' => 2,
|
|
|
937 'AtomIdentifierType' =>
|
|
|
938 'AtomicInvariantsAtomTypes',
|
|
|
939 'AtomicInvariantsToUse' =>
|
|
|
940 ['AS', 'X', 'BO', 'H', 'FC'] );
|
|
|
941
|
|
|
942 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
|
|
|
943 'Molecule' => $Molecule,
|
|
|
944 'AtomIdentifierType' =>
|
|
|
945 'SYBYLAtomTypes');
|
|
|
946
|
|
|
947 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
|
|
|
948 'Molecule' => $Molecule,
|
|
|
949 'AtomIdentifierType' =>
|
|
|
950 'MMFF94AtomTypes');
|
|
|
951
|
|
|
952 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
|
|
|
953 'Molecule' => $Molecule,
|
|
|
954 'AtomIdentifierType' =>
|
|
|
955 'AtomicInvariantsAtomTypes');
|
|
|
956
|
|
|
957 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
|
|
|
958 'Molecule' => $Molecule,
|
|
|
959 'MinNeighborhoodRadius' => 0,
|
|
|
960 'MaxNeighborhoodRadius' => 2,
|
|
|
961 'AtomIdentifierType' =>
|
|
|
962 'FunctionalClassAtomTypes',
|
|
|
963 'FunctionalClassesToUse' =>
|
|
|
964 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );
|
|
|
965
|
|
|
966 $AtomNeighborhoodsFingerprints->GenerateFingerprints();
|
|
|
967 print "$AtomNeighborhoodsFingerprints\n";
|
|
|
968
|
|
|
969 =item B<GenerateFingerprints>
|
|
|
970
|
|
|
971 $AtomNeighborhoodsFingerprints->GenerateFingerprints();
|
|
|
972
|
|
|
973 Generates atom neighborhood fingerprints and returns I<AtomNeighborhoodsFingerprints>.
|
|
|
974
|
|
|
975 =item B<GetDescription>
|
|
|
976
|
|
|
977 $Description = $AtomNeighborhoodsFingerprints->GetDescription();
|
|
|
978
|
|
|
979 Returns a string containing description of atom neighborhood fingerprints.
|
|
|
980
|
|
|
981 =item B<SetAtomIdentifierType>
|
|
|
982
|
|
|
983 $AtomNeighborhoodsFingerprints->SetAtomIdentifierType($IdentifierType);
|
|
|
984
|
|
|
985 Sets atom I<IdentifierType> to use during atom neighborhood fingerprints generation and
|
|
|
986 returns I<AtomNeighborhoodsFingerprints>.
|
|
|
987
|
|
|
988 Possible values: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
989 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
990 TPSAAtomTypes, UFFAtomTypes>.
|
|
|
991
|
|
|
992 =item B<SetAtomicInvariantsToUse>
|
|
|
993
|
|
|
994 $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse($ValuesRef);
|
|
|
995 $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse(@Values);
|
|
|
996
|
|
|
997 Sets atomic invariants to use during I<AtomicInvariantsAtomTypes> value of I<AtomIdentifierType>
|
|
|
998 for atom neighborhood fingerprints generation and returns I<AtomNeighborhoodsFingerprints>.
|
|
|
999
|
|
|
1000 Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB,
|
|
|
1001 H, Ar, RA, FC, MN, SM>. Default value: I<AS,X,BO,H,FC>.
|
|
|
1002
|
|
|
1003 The atomic invariants abbreviations correspond to:
|
|
|
1004
|
|
|
1005 AS = Atom symbol corresponding to element symbol
|
|
|
1006
|
|
|
1007 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
1008 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
1009 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
1010 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1011 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1012 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1013 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
1014 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
1015 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
1016 FC<+n/-n> = Formal charge assigned to atom
|
|
|
1017 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
1018 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
1019 3 (triplet)
|
|
|
1020
|
|
|
1021 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
1022
|
|
|
1023 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
1024
|
|
|
1025 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
1026 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
1027
|
|
|
1028 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
1029 are also allowed:
|
|
|
1030
|
|
|
1031 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
1032 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
1033 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
1034 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
1035 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
1036 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
1037 H : NumOfImplicitAndExplicitHydrogens
|
|
|
1038 Ar : Aromatic
|
|
|
1039 RA : RingAtom
|
|
|
1040 FC : FormalCharge
|
|
|
1041 MN : MassNumber
|
|
|
1042 SM : SpinMultiplicity
|
|
|
1043
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|
|
1044 I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant
|
|
|
1045 atom types.
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|
|
1046
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|
|
1047 =item B<SetFunctionalClassesToUse>
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|
|
1048
|
|
|
1049 $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse($ValuesRef);
|
|
|
1050 $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse(@Values);
|
|
|
1051
|
|
|
1052 Sets functional classes invariants to use during I<FunctionalClassAtomTypes> value of I<AtomIdentifierType>
|
|
|
1053 for atom neighborhoods fingerprints generation and returns I<AtomNeighborhoodsFingerprints>.
|
|
|
1054
|
|
|
1055 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
|
|
|
1056 Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>.
|
|
|
1057
|
|
|
1058 The functional class abbreviations correspond to:
|
|
|
1059
|
|
|
1060 HBD: HydrogenBondDonor
|
|
|
1061 HBA: HydrogenBondAcceptor
|
|
|
1062 PI : PositivelyIonizable
|
|
|
1063 NI : NegativelyIonizable
|
|
|
1064 Ar : Aromatic
|
|
|
1065 Hal : Halogen
|
|
|
1066 H : Hydrophobic
|
|
|
1067 RA : RingAtom
|
|
|
1068 CA : ChainAtom
|
|
|
1069
|
|
|
1070 Functional class atom type specification for an atom corresponds to:
|
|
|
1071
|
|
|
1072 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
|
|
|
1073
|
|
|
1074 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
|
|
|
1075 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
1076
|
|
|
1077 HydrogenBondDonor: NH, NH2, OH
|
|
|
1078 HydrogenBondAcceptor: N[!H], O
|
|
|
1079 PositivelyIonizable: +, NH2
|
|
|
1080 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1081
|
|
|
1082 =item B<SetMaxNeighborhoodRadius>
|
|
|
1083
|
|
|
1084 $AtomNeighborhoodsFingerprints->SetMaxNeighborhoodRadius($Radius);
|
|
|
1085
|
|
|
1086 Sets maximum neighborhood radius to use during atom neighborhood fingerprints generation and
|
|
|
1087 returns I<AtomNeighborhoodsFingerprints>.
|
|
|
1088
|
|
|
1089 =item B<SetMinNeighborhoodRadius>
|
|
|
1090
|
|
|
1091 $AtomNeighborhoodsFingerprints->SetMinNeighborhoodRadius($Radius);
|
|
|
1092
|
|
|
1093 Sets minimum neighborhood radius to use during atom neighborhood fingerprints generation and
|
|
|
1094 returns I<AtomNeighborhoodsFingerprints>.
|
|
|
1095
|
|
|
1096 =item B<StringifyAtomNeighborhoodsFingerprints>
|
|
|
1097
|
|
|
1098 $String = $Fingerprints->StringifyAtomNeighborhoodsFingerprints();
|
|
|
1099
|
|
|
1100 Returns a string containing information about I<AtomNeighborhoodsFingerprints> object.
|
|
|
1101
|
|
|
1102 =back
|
|
|
1103
|
|
|
1104 =head1 AUTHOR
|
|
|
1105
|
|
|
1106 Manish Sud <msud@san.rr.com>
|
|
|
1107
|
|
|
1108 =head1 SEE ALSO
|
|
|
1109
|
|
|
1110 Fingerprints.pm, FingerprintsStringUtil.pm, AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm,
|
|
|
1111 ExtendedConnectivityFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm,
|
|
|
1112 TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
|
|
|
1113 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
|
|
|
1114 TopologicalPharmacophoreAtomTripletsFingerprints.pm
|
|
|
1115
|
|
|
1116 =head1 COPYRIGHT
|
|
|
1117
|
|
|
1118 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
1119
|
|
|
1120 This file is part of MayaChemTools.
|
|
|
1121
|
|
|
1122 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1123 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1124 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1125 any later version.
|
|
|
1126
|
|
|
1127 =cut
|
