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1 package Fingerprints::EStateIndiciesFingerprints;
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2 #
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3 # $RCSfile: EStateIndiciesFingerprints.pm,v $
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4 # $Date: 2015/02/28 20:48:54 $
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5 # $Revision: 1.19 $
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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 Text::ParseWords;
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33 use TextUtil ();
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34 use FileUtil ();
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35 use MathUtil ();
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36 use Fingerprints::Fingerprints;
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37 use Molecule;
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38 use AtomTypes::EStateAtomTypes;
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39 use AtomicDescriptors::EStateValuesDescriptors;
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40
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41 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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42
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43 @ISA = qw(Fingerprints::Fingerprints Exporter);
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44 @EXPORT = qw();
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45 @EXPORT_OK = qw();
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46
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47 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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48
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49 # Setup class variables...
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50 my($ClassName);
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51 _InitializeClass();
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52
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53 # Overload Perl functions...
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54 use overload '""' => 'StringifyEStateIndiciesFingerprints';
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55
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56 # Class constructor...
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57 sub new {
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58 my($Class, %NamesAndValues) = @_;
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59
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60 # Initialize object...
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61 my $This = $Class->SUPER::new();
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62 bless $This, ref($Class) || $Class;
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63 $This->_InitializeEStateIndiciesFingerprints();
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64
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65 $This->_InitializeEStateIndiciesFingerprintsProperties(%NamesAndValues);
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66
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67 return $This;
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68 }
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69
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70 # Initialize object data...
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71 #
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72 sub _InitializeEStateIndiciesFingerprints {
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73 my($This) = @_;
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74
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75 # EStateIndicies is a vector containing sum of E-state values for E-state atom types
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76 #
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77 $This->{Type} = 'EStateIndicies';
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78
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79 # EStateAtomTypesSetToUse for EStateIndicies:
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80 #
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81 # ArbitrarySize - Corrresponds to only E-state atom types detected in molecule
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82 # FixedSize - Corresponds to fixed number of E-state atom types previously defined [ Ref 77 ]
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83 #
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84 # The default EStateAtomTypesSetToUse value for EStateIndicies fingerprints type: ArbitrarySize.
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85 # Possible values: ArbitrarySize or FixedSize.
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86 #
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87 $This->{EStateAtomTypesSetToUse} = '';
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88
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89 # Assigned E-state atom types...
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90 %{$This->{EStateAtomTypes}} = ();
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91
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92 # Vector values precision for real values during E-state indicies...
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93 $This->{ValuesPrecision} = 3;
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94
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95 # Calculated E-state values and indicies for generating E-state indicies fingerprints...
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96 %{$This->{EStateValues}} = ();
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97 %{$This->{EStateIndicies}} = ();
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98 }
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99
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100 # Initialize class ...
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101 sub _InitializeClass {
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102 #Class name...
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103 $ClassName = __PACKAGE__;
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104
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105 }
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106
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107 # Initialize object properties....
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108 sub _InitializeEStateIndiciesFingerprintsProperties {
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109 my($This, %NamesAndValues) = @_;
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110
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111 my($Name, $Value, $MethodName);
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112 while (($Name, $Value) = each %NamesAndValues) {
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113 $MethodName = "Set${Name}";
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114 $This->$MethodName($Value);
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115 }
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116
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117 # Make sure molecule object was specified...
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118 if (!exists $NamesAndValues{Molecule}) {
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119 croak "Error: ${ClassName}->New: Object can't be instantiated without specifying molecule...";
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120 }
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121
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122 $This->_InitializeEstateIndicies();
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123
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124 return $This;
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125 }
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126
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127 # Initialize E-state indicies...
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128 #
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129 sub _InitializeEstateIndicies {
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130 my($This) = @_;
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131
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132 # Set default EStateAtomTypesSetToUse...
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133 if (!$This->{EStateAtomTypesSetToUse}) {
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134 $This->{EStateAtomTypesSetToUse} = 'ArbitrarySize';
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135 }
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136
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137 # Vector type...
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138 $This->{VectorType} = 'FingerprintsVector';
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139
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140 if ($This->{EStateAtomTypesSetToUse} =~ /^FixedSize$/i) {
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141 $This->{FingerprintsVectorType} = 'OrderedNumericalValues';
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142 }
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143 else {
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144 $This->{FingerprintsVectorType} = 'NumericalValues';
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145 }
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146
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147 $This->_InitializeFingerprintsVector();
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148
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149 return $This;
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150 }
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151
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152 # Disable set size method...
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153 #
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154 sub SetSize {
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155 my($This, $Type) = @_;
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156
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157 croak "Error: ${ClassName}->SetSize: Can't change size: It's not allowed...";
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158 }
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159
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160 # Set E-state atom types set to use...
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161 #
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162 sub SetEStateAtomTypesSetToUse {
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163 my($This, $Value) = @_;
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164
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165 if ($This->{EStateAtomTypesSetToUse}) {
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166 croak "Error: ${ClassName}->SetEStateAtomTypesSetToUse: Can't change size: It's already set...";
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167 }
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168
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169 if ($Value !~ /^(ArbitrarySize|FixedSize)/i) {
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170 croak "Error: ${ClassName}->SetEStateAtomTypesSetToUse: Unknown EStateAtomTypesSetToUse value: $Value; Supported values: ArbitrarySize or FixedSize";
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171 }
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172
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173 $This->{EStateAtomTypesSetToUse} = $Value;
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174
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175 return $This;
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176 }
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177
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178 # Set vector values precision for real values for E-state indicies...
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179 #
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180 sub SetValuesPrecision {
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181 my($This, $Value) = @_;
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182
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183 if (!TextUtil::IsPositiveInteger($Value)) {
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184 croak "Error: ${ClassName}->SetValuesPrecision: ValuesPrecision value, $Value, is not valid: It must be a positive integer...";
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185 }
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186 $This->{ValuesPrecision} = $Value;
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187
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188 return $This;
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189 }
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190
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191 # Generate fingerprints description...
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192 #
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193 sub GetDescription {
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194 my($This) = @_;
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195
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196 # Is description explicity set?
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197 if (exists $This->{Description}) {
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198 return $This->{Description};
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199 }
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200
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201 # Generate fingerprints description...
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202
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203 return "$This->{Type}:$This->{EStateAtomTypesSetToUse}";
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204 }
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205
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206 # Generate electrotopological state indicies (E-state) [ Ref 75-78 ] fingerprints for
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207 # non-hydrogen atoms in a molecule...
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208 #
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209 # EStateIndicies fingerprints constitute a vector containing sum of E-state values
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210 # for E-state atom types. Two types of E-state atom types set size are allowed:
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211 #
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212 # ArbitrarySize - Corrresponds to only E-state atom types detected in molecule
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213 # FixedSize - Corresponds to fixed number of E-state atom types previously defined
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214 #
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215 # Module AtomTypes::EStateAtomTypes.pm is used to assign E-state atom types to
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216 # non-hydrogen atoms in the molecule which is able to assign atom types to any valid
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217 # atom group. However, for FixedSize value of EStateAtomTypesSetToUse, only a fixed
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218 # set of E-state atom types corresponding to specific atom groups [ Appendix III in
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219 # Ref 77 ] are used for fingerprints.
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220 #
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221 # The fixed size E-state atom type set size used during generation of fingerprints corresponding
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222 # FixedSize value of EStateAtomTypesSetToUse contains 87 E-state non-hydrogen atom types
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223 # in EStateAtomTypes.csv data file distributed with MayaChemTools.
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224 #
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225 # Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
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226 # E-state indicies fingerprints:
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227 #
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228 # Type EStateAtomTypesSetToUse
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229 #
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230 # EStateIndicies ArbitrarySize [ default fingerprints ]
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231 # EStateIndicies FixedSize
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232 #
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233 # The default is generate EStateIndicies type fingeprints corresponding to ArbitrarySize as
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234 # EStateAtomTypesSetToUse value.
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235 #
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236 #
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237 sub GenerateFingerprints {
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238 my($This) = @_;
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239
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240 # Cache appropriate molecule data...
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241 $This->_SetupMoleculeDataCache();
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242
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243 # Assign E-state atom types...
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244 if (!$This->_AssignEStateAtomTypes()) {
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245 carp "Warning: ${ClassName}->GenerateFingerprints: $This->{Type} fingerprints generation didn't succeed: Couldn't assign valid E-state atom types to all atoms...";
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246 return $This;
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247 }
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248
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249 # Calculate E-state indicies...
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250 if (!$This->_CalculateEStateIndicies()) {
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251 carp "Warning: ${ClassName}->GenerateFingerprints: $This->{Type} fingerprints generation didn't succeed: Couldn't calculate E-state values for all atoms...";
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252 return $This;
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253 }
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254
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255 # Set final fingerprints...
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256 $This->_SetFinalFingerprints();
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257
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258 # Clear cached molecule data...
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259 $This->_ClearMoleculeDataCache();
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260
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261 return $This;
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262 }
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263
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264 # Assign E-state atom types...
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265 #
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266 sub _AssignEStateAtomTypes {
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267 my($This) = @_;
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268 my($EStateAtomTypes, $Atom, $AtomID, $AtomType);
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269
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270 %{$This->{EStateAtomTypes}} = ();
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271
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272 # Assign E-state atom types...
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273 $EStateAtomTypes = new AtomTypes::EStateAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => 1);
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274 $EStateAtomTypes->AssignAtomTypes();
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275
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276 # Make sure atom types assignment is successful...
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277 if (!$EStateAtomTypes->IsAtomTypesAssignmentSuccessful()) {
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278 return undef;
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279 }
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280
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281 # Collect assigned atom types...
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282 for $Atom (@{$This->{Atoms}}) {
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283 $AtomID = $Atom->GetID();
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284
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285 $AtomType = $EStateAtomTypes->GetAtomType($Atom);
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286 $This->{EStateAtomTypes}{$AtomID} = $AtomType;
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287 }
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288 return $This;
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289 }
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290
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291 # Calculate E-state indicies by summing up E-state values for specific
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292 # E-state atom types...
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293 #
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294 sub _CalculateEStateIndicies {
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295 my($This) = @_;
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296 my($Atom, $AtomID, $AtomType, $EStateValue);
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297
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298 # Calculate E-state values to generate E-state indicies...
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299 if (!$This->_CalculateEStateValuesDescriptors()) {
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300 return undef;
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301 }
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302
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303 # Calculate E-state indicies...
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304 for $Atom (@{$This->{Atoms}}) {
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305 $AtomID = $Atom->GetID();
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306
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307 $AtomType = $This->{EStateAtomTypes}{$AtomID};
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308 $EStateValue = $This->{EStateValues}{$AtomID};
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309
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310 if (!exists $This->{EStateIndicies}{$AtomType}) {
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311 $This->{EStateIndicies}{$AtomType} = 0;
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312 }
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313
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314 $This->{EStateIndicies}{$AtomType} += $EStateValue;
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315 }
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316 return $This;
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317 }
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318
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319 # Calculate E-state values for E-state indicies...
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320 #
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321 sub _CalculateEStateValuesDescriptors {
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322 my($This) = @_;
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323 my($EStateValuesDescriptors, $Atom, $AtomID, $EStateValue);
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324
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325 %{$This->{EStateValues}} = ();
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326
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327 # Calculate and assign E-state values...
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328 $EStateValuesDescriptors = new AtomicDescriptors::EStateValuesDescriptors('Molecule' => $This->{Molecule});
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329 $EStateValuesDescriptors->GenerateDescriptors();
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330
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331 # Make sure E-state values calculation is successful...
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332 if (!$EStateValuesDescriptors->IsDescriptorsGenerationSuccessful()) {
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333 return undef;
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334 }
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335
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336 # Collect assigned E-state values...
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337 for $Atom (@{$This->{Atoms}}) {
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338 $AtomID = $Atom->GetID();
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339 $EStateValue = $EStateValuesDescriptors->GetDescriptorValue($Atom);
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340 $This->{EStateValues}{$AtomID} = $EStateValue;
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341 }
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342 return $This;
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343 }
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344
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345 # Set final final fingerpritns for E-state indicies...
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346 #
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347 sub _SetFinalFingerprints {
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348 my($This) = @_;
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349 my($AtomType, $ValuesPrecision, $EStateAtomTypesDataRef, @Values, @IDs);
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350
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351 # Mark successful generation of fingerprints...
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352 $This->{FingerprintsGenerated} = 1;
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353
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354 @Values = ();
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355 @IDs = ();
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356
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357 $ValuesPrecision = $This->{ValuesPrecision};
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358
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359 if ($This->{EStateAtomTypesSetToUse} =~ /^FixedSize$/i) {
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360 # Use fixed size E-state atom types set for non-hydrogen atoms...
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361 for $AtomType (@{AtomTypes::EStateAtomTypes::GetAllPossibleEStateNonHydrogenAtomTypes()}) {
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362 push @IDs, "S${AtomType}";
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363 push @Values, exists($This->{EStateIndicies}{$AtomType}) ? MathUtil::round($This->{EStateIndicies}{$AtomType}, $ValuesPrecision) : 0;
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364 }
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365 }
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366 else {
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367 for $AtomType (sort keys %{$This->{EStateIndicies}}) {
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368 push @IDs, "S${AtomType}";
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369 push @Values, MathUtil::round($This->{EStateIndicies}{$AtomType}, $ValuesPrecision);
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370 }
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371 }
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372
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373 # Add IDs and values to fingerprint vector...
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374 if (@IDs) {
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375 $This->{FingerprintsVector}->AddValueIDs(\@IDs);
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376 }
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377 $This->{FingerprintsVector}->AddValues(\@Values);
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378
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379 return $This;
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380 }
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381
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382 # Cache appropriate molecule data...
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383 #
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384 sub _SetupMoleculeDataCache {
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385 my($This) = @_;
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386
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387 # Get all non-hydrogen atoms...
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388 my($NegateAtomCheckMethod);
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389 $NegateAtomCheckMethod = 1;
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390 @{$This->{Atoms}} = $This->GetMolecule()->GetAtoms("IsHydrogen", $NegateAtomCheckMethod);
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391
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392 return $This;
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393 }
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394
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395 # Clear cached molecule data...
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396 #
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397 sub _ClearMoleculeDataCache {
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398 my($This) = @_;
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399
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400 @{$This->{Atoms}} = ();
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401
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402 return $This;
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403 }
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404
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405 # Return a string containg data for EStateIndiciesFingerprints object...
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406 sub StringifyEStateIndiciesFingerprints {
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407 my($This) = @_;
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408 my($EStateIndiciesFingerprintsString);
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409
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410 # Type of Keys...
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411 $EStateIndiciesFingerprintsString = "Type: $This->{Type}; EStateAtomTypesSetToUse: $This->{EStateAtomTypesSetToUse}";
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412
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413 # Fingerprint vector...
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414 $EStateIndiciesFingerprintsString .= "; FingerprintsVector: < $This->{FingerprintsVector} >";
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415
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416 return $EStateIndiciesFingerprintsString;
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417 }
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418
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419 1;
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420
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421 __END__
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422
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423 =head1 NAME
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424
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425 EStateIndiciesFingerprints
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426
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427 =head1 SYNOPSIS
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428
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429 use Fingerprints::EStateIndiciesFingerprints;
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430
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431 use Fingerprints::EStateIndiciesFingerprints qw(:all);
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432
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433 =head1 DESCRIPTION
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434
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435 B<EStateIndiciesFingerprints> [ Ref 75-78 ] class provides the following methods:
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436
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437 new, GenerateFingerprints, GetDescription, SetEStateAtomTypesSetToUse,
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438 SetValuesPrecision, StringifyEStateIndiciesFingerprints
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439
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440 B<EStateIndiciesFingerprints> is derived from B<Fingerprints> class which in turn
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441 is derived from B<ObjectProperty> base class that provides methods not explicitly defined
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442 in B<AtomNeighborhoodsFingerprints>, B<Fingerprints> or B<ObjectProperty> classes using Perl's
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443 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:
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444
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445 Set<PropertyName>(<PropertyValue>);
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446 $PropertyValue = Get<PropertyName>();
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447 Delete<PropertyName>();
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448
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449 E-state atom types are assigned to all non-hydrogen atoms in a molecule using module
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450 AtomTypes::EStateAtomTypes.pm and E-state values are calculated using module
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451 AtomicDescriptors::EStateValues.pm. Using E-state atom types and E-state values,
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452 B<EStateIndiciesFingerprints> constituting sum of E-state values for E-sate atom types
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453 are generated.
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454
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455 Two types of E-state atom types set size are allowed:
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456
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457 ArbitrarySize - Corresponds to only E-state atom types detected
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458 in molecule
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459 FixedSize - Corresponds to fixed number of E-state atom types previously
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460 defined
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461
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462 Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types to
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463 non-hydrogen atoms in the molecule, is able to assign atom types to any valid
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464 atom group. However, for I<FixedSize> value of B<EStateAtomTypesSetToUse>, only a
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465 fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in
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466 Ref 77 ] are used for fingerprints.
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467
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468 The fixed size E-state atom type set size used during generation of fingerprints contains
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469 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
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470 MayaChemTools.
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471
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472 Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
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473 E-state indicies fingerprints:
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474
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475 Type EStateAtomTypesSetToUse
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476
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477 EStateIndicies ArbitrarySize [ default fingerprints ]
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478 EStateIndicies FixedSize
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479
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480 The current release of MayaChemTools generates the following types of E-state
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481 fingerprints vector strings:
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482
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483 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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484 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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485 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
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486 .024 -2.270
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487
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488 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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489 ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
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490 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
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491 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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492 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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493
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494 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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495 IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
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496 SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
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497 C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
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498 0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 4.387 0 0 0
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499 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
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500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...
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501
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502 =head2 METHODS
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503
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504 =over 4
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505
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506 =item B<new>
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507
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508 $EStateIndiciesFingerprints = new EStateIndiciesFingerprints(%NamesAndValues);
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509
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510 Using specified I<EStateIndiciesFingerprints> property names and values hash, B<new> method creates a new object
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511 and returns a reference to newly created B<PathLengthFingerprints> object. By default, the
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512 following properties are initialized:
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513
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514 Molecule = '';
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515 Type = 'EStateIndicies'
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516 EStateAtomTypesSetToUse = 'ArbitrarySize'
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517 ValuesPrecision = 3
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518
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519 Examples:
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520
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521 $EStateIndiciesFingerprints = new AtomTypesFingerprints(
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522 'Molecule' => $Molecule,
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523 'EStateAtomTypesSetToUse' =>
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524 'ArbitrarySize');
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525
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526 $EStateIndiciesFingerprints = new AtomTypesFingerprints(
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527 'Molecule' => $Molecule,
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528 'EStateAtomTypesSetToUse' =>
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529 'FixedSize');
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530
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531 $EStateIndiciesFingerprints->GenerateFingerprints();
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532 print "$EStateIndiciesFingerprints\n";
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533
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534 =item B<GenerateFingerprints>
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535
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536 $EStateIndiciesFingerprints = $EStateIndiciesFingerprints->
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537 GenerateEStateIndiciesFingerprints();
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538
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539 Generates EState keys fingerprints and returns I<EStateIndiciesFingerprints>.
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540
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541 =item B<GetDescription>
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542
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543 $Description = $EStateIndiciesFingerprints->GetDescription();
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544
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545 Returns a string containing description of EState keys fingerprints.
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546
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547 =item B<SetEStateAtomTypesSetToUse>
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548
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549 $EStateIndiciesFingerprints->SetEStateAtomTypesSetToUse($Value);
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550
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551 Sets I<Value> of I<EStateAtomTypesSetToUse> and returns I<EStateIndiciesFingerprints>.
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552 Possible values: I<ArbitrarySize or FixedSize>. Default value: I<ArbitrarySize>.
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553
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554 =item B<SetValuesPrecision>
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555
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556 $EStateIndiciesFingerprints->SetValuesPrecision($Precision);
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557
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558 Sets precesion of E-state values to use during generation of E-state indices fingerprints
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559 and returns I<EStateIndiciesFingerprints>. Possible values: I<Positive integers>.
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560 Default value: I<3>.
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561
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562 =item B<StringifyEStateIndiciesFingerprints>
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563
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564 $String = $EStateIndiciesFingerprints->StringifyEStateIndiciesFingerprints();
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565
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566 Returns a string containing information about I<EStateIndiciesFingerprints> object.
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567
|
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568 =back
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569
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570 =head1 AUTHOR
|
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571
|
|
|
572 Manish Sud <msud@san.rr.com>
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573
|
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|
574 =head1 SEE ALSO
|
|
|
575
|
|
|
576 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
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|
|
577 ExtendedConnectivityFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm,
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|
|
578 TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
|
|
|
579 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
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580 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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581
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582 =head1 COPYRIGHT
|
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583
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584 Copyright (C) 2015 Manish Sud. All rights reserved.
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585
|
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586 This file is part of MayaChemTools.
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587
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588 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
589 the terms of the GNU Lesser General Public License as published by the Free
|
|
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590 Software Foundation; either version 3 of the License, or (at your option)
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591 any later version.
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592
|
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593 =cut
|
