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1 package AtomicDescriptors::EStateValuesDescriptors;
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2 #
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3 # $RCSfile: EStateValuesDescriptors.pm,v $
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4 # $Date: 2015/02/28 20:47:49 $
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5 # $Revision: 1.16 $
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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 Scalar::Util ();
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33 use Matrix;
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34 use Constants;
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35 use TextUtil ();
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36 use MathUtil ();
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37 use StatisticsUtil ();
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38 use Atom;
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39 use Molecule;
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40 use AtomicDescriptors::AtomicDescriptors;
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41
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42 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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43
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44 @ISA = qw(AtomicDescriptors::AtomicDescriptors Exporter);
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45 @EXPORT = qw();
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46 @EXPORT_OK = qw();
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47
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48 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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49
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50 # Setup class variables...
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51 my($ClassName);
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52 _InitializeClass();
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53
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54 # Overload Perl functions...
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55 use overload '""' => 'StringifyEStateValuesDescriptors';
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56
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57 # Class constructor...
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58 sub new {
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59 my($Class, %NamesAndValues) = @_;
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60
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61 # Initialize object...
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62 my $This = $Class->SUPER::new();
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63 bless $This, ref($Class) || $Class;
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64 $This->_InitializeEStateValuesDescriptors();
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65
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66 $This->_InitializeEStateValuesDescriptorsProperties(%NamesAndValues);
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67
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68 return $This;
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69 }
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70
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71 # Initialize class ...
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72 sub _InitializeClass {
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73 #Class name...
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74 $ClassName = __PACKAGE__;
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75 }
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76
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77
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78 # Initialize object data...
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79 #
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80 sub _InitializeEStateValuesDescriptors {
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81 my($This) = @_;
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82
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83 # Type of AtomicDescriptor...
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84 $This->{Type} = 'EStateValue';
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85
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86 # Intrinsic state values calculated for non-hydrogen atom...
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87 #
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88 %{$This->{IStateValues}} = ();
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89
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90 # Calculatetion of E-state values for types for hydrogens is not supported...
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91 $This->{IgnoreHydrogens} = 1;
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92
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93 # Perturbation to intrinsic state values of atoms corresponding to all non-hydrogen
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94 # atom pairs...
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95 #
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96 %{$This->{DeltaIStateMatrix}} = ();
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97
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98 # E-state values calculated for non-hydrogen atoms...
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99 #
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100 %{$This->{EStateValues}} = ();
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101
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102 return $This;
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103 }
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104
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105 # Initialize object properties...
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106 #
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107 sub _InitializeEStateValuesDescriptorsProperties {
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108 my($This, %NamesAndValues) = @_;
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109
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110 my($Name, $Value, $MethodName);
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111 while (($Name, $Value) = each %NamesAndValues) {
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112 $MethodName = "Set${Name}";
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113 $This->$MethodName($Value);
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114 }
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115
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116 # Make sure molecule object was specified...
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117 if (!exists $NamesAndValues{Molecule}) {
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118 croak "Error: ${ClassName}->New: Object can't be instantiated without specifying molecule...";
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119 }
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120
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121 # Intialize atomic descriptor values...
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122 $This->_InitializeDescriptorValues();
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123
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124 return $This;
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125 }
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126
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127 # Disable change of ignore hydrogens...
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128 #
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129 sub SetIgnoreHydrogens {
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130 my($This, $IgnoreHydrogens) = @_;
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131
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132 carp "Warning: ${ClassName}->SetIgnoreHydrogens: Ignore hydrogens value can't be changed: It's not supported...";
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133
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134 return $This;
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135 }
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136
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137 # Generate electrotopological state (E-state) values [ Ref 75-78 ] for all atoms
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138 # in the molecule...
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139 #
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140 # Calculation of E-state values for non-hydrogen atoms:
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141 #
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142 # Let:
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143 #
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144 # N = Principal quantum number or period number corresponding to element symbol
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145 #
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146 # Sigma = Number of sigma electrons involves in bonds to hydrogen and non-hydrogen atoms
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147 # attached to atom
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148 # = Number of sigma bonds to hydrogen and non-hydrogen atoms attached to atom
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149 # PI = Number of PI electrons involved in bonds to non-hydrogen atoms attached to atom
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150 # = Number of PI bonds to non-hydrogen atoms attached to atom
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151 #
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152 # LP = Number of lone pair electrons on atom
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153 #
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154 # Zv = Number of electrons in valence shell of atom
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155 #
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156 # X = Number of non-hydrogen atom neighbors or heavy atoms attached to atom
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157 # H = Number of implicit and explicit hydrogens for atom
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158 #
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159 # Delta = Number of sigma electrons involved to bonds to non-hydrogen atoms
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160 # DeltaV = ValenceDelta = Number of valence shell electrons not involved in bonding to hydrogen atoms
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161 #
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162 # Ii = Intrinsic state value for atom i
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163 #
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164 # DeltaIi = Sum of perturbations to intrinsic state value Ii of atom i by all other atoms besides atom i
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165 #
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166 # DeltaIij = Perturbation to intrinsic state value Ii of atom i by atom j
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167 #
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168 # Dij = Graph/bond distance between atom i and j
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169 # Rij = Dij + 1
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170 #
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171 # Si = E-state value for atom i
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172 #
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173 #
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174 # Then:
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175 #
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176 # Delta = Sigma - H = X
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177 #
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178 # DeltaV = Zv - H
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179 # = Sigma + PI + LP - H
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180 #
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181 # Ii = ( ( ( 2 / N ) ** 2 ) * DeltaV + 1 ) / Delta
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182 #
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183 # Si = Ii + DeltaIi
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184 #
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185 # DeltaIij = (Ii - Ij) / (Rij ** 2) for j not equal to i
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186 #
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187 # DeltaIji = - DeltaIij
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188 #
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189 # DeltaIi = SUM ( (Ii - Ij) / (Rij ** 2) ) for j = 1 to num of atoms skipping atom i
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190 #
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191 # Methodology:
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192 # . Calculate intrinsic state values for atoms.
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193 # . Generate a distance matrix.
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194 # . Use distance matrix to calculate DeltaIij matrix with each row i containing
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195 # DeltaIij values corresponding to perturbation to intrinsic state value of atom
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196 # i by atom j.
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197 # . Calculate E-state values using DeltaIij matrix.
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198 # . Assign E-state values to atoms.
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199 #
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200 # Notes:
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201 # . The current release of MayaChemTools doesn't support calculation of Hydrogen
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202 # E-state values.
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203 #
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204 sub GenerateDescriptors {
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205 my($This) = @_;
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206
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207 # Cache appropriate molecule data...
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208 $This->_SetupMoleculeDataCache();
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209
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210 # Generate distance matrix...
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211 if (!$This->_SetupDistanceMatrix()) {
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212 carp "Warning: ${ClassName}->GenerateDescriptors: E-state values description generation didn't succeed: Couldn't generate a distance matrix...";
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213 return $This;
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214 }
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215
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216 # Calculate EState values..
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217 if (!$This->_CalculateEStateValuesDescriptors()) {
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218 carp "Warning: ${ClassName}->GenerateDescriptors: E-state values description generation didn't succeed: Couldn't calculate IState values for all atoms...";
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219 return $This;
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220 }
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221
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222 # Set final descriptor values...
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223 $This->_SetFinalValues();
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224
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225 # Clear cached molecule data...
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226 $This->_ClearMoleculeDataCache();
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227
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228 return $This;
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229 }
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230
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231 # Calculate E-state values for non-hydrogen atoms...
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232 #
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233 sub _CalculateEStateValuesDescriptors {
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234 my($This) = @_;
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235 my($DeltaIStateMatrix, $NumOfRows, $NumOfCols, $RowIndex, $AtomID, $EStateValue, $IStateValue, $DeltaIStateValue, @DeltaIStateMatrixRowValues);
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236
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237 %{$This->{EStateValues}} = ();
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238
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239 # Calculate intrinsic state values for non-hydrogen atoms...
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240 if (!$This->_CalculateIStateValues()) {
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241 return undef;
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242 }
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243
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244 # Calculate delta intrinsic state matrix for non-hydrogen atoms...
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245 $This->_CalculateDeltaIStateMatrix();
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246
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247 # Get DeltaIState matrix information...
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248 $DeltaIStateMatrix = $This->{DeltaIStateMatrix};
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249 ($NumOfRows, $NumOfCols) = $DeltaIStateMatrix->GetSize();
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250
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251 # Calculate EState values...
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252 ROWINDEX: for $RowIndex (0 .. ($NumOfRows - 1) ) {
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253 $AtomID = $This->{AtomIndexToID}{$RowIndex};
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254 if ( !(exists($This->{IStateValues}{$AtomID})) ) {
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255 next ROWINDEX;
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256 }
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257 $IStateValue = $This->{IStateValues}{$AtomID};
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258
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259 @DeltaIStateMatrixRowValues = $DeltaIStateMatrix->GetRowValues($RowIndex);
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260 $DeltaIStateValue = StatisticsUtil::Sum(\@DeltaIStateMatrixRowValues);
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261
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262 $EStateValue = $IStateValue + $DeltaIStateValue;
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263
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264 $This->{EStateValues}{$AtomID} = $EStateValue;
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265 }
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266 return $This;
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267 }
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268
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269 # Calculate intrinsic state values for non-hydrogen atoms...
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270 #
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271 sub _CalculateIStateValues {
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272 my($This) = @_;
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273 my($Atom, $AtomID);
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274
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275 %{$This->{IStateValues}} = ();
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276
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277 ATOM: for $Atom (@{$This->{Atoms}}) {
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278 # Irrespective of IgoreHydrogens value, just ignore hydrogens...
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279 if ($Atom->IsHydrogen()) {
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280 next ATOM;
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281 }
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282 $AtomID = $Atom->GetID();
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283 $This->{IStateValues}{$AtomID} = $This->_CalculateIStateValue($Atom);
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284 if (!defined($This->{IStateValues}{$AtomID})) {
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285 return undef;
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286 }
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287 }
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288 return $This;
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289 }
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290
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291 # Calculation intrinsic state value for non-hydrogen...
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292 #
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293 sub _CalculateIStateValue {
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294 my($This, $Atom) = @_;
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295 my($IStateValue, $Delta, $DeltaV, $PeriodNumber);
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296
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297 $PeriodNumber = $Atom->GetPeriodNumber();
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298 ($Delta, $DeltaV) = $This->_GetDeltaValues($Atom);
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299
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300 if (!(defined($Delta) && defined($PeriodNumber) && defined($DeltaV))) {
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301 return undef;
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302 }
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303
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304 $IStateValue = ($PeriodNumber && $Delta) ? (((2/$PeriodNumber)**2)*$DeltaV + 1)/$Delta : 0;
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305
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306 return $IStateValue;
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307 }
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308
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309 # Get Delta and DeltaV values for atom...
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310 #
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311 sub _GetDeltaValues {
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312 my($This, $Atom) = @_;
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313 my($Delta, $DeltaV, $ValenceElectrons, $NumOfHydrogens);
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314
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315 ($Delta, $DeltaV) = (undef, undef);
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316
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317 $ValenceElectrons = $Atom->GetValenceElectrons();
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318 $NumOfHydrogens = $Atom->GetAtomicInvariantValue('H');
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319
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320 $Delta = $Atom->GetAtomicInvariantValue('X');
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321 if (defined($ValenceElectrons) && defined($NumOfHydrogens)) {
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322 $DeltaV = $ValenceElectrons - $NumOfHydrogens;
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323 }
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324
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325 return ($Delta, $DeltaV);
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326 }
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327
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328 # Calculate DeltaIState matrix for atoms with each row i containing DeltaIij values
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329 # corresponding atom atoms i and j.
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330 #
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331 # Notes:
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332 # . Matrix elements corresponding to hydrogen atoms or unconnected
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333 # are assigned zero value.
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334 #
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335 sub _CalculateDeltaIStateMatrix {
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336 my($This) = @_;
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337 my($DistanceMatrix, $NumOfRows, $NumOfCols, $RowIndex, $ColIndex, $AtomID1, $AtomID2, $DeltaIStateMatrix, $IStateValue1, $IStateValue2, $GraphDistance, $DeltaIState12, $DeltaIState21, $SkipIndexCheck);
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338
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339 # Get distance matrix information...
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340 $DistanceMatrix = $This->{DistanceMatrix};
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341 ($NumOfRows, $NumOfCols) = $DistanceMatrix->GetSize();
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342
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343 # Initialize DeltaIState matrix...
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344 $This->{DeltaIStateMatrix} = new Matrix($NumOfRows, $NumOfCols);
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345 $DeltaIStateMatrix = $This->{DeltaIStateMatrix};
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346
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347 $SkipIndexCheck = 1;
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348
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349 # Calculate DeltaIState matrix values...
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350 ROWINDEX: for $RowIndex (0 .. ($NumOfRows - 1) ) {
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351 $AtomID1 = $This->{AtomIndexToID}{$RowIndex};
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352 if (!exists($This->{IStateValues}{$AtomID1})) {
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353 next ROWINDEX;
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354 }
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355 $IStateValue1 = $This->{IStateValues}{$AtomID1};
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356
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357 COLINDEX: for $ColIndex (($RowIndex + 1) .. ($NumOfCols - 1) ) {
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358 $AtomID2 = $This->{AtomIndexToID}{$ColIndex};
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359 if (!exists($This->{IStateValues}{$AtomID2})) {
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360 next COLINDEX;
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361 }
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362 $IStateValue2 = $This->{IStateValues}{$AtomID2};
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363
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364 # Make sure it's a connected atom...
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365 $GraphDistance = $DistanceMatrix->GetValue($RowIndex, $ColIndex, $SkipIndexCheck);
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366 if ($GraphDistance >= BigNumber) {
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367 next COLINDEX;
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368 }
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369
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370 $DeltaIState12 = ($IStateValue1 - $IStateValue2)/(($GraphDistance + 1)**2);
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371 $DeltaIState21 = -$DeltaIState12;
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372
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373 # Set DeltaIState values...
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374 $DeltaIStateMatrix->SetValue($RowIndex, $ColIndex, $DeltaIState12, $SkipIndexCheck);
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375 $DeltaIStateMatrix->SetValue($ColIndex, $RowIndex, $DeltaIState21, $SkipIndexCheck);
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376 }
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377 }
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378 }
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379
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380 # Setup distance matrix...
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381 #
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382 sub _SetupDistanceMatrix {
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383 my($This) = @_;
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384
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385 $This->{DistanceMatrix} = $This->GetMolecule()->GetDistanceMatrix();
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386
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387 if (!defined($This->{DistanceMatrix})) {
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388 return undef;
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389 }
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390
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391 return $This;
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392 }
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393
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394 # Setup final descriptor values...
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395 #
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396 sub _SetFinalValues {
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397 my($This) = @_;
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398 my($Atom, $AtomID, $EStateValue);
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399
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400 ATOM: for $Atom (@{$This->{Atoms}}) {
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401 $AtomID = $Atom->GetID();
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402 if (!exists $This->{EStateValues}{$AtomID}) {
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403 next ATOM;
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404 }
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405 $EStateValue = $This->{EStateValues}{$AtomID};
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406 $This->SetDescriptorValue($Atom, $EStateValue);
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407 }
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408
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409 return $This;
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410 }
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411
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412 # Cache appropriate molecule data...
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413 #
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414 sub _SetupMoleculeDataCache {
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415 my($This) = @_;
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416
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417 # Get all atoms including hydrogens to correctly map atom indicies to atom IDs for
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418 # usage of distance matrix.
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419 #
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420 @{$This->{Atoms}} = $This->GetMolecule()->GetAtoms();
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421
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422 # Get all atom IDs...
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423 my(@AtomIDs);
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424 @AtomIDs = ();
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425 @AtomIDs = map { $_->GetID() } @{$This->{Atoms}};
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426
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427 # Set AtomIndex to AtomID hash...
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428 %{$This->{AtomIndexToID}} = ();
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429 @{$This->{AtomIndexToID}}{ (0 .. $#AtomIDs) } = @AtomIDs;
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430
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431 return $This;
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432 }
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433
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434 # Clear cached molecule data...
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435 #
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436 sub _ClearMoleculeDataCache {
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437 my($This) = @_;
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438
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439 @{$This->{Atoms}} = ();
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440
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441 return $This;
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442 }
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443
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444 # Return a string containg data for EStateValuesDescriptors object...
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445 #
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446 sub StringifyEStateValuesDescriptors {
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447 my($This) = @_;
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448 my($EStateValuesDescriptorsString);
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449
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450 # Type of AtomicValues...
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451 $EStateValuesDescriptorsString = "AtomicDescriptorType: $This->{Type}; IgnoreHydrogens: " . ($This->{IgnoreHydrogens} ? "Yes" : "No");
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452
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453 # Setup atomic descriptor information...
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454 my($AtomID, $DescriptorValue, @DescriptorValuesInfo, %DescriptorValues);
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455
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456 @DescriptorValuesInfo = ();
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457 %DescriptorValues = $This->GetDescriptorValues();
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458
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459 for $AtomID (sort { $a <=> $b } keys %DescriptorValues) {
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460 $DescriptorValue = $DescriptorValues{$AtomID};
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461 $DescriptorValue = (TextUtil::IsEmpty($DescriptorValue) || $DescriptorValue =~ /^None$/i) ? 'None' : MathUtil::round($DescriptorValue, 3) + 0;
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462 push @DescriptorValuesInfo, "$AtomID:$DescriptorValue";
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463 }
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464 $EStateValuesDescriptorsString .= "; AtomIDs:EStateValuesDescriptors: <" . TextUtil::JoinWords(\@DescriptorValuesInfo, ", ", 0) . ">";
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465
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466 return $EStateValuesDescriptorsString;
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467 }
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468
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469 # Is it a EStateValuesDescriptors object?
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470 sub _IsEStateValuesDescriptors {
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471 my($Object) = @_;
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|
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472
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473 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
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|
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474 }
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475
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476 1;
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477
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478 __END__
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479
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480 =head1 NAME
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481
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482 EStateValuesDescriptors
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483
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484 =head1 SYNOPSIS
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485
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486 use AtomicDescriptors::EStateValuesDescriptors;
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487
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488 use AtomicDescriptors::EStateValuesDescriptors qw(:all);
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489
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|
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490 =head1 DESCRIPTION
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|
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491
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|
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492 B<EStateValuesDescriptors> class provides the following methods:
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493
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|
|
494 new, GenerateDescriptors, StringifyEStateValuesDescriptors
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|
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495
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|
|
496 B<EStateValuesDescriptors> is derived from B<AtomicValues> class which in turn
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|
|
497 is derived from B<ObjectProperty> base class that provides methods not explicitly defined
|
|
|
498 in B<EStateValuesDescriptors>, B<AtomicValues> or B<ObjectProperty> classes using Perl's
|
|
|
499 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:
|
|
|
500
|
|
|
501 Set<PropertyName>(<PropertyValue>);
|
|
|
502 $PropertyValue = Get<PropertyName>();
|
|
|
503 Delete<PropertyName>();
|
|
|
504
|
|
|
505 For calculation of electrotopological state (E-state) values for non-hydrogen atoms:
|
|
|
506
|
|
|
507 Let:
|
|
|
508
|
|
|
509 N = Principal quantum number or period number corresponding to
|
|
|
510 element symbol
|
|
|
511
|
|
|
512 Sigma = Number of sigma electrons involves in bonds to hydrogen and
|
|
|
513 non-hydrogen atoms attached to atom
|
|
|
514 = Number of sigma bonds to hydrogen and non-hydrogen atoms
|
|
|
515 attached to atom
|
|
|
516 PI = Number of PI electrons involved in bonds to non-hydrogen atoms
|
|
|
517 attached to atom
|
|
|
518 = Number of PI bonds to non-hydrogen atoms attached to atom
|
|
|
519
|
|
|
520 LP = Number of lone pair electrons on atom
|
|
|
521
|
|
|
522 Zv = Number of electrons in valence shell of atom
|
|
|
523
|
|
|
524 X = Number of non-hydrogen atom neighbors or heavy atoms attached
|
|
|
525 to atom
|
|
|
526 H = Number of implicit and explicit hydrogens for atom
|
|
|
527
|
|
|
528 Delta = Number of sigma electrons involved to bonds to non-hydrogen
|
|
|
529 atoms
|
|
|
530 DeltaV = ValenceDelta = Number of valence shell electrons not involved
|
|
|
531 in bonding to hydrogen atoms
|
|
|
532
|
|
|
533 Ii = Intrinsic state value for atom i
|
|
|
534
|
|
|
535 DeltaIi = Sum of perturbations to intrinsic state value Ii of atom i
|
|
|
536 by all other atoms besides atom i
|
|
|
537
|
|
|
538 DeltaIij = Perturbation to intrinsic state value Ii of atom i by atom j
|
|
|
539
|
|
|
540 Dij = Graph/bond distance between atom i and j
|
|
|
541 Rij = Dij + 1
|
|
|
542
|
|
|
543 Si = E-state value for atom i
|
|
|
544
|
|
|
545 Then:
|
|
|
546
|
|
|
547 Delta = Sigma - H = X
|
|
|
548
|
|
|
549 DeltaV = Zv - H
|
|
|
550 = Sigma + PI + LP - H
|
|
|
551
|
|
|
552 Ii = ( ( ( 2 / N ) ** 2 ) * DeltaV + 1 ) / Delta
|
|
|
553
|
|
|
554 DeltaIi = SUM ( (Ii - Ij) / (Rij ** 2) ) for j = 1 to num of atoms skipping atom i
|
|
|
555
|
|
|
556 Si = Ii + DeltaIi
|
|
|
557
|
|
|
558 The current release of MayaChemTools doesn't support calculation of E-state
|
|
|
559 values [ Ref 75-78 ] for hydrogens.
|
|
|
560
|
|
|
561 =head2 METHODS
|
|
|
562
|
|
|
563 =over 4
|
|
|
564
|
|
|
565 =item B<new>
|
|
|
566
|
|
|
567 $NewEStateValuesDescriptors = new AtomicDescriptors::
|
|
|
568 EStateValuesDescriptors(%NamesAndValues);
|
|
|
569
|
|
|
570 Using specified I<EStateValuesDescriptors> property names and values hash, B<new>
|
|
|
571 method creates a new object and returns a reference to newly created B<EStateValuesDescriptors>
|
|
|
572 object. By default, the following properties are initialized:
|
|
|
573
|
|
|
574 Molecule = ''
|
|
|
575 Type = 'EState'
|
|
|
576 IgnoreHydrogens = 1
|
|
|
577
|
|
|
578 Examples:
|
|
|
579
|
|
|
580 $EStateValuesDescriptors = new AtomicDescriptors::EStateValuesDescriptors(
|
|
|
581 'Molecule' => $Molecule,
|
|
|
582 'IgnoreHydrogens' => 1);
|
|
|
583
|
|
|
584 =item B<GenerateDescriptors>
|
|
|
585
|
|
|
586 $EStateValuesDescriptors->GenerateDescriptors();
|
|
|
587
|
|
|
588 Calculates E-state atomic descriptors for all the atoms in a molecule and returns
|
|
|
589 I<EStateValuesDescriptors>.
|
|
|
590
|
|
|
591 =item B<StringifyEStateValuesDescriptors>
|
|
|
592
|
|
|
593 $String = $EStateValuesDescriptors->StringifyEStateValuesDescriptors();
|
|
|
594
|
|
|
595 Returns a string containing information about I<EStateValuesDescriptors> object.
|
|
|
596
|
|
|
597 =back
|
|
|
598
|
|
|
599 =head1 AUTHOR
|
|
|
600
|
|
|
601 Manish Sud <msud@san.rr.com>
|
|
|
602
|
|
|
603 =head1 SEE ALSO
|
|
|
604
|
|
|
605 AtomicDescriptors.pm
|
|
|
606
|
|
|
607 =head1 COPYRIGHT
|
|
|
608
|
|
|
609 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
610
|
|
|
611 This file is part of MayaChemTools.
|
|
|
612
|
|
|
613 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
614 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
615 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
616 any later version.
|
|
|
617
|
|
|
618 =cut
|
