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1 package MolecularDescriptors::SLogPAndSMRDescriptors;
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2 #
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3 # $RCSfile: SLogPAndSMRDescriptors.pm,v $
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4 # $Date: 2015/02/28 20:49:20 $
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5 # $Revision: 1.18 $
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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 TextUtil ();
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34 use MathUtil ();
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35 use Atom;
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36 use Molecule;
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37 use MolecularDescriptors::MolecularDescriptors;
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38 use AtomTypes::SLogPAtomTypes;
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39
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40 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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41
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42 @ISA = qw(MolecularDescriptors::MolecularDescriptors Exporter);
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43 @EXPORT = qw();
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44 @EXPORT_OK = qw(GetDescriptorNames);
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45
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46 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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47
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48 # Setup class variables...
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49 my($ClassName, @DescriptorNames);
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50 _InitializeClass();
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51
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52 # Overload Perl functions...
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53 use overload '""' => 'StringifySLogPAndSMRDescriptors';
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54
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55 # Class constructor...
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56 sub new {
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57 my($Class, %NamesAndValues) = @_;
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58
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59 # Initialize object...
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60 my $This = $Class->SUPER::new();
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61 bless $This, ref($Class) || $Class;
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62 $This->_InitializeSLogPAndSMRDescriptors();
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63
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64 $This->_InitializeSLogPAndSMRDescriptorsProperties(%NamesAndValues);
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65
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66 return $This;
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67 }
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68
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69 # Initialize class ...
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70 sub _InitializeClass {
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71 #Class name...
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72 $ClassName = __PACKAGE__;
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73
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74 # Descriptor names...
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75 @DescriptorNames = ('SLogP', 'SMR');
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76 }
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77
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78 # Get descriptor names as an array.
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79 #
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80 # This functionality can be either invoked as a class function or an
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81 # object method.
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82 #
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83 sub GetDescriptorNames {
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84 return @DescriptorNames;
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85 }
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86
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87 # Initialize object data...
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88 #
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89 sub _InitializeSLogPAndSMRDescriptors {
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90 my($This) = @_;
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91
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92 # Type of MolecularDescriptor...
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93 $This->{Type} = 'SLogPAndSMR';
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94
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95 # SLogPAndSMR atom types assigned to hydrogen and non-hydrogen atoms...
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96 %{$This->{AtomTypes}} = ();
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97
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98 # Intialize descriptor names and values...
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99 $This->_InitializeDescriptorNamesAndValues(@DescriptorNames);
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100
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101 return $This;
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102 }
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103
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104 # Initialize object properties...
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105 #
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106 sub _InitializeSLogPAndSMRDescriptorsProperties {
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107 my($This, %NamesAndValues) = @_;
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108
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109 my($Name, $Value, $MethodName);
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110 while (($Name, $Value) = each %NamesAndValues) {
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111 $MethodName = "Set${Name}";
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112 $This->$MethodName($Value);
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113 }
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114
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115 return $This;
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116 }
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117
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118
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119 # Calculate SLogPAndSMR value [ Ref 89 ] for a molecule...
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120 #
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121 # Methodology:
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122 # . Assign SLogP atom types to all atoms.
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123 # . Calculate SLogP and SMR value by adding contribution of each atom type.
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124 #
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125 # Caveats:
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126 # . All hydrogens must be added to molecule before calling GenerateDescriptors.
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127 #
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128 sub GenerateDescriptors {
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129 my($This) = @_;
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130
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131 # Initialize descriptor values...
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132 $This->_InitializeDescriptorValues();
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133
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134 # Check availability of molecule...
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135 if (!$This->{Molecule}) {
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136 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set...";
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137 return undef;
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138 }
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139
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140 # Cache appropriate molecule data...
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141 $This->_SetupMoleculeDataCache();
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142
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143 # Assign SLogP atom types...
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144 if (!$This->_AssignAtomTypes()) {
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145 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't assign valid SLogPAndSMR atom types to all atoms...";
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146 return undef;
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147 }
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148
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149 # Calculate descriptor values...
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150 if (!$This->_CalculateDescriptorValues()) {
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151 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular description generation didn't succeed: Couldn't calculate SLogPAndSMR values corresponding to assigned SLogP atom types...";
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152 return undef;
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153 }
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154
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155 # Set final descriptor values...
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156 $This->_SetFinalDescriptorValues();
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157
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158 # Clear cached molecule data...
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159 $This->_ClearMoleculeDataCache();
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160
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161 return $This;
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162 }
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163
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164 # Assign SLogPAndSMR atom types..
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165 #
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166 sub _AssignAtomTypes {
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167 my($This) = @_;
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168 my($SLogPAtomTypes, $Atom, $AtomID);
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169
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170 %{$This->{AtomTypes}} = ();
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171
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172 # Assign atom types...
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173 $SLogPAtomTypes = new AtomTypes::SLogPAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => 0);
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174 $SLogPAtomTypes->AssignAtomTypes();
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175
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176 # Make sure SLogP atom types assignment is successful...
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177 if (!$SLogPAtomTypes->IsAtomTypesAssignmentSuccessful()) {
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178 return undef;
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179 }
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180
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181 # Collect assigned atom types...
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182 for $Atom (@{$This->{Atoms}}) {
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183 $AtomID = $Atom->GetID();
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184 $This->{AtomTypes}{$AtomID} = $SLogPAtomTypes->GetAtomType($Atom);
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185 }
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186
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187 return $This;
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188 }
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189
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190 # Calculate SLogP and SMR values...
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191 #
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192 sub _CalculateDescriptorValues {
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193 my($This) = @_;
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194 my($SLogP, $SMR, $AtomID, $SLogPAndSMRDataRef, $AtomType);
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195
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196 $SLogP = 0; $SMR = 0;
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197
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198 # Get SLogP and SMR atom types data...
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199 $SLogPAndSMRDataRef = AtomTypes::SLogPAtomTypes::GetSLogPAtomTypesData();
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200
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201 for $AtomID (keys %{$This->{AtomTypes}}) {
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202 $AtomType = $This->{AtomTypes}{$AtomID};
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203
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204 # Makes sure data for SLogp and SMR contribution exists for atom type...
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205 if (!(exists($SLogPAndSMRDataRef->{DataCol4}{$AtomType}) && exists($SLogPAndSMRDataRef->{DataCol5}{$AtomType}))) {
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206 return undef;
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207 }
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208
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209 # Data for SLogP contribution is in column number 4...
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210 $SLogP += $SLogPAndSMRDataRef->{DataCol4}{$AtomType};
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211
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212 # Data for SMR contribution is in column number 5...
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213 $SMR += $SLogPAndSMRDataRef->{DataCol5}{$AtomType};
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214 }
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215
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216 # Track the calculated values...
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217 $This->{SLogP} = MathUtil::round($SLogP, 2);
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218 $This->{SMR} = MathUtil::round($SMR, 2);
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219
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220 return $This;
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221 }
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222
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223 # Setup final descriptor values...
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224 #
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225 sub _SetFinalDescriptorValues {
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226 my($This) = @_;
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227
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228 $This->{DescriptorsGenerated} = 1;
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229
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230 $This->SetDescriptorValues($This->{SLogP}, $This->{SMR});
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231
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232 return $This;
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233 }
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234
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235 # Cache appropriate molecule data...
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236 #
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237 sub _SetupMoleculeDataCache {
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238 my($This) = @_;
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239
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240 @{$This->{Atoms}} = $This->GetMolecule()->GetAtoms();
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241
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242 return $This;
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243 }
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244
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245 # Clear cached molecule data...
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246 #
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247 sub _ClearMoleculeDataCache {
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248 my($This) = @_;
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249
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250 @{$This->{Atoms}} = ();
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251
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252 return $This;
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253 }
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254
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255 # Return a string containg data for SLogPAndSMRDescriptors object...
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256 #
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257 sub StringifySLogPAndSMRDescriptors {
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258 my($This) = @_;
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259 my($SLogPAndSMRDescriptorsString);
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260
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261 $SLogPAndSMRDescriptorsString = "MolecularDescriptorType: $This->{Type}; " . $This->_StringifyDescriptorNamesAndValues();
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262
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263 return $SLogPAndSMRDescriptorsString;
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264 }
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265
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266 # Is it a SLogPAndSMRDescriptors object?
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267 sub _IsSLogPAndSMRDescriptors {
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268 my($Object) = @_;
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269
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270 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
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271 }
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272
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273 1;
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274
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275 __END__
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276
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277 =head1 NAME
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278
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279 SLogPAndSMRDescriptors
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280
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281 =head1 SYNOPSIS
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282
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283 use MolecularDescriptors::SLogPAndSMRDescriptors;
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284
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285 use MolecularDescriptors::SLogPAndSMRDescriptors qw(:all);
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286
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287 =head1 DESCRIPTION
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288
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289 B<SLogPAndSMRDescriptors> class provides the following methods:
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290
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291 new, GenerateDescriptors, GetDescriptorNames,
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292 StringifySLogPAndSMRDescriptors
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293
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294 B<SLogPAndSMRDescriptors> is derived from B<MolecularDescriptors> class which in turn
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295 is derived from B<ObjectProperty> base class that provides methods not explicitly defined
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296 in B<SLogPAndSMRDescriptors>, B<MolecularDescriptors> or B<ObjectProperty> classes using Perl's
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297 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:
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298
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299 Set<PropertyName>(<PropertyValue>);
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300 $PropertyValue = Get<PropertyName>();
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301 Delete<PropertyName>();
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302
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303 After SLogP atom types [ Ref 89 ] has been assigned to all atoms in a molecule using
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304 AtomTypes::SLogPAndSMR.pm module, SLogP (calculated logP) and SMR (calculated molar
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305 refractivity) values are calculated by adding up LogP and MR contributions of each atom
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306 type.
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307
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308 =head2 METHODS
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309
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310 =over 4
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311
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312 =item B<new>
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313
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314 $NewSLogPAndSMRDescriptors = new MolecularDescriptors::
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315 SLogPAndSMRDescriptors(
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316 %NamesAndValues);
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317
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318 Using specified I<SLogPAndSMRDescriptors> property names and values hash, B<new>
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319 method creates a new object and returns a reference to newly created B<SLogPAndSMRDescriptors>
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320 object. By default, the following properties are initialized:
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321
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322 Molecule = ''
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323 Type = 'SLogPAndSMR'
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324 @DescriptorNames = ('SLogP', 'SMR')
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325 @DescriptorValues = ('None', 'None')
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326
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327 Examples:
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328
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329 $SLogPAndSMRDescriptors = new MolecularDescriptors::
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330 SLogPAndSMRDescriptors();
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331
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332 $SLogPAndSMRDescriptors->SetMolecule($Molecule);
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333 $SLogPAndSMRDescriptors->GenerateDescriptors();
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334 print "SLogPAndSMRDescriptors: $SLogPAndSMRDescriptors\n";
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335
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336 =item B<GenerateDescriptors>
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337
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338 $SLogPAndSMRDescriptors->GenerateDescriptors();
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339
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340 Calculate SLogP and SMR values for a molecule and returns I<SLogPAndSMRDescriptors>.
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341
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342 =item B<GetDescriptorNames>
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343
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344 @DescriptorNames = $SLogPAndSMRDescriptors->GetDescriptorNames();
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345 @DescriptorNames = MolecularDescriptors::SLogPAndSMRDescriptors::
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346 GetDescriptorNames();
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347
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348 Returns all available descriptor names as an array.
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349
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350 =item B<StringifySLogPAndSMRDescriptors>
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351
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352 $String = $SLogPAndSMRDescriptors->StringifySLogPAndSMRDescriptors();
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353
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354 Returns a string containing information about I<SLogPAndSMRDescriptors> object.
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355
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356 =back
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357
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358 =head1 AUTHOR
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359
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360 Manish Sud <msud@san.rr.com>
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361
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362 =head1 SEE ALSO
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363
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364 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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365
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366 =head1 COPYRIGHT
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367
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368 Copyright (C) 2015 Manish Sud. All rights reserved.
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369
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370 This file is part of MayaChemTools.
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371
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372 MayaChemTools is free software; you can redistribute it and/or modify it under
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373 the terms of the GNU Lesser General Public License as published by the Free
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374 Software Foundation; either version 3 of the License, or (at your option)
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375 any later version.
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376
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377 =cut
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