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1 package MolecularDescriptors::RingsCountDescriptors;
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2 #
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3 # $RCSfile: RingsCountDescriptors.pm,v $
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4 # $Date: 2015/02/28 20:49:20 $
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5 # $Revision: 1.10 $
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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 Molecule;
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34 use MolecularDescriptors::MolecularDescriptors;
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35
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36 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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37
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38 @ISA = qw(MolecularDescriptors::MolecularDescriptors Exporter);
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39 @EXPORT = qw();
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40 @EXPORT_OK = qw(GetDescriptorNames);
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41
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42 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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43
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44 # Setup class variables...
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45 my($ClassName, @DescriptorNames);
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46 _InitializeClass();
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47
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48 # Overload Perl functions...
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49 use overload '""' => 'StringifyRingsCountDescriptors';
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50
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51 # Class constructor...
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52 sub new {
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53 my($Class, %NamesAndValues) = @_;
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54
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55 # Initialize object...
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56 my $This = $Class->SUPER::new();
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57 bless $This, ref($Class) || $Class;
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58 $This->_InitializeRingsCountDescriptors();
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59
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60 $This->_InitializeRingsCountDescriptorsProperties(%NamesAndValues);
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61
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62 return $This;
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63 }
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64
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65 # Initialize class ...
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66 sub _InitializeClass {
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67 #Class name...
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68 $ClassName = __PACKAGE__;
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69
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70 # Descriptor names...
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71 @DescriptorNames = ('Rings', 'AromaticRings');
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72
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73 }
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74
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75 # Get descriptor names as an array.
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76 #
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77 # This functionality can be either invoked as a class function or an
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78 # object method.
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79 #
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80 sub GetDescriptorNames {
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81 return @DescriptorNames;
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82 }
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83
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84 # Initialize object data...
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85 #
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86 sub _InitializeRingsCountDescriptors {
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87 my($This) = @_;
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88
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89 # Type of MolecularDescriptor...
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90 $This->{Type} = 'RingsCount';
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91
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92 # Intialize descriptor names and values...
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93 $This->_InitializeDescriptorNamesAndValues(@DescriptorNames);
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94
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95 return $This;
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96 }
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97
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98 # Initialize object properties...
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99 #
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100 sub _InitializeRingsCountDescriptorsProperties {
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101 my($This, %NamesAndValues) = @_;
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102
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103 my($Name, $Value, $MethodName);
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104 while (($Name, $Value) = each %NamesAndValues) {
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105 $MethodName = "Set${Name}";
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106 $This->$MethodName($Value);
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107 }
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108
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109 return $This;
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110 }
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111
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112 # Generate molecular weight and exact mass values...
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113 #
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114 sub GenerateDescriptors {
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115 my($This) = @_;
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116
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117 # Initialize descriptor values...
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118 $This->_InitializeDescriptorValues();
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119
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120 # Check availability of molecule...
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121 if (!$This->{Molecule}) {
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122 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set...";
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123 return undef;
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124 }
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125
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126 # Calculate descriptor values...
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127 if (!$This->_CalculateDescriptorValues()) {
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128 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed...";
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129 return undef;
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130 }
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131
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132 # Set final descriptor values...
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133 $This->_SetFinalDescriptorValues();
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134
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135 return $This;
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136 }
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137
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138 # Calculate molecular weight and exact mass values..
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139 #
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140 sub _CalculateDescriptorValues {
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141 my($This) = @_;
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142 my($MolecularWeight, $ExactMass);
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143
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144 $This->{Rings} = $This->{Molecule}->GetNumOfRings();
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145 $This->{AromaticRings} = $This->{Molecule}->GetNumOfAromaticRings();
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146
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147 return $This;
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148 }
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149
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150 # Setup final descriptor values...
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151 #
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152 sub _SetFinalDescriptorValues {
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153 my($This) = @_;
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154
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155 $This->{DescriptorsGenerated} = 1;
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156
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157 $This->SetDescriptorValues($This->{Rings}, $This->{AromaticRings});
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158
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159 return $This;
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160 }
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161
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162 # Return a string containg data for RingsCountDescriptors object...
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163 #
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164 sub StringifyRingsCountDescriptors {
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165 my($This) = @_;
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166 my($TheString);
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167
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168 $TheString = "MolecularDescriptorType: $This->{Type}; " . $This->_StringifyDescriptorNamesAndValues();
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169
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170 return $TheString;
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171 }
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172
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173 # Is it a RingsCountDescriptors object?
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174 sub _IsRingsCountDescriptors {
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175 my($Object) = @_;
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176
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177 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
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178 }
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179
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180 1;
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181
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182 __END__
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183
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184 =head1 NAME
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185
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186 RingsCountDescriptors
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187
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188 =head1 SYNOPSIS
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189
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190 use MolecularDescriptors::RingsCountDescriptors;
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191
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192 use MolecularDescriptors::RingsCountDescriptors qw(:all);
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193
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194 =head1 DESCRIPTION
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195
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196 B<RingsCountDescriptors> class provides the following methods:
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197
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198 new, GenerateDescriptors, GetDescriptorNames, StringifyRingsCountDescriptors
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199
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200 B<RingsCountDescriptors> is derived from B<MolecularDescriptors> class which in turn
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201 is derived from B<ObjectProperty> base class that provides methods not explicitly defined
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202 in B<RingsCountDescriptors>, B<MolecularDescriptors> or B<ObjectProperty> classes using Perl's
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203 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:
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204
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205 Set<PropertyName>(<PropertyValue>);
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206 $PropertyValue = Get<PropertyName>();
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207 Delete<PropertyName>();
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208
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209 B<RingsCountDescriptors> class doesn't perform any ring or aromaticity detection before
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210 counting their number in a molecule. Instead, it assumes ring and aromaticity detection have
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211 been performed by caller using B<DetectRings> [Ref 31] and B<DetectAromaticity> methods
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212 available in B<Molecule>.
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213
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214 B<DetectAromaticity> method available in B<Molecule> class assigns aromaticity to rings
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215 using Huckel rule as explained below:
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216
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217 o Ring aromaticity is determined using Huckel's rule: a ring containing 4n + 2 pi electrons is
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218 considered aromatic.
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219
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220 o Hetrocyclic rings containing N, O and S atoms fall into two classes: Basic aromatic and
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221 Non-basic aromatic. In Basic aromatic hetrocyclic rings, heteroatom itself is involved in a
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222 double bond. (e.g. Pyridine) However, in non-basic hetrocyclic rings, heteroatom might have
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223 an attached hydrogen atom and the remaining lone pair contribute to electron delocalization
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224 and contributes to 4n + 2 electrons. (e.g. Pyrrole, Furan)
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225
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226 o For molecules containing fused rings, each fused ring set is considered as one aromatic
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227 system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in
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228 fused set are treated individually for aromaticity detection. Additionally, non-fused
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229 rings are handled on their own during aromaticity detection.
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230
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231 =head2 METHODS
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232
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233 =over 4
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234
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235 =item B<new>
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236
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237 $NewRingsCountDescriptors = new MolecularDescriptors::
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238 RingsCountDescriptors(
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239 %NamesAndValues);
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240
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241 Using specified I<RingsCountDescriptors> property names and values hash, B<new>
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242 method creates a new object and returns a reference to newly created B<RingsCountDescriptors>
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243 object. By default, the following properties are initialized:
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244
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245 Molecule = ''
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246 Type = 'RingsCount'
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247
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248 @DescriptorNames = ('Rings', 'AromaticRings')
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249 @DescriptorValues = ('None', 'None')
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250
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251 Examples:
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252
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253 $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors(
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254 'Molecule' => $Molecule);
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255
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256 $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();
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257
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258 $RingsCountDescriptors->SetMolecule($Molecule);
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259 $RingsCountDescriptors->GenerateDescriptors();
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260 print "RingsCountDescriptors: $RingsCountDescriptors\n";
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261
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262 =item B<GenerateDescriptors>
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263
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264 $RingsCountDescriptors->GenerateDescriptors();
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265
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266 Calculate number of rings and aromatic rings in a molecule and returns
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267 I<RingsCountDescriptors>.
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268
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269 =item B<GetDescriptorNames>
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270
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271 @DescriptorNames = $RingsCountDescriptors->GetDescriptorNames();
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272 @DescriptorNames = MolecularDescriptors::RingsCountDescriptors::
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273 GetDescriptorNames();
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274
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275 Returns all available descriptor names as an array.
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276
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277 =item B<StringifyRingsCountDescriptors>
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278
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279 $String = $RingsCountDescriptors->
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280 StringifyRingsCountDescriptors();
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281
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282 Returns a string containing information about I<RingsCountDescriptors> object.
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283
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284 =back
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285
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286 =head1 AUTHOR
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287
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288 Manish Sud <msud@san.rr.com>
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289
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290 =head1 SEE ALSO
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291
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292 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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293
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294 =head1 COPYRIGHT
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295
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296 Copyright (C) 2015 Manish Sud. All rights reserved.
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297
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298 This file is part of MayaChemTools.
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299
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300 MayaChemTools is free software; you can redistribute it and/or modify it under
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301 the terms of the GNU Lesser General Public License as published by the Free
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302 Software Foundation; either version 3 of the License, or (at your option)
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303 any later version.
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304
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305 =cut
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