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1 package MolecularDescriptors::Fsp3CarbonsDescriptors;
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2 #
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3 # $RCSfile: Fsp3CarbonsDescriptors.pm,v $
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4 # $Date: 2015/02/28 20:49:19 $
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5 # $Revision: 1.12 $
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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
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39 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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40
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41 @ISA = qw(MolecularDescriptors::MolecularDescriptors Exporter);
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42 @EXPORT = qw();
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43 @EXPORT_OK = qw(GetDescriptorNames);
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44
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45 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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46
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47 # Setup class variables...
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48 my($ClassName, @DescriptorNames);
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49 _InitializeClass();
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50
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51 # Overload Perl functions...
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52 use overload '""' => 'StringifyFsp3CarbonsDescriptors';
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53
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54 # Class constructor...
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55 sub new {
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56 my($Class, %NamesAndValues) = @_;
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57
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58 # Initialize object...
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59 my $This = $Class->SUPER::new();
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60 bless $This, ref($Class) || $Class;
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61 $This->_InitializeFsp3CarbonsDescriptors();
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62
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63 $This->_InitializeFsp3CarbonsDescriptorsProperties(%NamesAndValues);
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64
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65 return $This;
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66 }
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67
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68 # Initialize class ...
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69 sub _InitializeClass {
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70 #Class name...
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71 $ClassName = __PACKAGE__;
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72
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73 # Descriptor names...
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74 @DescriptorNames = ('Fsp3Carbons', 'Sp3Carbons');
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75
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76 }
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77
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78 # Get descriptor names as an array.
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79 #
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80 # This functionality can be either invoked as a class function or an
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81 # object method.
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82 #
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83 sub GetDescriptorNames {
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84 return @DescriptorNames;
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85 }
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86
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87 # Initialize object data...
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88 #
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89 sub _InitializeFsp3CarbonsDescriptors {
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90 my($This) = @_;
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91
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92 # Type of MolecularDescriptor...
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93 $This->{Type} = 'Fsp3Carbons';
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94
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95 # Intialize descriptor names and values...
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96 $This->_InitializeDescriptorNamesAndValues(@DescriptorNames);
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97
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98 return $This;
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99 }
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100
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101 # Initialize object properties...
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102 #
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103 sub _InitializeFsp3CarbonsDescriptorsProperties {
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104 my($This, %NamesAndValues) = @_;
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105
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106 my($Name, $Value, $MethodName);
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107 while (($Name, $Value) = each %NamesAndValues) {
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108 $MethodName = "Set${Name}";
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109 $This->$MethodName($Value);
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110 }
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111
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112 return $This;
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113 }
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114
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115 # Calculate fraction of SP3 carbons (Fsp3Carbons) [ Ref 115-116, Ref 119 ] in a molecule...
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116 #
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117 # It is defined as follows:
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118 #
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119 # Fsp3 = Number of SP3 carbons/Total number of carbons
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120 #
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121 sub GenerateDescriptors {
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122 my($This) = @_;
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123
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124 # Initialize descriptor values...
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125 $This->_InitializeDescriptorValues();
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126
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127 # Check availability of molecule...
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128 if (!$This->{Molecule}) {
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129 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set...";
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130 return undef;
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131 }
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132
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133 # Calculate descriptor values...
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134 if (!$This->_CalculateDescriptorValues()) {
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135 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate Fsp3Carbons values corresponding to assigned Fsp3Carbons atom types...";
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136 return undef;
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137 }
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138
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139 # Set final descriptor values...
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140 $This->_SetFinalDescriptorValues();
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141
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142 return $This;
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143 }
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144
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145 # Calculate Fsp3Carbons value...
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146 #
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147 sub _CalculateDescriptorValues {
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148 my($This) = @_;
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149 my($Atom, $AtomID, $TotalCarbons, $NumOfSp3Carbons, $Fsp3Carbons);
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150
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151 $TotalCarbons = 0;
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152 $NumOfSp3Carbons = 0;
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153
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154 ATOM: for $Atom ($This->{Molecule}->GetAtoms()) {
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155 if (!$Atom->IsCarbon()) {
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156 next ATOM;
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157 }
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158 $TotalCarbons += 1;
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159
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160 if ($Atom->DoesAtomNeighborhoodMatch('C.T4.TSB4')) {
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161 $NumOfSp3Carbons += 1;
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162 }
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163 }
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164
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165 $Fsp3Carbons = $NumOfSp3Carbons ? $NumOfSp3Carbons/$TotalCarbons : 0;
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166
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167 # Track values...
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168 $This->{Fsp3Carbons} = MathUtil::round($Fsp3Carbons, 2);
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169 $This->{Sp3Carbons} = $NumOfSp3Carbons;
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170
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171 return $This;
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172 }
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173
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174 # Setup final descriptor values...
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175 #
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176 sub _SetFinalDescriptorValues {
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177 my($This) = @_;
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178
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179 $This->{DescriptorsGenerated} = 1;
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180
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181 $This->SetDescriptorValues($This->{Fsp3Carbons}, $This->{Sp3Carbons});
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182
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183 return $This;
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184 }
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185
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186 # Return a string containg data for Fsp3CarbonsDescriptors object...
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187 #
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188 sub StringifyFsp3CarbonsDescriptors {
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189 my($This) = @_;
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190 my($Fsp3CarbonsDescriptorsString);
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191
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192 $Fsp3CarbonsDescriptorsString = "MolecularDescriptorType: $This->{Type}; " . $This->_StringifyDescriptorNamesAndValues();
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193
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194 return $Fsp3CarbonsDescriptorsString;
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195 }
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196
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197 # Is it a Fsp3CarbonsDescriptors object?
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198 sub _IsFsp3CarbonsDescriptors {
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199 my($Object) = @_;
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200
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201 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
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202 }
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203
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204 1;
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205
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206 __END__
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207
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208 =head1 NAME
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209
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210 Fsp3CarbonsDescriptors
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211
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212 =head1 SYNOPSIS
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213
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214 use MolecularDescriptors::Fsp3CarbonsDescriptors;
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215
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216 use MolecularDescriptors::Fsp3CarbonsDescriptors qw(:all);
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217
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218 =head1 DESCRIPTION
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219
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220 B<Fsp3CarbonsDescriptors> class provides the following methods:
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221
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222 new, GenerateDescriptors, GetDescriptorNames, StringifyFsp3CarbonsDescriptors
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223
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224 B<Fsp3CarbonsDescriptors> is derived from B<MolecularDescriptors> class which in turn
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225 is derived from B<ObjectProperty> base class that provides methods not explicitly defined
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226 in B<Fsp3CarbonsDescriptors>, B<MolecularDescriptors> or B<ObjectProperty> classes using Perl's
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227 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:
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228
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229 Set<PropertyName>(<PropertyValue>);
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230 $PropertyValue = Get<PropertyName>();
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231 Delete<PropertyName>();
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232
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233 Fraction sp3 carbons (Fsp3Carbons) [ Ref 115-116, Ref 119 ] value is calculated by dividing the number of sp3
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234 carbons (Sp3Carbons) with the total number of carbons in a molecule.
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235
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236 =head2 METHODS
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237
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238 =over 4
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239
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240 =item B<new>
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241
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242 $NewFsp3CarbonsDescriptors = new MolecularDescriptors::
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243 Fsp3CarbonsDescriptors(%NamesAndValues);
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244
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245 Using specified I<Fsp3CarbonsDescriptors> property names and values hash, B<new>
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246 method creates a new object and returns a reference to newly created B<Fsp3CarbonsDescriptors>
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247 object. By default, the following properties are initialized:
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248
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249 Molecule = ''
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250 Type = 'Fsp3Carbons'
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251 @DescriptorNames = ('Fsp3Carbons', 'Sp3Carbons')
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252 @DescriptorValues = ('None', 'None')
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253
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254 Examples:
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255
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256 $Fsp3CarbonsDescriptors = new MolecularDescriptors::Fsp3CarbonsDescriptors(
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257 'Molecule' => $Molecule);
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258
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259 $Fsp3CarbonsDescriptors = new MolecularDescriptors::Fsp3CarbonsDescriptors();
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260
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261 $Fsp3CarbonsDescriptors->SetMolecule($Molecule);
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262 $Fsp3CarbonsDescriptors->GenerateDescriptors();
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263 print "Fsp3CarbonsDescriptors: $Fsp3CarbonsDescriptors\n";
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264
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265 =item B<GenerateDescriptors>
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266
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267 $Fsp3CarbonsDescriptors->GenerateDescriptors();
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268
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269 Calculates Fsp3Carbons and Sp3Carbons values for a molecule and returns I<Fsp3CarbonsDescriptors>.
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270
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271 =item B<GetDescriptorNames>
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272
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273 @DescriptorNames = $Fsp3CarbonsDescriptors->GetDescriptorNames();
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274 @DescriptorNames = MolecularDescriptors::Fsp3CarbonsDescriptors::
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275 GetDescriptorNames();
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276
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277 Returns all available descriptor names as an array.
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278
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279 =item B<StringifyFsp3CarbonsDescriptors>
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280
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281 $String = $Fsp3CarbonsDescriptors->StringifyFsp3CarbonsDescriptors();
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282
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283 Returns a string containing information about I<Fsp3CarbonsDescriptors> object.
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284
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285 =back
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286
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287 =head1 AUTHOR
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288
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289 Manish Sud <msud@san.rr.com>
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290
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291 =head1 SEE ALSO
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292
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293 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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294
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295 =head1 COPYRIGHT
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296
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297 Copyright (C) 2015 Manish Sud. All rights reserved.
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298
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299 This file is part of MayaChemTools.
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300
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301 MayaChemTools is free software; you can redistribute it and/or modify it under
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302 the terms of the GNU Lesser General Public License as published by the Free
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303 Software Foundation; either version 3 of the License, or (at your option)
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304 any later version.
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305
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306 =cut
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