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1 package MolecularDescriptors::MolecularDescriptors;
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2 #
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3 # $RCSfile: MolecularDescriptors.pm,v $
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4 # $Date: 2015/02/28 20:49:20 $
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5 # $Revision: 1.14 $
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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 ObjectProperty;
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34 use TextUtil ();
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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(ObjectProperty Exporter);
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39 @EXPORT = qw();
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40 @EXPORT_OK = qw();
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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($ClassName);
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46 _InitializeClass();
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47
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48 # Class constructor...
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49 sub new {
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50 my($Class, %NamesAndValues) = @_;
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51
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52 # Initialize object...
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53 my $This = {};
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54 bless $This, ref($Class) || $Class;
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55 $This->_InitializeMolecularDescriptors();
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56
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57 $This->_InitializeMolecularDescriptorsProperties(%NamesAndValues);
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58
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59 return $This;
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60 }
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61
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62 # Initialize object data...
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63 #
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64 sub _InitializeMolecularDescriptors {
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65 my($This) = @_;
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66
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67 # Molecule object...
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68 $This->{Molecule} = '';
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69
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70 # Type of molecular descriptors...
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71 $This->{Type} = '';
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72
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73 # Names and calculated value of molecular descriptors...
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74 #
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75 # The specific descriptor class, derived from this base class, populate descriptor names and values
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76 # arrays...
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77 #
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78 @{$This->{DescriptorNames}} = ();
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79 @{$This->{DescriptorValues}} = ();
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80
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81 # Marks successful generation of descriptors...
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82 $This->{DescriptorsGenerated} = 0;
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83
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84 }
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85
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86 # Initialize class ...
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87 sub _InitializeClass {
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88 #Class name...
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89 $ClassName = __PACKAGE__;
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90 }
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91
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92
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93 # Initialize object properties....
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94 sub _InitializeMolecularDescriptorsProperties {
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95 my($This, %NamesAndValues) = @_;
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96
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97 my($Name, $Value, $MethodName);
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98 while (($Name, $Value) = each %NamesAndValues) {
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99 $MethodName = "Set${Name}";
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100 $This->$MethodName($Value);
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101 }
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102
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103 return $This;
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104 }
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105
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106 # Initialize descriptor names and values...
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107 #
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108 sub _InitializeDescriptorNamesAndValues {
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109 my($This, @Names) = @_;
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110
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111 @{$This->{DescriptorNames}} = @Names;
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112
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113 $This->_InitializeDescriptorValues();
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114
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115 return $This;
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116 }
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117
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118 # Initialize descriptor values...
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119 #
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120 sub _InitializeDescriptorValues {
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121 my($This) = @_;
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122
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123 $This->{DescriptorsGenerated} = 0;
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124
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125 @{$This->{DescriptorValues}} = ();
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126
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127 return $This;
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128 }
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129
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130 # Set molecule object...
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131 #
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132 sub SetMolecule {
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133 my($This, $Molecule) = @_;
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134
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135 $This->{Molecule} = $Molecule;
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136
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137 # Weaken the reference to disable increment of reference count...
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138 Scalar::Util::weaken($This->{Molecule});
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139
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140 return $This;
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141 }
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142
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143 # Set type and make sure it's not already set...
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144 #
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145 sub SetType {
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146 my($This, $Type) = @_;
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147
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148 if ($This->{Type}) {
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149 croak "Error: ${ClassName}->SetType: Can't change MolecularDescriptors type: It's already set...";
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150 }
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151 $This->{Type} = $Type;
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152
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153 return $This;
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154 }
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155
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156 # Get molecular descriptor names as an array...
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157 #
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158 sub GetDescriptorNames {
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159 my($This) = @_;
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160
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161 return @{$This->{DescriptorNames}};
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162 }
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163
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164 # Set descriptor names...
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165 #
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166 sub SetDescriptorNames {
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167 my($This, @Names) = @_;
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168
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169 @{$This->{DescriptorNames}} = @Names;
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170
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171 return $This;
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172 }
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173
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174 # Add descriptor names...
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175 #
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176 sub AddDescriptorNames {
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177 my($This, @Names) = @_;
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178
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179 push @{$This->{DescriptorNames}}, @Names;
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180
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181 return $This;
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182 }
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183
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184 # Set descriptor values...
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185 #
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186 sub SetDescriptorValues {
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187 my($This, @Values) = @_;
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188
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189 @{$This->{DescriptorValues}} = @Values;
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190
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191 return $This;
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192 }
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193
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194 # Add descriptor values...
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195 #
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196 sub AddDescriptorValues {
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197 my($This, @Values) = @_;
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198
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199 push @{$This->{DescriptorValues}}, @Values;
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200
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201 return $This;
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202 }
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203
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204 # Is descriptors generation successful?
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205 #
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206 # Notes:
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207 # . The specific molecular descriptor class generation class sets the value of
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208 # DescriptorsCalculated to 1 after the successful generation of descriptors;
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209 # otherwise, it's set to 0.
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210 #
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211 sub IsDescriptorsGenerationSuccessful {
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212 my($This) = @_;
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213
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214 return $This->{DescriptorsGenerated} ? 1 : 0;
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215 }
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216
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217 # Get all descriptor values as an array...
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218 #
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219 sub GetDescriptorValues {
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220 my($This) = @_;
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221
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222 if ($This->{DescriptorsGenerated}) {
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223 return wantarray ? @{$This->{DescriptorValues}} : scalar @{$This->{DescriptorValues}};
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224 }
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225 else {
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226 my(@DescriptorValues);
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227
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228 @DescriptorValues = ('None') x scalar @{$This->{DescriptorNames}};
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229
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230 return wantarray ? @DescriptorValues : scalar @DescriptorValues;
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231 }
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232 }
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233
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234 # Get descriptor value for a specified descriptor name...
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235 #
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236 sub GetDescriptorValueByName {
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237 my($This, $Name) = @_;
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238 my(%NamesAndValues);
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239
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240 %NamesAndValues = $This->GetDescriptorNamesAndValues();
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241
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242 return exists $NamesAndValues{$Name} ? $NamesAndValues{$Name} : 'None';
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243
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244 }
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245
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246 # Get calculated molecular descriptor names sand values as a to a hash with names
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247 # and values as key/value pairs...
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248 #
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249 sub GetDescriptorNamesAndValues {
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250 my($This) = @_;
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251 my(%NamesAndValues);
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252
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253 %NamesAndValues = ();
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254 @NamesAndValues{ @{$This->{DescriptorNames}} } = $This->GetDescriptorValues();
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255
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256 return %NamesAndValues;
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257 }
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258
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259 # Return a string containing descriptor names and values...
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260 #
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261 sub _StringifyDescriptorNamesAndValues {
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262 my($This) = @_;
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263 my($NamesAndValuesString, $Name, $Value, @NamesAndValuesInfo, %NamesAndValues);
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264
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265 @NamesAndValuesInfo = ();
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266 %NamesAndValues = $This->GetDescriptorNamesAndValues();
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267
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268 for $Name (@{$This->{DescriptorNames}}) {
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269 $Value = $NamesAndValues{$Name};
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270 $Value = (TextUtil::IsEmpty($Value) || $Value =~ /^None$/i) ? 'None' : $Value;
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271 push @NamesAndValuesInfo, "$Name - $Value";
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272 }
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273 if (@NamesAndValuesInfo) {
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274 $NamesAndValuesString = "Names - Values: <" . TextUtil::JoinWords(\@NamesAndValuesInfo, ", ", 0) . ">";
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275 }
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276 else {
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277 $NamesAndValuesString = "Names - Values: < None>";
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278 }
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279 return $NamesAndValuesString;
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280 }
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281
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282 1;
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283
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284 __END__
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285
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286 =head1 NAME
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287
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288 MolecularDescriptors - MolecularDescriptors class
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289
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290 =head1 SYNOPSIS
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291
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292 use MolecularDescriptors::MolecularDescriptors;
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293
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294 use MolecularDescriptors::MolecularDescriptors qw(:all);
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295
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296 =head1 DESCRIPTION
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297
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298 B<MolecularDescriptors> base class used to derive all other molecular descriptors classes provides the following methods:
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299
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300 new, AddDescriptorNames, AddDescriptorValues, GetDescriptorNames,
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301 GetDescriptorNamesAndValues, GetDescriptorValueByName, GetDescriptorValues,
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302 IsDescriptorsGenerationSuccessful, SetDescriptorNames, SetDescriptorValues,
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303 SetMolecule, SetType
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304
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305 B<MolecularDescriptors> class is derived from B<ObjectProperty> base class which provides methods not
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306 explicitly defined in B<Fingerprints> or B<ObjectProperty> classes using Perl's AUTOLOAD functionality.
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307 These methods are generated on-the-fly for a specified object property:
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308
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309 Set<PropertyName>(<PropertyValue>);
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310 $PropertyValue = Get<PropertyName>();
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311 Delete<PropertyName>();
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312
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313 =head2 METHODS
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314
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315 =over 4
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316
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317 =item B<new>
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318
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319 $NewMolecularDescriptors = new MolecularDescriptors::
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320 MolecularDescriptors(%NamesAndValues);
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321
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322 Using specified I<MolecularDescriptors> property names and values hash, B<new> method creates a new object
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323 and returns a reference to newly created B<MolecularDescriptors> object. By default, following properties are
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324 initialized:
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325
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326 Molecule = '';
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327 Type = '';
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328
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329 =item B<AddDescriptorNames>
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330
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331 $MolecularDescriptors->AddDescriptorNames(@Name);
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332
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333 Adds specified descriptor I<Names> to the list of available descriptor names and returns
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334 I<MolecularDescriptors>.
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335
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336 =item B<AddDescriptorValues>
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337
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338 $MolecularDescriptors->AddDescriptorValues(@Values);
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339
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340 Adds specified descriptor I<Values> to the list of calculated descriptor values and returns
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341 I<MolecularDescriptors>.
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342
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343 =item B<GetDescriptorNames>
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344
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345 @Names = $MolecularDescriptors->GetDescriptorNames();
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346
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347 Returns an array containing all available descriptor names.
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348
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349 =item B<GetDescriptorNamesAndValues>
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350
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351 %NamesAndValuesReturn = $MolecularDescriptors->
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352 GetDescriptorNamesAndValues();
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353
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354 Returns a hash containing all available descriptor names and calculated values.
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355
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356 =item B<GetDescriptorValueByName>
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357
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358 $Value = $MolecularDescriptors->
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359 GetDescriptorValueByName($Name);
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360
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361 Returns calculated value for a specified descriptor name. A string B<None> is returned for
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362 unknown descriptor names or for those descriptors whose values haven't been calculated.
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363
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364 =item B<GetDescriptorValues>
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365
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366 @Values = $MolecularDescriptors->GetDescriptorValues();
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367
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368 Returns an array containing calculated descriptor values for all available descriptors.
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369 Unless B<CalculateDescriptorsValues> method has been successfully invoked on a
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370 I<MolecularDescriptors> object, value of each descriptor corresponds to string B<None>.
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371
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372 =item B<IsDescriptorsGenerationSuccessful>
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373
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374 $Status = $MolecularDescriptors->
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375 IsDescriptorsGenerationSuccessful();
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376
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377 Returns 1 or 0 based on whether molecular descriptors generation was successful.
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378 For a successful molecular descriptors calculation, all available descriptors must have
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379 a values other than a string I<None> which are set by B<CalculateDescriptorsValues>
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380 method after successful completion of descriptors calculation.
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381
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382 =item B<SetDescriptorNames>
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383
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384 $MolecularDescriptors->SetDescriptorNames(@Names);
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385
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386 Sets names of available descriptors to specified names and returns I<MolecularDescriptors>.
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387
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388 =item B<SetDescriptorValues>
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389
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390 $MolecularDescriptors->SetDescriptorValues(@Values);
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391
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392 Sets values of available descriptors to specified values and returns I<MolecularDescriptors>.
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393
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394 =item B<SetMolecule>
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395
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396 $MolecularDescriptors->SetMolecule($Molecule);
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397
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398 Sets molecule to use during calculation of molecular descriptors and returns I<MolecularDescriptors>.
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399
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400 =item B<SetType>
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401
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402 $MolecularDescriptors->SetType($Type);
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403
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404 Sets I<Type> for I<MolecularDescriptors> object and returns I<MolecularDescriptors>.
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405
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406 =back
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407
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408 =head1 AUTHOR
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409
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410 Manish Sud <msud@san.rr.com>
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411
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412 =head1 SEE ALSO
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413
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414 MolecularDescriptorsGenerator.pm
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415
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416 =head1 COPYRIGHT
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417
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418 Copyright (C) 2015 Manish Sud. All rights reserved.
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419
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420 This file is part of MayaChemTools.
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421
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422 MayaChemTools is free software; you can redistribute it and/or modify it under
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423 the terms of the GNU Lesser General Public License as published by the Free
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424 Software Foundation; either version 3 of the License, or (at your option)
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425 any later version.
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426
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427 =cut
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