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1 package MolecularDescriptors::WeightAndMassDescriptors;
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2 #
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3 # $RCSfile: WeightAndMassDescriptors.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 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($ClassName, @DescriptorNames);
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49 _InitializeClass();
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50
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51 # Overload Perl functions...
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52 use overload '""' => 'StringifyWeightAndMassDescriptors';
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53
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54 # Class constructor...
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55 sub new {
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56 my($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->_InitializeWeightAndMassDescriptors();
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62
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63 $This->_InitializeWeightAndMassDescriptorsProperties(%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 $ClassName = __PACKAGE__;
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72
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73 # Descriptor names...
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74 @DescriptorNames = ('MolecularWeight', 'ExactMass');
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75
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76 }
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77
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78 # Get descriptor names as an array.
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79 #
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80 # This functionality can be either invoked as a class function or an
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81 # object method.
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82 #
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83 sub GetDescriptorNames {
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84 return @DescriptorNames;
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85 }
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86
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87 # Initialize object data...
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88 #
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89 sub _InitializeWeightAndMassDescriptors {
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90 my($This) = @_;
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91
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92 # Type of MolecularDescriptor...
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93 $This->{Type} = 'WeightAndMass';
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94
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95 # Precision for molecular weight and exact mass values...
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96 $This->{WeightPrecision} = 2;
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97 $This->{MassPrecision} = 4;
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98
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99 # Intialize descriptor names and values...
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100 $This->_InitializeDescriptorNamesAndValues(@DescriptorNames);
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101
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102 return $This;
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103 }
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104
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105 # Initialize object properties...
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106 #
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107 sub _InitializeWeightAndMassDescriptorsProperties {
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108 my($This, %NamesAndValues) = @_;
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109
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110 my($Name, $Value, $MethodName);
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111 while (($Name, $Value) = each %NamesAndValues) {
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112 $MethodName = "Set${Name}";
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113 $This->$MethodName($Value);
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114 }
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115
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116 return $This;
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117 }
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118
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119 # Set weight precision for moelcular weight...
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120 #
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121 sub SetWeightPrecision {
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122 my($This, $Value) = @_;
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123
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124 if (!TextUtil::IsInteger($Value)) {
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125 croak "Error: ${ClassName}->SetWeightPrecision: WeightPrecision value, $Value, is not valid: It must be a an integer...";
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126 }
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127 $This->{WeightPrecision} = $Value;
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128
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129 return $This;
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130 }
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131
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132 # Set mass precision for exact weight...
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133 #
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134 sub SetMassPrecision {
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135 my($This, $Value) = @_;
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136
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137 if (!TextUtil::IsInteger($Value)) {
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138 croak "Error: ${ClassName}->SetMassPrecision: MassPrecision value, $Value, is not valid: It must be a an integer...";
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139 }
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140 $This->{MassPrecision} = $Value;
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141
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142 return $This;
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143 }
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144
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145 # Generate molecular weight and exact mass values...
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146 #
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147 sub GenerateDescriptors {
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148 my($This) = @_;
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149
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150 # Initialize descriptor values...
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151 $This->_InitializeDescriptorValues();
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152
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153 # Check availability of molecule...
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154 if (!$This->{Molecule}) {
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155 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set...";
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156 return undef;
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157 }
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158
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159 # Calculate descriptor values...
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160 if (!$This->_CalculateDescriptorValues()) {
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161 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed...";
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162 return undef;
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163 }
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164
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165 # Set final descriptor values...
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166 $This->_SetFinalDescriptorValues();
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167
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168 return $This;
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169 }
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170
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171 # Calculate molecular weight and exact mass values..
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172 #
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173 sub _CalculateDescriptorValues {
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174 my($This) = @_;
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175 my($MolecularWeight, $ExactMass);
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176
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177 $MolecularWeight = $This->{Molecule}->GetMolecularWeight();
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178 $ExactMass = $This->{Molecule}->GetExactMass();
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179
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180 # Track values...
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181 $This->{MolecularWeight} = MathUtil::round($MolecularWeight, $This->{WeightPrecision});
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182 $This->{ExactMass} = MathUtil::round($ExactMass, $This->{MassPrecision});
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183
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184 return $This;
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185 }
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186
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187 # Setup final descriptor values...
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188 #
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189 sub _SetFinalDescriptorValues {
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190 my($This) = @_;
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191
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192 $This->{DescriptorsGenerated} = 1;
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193
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194 $This->SetDescriptorValues($This->{MolecularWeight}, $This->{ExactMass});
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195
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196 return $This;
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197 }
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198
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199 # Return a string containg data for WeightAndMassDescriptors object...
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200 #
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201 sub StringifyWeightAndMassDescriptors {
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202 my($This) = @_;
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203 my($TheString);
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204
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205 $TheString = "MolecularDescriptorType: $This->{Type}; " . $This->_StringifyDescriptorNamesAndValues();
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206
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207 return $TheString;
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208 }
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209
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210 # Is it a WeightAndMassDescriptors object?
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211 sub _IsWeightAndMassDescriptors {
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212 my($Object) = @_;
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213
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214 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
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215 }
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216
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217 1;
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218
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219 __END__
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220
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221 =head1 NAME
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222
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223 WeightAndMassDescriptors
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224
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225 =head1 SYNOPSIS
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226
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227 use MolecularDescriptors::WeightAndMassDescriptors;
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228
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229 use MolecularDescriptors::WeightAndMassDescriptors qw(:all);
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230
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231 =head1 DESCRIPTION
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232
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233 B<WeightAndMassDescriptors> class provides the following methods:
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234
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235 new, GenerateDescriptors, GetDescriptorNames, StringifyWeightAndMassDescriptors
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236
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237 B<WeightAndMassDescriptors> is derived from B<MolecularDescriptors> class which in turn
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238 is derived from B<ObjectProperty> base class that provides methods not explicitly defined
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239 in B<WeightAndMassDescriptors>, B<MolecularDescriptors> or B<ObjectProperty> classes using Perl's
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240 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:
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241
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242 Set<PropertyName>(<PropertyValue>);
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243 $PropertyValue = Get<PropertyName>();
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244 Delete<PropertyName>();
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245
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246 B<WeightAndMassDescriptors> calculates molecular weight and exact mass descriptors using
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247 methods available in B<Molecule> class.
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248
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249 =head2 METHODS
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250
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251 =over 4
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252
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253 =item B<new>
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254
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255 $NewWeightAndMassDescriptors = new MolecularDescriptors::
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256 WeightAndMassDescriptors(
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257 %NamesAndValues);
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258
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259 Using specified I<WeightAndMassDescriptors> property names and values hash, B<new>
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260 method creates a new object and returns a reference to newly created B<WeightAndMassDescriptors>
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261 object. By default, the following properties are initialized:
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262
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263 Molecule = ''
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264 Type = 'WeightAndMass'
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265 WeightPrecision = 2;
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266 MassPrecision = 4;
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267
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268 @DescriptorNames = ('MolecularWeight', 'ExactMass')
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269 @DescriptorValues = ('None', 'None')
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270
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271 Examples:
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272
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273 $WeightAndMassDescriptors = new MolecularDescriptors::
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274 WeightAndMassDescriptors(
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275 'Molecule' => $Molecule);
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276
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277 $WeightAndMassDescriptors = new MolecularDescriptors::
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278 WeightAndMassDescriptors();
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279
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280 $WeightAndMassDescriptors->SetMolecule($Molecule);
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281 $WeightAndMassDescriptors->GenerateDescriptors();
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282 print "WeightAndMassDescriptors: $WeightAndMassDescriptors\n";
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283
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284 =item B<GenerateDescriptors>
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285
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286 $WeightAndMassDescriptors->GenerateDescriptors();
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287
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288 Calculates molecular weight and exact mass of a molecule and returns
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289 I<WeightAndMassDescriptors>.
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290
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291 =item B<GetDescriptorNames>
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292
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293 @DescriptorNames = $WeightAndMassDescriptors->GetDescriptorNames();
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294 @DescriptorNames = MolecularDescriptors::WeightAndMassDescriptors::
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295 GetDescriptorNames();
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296
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297 Returns all available descriptor names as an array.
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298
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299 =item B<SetMassPrecision>
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300
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301 $WeightAndMassDescriptors->SetMassPrecision($Precision);
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302
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303 Sets precision for calculated exact mass value and returns
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304 I<WeightAndMassDescriptors>.
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305
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306 =item B<SetWeightPrecision>
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307
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308 $WeightAndMassDescriptors->SetWeightPrecision($Precision);
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309
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310 Sets precision for calculated molecular weight value and returns
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311 I<WeightAndMassDescriptors>.
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312
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313 =item B<StringifyWeightAndMassDescriptors>
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314
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315 $String = $WeightAndMassDescriptors->StringifyWeightAndMassDescriptors();
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316
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317 Returns a string containing information about I<WeightAndMassDescriptors> object.
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318
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319 =back
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320
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321 =head1 AUTHOR
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322
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323 Manish Sud <msud@san.rr.com>
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324
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325 =head1 SEE ALSO
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326
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327 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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328
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329 =head1 COPYRIGHT
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330
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331 Copyright (C) 2015 Manish Sud. All rights reserved.
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332
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333 This file is part of MayaChemTools.
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334
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335 MayaChemTools is free software; you can redistribute it and/or modify it under
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336 the terms of the GNU Lesser General Public License as published by the Free
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337 Software Foundation; either version 3 of the License, or (at your option)
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338 any later version.
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339
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340 =cut
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