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1 package AtomicDescriptors::AtomicDescriptors;
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2 #
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3 # $RCSfile: AtomicDescriptors.pm,v $
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4 # $Date: 2015/02/28 20:47:48 $
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5 # $Revision: 1.17 $
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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, %PropertyNamesAndValues) = @_;
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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->_InitializeAtomicDescriptors();
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56
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57 $This->_InitializeAtomicDescriptorsProperties(%PropertyNamesAndValues);
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58
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59 return $This;
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60 }
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61
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62 # Initialize object data...
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63 #
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64 sub _InitializeAtomicDescriptors {
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65 my($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 atomic descriptors...
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71 $This->{Type} = '';
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72
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73 # By default, atomic decriptor values are also calculated for hydrogens...
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74 $This->{IgnoreHydrogens} = 0;
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75
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76 # Calculated atomic descriptor values hash. Instead of assigning the calculated values to Atom
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77 # objects, these values are stored in the current object in a hash with atom ID and atomic descriptor
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78 # values as key/value pairs.
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79 #
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80 # Unlike molecular descriptors, no descriptor names are assigned to individual atomic descriptor
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81 # values.
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82 #
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83 %{$This->{DescriptorValues}} = ();
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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 $ClassName = __PACKAGE__;
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90 }
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91
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92 # Initialize object properties....
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93 sub _InitializeAtomicDescriptorsProperties {
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94 my($This, %PropertiesNamesAndValues) = @_;
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95
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96 my($Name, $Value, $MethodName);
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97 while (($Name, $Value) = each %PropertiesNamesAndValues) {
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98 $MethodName = "Set${Name}";
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99 $This->$MethodName($Value);
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100 }
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101
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102 return $This;
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103 }
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104
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105 # Initialize descriptor values for all atoms in a molecule...
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106 #
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107 sub _InitializeDescriptorValues {
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108 my($This) = @_;
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109
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110 if (!$This->{Molecule}) {
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111 return $This;
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112 }
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113
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114 # Assign 'None' to all atomic descriptor values...
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115 #
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116 my($Atom, $AtomID);
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117
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118 ATOM: for $Atom ($This->{Molecule}->GetAtoms()) {
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119 $AtomID = $Atom->GetID();
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120 $This->{DescriptorValues}{$AtomID} = 'None';
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121 }
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122
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123 return $This;
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124 }
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125
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126 # Set molecule object and make sure it's not already set...
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127 #
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128 sub SetMolecule {
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129 my($This, $Molecule) = @_;
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130
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131 if ($This->{Molecule}) {
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132 croak "Error: ${ClassName}->SetMolecule: Can't change molecule object: It's already set...";
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133 }
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134 $This->{Molecule} = $Molecule;
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135
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136 # Weaken the reference to disable increment of reference count...
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137 Scalar::Util::weaken($This->{Molecule});
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138
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139 return $This;
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140 }
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141
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142 # Set type and make sure it's not already set...
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143 #
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144 sub SetType {
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145 my($This, $Type) = @_;
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146
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147 if ($This->{Type}) {
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148 croak "Error: ${ClassName}->SetType: Can't change AtomicDescriptors type: It's already set...";
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149 }
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150 $This->{Type} = $Type;
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151
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152 return $This;
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153 }
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154
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155 # Set specific atomic descriptor value...
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156 #
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157 sub SetDescriptorValue {
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158 my($This, $Atom, $AtomicDescriptor) = @_;
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159 my($AtomID);
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160
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161 $AtomID = $Atom->GetID();
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162 $This->{DescriptorValues}{$AtomID} = $AtomicDescriptor;
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163
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164 return $This;
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165 }
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166
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167 # Get specific atomic descriptor value...
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168 #
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169 sub GetDescriptorValue {
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170 my($This, $Atom) = @_;
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171 my($AtomID);
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172
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173 $AtomID = $Atom->GetID();
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174
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175 return exists $This->{DescriptorValues}{$AtomID} ? $This->{DescriptorValues}{$AtomID} : 'None';
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176 }
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177
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178 # Get calculated atomic descriptor values as a hash with atom ID and atomic descriptor
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179 # values as key/value pairs...
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180 #
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181 sub GetDescriptorValues {
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182 my($This) = @_;
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183
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184 return %{$This->{DescriptorValues}};
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185 }
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186
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187 # Are all atomic descriptor values successfully calculated?
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188 #
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189 # Notes:
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190 # . Dynamic checking of calculated descriptor values for atoms eliminates the need
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191 # to check and synchronize valid descriptor values during SetDescriptorValue.
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192 #
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193 sub IsDescriptorsGenerationSuccessful {
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194 my($This) = @_;
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195 my($Atom, $DescriptorValue, @Atoms);
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196
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197 ATOM: for $Atom ($This->{Molecule}->GetAtoms()) {
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198 if ($This->{IgnoreHydrogens} && $Atom->IsHydrogen()) {
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199 next ATOM;
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200 }
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201 $DescriptorValue = $This->GetDescriptorValue($Atom);
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202 if ($DescriptorValue =~ /^None$/i) {
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203 return 0;
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204 }
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205 }
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206
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207 return 1;
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208 }
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209
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210 1;
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211
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212 __END__
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213
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214 =head1 NAME
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215
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216 AtomicDescriptors - AtomicDescriptors class
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217
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218 =head1 SYNOPSIS
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219
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220 use AtomicDescriptors::AtomicDescriptors;
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221
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222 use AtomicDescriptors::AtomicDescriptors qw(:all);
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223
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224 =head1 DESCRIPTION
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225
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226 B<AtomicDescriptors> base class used to derive all other atomic descriptors classes provides the following methods:
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227
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228 new, GetDescriptorValue, GetDescriptorValues,
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229 IsDescriptorsGenerationSuccessful, SetDescriptorValue
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230
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231 B<AtomicDescriptors> class is derived from B<ObjectProperty> base class which provides methods not
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232 explicitly defined in B<Fingerprints> or B<ObjectProperty> classes using Perl's AUTOLOAD functionality.
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233 These methods are generated on-the-fly for a specified object property:
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234
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235 Set<PropertyName>(<PropertyValue>);
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236 $PropertyValue = Get<PropertyName>();
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237 Delete<PropertyName>();
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238
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239 =head2 METHODS
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240
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241 =over 4
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242
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243 =item B<new>
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244
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245 $NewAtomicDescriptors = new AtomicDescriptors::
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246 AtomicDescriptors(%NamesAndValues);
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247
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248 Using specified I<AtomicDescriptors> property names and values hash, B<new> method creates a new object
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249 and returns a reference to newly created B<AtomicDescriptors> object. By default, following properties are
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250 initialized:
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251
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252 Molecule = '';
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253 Type = '';
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254 IgnoreHydrogens = 0;
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255
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256 =item B<GetDescriptorValue>
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257
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258 $Value = $AtomicDescriptors->GetDescriptorValue($Atom);
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259
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260 Returns calculated atomic descriptor I<Value> for specified I<Atom>.
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261
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262 =item B<GetDescriptorValues>
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263
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264 %Values = $AtomicDescriptors->GetDescriptorValues();
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265
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266 Returns calculated atomic descriptor values for all atoms as a hash with atom ID
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267 and atomic descriptor values as key/value pairs.
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268
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269 =item B<IsDescriptorsGenerationSuccessful>
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270
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271 $Status = $AtomicDescriptors->
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272 IsDescriptorsGenerationSuccessful();
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273
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274 Returns 1 or 0 based on whether atomic desctiptors calculations was successful.
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275 For a successful atomic descriptors calculation, all atoms must have a value of other
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276 than a string I<None>.
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277
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278 =item B<SetDescriptorValue>
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279
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280 $AtomicDescriptors->SetDescriptorValue($Atom, $Value);
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281
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282 Sets specified atomic descriptor I<Value> for I<Atom> and returns I<$AtomicDescriptors>.
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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 demo
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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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