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1 NAME
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2 MolecularDescriptorsGenerator
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3
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4 SYNOPSIS
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5 use MolecularDescriptors::MolecularDescriptorsGenerator;
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6
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7 use MolecularDescriptors::MolecularDescriptorsGenerator qw(:all);
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8
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9 DESCRIPTION
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10 MolecularDescriptorsGenerator class provides the following methods:
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11
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12 new, GenerateDescriptors, GetAvailableClassAndDescriptorNames,
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13 GetAvailableClassNameForDescriptorName,
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14 GetAvailableDescriptorClassNames, GetAvailableDescriptorNames,
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15 GetAvailableDescriptorNamesForDescriptorClass,
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16 GetDescriptorClassParameters, GetDescriptorNames,
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17 GetDescriptorNamesAndValues, GetDescriptorValueByName,
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18 GetDescriptorValues, GetRuleOf3DescriptorNames,
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19 GetRuleOf5DescriptorNames, IsDescriptorClassNameAvailable,
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20 IsDescriptorNameAvailable, IsDescriptorsGenerationSuccessful,
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21 SetDescriptorClassParameters, SetDescriptorNames, SetMode, SetMolecule,
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22 StringifyMolecularDescriptorsGenerator
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23
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24 MolecularDescriptorsGenerator is derived from is derived from
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25 ObjectProperty base class that provides methods not explicitly defined
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26 in MolecularDescriptorsGenerator or ObjectProperty classes using Perl's
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27 AUTOLOAD functionality. These methods are generated on-the-fly for a
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28 specified object property:
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29
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30 Set<PropertyName>(<PropertyValue>);
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31 $PropertyValue = Get<PropertyName>();
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32 Delete<PropertyName>();
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33
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34 MolecularDescriptorsGenerator is designed to provide a plug-in
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35 environment for molecular descriptors development. The molecular
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36 descriptor class modules available in MolecularDescriptors directory
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37 under MayaChemTools/lib directory are automatically detected and loaded
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38 into the system. The descriptor names provided by each descriptor class
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39 module through its GetDescriptorNames function are retrieved and are
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40 made available for calculations of their values for a specified
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41 molecule.
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42
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43 Any combination of available descriptor names can be specified during
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44 calculation of descriptor values using GenerateDescriptors method. The
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45 current release of MayaChemTools supports generation of four sets of
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46 descriptors: All available descriptors, rule of 5 or 3 descriptors, or a
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47 specified set of descriptor names.
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48
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49 RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight,
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50 HydrogenBondDonors, HydrogenBondAcceptors, SLogP. RuleOf5 states:
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51 MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors
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52 <= 10, and logP <= 5.
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53
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54 RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight,
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55 RotatableBonds, HydrogenBondDonors, HydrogenBondAcceptors, SLogP, TPSA.
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56 RuleOf3 states: MolecularWeight <= 300, RotatableBonds <= 3,
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57 HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA
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58 <= 60.
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59
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60 Before calculation of a specified set of descriptors by
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61 GenerateDescriptors method, a set of descriptor calculation control
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62 parameters for a specific descriptor class name can be set using
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63 SetDescriptorClassParameters method. The specified control parameter
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64 names and values are simply passed on to specified descriptor class
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65 during instantiation of descriptor class object without performing any
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66 validation of parameter names and associated values. It's up to the
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67 appropriate descriptor class methods to validate these parameters and
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68 values. In addition to specified parameter names and values, the
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69 parameter hash must also contain descriptor class name as key and value
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70 pair with DescriptorClassName as key with class name as value.
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71
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72 METHODS
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73 new
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74 $NewMolecularDescriptorsGenerator = new MolecularDescriptors::
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75 MolecularDescriptorsGenerator(
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76 %NamesAndValues);
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77
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78 Using specified *MolecularDescriptorsGenerator* property names and
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79 values hash, new method creates a new object and returns a reference
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80 to newly created MolecularDescriptorsGenerator object. By default,
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81 the following properties are initialized:
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82
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83 Mode = 'All'
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84 @{$This->{DescriptorNames}} = ()
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85 %{$This->{DescriptorClassParameters}} = ()
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86 @{$This->{DescriptorClassNames}} = ()
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87 %{$This->{DescriptorClassObjects}} = ()
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88 @{$This->{DescriptorValues}} = ()
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89
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90 Examples:
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91
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92 $MolecularDescriptorsGenerator = new MolecularDescriptors::
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93 MolecularDescriptorsGenerator(
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94 'Molecule' => $Molecule);
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95
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96 @DescriptorNames = qw(MolecularWeight HydrogenBondDonors Fsp3Carbons)
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97 $MolecularDescriptorsGenerator = new MolecularDescriptors::
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98 MolecularDescriptorsGenerator(
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99 'Mode' => 'Specify',
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100 'DescriptorNames' => \@DescriptorNames);
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101
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102 $MolecularDescriptorsGenerator->SetDescriptorClassParameters(
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103 'DescriptorClassName' => 'WeightAndMassDescriptors',
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104 'WeightPrecision' => 2,
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105 'MassPrecision' => 2);
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106
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107 $MolecularDescriptorsGenerator->SetDescriptorClassParameters(
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108 'DescriptorClassName' => 'HydrogenBondsDescriptors',
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109 'HydrogenBondsType' => 'HBondsType1');
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110
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111 $MolecularDescriptorsGenerator->SetMolecule($Molecule);
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112 $MolecularDescriptorsGenerator->GenerateDescriptors();
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113 print "MolecularDescriptorsGenerator: $MolecularDescriptorsGenerator\n";
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114
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115 GenerateDescriptors
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116 $MolecularDescriptorsGenerator->GenerateDescriptors();
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117
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118 Calculates descriptor values for specified descriptors and returns
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119 *MolecularDescriptorsGenerator*.
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120
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121 Descriptor class objects are instantiated only once at first
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122 invocation. During subsequent calls to GenerateDescriptors method,
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123 descriptor values are initialized and GenerateDescriptors method
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124 provided by descriptor class is used to calculate descriptor values
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125 for specified descriptors.
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126
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127 GetAvailableClassAndDescriptorNames
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128 %ClassAndDescriptorNames = $MolecularDescriptorsGenerator->
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129 GetAvailableClassAndDescriptorNames();
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130 %ClassAndDescriptorNames = MolecularDescriptors::
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131 MolecularDescriptorsGenerator::
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132 GetAvailableClassAndDescriptorNames();
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133
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134 Returns available descriptors class and descriptors names as a hash
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135 containing key and value pairs corresponding to class name and an
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136 array of descriptor names available for the class.
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137
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138 GetAvailableClassNameForDescriptorName
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139 $DescriptorClassName = $MolecularDescriptorsGenerator->
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140 GetAvailableClassNameForDescriptorName($DescriptorName);
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141
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142 $DescriptorClassName = MolecularDescriptors::MolecularDescriptorsGenerator::
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143 GetAvailableClassNameForDescriptorName($DescriptorName);
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144
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145 Returns available descriptor class name for a descriptor name.
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146
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147 GetAvailableDescriptorClassNames
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148 $Return = $MolecularDescriptorsGenerator->GetAvailableDescriptorClassNames();
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149
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150 @DescriptorClassNames = $MolecularDescriptorsGenerator->
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151 GetAvailableDescriptorClassNames();
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152 @DescriptorClassNames = MolecularDescriptors::
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153 MolecularDescriptorsGenerator::
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154 GetAvailableDescriptorClassNames();
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155
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156 Returns available descriptor class names as an array or number of
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157 available descriptor class names in scalar context.
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158
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159 GetAvailableDescriptorNames
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160 @DescriptorNames = $MolecularDescriptorsGenerator->
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161 GetAvailableDescriptorNames();
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162 @DescriptorNames = MolecularDescriptors::
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163 MolecularDescriptorsGenerator::
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164 GetAvailableDescriptorNames();
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165
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166 Returns available descriptor names as an array or number of
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167 available descriptor names in scalar context.
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168
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169 GetAvailableDescriptorNamesForDescriptorClass
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170 @DescriptorNames = $MolecularDescriptorsGenerator->
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171 GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
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172 @DescriptorNames = MolecularDescriptors::
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173 MolecularDescriptorsGenerator::
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174 GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
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175
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176 Returns available descriptors names for a descriptor class as an
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177 array or number of available descriptor names in scalar context.
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178
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179 GetDescriptorClassParameters
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180 $DescriptorClassParametersRef = $MolecularDescriptorsGenerator->
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181 GetDescriptorClassParameters();
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182 $DescriptorClassParametersRef = MolecularDescriptors::
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183 MolecularDescriptorsGenerator::
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184 GetDescriptorClassParameters();
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185
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186 Returns descriptor name parameters as a reference to hash of hashes
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187 with hash keys corresponding to class name and class parameter name
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188 with hash value as class parameter value.
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189
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190 GetDescriptorNames
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191 @DescriptorNames = $MolecularDescriptorsGenerator->GetDescriptorNames();
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192 @DescriptorNames = MolecularDescriptors::MolecularDescriptorsGenerator::
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193 GetDescriptorNames();
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194
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195 Returns all available descriptor names as an array or number of
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196 available descriptors in scalar context.
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197
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198 GetDescriptorNamesAndValues
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199 %NamesAndValues = $MolecularDescriptorsGenerator->
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200 GetDescriptorNamesAndValues();
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201
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202 Returns calculated molecular descriptor names and values as a hash
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203 with descriptor names and values as hash key and value pairs.
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204
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205 GetDescriptorValueByName
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206 $Value = $MolecularDescriptorsGenerator->
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207 GetDescriptorValueByName($Name);
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208
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209 Returns calculated descriptor values for a specified descriptor
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210 name.
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211
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212 GetDescriptorValues
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213 @DescriptorValues = $MolecularDescriptorsGenerator->GetDescriptorValues();
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214
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215 Returns all calculated descriptor values as an array corresponding
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216 to specified descriptor names.
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217
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218 GetRuleOf3DescriptorNames
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219 @DescriptorNames = $MolecularDescriptorsGenerator->
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220 GetRuleOf3DescriptorNames();
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221 @DescriptorNames = MolecularDescriptors::
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222 MolecularDescriptorsGenerator::
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223 GetRuleOf3DescriptorNames();
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224
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225 Returns rule of 3 descriptor names as an array or number of rule of
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226 3 descriptors in scalar context.
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227
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228 RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight,
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229 RotatableBonds, HydrogenBondDonors, HydrogenBondAcceptors, SLogP,
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230 TPSA. RuleOf3 states: MolecularWeight <= 300, RotatableBonds <= 3,
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231 HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and
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232 TPSA <= 60.
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233
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234 GetRuleOf5DescriptorNames
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235 @DescriptorNames = $MolecularDescriptorsGenerator->
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236 GetRuleOf5DescriptorNames();
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237 @DescriptorNames = $MolecularDescriptorsGenerator::
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238 GetRuleOf5DescriptorNames();
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239
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240 Returns rule of 5 descriptor names as an array or number of rule of
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241 4 descriptors in scalar context.
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242
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243 RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight,
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244 HydrogenBondDonors, HydrogenBondAcceptors, SLogP. RuleOf5 states:
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245 MolecularWeight <= 500, HydrogenBondDonors <= 5,
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246 HydrogenBondAcceptors <= 10, and logP <= 5.
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247
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248 IsDescriptorClassNameAvailable
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249 $Status = $MolecularDescriptorsGenerator->
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250 IsDescriptorClassNameAvailable($ClassName);
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251 $Status = MolecularDescriptors::
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252 MolecularDescriptorsGenerator::
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253 IsDescriptorClassNameAvailable($ClassName);
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254
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255 Returns 1 or 0 based on whether specified descriptor class name is
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256 available.
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257
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258 IsDescriptorNameAvailable
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259 $Status = $MolecularDescriptorsGenerator->
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260 IsDescriptorNameAvailable($DescriptorName);
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261 $Status = MolecularDescriptors::
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262 MolecularDescriptorsGenerator::
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263 IsDescriptorNameAvailable($DescriptorName);
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264
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265 Returns 1 or 0 based on whether specified descriptor name is
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266 available.
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267
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268 IsDescriptorsGenerationSuccessful
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269 $Status = $MolecularDescriptorsGenerator->
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270 IsDescriptorsGenerationSuccessful();
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271
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272 Returns 1 or 0 based on whether descriptors generation is
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273 successful.
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274
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275 SetDescriptorClassParameters
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276 $MolecularDescriptorsGenerator->SetDescriptorClassParameters(
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277 %NamesAndValues);
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278
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279 Sets descriptor calculation control parameters for a specified
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280 descriptor class name and returns *MolecularDescriptorsGenerator*.
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281
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282 The specified parameter names and values are simply passed on to
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283 specified descriptor class during instantiation of descriptor class
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284 object without any performing any validation of parameter names and
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285 associated values. It's up to the appropriate descriptor class
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286 methods to validate these parameters and values.
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287
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288 In addition to specified parameter names and values, the parameter
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289 hash must also contain descriptor class name as key and value pair
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290 with DescriptorClassName as key with class name as value.
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291
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292 SetDescriptorNames
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293 $MolecularDescriptorsGenerator->SetDescriptorNames(@Names);
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294 $MolecularDescriptorsGenerator->SetDescriptorNames(\@Names);
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295
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296 Sets descriptor names to use for generating descriptor values using
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297 an array or reference to an array and returns
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298 *MolecularDescriptorsGenerator*.
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299
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300 SetMode
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301 $MolecularDescriptorsGenerator->SetMode($Mode);
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302
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303 Sets descriptors generation mode and returns
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304 *MolecularDescriptorsGenerator*. Possible *Mode* values: *All,
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305 RuleOf5, RuleOf3, Specify*.
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306
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307 SetMolecule
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308 $MolecularDescriptorsGenerator->SetMolecule($Molecule);
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309
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310 Sets molecule to use during calculation of molecular descriptors and
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311 returns *MolecularDescriptorsGenerator*.
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312
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313 StringifyMolecularDescriptorsGenerator
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314 $String = $MolecularDescriptorsGenerator->StringifyMolecularDescriptorsGenerator();
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315
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316 Returns a string containing information about
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317 *MolecularDescriptorsGenerator* object.
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318
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319 AUTHOR
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320 Manish Sud <msud@san.rr.com>
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321
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322 SEE ALSO
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323 MolecularDescriptors.pm
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324
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325 COPYRIGHT
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326 Copyright (C) 2015 Manish Sud. All rights reserved.
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327
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328 This file is part of MayaChemTools.
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329
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330 MayaChemTools is free software; you can redistribute it and/or modify it
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331 under the terms of the GNU Lesser General Public License as published by
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332 the Free Software Foundation; either version 3 of the License, or (at
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333 your option) any later version.
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334
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