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1 NAME
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2 MolecularComplexityDescriptors
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3
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4 SYNOPSIS
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5 use MolecularDescriptors::MolecularComplexityDescriptors;
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6
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7 use MolecularDescriptors::MolecularComplexityDescriptors qw(:all);
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8
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9 DESCRIPTION
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10 MolecularComplexityDescriptors class provides the following methods:
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11
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12 new, GenerateDescriptors, GetDescriptorNames,
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13 GetMolecularComplexityTypeAbbreviation, MACCSKeysSize,
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14 SetAtomIdentifierType, SetAtomicInvariantsToUse, SetDistanceBinSize,
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15 SetFunctionalClassesToUse, SetMaxDistance, SetMaxPathLength,
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16 SetMinDistance, SetMinPathLength, SetMolecularComplexityType,
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17 SetNeighborhoodRadius, SetNormalizationMethodology,
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18 StringifyMolecularComplexityDescriptors
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19
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20 MolecularComplexityDescriptors is derived from MolecularDescriptors
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21 class which in turn is derived from ObjectProperty base class that
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22 provides methods not explicitly defined in
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23 MolecularComplexityDescriptors, MolecularDescriptors or ObjectProperty
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24 classes using Perl's AUTOLOAD functionality. These methods are generated
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25 on-the-fly for a specified object property:
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26
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27 Set<PropertyName>(<PropertyValue>);
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28 $PropertyValue = Get<PropertyName>();
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29 Delete<PropertyName>();
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30
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31 The current release of MayaChemTools supports calculation of molecular
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32 complexity using *MolecularComplexityType* parameter corresponding to
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33 number of bits-set or unique keys [ Ref 117-119 ] in molecular
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34 fingerprints. The valid values for *MolecularComplexityType* are:
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35
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36 AtomTypesFingerprints
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37 ExtendedConnectivityFingerprints
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38 MACCSKeys
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39 PathLengthFingerprints
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40 TopologicalAtomPairsFingerprints
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41 TopologicalAtomTripletsFingerprints
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42 TopologicalAtomTorsionsFingerprints
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43 TopologicalPharmacophoreAtomPairsFingerprints
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44 TopologicalPharmacophoreAtomTripletsFingerprints
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45
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46 Default value for *MolecularComplexityType*: *MACCSKeys*.
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47
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48 *AtomIdentifierType* parameter name corresponds to atom types used
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49 during generation of fingerprints. The valid values for
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50 *AtomIdentifierType* are: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
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51 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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52 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
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53 *AtomicInvariantsAtomTypes* is not supported for following values of
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54 *MolecularComplexityType*: *MACCSKeys,
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55 TopologicalPharmacophoreAtomPairsFingerprints,
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56 TopologicalPharmacophoreAtomTripletsFingerprints*.
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57 *FunctionalClassAtomTypes* is the only valid value of
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58 *AtomIdentifierType* for topological pharmacophore fingerprints.
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59
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60 Default value for *AtomIdentifierType*: *AtomicInvariantsAtomTypes* for
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61 all fingerprints; *FunctionalClassAtomTypes* for topological
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62 pharmacophore fingerprints.
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63
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64 *AtomicInvariantsToUse* parameter name and values are used during
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65 *AtomicInvariantsAtomTypes* value of parameter *AtomIdentifierType*.
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66 It's a list of space separated valid atomic invariant atom types.
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67
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68 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB, TB,
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69 H, Ar, RA, FC, MN, SM*. Default value for *AtomicInvariantsToUse*
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70 parameter are set differently for different fingerprints using
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71 *MolecularComplexityType* parameter as shown below:
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72
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73 MolecularComplexityType AtomicInvariantsToUse
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74
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75 AtomTypesFingerprints AS X BO H FC
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76 TopologicalAtomPairsFingerprints AS X BO H FC
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77 TopologicalAtomTripletsFingerprints AS X BO H FC
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78 TopologicalAtomTorsionsFingerprints AS X BO H FC
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79
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80 ExtendedConnectivityFingerprints AS X BO H FC MN
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81 PathLengthFingerprints AS
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82
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83 *FunctionalClassesToUse* parameter name and values are used during
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84 *FunctionalClassAtomTypes* value of parameter *AtomIdentifierType*. It's
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85 a list of space separated valid atomic invariant atom types.
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86
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87 Possible values for atom functional classes are: *Ar, CA, H, HBA, HBD,
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88 Hal, NI, PI, RA*.
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89
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90 Default value for *FunctionalClassesToUse* parameter is set to:
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91
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92 HBD HBA PI NI Ar Hal
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93
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94 for all fingerprints except for the following two
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95 *MolecularComplexityType* fingerints:
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96
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97 MolecularComplexityType FunctionalClassesToUse
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98
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99 TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H
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100 TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar
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101
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102 *MACCSKeysSize* parameter name is only used during *MACCSKeys* value of
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103 *MolecularComplexityType* and corresponds to size of MACCS key set.
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104 Possible values: *166 or 322*. Default value: *166*.
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105
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106 *NeighborhoodRadius* parameter name is only used during
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107 *ExtendedConnectivityFingerprints* value of *MolecularComplexityType*
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108 and corresponds to atomic neighborhoods radius for generating extended
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109 connectivity fingerprints. Possible values: positive integer. Default
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110 value: *2*.
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111
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112 *MinPathLength* and *MaxPathLength* parameters are only used during
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113 *PathLengthFingerprints* value of *MolecularComplexityType* and
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114 correspond to minimum and maximum path lengths to use for generating
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115 path length fingerprints. Possible values: positive integers. Default
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116 value: *MinPathLength - 1*; *MaxPathLength - 8*.
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117
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118 *UseBondSymbols* parameter is only used during *PathLengthFingerprints*
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119 value of *MolecularComplexityType* and indicates whether bond symbols
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120 are included in atom path strings used to generate path length
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121 fingerprints. Possible value: *Yes or No*. Default value: *Yes*.
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122
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123 *MinDistance* and *MaxDistance* parameters are only used during
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124 *TopologicalAtomPairsFingerprints* and
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125 *TopologicalAtomTripletsFingerprints* values of
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126 *MolecularComplexityType* and correspond to minimum and maximum bond
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127 distance between atom pairs during topological pharmacophore
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128 fingerprints. Possible values: positive integers. Default value:
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129 *MinDistance - 1*; *MaxDistance - 10*.
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130
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131 *UseTriangleInequality* parameter is used during these values for
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132 *MolecularComplexityType*: *TopologicalAtomTripletsFingerprints* and
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133 *TopologicalPharmacophoreAtomTripletsFingerprints*. Possible values:
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134 *Yes or No*. It determines wheter to apply triangle inequality to
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135 distance triplets. Default value: *TopologicalAtomTripletsFingerprints -
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136 No*; *TopologicalPharmacophoreAtomTripletsFingerprints - Yes*.
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137
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138 *DistanceBinSize* parameter is used during
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139 *TopologicalPharmacophoreAtomTripletsFingerprints* value of
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140 *MolecularComplexityType* and corresponds to distance bin size used for
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141 binning distances during generation of topological pharmacophore atom
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142 triplets fingerprints. Possible value: positive integer. Default value:
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143 *2*.
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144
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145 *NormalizationMethodology* is only used for these values for
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146 *MolecularComplexityType*: *ExtendedConnectivityFingerprints*,
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147 *TopologicalPharmacophoreAtomPairsFingerprints* and
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148 *TopologicalPharmacophoreAtomTripletsFingerprints*. It corresponds to
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149 normalization methodology to use for scaling the number of bits-set or
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150 unique keys during generation of fingerprints. Possible values during
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151 *ExtendedConnectivityFingerprints*: *None or ByHeavyAtomsCount*; Default
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152 value: *None*. Possible values during topological pharmacophore atom
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153 pairs and triplets fingerprints: *None or ByPossibleKeysCount*; Default
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154 value: *None*. *ByPossibleKeysCount* corresponds to total number of
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155 possible topological pharmacophore atom pairs or triplets in a molecule.
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156
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157 METHODS
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158 new
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159 $NewMolecularComplexityDescriptors = new MolecularDescriptors::
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160 MolecularComplexityDescriptors(
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161 %NamesAndValues);
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162
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163 Using specified *MolecularComplexityDescriptors* property names and
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164 values hash, new method creates a new object and returns a reference
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165 to newly created MolecularComplexityDescriptors object. By default,
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166 the following properties are initialized:
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167
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168 Molecule = ''
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169 Type = 'MolecularComplexity'
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170 MolecularComplexityType = 'MACCSKeys'
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171 AtomIdentifierType = ''
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172 MACCSKeysSize = 166
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173 NeighborhoodRadius = 2
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174 MinPathLength = 1
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175 MaxPathLength = 8
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176 UseBondSymbols = 1
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177 MinDistance = 1
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178 MaxDistance = 10
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179 UseTriangleInequality = ''
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180 DistanceBinSize = 2
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181 NormalizationMethodology = 'None'
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182 @DescriptorNames = ('MolecularComplexity')
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183 @DescriptorValues = ('None')
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184
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185 Examples:
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186
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187 $MolecularComplexityDescriptors = new MolecularDescriptors::
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188 MolecularComplexityDescriptors(
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189 'Molecule' => $Molecule);
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190
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191 $MolecularComplexityDescriptors = new MolecularDescriptors::
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192 MolecularComplexityDescriptors();
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193
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194 $MolecularComplexityDescriptors->SetMolecule($Molecule);
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195 $MolecularComplexityDescriptors->GenerateDescriptors();
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196 print "MolecularComplexityDescriptors: $MolecularComplexityDescriptors\n";
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197
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198 GenerateDescriptors
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199 $MolecularComplexityDescriptors->GenerateDescriptors();
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200
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201 Calculates MolecularComplexity value for a molecule and returns
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202 *MolecularComplexityDescriptors*.
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203
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204 GetDescriptorNames
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205 @DescriptorNames = $MolecularComplexityDescriptors->GetDescriptorNames();
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206 @DescriptorNames = MolecularDescriptors::MolecularComplexityDescriptors::
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207 GetDescriptorNames();
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208
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209 Returns all available descriptor names as an array.
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210
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211 GetMolecularComplexityTypeAbbreviation
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212 $Abbrev = $MolecularComplexityDescriptors->
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213 GetMolecularComplexityTypeAbbreviation();
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214 $Abbrev = MolecularDescriptors::MolecularComplexityDescriptors::
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215 GetMolecularComplexityTypeAbbreviation($ComplexityType);
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216
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217 Returns abbreviation for a specified molecular complexity type or
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218 corresponding to *MolecularComplexityDescriptors* object.
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219
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220 SetMACCSKeysSize
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221 $MolecularComplexityDescriptors->MACCSKeysSize($Size);
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222
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223 Sets MACCS keys size and returns *MolecularComplexityDescriptors*.
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224
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225 SetAtomIdentifierType
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226 $MolecularComplexityDescriptors->SetAtomIdentifierType($IdentifierType);
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227
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228 Sets atom *IdentifierType* to use during fingerprints generation
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229 corresponding to *MolecularComplexityType* and returns
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230 *MolecularComplexityDescriptors*.
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231
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232 Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
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233 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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234 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
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235
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236 SetAtomicInvariantsToUse
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237 $MolecularComplexityDescriptors->SetAtomicInvariantsToUse($ValuesRef);
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238 $MolecularComplexityDescriptors->SetAtomicInvariantsToUse(@Values);
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239
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240 Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
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241 value of *AtomIdentifierType* for fingerprints generation and
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242 returns *MolecularComplexityDescriptors*.
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243
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244 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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245 TB, H, Ar, RA, FC, MN, SM*. Default value [ Ref 24 ]:
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246 *AS,X,BO,H,FC,MN*.
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247
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248 The atomic invariants abbreviations correspond to:
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249
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250 AS = Atom symbol corresponding to element symbol
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251
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252 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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253 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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254 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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255 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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256 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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257 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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258 H<n> = Number of implicit and explicit hydrogens for atom
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259 Ar = Aromatic annotation indicating whether atom is aromatic
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260 RA = Ring atom annotation indicating whether atom is a ring
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261 FC<+n/-n> = Formal charge assigned to atom
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262 MN<n> = Mass number indicating isotope other than most abundant isotope
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263 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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264 3 (triplet)
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265
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266 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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267 corresponds to:
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268
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269 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
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270
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271 Except for AS which is a required atomic invariant in atom types,
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272 all other atomic invariants are optional. Atom type specification
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273 doesn't include atomic invariants with zero or undefined values.
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274
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275 In addition to usage of abbreviations for specifying atomic
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276 invariants, the following descriptive words are also allowed:
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277
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278 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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279 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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280 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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281 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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282 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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283 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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284 H : NumOfImplicitAndExplicitHydrogens
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285 Ar : Aromatic
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286 RA : RingAtom
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287 FC : FormalCharge
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288 MN : MassNumber
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289 SM : SpinMultiplicity
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290
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291 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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292 atomic invariant atom types.
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293
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294 SetDistanceBinSize
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295 $MolecularComplexityDescriptors->SetDistanceBinSize($BinSize);
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296
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297 Sets distance bin size used to bin distances between atom pairs in
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298 atom triplets for topological pharmacophore atom triplets
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299 fingerprints generation and returns
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300 *MolecularComplexityDescriptors*.
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301
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302 SetFunctionalClassesToUse
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303 $MolecularComplexityDescriptors->SetFunctionalClassesToUse($ValuesRef);
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304 $MolecularComplexityDescriptors->SetFunctionalClassesToUse(@Values);
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305
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306 Sets functional classes invariants to use during
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307 *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
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308 fingerprints generation and returns
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309 *MolecularComplexityDescriptors*.
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310
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311 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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312 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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313 *HBD,HBA,PI,NI,Ar,Hal*.
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314
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315 The functional class abbreviations correspond to:
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316
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317 HBD: HydrogenBondDonor
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318 HBA: HydrogenBondAcceptor
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319 PI : PositivelyIonizable
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320 NI : NegativelyIonizable
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321 Ar : Aromatic
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322 Hal : Halogen
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323 H : Hydrophobic
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324 RA : RingAtom
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325 CA : ChainAtom
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326
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327 Functional class atom type specification for an atom corresponds to:
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328
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329 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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330
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331 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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332 functional class atom types. It uses following definitions [ Ref
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333 60-61, Ref 65-66 ]:
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334
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335 HydrogenBondDonor: NH, NH2, OH
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336 HydrogenBondAcceptor: N[!H], O
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337 PositivelyIonizable: +, NH2
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338 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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339
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340 SetMaxDistance
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341 $MolecularComplexityDescriptors->SetMaxDistance($MaxDistance);
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342
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343 Sets maximum distance to use during topological atom pairs and
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344 triplets fingerprints generation and returns
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345 *MolecularComplexityDescriptors*.
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346
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347 SetMaxPathLength
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348 $MolecularComplexityDescriptors->SetMaxPathLength($Length);
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349
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350 Sets maximum path length to use during path length fingerprints
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351 generation and returns *MolecularComplexityDescriptors*.
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352
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353 SetMinDistance
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354 $MolecularComplexityDescriptors->SetMinDistance($MinDistance);
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355
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356 Sets minimum distance to use during topological atom pairs and
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357 triplets fingerprints generation and returns
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358 *MolecularComplexityDescriptors*.
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359
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360 SetMinPathLength
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361 $MolecularComplexityDescriptors->SetMinPathLength($MinPathLength);
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362
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363 Sets minimum path length to use during path length fingerprints
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364 generation and returns *MolecularComplexityDescriptors*.
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365
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366 SetMolecularComplexityType
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367 $MolecularComplexityDescriptors->SetMolecularComplexityType($ComplexityType);
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368
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369 Sets molecular complexity type to use for calculating its value and
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370 returns *MolecularComplexityDescriptors*.
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371
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372 SetNeighborhoodRadius
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373 $MolecularComplexityDescriptors->SetNeighborhoodRadius($Radius);
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374
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375 Sets neighborhood radius to use during extended connectivity
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376 fingerprints generation and returns
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377 *MolecularComplexityDescriptors*.
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378
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379 SetNormalizationMethodology
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380 $MolecularComplexityDescriptors->SetNormalizationMethodology($Methodology);
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381
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382 Sets normalization methodology to use during calculation of
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383 molecular complexity corresponding to extended connectivity,
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384 topological pharmacophore atom pairs and tripletes fingerprints
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385 returns *MolecularComplexityDescriptors*.
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386
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387 StringifyMolecularComplexityDescriptors
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388 $String = $MolecularComplexityDescriptors->
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389 StringifyMolecularComplexityDescriptors();
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390
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391 Returns a string containing information about
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392 *MolecularComplexityDescriptors* object.
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393
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394 AUTHOR
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395 Manish Sud <msud@san.rr.com>
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396
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397 SEE ALSO
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398 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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399
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400 COPYRIGHT
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401 Copyright (C) 2015 Manish Sud. All rights reserved.
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402
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403 This file is part of MayaChemTools.
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404
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405 MayaChemTools is free software; you can redistribute it and/or modify it
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406 under the terms of the GNU Lesser General Public License as published by
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407 the Free Software Foundation; either version 3 of the License, or (at
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408 your option) any later version.
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409
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