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1 NAME
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2 TopologicalPharmacophoreAtomPairsFingerprints
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3
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4 SYNOPSIS
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5 use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints;
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6
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7 use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints
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8 qw(:all);
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9
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10 DESCRIPTION
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11 TopologicalPharmacophoreAtomPairsFingerprints [ Ref 60-62, Ref 65, Ref
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12 68 ] class provides the following methods:
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13
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14 new, GenerateFingerprints, GetDescription, GetAtomPairIDs,
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15 SetAtomTypesToUse, SetAtomTypesWeight, SetFuzzFactor,
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16 SetFuzzificationMethodology, SetFuzzificationMode, SetMaxDistance,
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17 SetMinDistance, SetNormalizationMethodology, SetValuesPrecision,
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18 StringifyTopologicalPharmacophoreAtomPairsFingerprints
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19
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20 TopologicalPharmacophoreAtomPairsFingerprints is derived from
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21 Fingerprints class which in turn is derived from ObjectProperty base
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22 class that provides methods not explicitly defined in
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23 TopologicalPharmacophoreAtomPairsFingerprints, Fingerprints or
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24 ObjectProperty classes using Perl's AUTOLOAD functionality. These
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25 methods are generated 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 Based on the values specified for AtomTypesToUse, pharmacophore atom
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32 types are assigned to all non-hydrogen atoms in a molecule and a
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33 distance matrix is generated. A pharmacophore atom pairs basis set is
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34 initialized for all unique possible pairs within MinDistance and
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35 MaxDistance range.
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36
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37 Let:
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38
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39 P = Valid pharmacophore atom type
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40
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41 Px = Pharmacophore atom type x
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42 Py = Pharmacophore atom type y
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43
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44 Dmin = Minimum distance corresponding to number of bonds between two atoms
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45 Dmax = Maximum distance corresponding to number of bonds between two atoms
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46 D = Distance corresponding to number of bonds between two atoms
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47
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48 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn
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49
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50 P = Number of pharmacophore atom types to consider
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51 PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn
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52
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53 PPT = Total number of possible pharmacophore atom pairs at all distances between Dmin and Dmax
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54
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55 Then:
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56
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57 PPD = (P * (P - 1))/2 + P
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58
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59 PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)
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60 = ((Dmax - Dmin) + 1) * PPD
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61
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62 So for default values of Dmin = 1, Dmax = 10 and P = 5,
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63
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64 PPD = (5 * (5 - 1))/2 + 5 = 15
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65 PPT = ((10 - 1) + 1) * 15 = 150
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66
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67 The pharmacophore atom pairs bais set includes 150 values.
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68
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69 The atom pair IDs correspond to:
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70
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71 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn
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72
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73 For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on
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74
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75 Using distance matrix and pharmacohore atom types, occurrence of unique
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76 pharmacohore atom pairs is counted. The contribution of each atom type
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77 to atom pair interaction is optionally weighted by specified
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78 AtomTypesWeight before assigning its count to appropriate distance bin.
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79 Based on NormalizationMethodology option, pharmacophore atom pairs count
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80 is optionally normalized. Additionally, pharmacohore atom pairs count is
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81 optionally fuzzified before or after the normalization controlled by
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82 values of FuzzifyAtomPairsCount, FuzzificationMode,
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83 FuzzificationMethodology and FuzzFactor.
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84
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85 The final pharmacophore atom pairs count along with atom pair
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86 identifiers involving all non-hydrogen atoms, with optional
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87 normalization and fuzzification, constitute pharmacophore topological
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88 atom pairs fingerprints of the molecule.
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89
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90 For *ArbitrarySize* value of AtomPairsSetSizeToUse, the fingerprint
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91 vector correspond to only those topological pharmacophore atom pairs
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92 which are present and have non-zero count. However, for *FixedSize*
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93 value of AtomPairsSetSizeToUse, the fingerprint vector contains all
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94 possible valid topological pharmacophore atom pairs with both zero and
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95 non-zero count values.
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96
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97 The current release of MayaChemTools generates the following types of
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98 topological pharmacophore atom pairs fingerprints vector strings:
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99
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100 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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101 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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102 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
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103 HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
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104 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
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105 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
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106 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
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107
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108 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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109 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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110 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
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111 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
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112 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
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113 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
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114
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115 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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116 ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
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117 -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
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118 BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
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119 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
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120 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
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121 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
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122 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0
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123
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124 METHODS
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125 new
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126 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
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127 %NamesAndValues);
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128
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129 Using specified *TopologicalPharmacophoreAtomPairsFingerprints*
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130 property names and values hash, new method creates a new object and
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131 returns a reference to newly created
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132 TopologicalPharmacophoreAtomPairsFingerprints object. By default,
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133 the following properties are initialized:
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134
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135 Molecule = ''
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136 Type = 'TopologicalPharmacophoreAtomPairs'
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137 MinDistance = 1
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138 MaxDistance = 10
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139 NormalizationMethodology = 'None'
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140 AtomTypesToUse = ['HBD', 'HBA', 'PI', 'NI', 'H']
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141
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142 FuzzifyAtomPairsCount = 0
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143 FuzzificationMode = 'AfterNormalization'
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144 FuzzificationMethodology = 'FuzzyBinning'
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145 FuzzFactor = 0.15
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146
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147 ValuesPrecision = 2
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148
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149 Examples:
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150
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151 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
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152 'Molecule' => $Molecule);
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153
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154 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
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155 'Molecule' => $Molecule,
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156 'AtomPairsSetSizeToUse' => 'ArbitrarySize',
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157 'MinDistance' => 1,
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158 'MaxDistance' => 10,
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159 'NormalizationMethodology' => 'None',
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160 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H'],
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161 'FuzzifyAtomPairsCount' => 0);
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162
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163 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
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164 'Molecule' => $Molecule,
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165 'AtomPairsSetSizeToUse' => 'FizedSize',
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166 'MinDistance' => 1,
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167 'MaxDistance' => 10,
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168 'NormalizationMethodology' => 'None',
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169 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H'],
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170 'FuzzifyAtomPairsCount' => 1,
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171 'FuzzificationMethodology' => 'FuzzyBinning',
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172 'FuzzFactor' => 0.15,
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173 'ValuesPrecision' => 2);
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174
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175 $TPAPFP->GenerateFingerprints();
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176 print "$TPAPFP\n";
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177
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178 GetDescription
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179 $Description = $TopologicalPharmacophoreAtomPairsFP->GetDescription();
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180
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181 Returns a string containing description of topological pharmacophore
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182 atom pairs fingerprints.
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183
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184 GenerateFingerprints
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185 $TopologicalPharmacophoreAtomPairsFP->GenerateFingerprints();
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186
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187 Generates topological pharmacophore atom pairs fingerprints and
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188 returns *TopologicalPharmacophoreAtomPairsFP*.
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189
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190 GetAtomPairIDs
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191 $AtomPairIDsRef = $TopologicalPharmacophoreAtomPairsFP->GetAtomPairIDs();
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192 @AtomPairIDs = $TopologicalPharmacophoreAtomPairsFP->GetAtomPairIDs();
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193
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194 Returns atom pair IDs corresponding to atom pairs count values in
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195 topological pharmacophore atom pairs fingerprints vector as an array
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196 or reference to an array.
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197
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198 SetAtomPairsSetSizeToUse
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199 $TopologicalPharmacophoreAtomPairsFP->SetAtomPairsSetSizeToUse($Values);
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200
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201 Sets pharmacophore atom pairs set size to use for topological
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202 pharmacophore fingerprints generation and returns
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203 *TopologicalPharmacophoreAtomPairsFingerprints*.
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204
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205 Possible values for pharmacophore atom pairs set size are:
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206 *ArbitrarySize, FizedSize*. Default value: *ArbitrarySize*.
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207
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208 For *ArbitrarySize* value of AtomPairsSetSizeToUse, the fingerprint
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209 vector correspond to only those topological pharmacophore atom pairs
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210 which are present and have non-zero count. However, for *FixedSize*
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211 value of AtomPairsSetSizeToUse, the fingerprint vector contains all
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212 possible valid topological pharmacophore atom pairs with both zero
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213 and non-zero count values.
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214
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215 SetAtomTypesToUse
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216 $TopologicalPharmacophoreAtomPairsFP->SetAtomTypesToUse($ValuesRef);
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217 $TopologicalPharmacophoreAtomPairsFP->SetAtomTypesToUse(@Values);
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218
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219 Sets pharmacophore atom types to use for topological pharmacophore
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220 fingerprints generation and returns
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221 *TopologicalPharmacophoreAtomPairsFingerprints*.
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222
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223 Possible values for pharmacophore atom types are: *Ar, CA, H, HBA,
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224 HBD, Hal, NI, PI, RA*. Default value [ Ref 60-62 ] :
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225 *HBD,HBA,PI,NI,H*.
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226
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227 The pharmacophore atom types abbreviations correspond to:
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228
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229 HBD: HydrogenBondDonor
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230 HBA: HydrogenBondAcceptor
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231 PI : PositivelyIonizable
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232 NI : NegativelyIonizable
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233 Ar : Aromatic
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234 Hal : Halogen
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235 H : Hydrophobic
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236 RA : RingAtom
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237 CA : ChainAtom
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238
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239 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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240 pharmacophore atom types. It uses following definitions [ Ref 60-61,
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241 Ref 65-66 ]:
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242
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243 HydrogenBondDonor: NH, NH2, OH
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244 HydrogenBondAcceptor: N[!H], O
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245 PositivelyIonizable: +, NH2
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246 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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247
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248 SetAtomTypesWeight
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249 $TopologicalPharmacophoreAtomPairsFP->SetAtomTypesWeight(
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250 %AtomTypesToWeight);
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251
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252 Sets weights of specified pharmacophore atom types to use during
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253 calculation of their contribution to atom pair count and returns
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254 *TopologicalPharmacophoreAtomPairsFP*. Default values: *1 for each
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255 atom type*.
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256
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257 The weight values allow to increase the importance of specific
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258 pharmacophore atom type in the generated fingerprints. A weight
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259 value of 0 for an atom type eliminates its contribution to atom pair
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260 count where as weight value of 2 doubles its contribution.
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261
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262 SetFuzzFactor
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263 $TopologicalPharmacophoreAtomPairsFP->SetFuzzFactor($Value);
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264
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265 Sets fuzz factor value to use during fuzzification of atom pairs
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266 count and returns *TopologicalPharmacophoreAtomPairsFP*. Default
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267 value: *0.15*.
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268
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269 Valid values: For *FuzzyBinning* value of FuzzificationMethodology:
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270 *between 0 and 1.0*; For *FuzzyBinSmoothing* value of
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271 FuzzificationMethodology: *between 0 and 0.5*.
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272
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273 SetFuzzificationMethodology
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274 $TopologicalPharmacophoreAtomPairsFP->SetFuzzificationMethodology($Value);
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275
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276 Sets fuzzification methodology to use for fuzzification of atom
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277 pairs count and returns *TopologicalPharmacophoreAtomPairsFP*.
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278 Default value: *FuzzyBinning*. Possible values: *FuzzyBinning |
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279 FuzzyBinSmoothing*.
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280
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281 In conjunction with values for options FuzzifyAtomPairsCount,
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282 FuzzificationMode and FuzzFactor, FuzzificationMethodology option is
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283 used to fuzzify pharmacophore atom pairs count.
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284
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285 Let:
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286
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287 Px = Pharmacophore atom type x
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288 Py = Pharmacophore atom type y
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289 PPxy = Pharmacophore atom pair between atom type Px and Py
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290
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291 PPxyDn = Pharmacophore atom pairs count between atom type Px and Py
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292 at distance Dn
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293 PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py
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294 at distance Dn - 1
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295 PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py
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296 at distance Dn + 1
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297
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298 FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing
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299
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300 Then:
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301
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302 For *FuzzyBinning*:
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303
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304 PPxyDn = PPxyDn (Unchanged)
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305
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306 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
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307 PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
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308
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309 For *FuzzyBinSmoothing*:
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310
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311 PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax
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312 PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax
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313
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314 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
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315 PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
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316
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317 In both fuzzification schemes, a value of 0 for FF implies no
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318 fuzzification of occurrence counts. A value of 1 during
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319 *FuzzyBinning* corresponds to maximum fuzzification of occurrence
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320 counts; however, a value of 1 during *FuzzyBinSmoothing* ends up
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321 completely distributing the value over the previous and next
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322 distance bins.
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323
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324 So for default value of FuzzFactor (FF) 0.15, the occurrence count
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325 of pharmacohore atom pairs at distance Dn during FuzzyBinning is
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326 left unchanged and the counts at distances Dn -1 and Dn + 1 are
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327 incremented by PPxyDn * 0.15.
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328
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329 And during *FuzzyBinSmoothing* the occurrence counts at Distance Dn
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330 is scaled back using multiplicative factor of (1 - 2*0.15) and the
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331 occurrence counts at distances Dn -1 and Dn + 1 are incremented by
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332 PPxyDn * 0.15. In other words, occurrence bin count is smoothed out
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333 by distributing it over the previous and next distance value.
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334
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335 SetFuzzificationMode
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336 $TopologicalPharmacophoreAtomPairsFP->SetFuzzificationMode($Value);
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337
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338 Sets fuzzification mode to use for fuzzification of atom pairs count
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339 and returns *TopologicalPharmacophoreAtomPairsFP*. Default value:
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340 *AfterNormalization*. Possible values: *BeforeNormalization |
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341 AfterNormalization*.
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342
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343 SetMaxDistance
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344 $TopologicalPharmacophoreAtomPairsFP->SetMaxDistance($Value);
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345
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346 Sets maximum bond distance between atom pairs for generating
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347 topological pharmacophore atom pairs fingerprints and returns
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348 *TopologicalPharmacophoreAtomPairsFP*.
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349
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350 SetMinDistance
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351 $TopologicalPharmacophoreAtomPairsFP->SetMinDistance($Value);
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352
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353 Sets minimum bond distance between atom pairs for generating
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354 topological pharmacophore atom pairs fingerprints and returns
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355 *TopologicalPharmacophoreAtomPairsFP*.
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356
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357 SetNormalizationMethodology
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358 $TopologicalPharmacophoreAtomPairsFP->SetNormalizationMethodology($Value);
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359
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360 Sets normalization methodology to use for scaling the occurrence
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361 count of pharmacophore atom pairs within specified distance range
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362 and returns *TopologicalPharmacophoreAtomPairsFP*. Default value:
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363 *None*. Possible values: *None, ByHeavyAtomsCount or
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364 ByAtomTypesCount*.
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365
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366 SetValuesPrecision
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367 $TopologicalPharmacophoreAtomPairsFP->SetValuesPrecision($Value);
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368
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369 Sets precision of atom pairs count real values which might be
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370 generated after normalization or fuzzification and returns
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371 *TopologicalPharmacophoreAtomPairsFP*. Default: up to *2* decimal
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372 places.
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373
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374 StringifyTopologicalPharmacophoreAtomPairsFingerprints
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375 $String = $TopologicalPharmacophoreAtomPairsFP->
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376 StringifyTopologicalPharmacophoreAtomPairsFingerprints();
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377
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378 Returns a string containing information about
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379 *TopologicalPharmacophoreAtomPairsFingerprints* object.
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380
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381 AUTHOR
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382 Manish Sud <msud@san.rr.com>
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383
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384 SEE ALSO
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385 Fingerprints.pm, FingerprintsStringUtil.pm,
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386 AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
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387 EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
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388 MACCSKeys.pm, PathLengthFingerprints.pm,
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389 TopologicalAtomPairsFingerprints.pm,
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390 TopologicalAtomTripletsFingerprints.pm,
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391 TopologicalAtomTorsionsFingerprints.pm,
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392 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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393
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394 COPYRIGHT
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395 Copyright (C) 2015 Manish Sud. All rights reserved.
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396
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397 This file is part of MayaChemTools.
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398
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399 MayaChemTools is free software; you can redistribute it and/or modify it
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400 under the terms of the GNU Lesser General Public License as published by
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401 the Free Software Foundation; either version 3 of the License, or (at
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402 your option) any later version.
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403
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