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1 NAME
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2 FingerprintsVector
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3
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4 SYNOPSIS
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5 use Fingerprints::FingerprintsVector;
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6
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7 use Fingerprints::FingerprintsVector qw(:all);
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8
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9 DESCRIPTION
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10 FingerprintsVector class provides the following methods:
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11
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12 new, AddValueIDs, AddValues, CityBlockDistanceCoefficient,
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13 CosineSimilarityCoefficient, CzekanowskiSimilarityCoefficient,
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14 DiceSimilarityCoefficient, EuclideanDistanceCoefficient, GetDescription,
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15 GetFingerprintsVectorString, GetID, GetIDsAndValuesPairsString,
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16 GetIDsAndValuesString, GetNumOfNonZeroValues, GetNumOfValueIDs,
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17 GetNumOfValues, GetSupportedDistanceAndSimilarityCoefficients,
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18 GetSupportedDistanceCoefficients, GetSupportedSimilarityCoefficients,
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19 GetType, GetValue, GetValueID, GetValueIDs, GetValueIDsString,
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20 GetValues, GetValuesAndIDsPairsString, GetValuesAndIDsString,
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21 GetValuesString, GetVectorType, HammingDistanceCoefficient,
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22 IsFingerprintsVector, JaccardSimilarityCoefficient,
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23 ManhattanDistanceCoefficient, NewFromIDsAndValuesPairsString,
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24 NewFromIDsAndValuesString, NewFromValuesAndIDsPairsString,
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25 NewFromValuesAndIDsString, NewFromValuesString,
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26 OchiaiSimilarityCoefficient, SetDescription, SetID, SetType, SetValue,
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27 SetValueID, SetValueIDs, SetValues, SetVectorType,
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28 SoergelDistanceCoefficient, SorensonSimilarityCoefficient,
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29 StringifyFingerprintsVector, TanimotoSimilarityCoefficient
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30
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31 The methods available to create fingerprints vector from strings and to
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32 calculate similarity and distance coefficients between two vectors can
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33 also be invoked as class functions.
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34
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35 FingerprintsVector class provides support to perform comparison between
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36 vectors containing three different types of values:
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37
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38 Type I: OrderedNumericalValues
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39
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40 o Size of two vectors are same
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41 o Vectors contain real values in a specific order. For example: MACCS keys
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42 count, Topological pharmacophore atom pairs and so on.
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43
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44 Type II: UnorderedNumericalValues
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45
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46 o Size of two vectors might not be same
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47 o Vectors contain unordered real value identified by value IDs. For example:
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48 Topological atom pairs, Topological atom torsions and so on
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49
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50 Type III: AlphaNumericalValues
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51
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52 o Size of two vectors might not be same
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53 o Vectors contain unordered alphanumerical values. For example: Extended
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54 connectivity fingerprints, atom neighborhood fingerprints.
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55
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56 Before performing similarity or distance calculations between vectors
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57 containing UnorderedNumericalValues or AlphaNumericalValues, the vectors
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58 are transformed into vectors containing unique OrderedNumericalValues
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59 using value IDs for UnorderedNumericalValues and values itself for
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60 AlphaNumericalValues.
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61
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62 Three forms of similarity and distance calculation between two vectors,
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63 specified using CalculationMode option, are supported: *AlgebraicForm,
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64 BinaryForm or SetTheoreticForm*.
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65
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66 For *BinaryForm*, the ordered list of processed final vector values
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67 containing the value or count of each unique value type is simply
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68 converted into a binary vector containing 1s and 0s corresponding to
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69 presence or absence of values before calculating similarity or distance
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70 between two vectors.
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71
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72 For two fingerprint vectors A and B of same size containing
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73 OrderedNumericalValues, let:
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74
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75 N = Number values in A or B
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76
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77 Xa = Values of vector A
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78 Xb = Values of vector B
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79
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80 Xai = Value of ith element in A
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81 Xbi = Value of ith element in B
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82
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83 SUM = Sum of i over N values
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84
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85 For SetTheoreticForm of calculation between two vectors, let:
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86
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87 SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) )
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88 SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) )
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89
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90 For BinaryForm of calculation between two vectors, let:
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91
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92 Na = Number of bits set to "1" in A = SUM ( Xai )
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93 Nb = Number of bits set to "1" in B = SUM ( Xbi )
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94 Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi )
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95 Nd = Number of bits set to "0" in both A and B
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96 = SUM ( 1 - Xai - Xbi + Xai * Xbi)
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97
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98 N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd
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99
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100 Additionally, for BinaryForm various values also correspond to:
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101
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102 Na = | Xa |
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103 Nb = | Xb |
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104 Nc = | SetIntersectionXaXb |
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105 Nd = N - | SetDifferenceXaXb |
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106
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107 | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc
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108 = | Xa | + | Xb | - | SetIntersectionXaXb |
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109
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110 Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ]
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111 for a pair of vectors A and B in *AlgebraicForm, BinaryForm and
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112 SetTheoreticForm* are defined as follows:
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113
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114 CityBlockDistance: ( same as HammingDistance and ManhattanDistance)
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115
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116 *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) )
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117
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118 *BinaryForm*: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc
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119
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120 *SetTheoreticForm*: | SetDifferenceXaXb | - | SetIntersectionXaXb | =
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121 SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )
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122
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123 CosineSimilarity: ( same as OchiaiSimilarityCoefficient)
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124
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125 *AlgebraicForm*: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi
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126 ** 2) )
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127
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128 *BinaryForm*: Nc / SQRT ( Na * Nb)
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129
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130 *SetTheoreticForm*: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM
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131 ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )
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132
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133 CzekanowskiSimilarity: ( same as DiceSimilarity and SorensonSimilarity)
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134
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135 *AlgebraicForm*: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM
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136 ( Xbi **2 ) )
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137
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138 *BinaryForm*: 2 * Nc / ( Na + Nb )
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139
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140 *SetTheoreticForm*: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 *
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141 ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )
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142
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143 DiceSimilarity: ( same as CzekanowskiSimilarity and SorensonSimilarity)
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144
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145 *AlgebraicForm*: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM
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146 ( Xbi **2 ) )
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147
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148 *BinaryForm*: 2 * Nc / ( Na + Nb )
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149
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150 *SetTheoreticForm*: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 *
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151 ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )
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152
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153 EuclideanDistance:
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154
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155 *AlgebraicForm*: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) )
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156
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157 *BinaryForm*: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 *
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158 Nc )
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159
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160 *SetTheoreticForm*: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb
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161 | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) )
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162 ) )
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163
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164 HammingDistance: ( same as CityBlockDistance and ManhattanDistance)
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165
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166 *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) )
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167
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168 *BinaryForm*: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc
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169
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170 *SetTheoreticForm*: | SetDifferenceXaXb | - | SetIntersectionXaXb | =
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171 SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )
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172
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173 JaccardSimilarity: ( same as TanimotoSimilarity)
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174
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175 *AlgebraicForm*: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2
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176 ) - SUM ( Xai * Xbi ) )
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177
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178 *BinaryForm*: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb -
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179 Nc )
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180
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181 *SetTheoreticForm*: | SetIntersectionXaXb | / | SetDifferenceXaXb | =
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182 SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN (
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183 Xai, Xbi ) ) )
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184
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185 ManhattanDistance: ( same as CityBlockDistance and HammingDistance)
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186
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187 *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) )
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188
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189 *BinaryForm*: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc
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190
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191 *SetTheoreticForm*: | SetDifferenceXaXb | - | SetIntersectionXaXb | =
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192 SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )
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193
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194 OchiaiSimilarity: ( same as CosineSimilarity)
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195
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196 *AlgebraicForm*: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi
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197 ** 2) )
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198
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199 *BinaryForm*: Nc / SQRT ( Na * Nb)
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200
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201 *SetTheoreticForm*: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM
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202 ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )
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203
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204 SorensonSimilarity: ( same as CzekanowskiSimilarity and DiceSimilarity)
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205
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206 *AlgebraicForm*: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM
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207 ( Xbi **2 ) )
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208
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209 *BinaryForm*: 2 * Nc / ( Na + Nb )
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210
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211 *SetTheoreticForm*: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 *
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212 ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )
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213
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214 SoergelDistance:
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215
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216 *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) )
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217
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218 *BinaryForm*: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na +
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219 Nb - Nc )
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220
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221 *SetTheoreticForm*: ( | SetDifferenceXaXb | - | SetIntersectionXaXb | )
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222 / | SetDifferenceXaXb | = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN
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223 ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi
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224 ) ) )
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225
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226 TanimotoSimilarity: ( same as JaccardSimilarity)
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227
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228 *AlgebraicForm*: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2
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229 ) - SUM ( Xai * Xbi ) )
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230
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231 *BinaryForm*: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb -
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232 Nc )
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233
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234 *SetTheoreticForm*: | SetIntersectionXaXb | / | SetDifferenceXaXb | =
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235 SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN (
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236 Xai, Xbi ) ) )
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237
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238 METHODS
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239 new
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240 $FPVector = new Fingerprints::FingerprintsVector(%NamesAndValues);
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241
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242 Using specified *FingerprintsVector* property names and values hash,
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243 new method creates a new object and returns a reference to newly
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244 created FingerprintsVectorsVector object. By default, the following
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245 properties are initialized:
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246
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247 Type = ''
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248 @{Values} = ()
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249 @{ValuesIDs} = ()
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250
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251 Examples:
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252
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253 $FPVector = new Fingerprints::FingerprintsVector('Type' => 'OrderedNumericalValues',
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254 'Values' => [1, 2, 3, 4]);
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255 $FPVector = new Fingerprints::FingerprintsVector('Type' => 'NumericalValues',
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256 'Values' => [10, 22, 33, 44],
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257 'ValueIDs' => ['ID1', 'ID2', 'ID3', 'ID4']);
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258 $FPVector = new Fingerprints::FingerprintsVector('Type' => 'AlphaNumericalValues',
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259 'Values' => ['a1', 2, 'a3', 4]);
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260
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261 AddValueIDs
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262 $FingerprintsVector->AddValueIDs($ValueIDsRef);
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263 $FingerprintsVector->AddValueIDs(@ValueIDs);
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264
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265 Adds specified *ValueIDs* to *FingerprintsVector* and returns
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266 *FingerprintsVector*.
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267
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268 AddValues
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269 $FingerprintsVector->AddValues($ValuesRef);
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270 $FingerprintsVector->AddValues(@Values);
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271 $FingerprintsVector->AddValues($Vector);
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272
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273 Adds specified *Values* to *FingerprintsVector* and returns
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274 *FingerprintsVector*.
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275
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276 CityBlockDistanceCoefficient
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277 $Value = $FingerprintsVector->CityBlockDistanceCoefficient(
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278 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
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279 $Value = Fingerprints::FingerprintsVector::CityBlockDistanceCoefficient(
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280 $FingerprintsVectorA, $FingerprintVectorB,
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281 [$CalculationMode, $SkipValuesCheck]);
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282
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283 Returns value of *CityBlock* distance coefficient between two
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284 *FingerprintsVectors* using optionally specified *CalculationMode*
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285 and optional checking of vector values.
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286
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287 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
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288 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
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289 Default *SkipValuesCheck* value: *0*.
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290
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291 CosineSimilarityCoefficient
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292 $Value = $FingerprintsVector->CosineSimilarityCoefficient(
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293 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
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294 $Value = Fingerprints::FingerprintsVector::CosineSimilarityCoefficient(
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295 $FingerprintsVectorA, $FingerprintVectorB,
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296 [$CalculationMode, $SkipValuesCheck]);
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297
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298 Returns value of *Cosine* similarity coefficient between two
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299 *FingerprintsVectors* using optionally specified *CalculationMode*
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300 and optional checking of vector values.
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301
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302 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
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303 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
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304 Default *SkipValuesCheck* value: *0*.
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305
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306 CzekanowskiSimilarityCoefficient
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307 $Value = $FingerprintsVector->CzekanowskiSimilarityCoefficient(
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308 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
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309 $Value = Fingerprints::FingerprintsVector::CzekanowskiSimilarityCoefficient(
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310 $FingerprintsVectorA, $FingerprintVectorB,
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311 [$CalculationMode, $SkipValuesCheck]);
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312
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313 Returns value of *Czekanowski* similarity coefficient between two
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314 *FingerprintsVectors* using optionally specified *CalculationMode*
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315 and optional checking of vector values.
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316
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317 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
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318 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
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319 Default *SkipValuesCheck* value: *0*.
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320
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321 DiceSimilarityCoefficient
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322 $Value = $FingerprintsVector->DiceSimilarityCoefficient(
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323 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
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324 $Value = Fingerprints::FingerprintsVector::DiceSimilarityCoefficient(
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325 $FingerprintsVectorA, $FingerprintVectorB,
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326 [$CalculationMode, $SkipValuesCheck]);
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327
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328 Returns value of *Dice* similarity coefficient between two
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329 *FingerprintsVectors* using optionally specified *CalculationMode*
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330 and optional checking of vector values.
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331
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332 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
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333 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
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334 Default *SkipValuesCheck* value: *0*.
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335
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336 EuclideanDistanceCoefficient
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337 $Value = $FingerprintsVector->EuclideanDistanceCoefficient(
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338 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
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339 $Value = Fingerprints::FingerprintsVector::EuclideanDistanceCoefficient(
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340 $FingerprintsVectorA, $FingerprintVectorB,
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341 [$CalculationMode, $SkipValuesCheck]);
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342
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343 Returns value of *Euclidean* distance coefficient between two
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344 *FingerprintsVectors* using optionally specified *CalculationMode*
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345 and optional checking of vector values.
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346
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347 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
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348 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
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349 Default *SkipValuesCheck* value: *0*.
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350
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351 GetDescription
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352 $Description = $FingerprintsVector->GetDescription();
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353
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354 Returns a string containing description of fingerprints vector.
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355
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356 GetFingerprintsVectorString
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357 $FPString = $FingerprintsVector->GetFingerprintsVectorString($Format);
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358
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359 Returns a FingerprintsString containing vector values and/or IDs in
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360 *FingerprintsVector* corresponding to specified *Format*.
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361
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362 Possible *Format* values: *IDsAndValuesString, IDsAndValues,
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363 IDsAndValuesPairsString, IDsAndValuesPairs, ValuesAndIDsString,
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364 ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs,
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365 ValueIDsString, ValueIDs, ValuesString, or Values*.
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366
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367 GetID
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368 $ID = $FingerprintsVector->GetID();
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369
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370 Returns *ID* of *FingerprintsVector*.
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371
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372 GetVectorType
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373 $VectorType = $FingerprintsVector->GetVectorType();
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374
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375 Returns *VectorType* of *FingerprintsVector*.
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376
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377 GetIDsAndValuesPairsString
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378 $IDsValuesPairsString = $FingerprintsVector->GetIDsAndValuesPairsString();
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379
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380 Returns *FingerprintsVector* value IDs and values as space delimited
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381 ID/value pair string.
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382
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383 GetIDsAndValuesString
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384 $IDsValuesString = $FingerprintsVector->GetIDsAndValuesString();
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385
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386 Returns *FingerprintsVector* value IDs and values as string
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387 containing space delimited IDs followed by values with semicolon as
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388 IDs and values delimiter.
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389
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390 GetNumOfNonZeroValues
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391 $NumOfNonZeroValues = $FingerprintsVector->GetNumOfNonZeroValues();
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392
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393 Returns number of non-zero values in *FingerprintsVector*.
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394
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395 GetNumOfValueIDs
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396 $NumOfValueIDs = $FingerprintsVector->GetNumOfValueIDs();
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397
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|
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398 Returns number of value IDs *FingerprintsVector*.
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399
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400 GetNumOfValues
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401 $NumOfValues = $FingerprintsVector->GetNumOfValues();
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402
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403 Returns number of values *FingerprintsVector*.
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404
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405 GetSupportedDistanceAndSimilarityCoefficients
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406 @SupportedDistanceAndSimilarityCoefficientsReturn =
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407 Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients();
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408
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409 Returns an array containing names of supported distance and
|
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|
410 similarity coefficients.
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|
411
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412 GetSupportedDistanceCoefficients
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413 @SupportedDistanceCoefficientsReturn =
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414 Fingerprints::FingerprintsVector::GetSupportedDistanceCoefficients();
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415
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416 Returns an array containing names of supported disyance
|
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|
417 coefficients.
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418
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|
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419 GetSupportedSimilarityCoefficients
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420 @SupportedSimilarityCoefficientsReturn =
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421 Fingerprints::FingerprintsVector::GetSupportedSimilarityCoefficients();
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422
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|
423 Returns an array containing names of supported similarity
|
|
|
424 coefficients.
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|
425
|
|
|
426 GetType
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|
427 $VectorType = $FingerprintsVector->GetType();
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428
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429 Returns *FingerprintsVector* vector type.
|
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430
|
|
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431 GetValue
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432 $Value = $FingerprintsVector->GetValue($Index);
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433
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|
434 Returns fingerprints vector Value specified using *Index* starting
|
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|
435 at 0.
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|
436
|
|
|
437 GetValueID
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|
438 $ValueID = $FingerprintsVector->GetValueID();
|
|
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439
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|
|
440 Returns fingerprints vector ValueID specified using *Index* starting
|
|
|
441 at 0.
|
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|
442
|
|
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443 GetValueIDs
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|
444 $ValueIDs = $FingerprintsVector->GetValueIDs();
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|
|
445 @ValueIDs = $FingerprintsVector->GetValueIDs();
|
|
|
446
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|
|
447 Returns fingerprints vector ValueIDs as an array or reference to an
|
|
|
448 array.
|
|
|
449
|
|
|
450 GetValueIDsString
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|
|
451 $ValueIDsString = $FingerprintsVector->GetValueIDsString();
|
|
|
452
|
|
|
453 Returns fingerprints vector ValueIDsString with value IDs delimited
|
|
|
454 by space.
|
|
|
455
|
|
|
456 GetValues
|
|
|
457 $ValuesRef = $FingerprintsVector->GetValues();
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|
|
458 @Values = $FingerprintsVector->GetValues();
|
|
|
459
|
|
|
460 Returns fingerprints vector Values as an array or reference to an
|
|
|
461 array.
|
|
|
462
|
|
|
463 GetValuesAndIDsPairsString
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|
|
464 $ValuesIDsPairsString = $FingerprintsVector->GetValuesAndIDsPairsString();
|
|
|
465
|
|
|
466 Returns *FingerprintsVector* value and value IDs as space delimited
|
|
|
467 ID/value pair string.
|
|
|
468
|
|
|
469 GetValuesAndIDsString
|
|
|
470 $ValuesIDsString = $FingerprintsVector->GetValuesAndIDsString();
|
|
|
471
|
|
|
472 Returns *FingerprintsVector* values and value IDs as string
|
|
|
473 containing space delimited IDs followed by values with semicolon as
|
|
|
474 IDs and values delimiter.
|
|
|
475
|
|
|
476 GetValuesString
|
|
|
477 $Return = $FingerprintsVector->GetValuesString();
|
|
|
478
|
|
|
479 Returns *FingerprintsVector* values as space delimited string.
|
|
|
480
|
|
|
481 HammingDistanceCoefficient
|
|
|
482 $Value = $FingerprintsVector->HammingDistanceCoefficient(
|
|
|
483 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
|
|
|
484 $Value = Fingerprints::FingerprintsVector::HammingDistanceCoefficient(
|
|
|
485 $FingerprintsVectorA, $FingerprintVectorB,
|
|
|
486 [$CalculationMode, $SkipValuesCheck]);
|
|
|
487
|
|
|
488 Returns value of *Hamming* distance coefficient between two
|
|
|
489 *FingerprintsVectors* using optionally specified *CalculationMode*
|
|
|
490 and optional checking of vector values.
|
|
|
491
|
|
|
492 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
|
|
|
493 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
|
|
|
494 Default *SkipValuesCheck* value: *0*.
|
|
|
495
|
|
|
496 IsFingerprintsVector
|
|
|
497 $Status = Fingerprints::FingerprintsVector::IsFingerprintsVector($Object);
|
|
|
498
|
|
|
499 Returns 1 or 0 based on whether *Object* is a *FingerprintsVector*.
|
|
|
500
|
|
|
501 JaccardSimilarityCoefficient
|
|
|
502 $Value = $FingerprintsVector->JaccardSimilarityCoefficient(
|
|
|
503 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
|
|
|
504 $Value = Fingerprints::FingerprintsVector::JaccardSimilarityCoefficient(
|
|
|
505 $FingerprintsVectorA, $FingerprintVectorB,
|
|
|
506 [$CalculationMode, $SkipValuesCheck]);
|
|
|
507
|
|
|
508 Returns value of *Jaccard* similarity coefficient between two
|
|
|
509 *FingerprintsVectors* using optionally specified *CalculationMode*
|
|
|
510 and optional checking of vector values.
|
|
|
511
|
|
|
512 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
|
|
|
513 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
|
|
|
514 Default *SkipValuesCheck* value: *0*.
|
|
|
515
|
|
|
516 ManhattanDistanceCoefficient
|
|
|
517 $Value = $FingerprintsVector->ManhattanDistanceCoefficient(
|
|
|
518 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
|
|
|
519 $Value = Fingerprints::FingerprintsVector::ManhattanDistanceCoefficient(
|
|
|
520 $FingerprintsVectorA, $FingerprintVectorB,
|
|
|
521 [$CalculationMode, $SkipValuesCheck]);
|
|
|
522
|
|
|
523 Returns value of *Manhattan* distance coefficient between two
|
|
|
524 *FingerprintsVectors* using optionally specified *CalculationMode*
|
|
|
525 and optional checking of vector values.
|
|
|
526
|
|
|
527 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
|
|
|
528 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
|
|
|
529 Default *SkipValuesCheck* value: *0*.
|
|
|
530
|
|
|
531 NewFromIDsAndValuesPairsString
|
|
|
532 $FingerprintsVector = $FingerprintsVector->NewFromIDsAndValuesPairsString(
|
|
|
533 $ValuesType, $IDsAndValuesPairsString);
|
|
|
534 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesPairsString(
|
|
|
535 $ValuesType, $IDsAndValuesPairsString);
|
|
|
536
|
|
|
537 Creates a new *FingerprintsVector* of *ValuesType* using
|
|
|
538 *IDsAndValuesPairsString* containing space delimited value IDs and
|
|
|
539 values pairs and returns new FingerprintsVector object. Possible
|
|
|
540 *ValuesType* values: *OrderedNumericalValues, NumericalValues, or
|
|
|
541 AlphaNumericalValues*.
|
|
|
542
|
|
|
543 NewFromIDsAndValuesString
|
|
|
544 $FingerprintsVector = $FingerprintsVector->NewFromIDsAndValuesString(
|
|
|
545 $ValuesType, $IDsAndValuesString);
|
|
|
546 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesString(
|
|
|
547 $ValuesType, $IDsAndValuesString);
|
|
|
548
|
|
|
549 Creates a new *FingerprintsVector* of *ValuesType* using
|
|
|
550 *IDsAndValuesString* containing semicolon delimited value IDs string
|
|
|
551 followed by values strings and returns new FingerprintsVector
|
|
|
552 object. The values within value and value IDs tring are delimited by
|
|
|
553 spaces. Possible *ValuesType* values: *OrderedNumericalValues,
|
|
|
554 NumericalValues, or AlphaNumericalValues*.
|
|
|
555
|
|
|
556 NewFromValuesAndIDsPairsString
|
|
|
557 $FingerprintsVector = $FingerprintsVector->NewFromValuesAndIDsPairsString(
|
|
|
558 $ValuesType, $ValuesAndIDsPairsString);
|
|
|
559 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsPairsString(
|
|
|
560 $ValuesType, $ValuesAndIDsPairsString);
|
|
|
561
|
|
|
562 Creates a new *FingerprintsVector* of *ValuesType* using
|
|
|
563 *ValuesAndIDsPairsString* containing space delimited value and value
|
|
|
564 IDs pairs and returns new FingerprintsVector object. Possible
|
|
|
565 *ValuesType* values: *OrderedNumericalValues, NumericalValues, or
|
|
|
566 AlphaNumericalValues*.
|
|
|
567
|
|
|
568 NewFromValuesAndIDsString
|
|
|
569 $FingerprintsVector = $FingerprintsVector->NewFromValuesAndIDsString(
|
|
|
570 $ValuesType, $IDsAndValuesString);
|
|
|
571 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsString(
|
|
|
572 $ValuesType, $IDsAndValuesString);
|
|
|
573
|
|
|
574 Creates a new *FingerprintsVector* of *ValuesType* using
|
|
|
575 *ValuesAndIDsString* containing semicolon delimited values string
|
|
|
576 followed by value IDs strings and returns new FingerprintsVector
|
|
|
577 object. The values within values and value IDs tring are delimited
|
|
|
578 by spaces. Possible *ValuesType* values: *OrderedNumericalValues,
|
|
|
579 NumericalValues, or AlphaNumericalValues*.
|
|
|
580
|
|
|
581 NewFromValuesString
|
|
|
582 $FingerprintsVector = $FingerprintsVector->NewFromValuesString(
|
|
|
583 $ValuesType, $ValuesString);
|
|
|
584 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesString(
|
|
|
585 $ValuesType, $ValuesString);
|
|
|
586
|
|
|
587 Creates a new *FingerprintsVector* of *ValuesType* using
|
|
|
588 *ValuesString* containing space delimited values string and returns
|
|
|
589 new FingerprintsVector object. The values within values and value
|
|
|
590 IDs tring are delimited by spaces. Possible *ValuesType* values:
|
|
|
591 *OrderedNumericalValues, NumericalValues, or AlphaNumericalValues*.
|
|
|
592
|
|
|
593 OchiaiSimilarityCoefficient
|
|
|
594 $Value = $FingerprintsVector->OchiaiSimilarityCoefficient(
|
|
|
595 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
|
|
|
596 $Value = Fingerprints::FingerprintsVector::OchiaiSimilarityCoefficient(
|
|
|
597 $FingerprintsVectorA, $FingerprintVectorB,
|
|
|
598 [$CalculationMode, $SkipValuesCheck]);
|
|
|
599
|
|
|
600 Returns value of *Ochiai* similarity coefficient between two
|
|
|
601 *FingerprintsVectors* using optionally specified *CalculationMode*
|
|
|
602 and optional checking of vector values.
|
|
|
603
|
|
|
604 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
|
|
|
605 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
|
|
|
606 Default *SkipValuesCheck* value: *0*.
|
|
|
607
|
|
|
608 SetDescription
|
|
|
609 $FingerprintsVector->SetDescription($Description);
|
|
|
610
|
|
|
611 Sets *Description* of fingerprints vector and returns
|
|
|
612 *FingerprintsVector*.
|
|
|
613
|
|
|
614 SetID
|
|
|
615 $FingerprintsVector->SetID($ID);
|
|
|
616
|
|
|
617 Sets *ID* of fingerprints vector and returns *FingerprintsVector*.
|
|
|
618
|
|
|
619 SetVectorType
|
|
|
620 $FingerprintsVector->SetVectorType($VectorType);
|
|
|
621
|
|
|
622 Sets *VectorType* of fingerprints vector and returns
|
|
|
623 *FingerprintsVector*.
|
|
|
624
|
|
|
625 SetType
|
|
|
626 $FingerprintsVector->SetType($Type);
|
|
|
627
|
|
|
628 Sets *FingerprintsVector* values *Type* and returns
|
|
|
629 *FingerprintsVector*. Possible *Type* values:
|
|
|
630 *OrderedNumericalValues, NumericalValues, or AlphaNumericalValues*.
|
|
|
631
|
|
|
632 During calculation of similarity and distance coefficients between
|
|
|
633 two *FingerprintsVectors*, the following conditions apply to vector
|
|
|
634 type, size, value and value IDs:
|
|
|
635
|
|
|
636 o For OrderedNumericalValues type, both vectors must be of the same size
|
|
|
637 and contain similar types of numerical values in the same order.
|
|
|
638
|
|
|
639 o For NumericalValues type, vector value IDs for both vectors must be
|
|
|
640 specified; however, their size and order of IDs and numerical values may
|
|
|
641 be different. For each vector, value IDs must correspond to vector values.
|
|
|
642
|
|
|
643 o For AlphaNumericalValues type, vectors may contain both numerical and
|
|
|
644 alphanumerical values and their sizes may be different.
|
|
|
645
|
|
|
646 SetValue
|
|
|
647 $FingerprintsVector->SetValue($Index, $Value, [$SkipIndexCheck]);
|
|
|
648
|
|
|
649 Sets a *FingerprintsVector* value specified by *Index* starting at 0
|
|
|
650 to *Value* along with optional index range check and returns
|
|
|
651 *FingerprintsVector*.
|
|
|
652
|
|
|
653 SetValueID
|
|
|
654 $FingerprintsVector->SetValueID($Index, $ValueID, [$SkipIndexCheck]);
|
|
|
655
|
|
|
656 Sets a *FingerprintsVector* value ID specified by *Index* starting
|
|
|
657 at 0 to *ValueID* along with optional index range check and returns
|
|
|
658 *FingerprintsVector*.
|
|
|
659
|
|
|
660 SetValueIDs
|
|
|
661 $FingerprintsVector->SetValueIDs($ValueIDsRef);
|
|
|
662 $FingerprintsVector->SetValueIDs(@ValueIDs);
|
|
|
663
|
|
|
664 Sets *FingerprintsVector* value IDs to specified *ValueIDs* and
|
|
|
665 returns *FingerprintsVector*.
|
|
|
666
|
|
|
667 SetValues
|
|
|
668 $FingerprintsVector->SetValues($ValuesRef);
|
|
|
669 $FingerprintsVector->SetValues(@Values);
|
|
|
670
|
|
|
671 Sets *FingerprintsVector* value to specified *Values* and returns
|
|
|
672 *FingerprintsVector*.
|
|
|
673
|
|
|
674 SoergelDistanceCoefficient
|
|
|
675 $Value = $FingerprintsVector->SoergelDistanceCoefficient(
|
|
|
676 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
|
|
|
677 $Value = Fingerprints::FingerprintsVector::SoergelDistanceCoefficient(
|
|
|
678 $FingerprintsVectorA, $FingerprintVectorB,
|
|
|
679 [$CalculationMode, $SkipValuesCheck]);
|
|
|
680
|
|
|
681 Returns value of *Soergel* distance coefficient between two
|
|
|
682 *FingerprintsVectors* using optionally specified *CalculationMode*
|
|
|
683 and optional checking of vector values.
|
|
|
684
|
|
|
685 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
|
|
|
686 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
|
|
|
687 Default *SkipValuesCheck* value: *0*.
|
|
|
688
|
|
|
689 SorensonSimilarityCoefficient
|
|
|
690 $Value = $FingerprintsVector->SorensonSimilarityCoefficient(
|
|
|
691 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
|
|
|
692 $Value = Fingerprints::FingerprintsVector::SorensonSimilarityCoefficient(
|
|
|
693 $FingerprintsVectorA, $FingerprintVectorB,
|
|
|
694 [$CalculationMode, $SkipValuesCheck]);
|
|
|
695
|
|
|
696 Returns value of *Sorenson* similarity coefficient between two
|
|
|
697 *FingerprintsVectors* using optionally specified *CalculationMode*
|
|
|
698 and optional checking of vector values.
|
|
|
699
|
|
|
700 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
|
|
|
701 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
|
|
|
702 Default *SkipValuesCheck* value: *0*.
|
|
|
703
|
|
|
704 TanimotoSimilarityCoefficient
|
|
|
705 $Value = $FingerprintsVector->TanimotoSimilarityCoefficient(
|
|
|
706 $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
|
|
|
707 $Value = Fingerprints::FingerprintsVector::TanimotoSimilarityCoefficient(
|
|
|
708 $FingerprintsVectorA, $FingerprintVectorB,
|
|
|
709 [$CalculationMode, $SkipValuesCheck]);
|
|
|
710
|
|
|
711 Returns value of *Tanimoto* similarity coefficient between two
|
|
|
712 *FingerprintsVectors* using optionally specified *CalculationMode*
|
|
|
713 and optional checking of vector values.
|
|
|
714
|
|
|
715 Possible *CalculationMode* values: *AlgebraicForm, BinaryForm or
|
|
|
716 SetTheoreticForm*. Default *CalculationMode* value: *AlgebraicForm*.
|
|
|
717 Default *SkipValuesCheck* value: *0*.
|
|
|
718
|
|
|
719 StringifyFingerprintsVector
|
|
|
720 $String = $FingerprintsVector->StringifyFingerprintsVector();
|
|
|
721
|
|
|
722 Returns a string containing information about *FingerprintsVector*
|
|
|
723 object.
|
|
|
724
|
|
|
725 AUTHOR
|
|
|
726 Manish Sud <msud@san.rr.com>
|
|
|
727
|
|
|
728 SEE ALSO
|
|
|
729 BitVector.pm, FingerprintsStringUtil.pm, FingerprintsBitVector.pm,
|
|
|
730 Vector.pm
|
|
|
731
|
|
|
732 COPYRIGHT
|
|
|
733 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
734
|
|
|
735 This file is part of MayaChemTools.
|
|
|
736
|
|
|
737 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
738 under the terms of the GNU Lesser General Public License as published by
|
|
|
739 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
740 your option) any later version.
|
|
|
741
|
