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1 NAME
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2 TopologicalPharmacophoreAtomTripletsFingerprints.pl - Generate
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3 topological pharmacophore atom triplets fingerprints for SD files
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4
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5 SYNOPSIS
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6 TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)...
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7
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8 TopologicalPharmacophoreAtomTripletsFingerprints.pl [--AromaticityModel
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9 *AromaticityModelType*] [--AtomTripletsSetSizeToUse *ArbitrarySize |
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10 FixedSize*] [-a, --AtomTypesToUse *"AtomType1, AtomType2..."*]
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11 [--AtomTypesWeight *"AtomType1, Weight1, AtomType2, Weight2..."*]
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12 [--CompoundID *DataFieldName or LabelPrefixString*] [--CompoundIDLabel
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13 *text*] [--CompoundIDMode] [--DataFields *"FieldLabel1,
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14 FieldLabel2,..."*] [-d, --DataFieldsMode *All | Common | Specify |
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15 CompoundID*] [--DistanceBinSize *number*] [-f, --Filter *Yes | No*]
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16 [--FingerprintsLabelMode *FingerprintsLabelOnly |
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17 FingerprintsLabelWithIDs*] [--FingerprintsLabel *text*] [-h, --help]
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18 [-k, --KeepLargestComponent *Yes | No*] [--MinDistance *number*]
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19 [--MaxDistance *number*] [--OutDelim *comma | tab | semicolon*]
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20 [--output *SD | FP | text | all*] [-o, --overwrite] [-q, --quote *Yes |
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21 No*] [-r, --root *RootName*] [-u, --UseTriangleInequality *Yes | No*]
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22 [-v, --VectorStringFormat *ValuesString, IDsAndValuesString |
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23 IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*]
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24 [-w, --WorkingDir dirname] SDFile(s)...
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25
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26 DESCRIPTION
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27 Generate topological pharmacophore atom triplets fingerprints [ Ref 66,
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28 Ref 68-71 ] for *SDFile(s)* and create appropriate SD, FP or CSV/TSV
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29 text file(s) containing fingerprints vector strings corresponding to
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30 molecular fingerprints.
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31
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32 Multiple SDFile names are separated by spaces. The valid file extensions
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33 are *.sdf* and *.sd*. All other file names are ignored. All the SD files
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34 in a current directory can be specified either by **.sdf* or the current
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35 directory name.
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36
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37 Based on the values specified for --AtomTypesToUse, pharmacophore atom
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38 types are assigned to all non-hydrogen atoms in a molecule and a
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39 distance matrix is generated. Using --MinDistance, --MaxDistance, and
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40 --DistanceBinSize values, a binned distance matrix is generated with
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41 lower bound on the distance bin as the distance in distance matrix; the
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42 lower bound on the distance bin is also used as the distance between
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43 atom pairs for generation of atom triplet identifiers.
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44
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45 A pharmacophore atom triplets basis set is generated for all unique atom
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46 triplets constituting atom pairs binned distances between --MinDistance
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47 and --MaxDistance. The value of --UseTriangleInequality determines
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48 whether the triangle inequality test is applied during generation of
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49 atom triplets basis set. The lower distance bound, along with specified
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50 pharmacophore types, is used during generation of atom triplet IDs.
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51
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52 Let:
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53
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54 P = Valid pharmacophore atom type
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55
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56 Px = Pharmacophore atom x
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57 Py = Pharmacophore atom y
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58 Pz = Pharmacophore atom z
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59
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60 Dmin = Minimum distance corresponding to number of bonds between two atoms
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61 Dmax = Maximum distance corresponding to number of bonds between two atoms
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62 D = Distance corresponding to number of bonds between two atom
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63
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64 Bsize = Distance bin size
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65 Nbins = Number of distance bins
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66
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67 Dxy = Distance or lower bound of binned distance between Px and Py
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68 Dxz = Distance or lower bound of binned distance between Px and Pz
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69 Dyz = Distance or lower bound of binned distance between Py and Pz
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70
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71 Then:
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72
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73 PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet IDs for atom types Px,
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74 Py, and Pz
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75
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76 For example: H1-H1-H1, H2-HBA-H2 and so on
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77
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78 For default values of Dmin = 1 , Dmax = 10 and Bsize = 2:
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79
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80 the number of distance bins, Nbins = 5, are:
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81
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82 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]
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83
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84 and atom triplet basis set size is 2692.
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85
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86 Atom triplet basis set size for various values of Dmin, Dmax and Bsize in
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87 conjunction with usage of triangle inequality is:
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88
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89 Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize
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90 1 10 2 No 4960
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91 1 10 2 Yes 2692 [ Default ]
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92 2 12 2 No 8436
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93 2 12 2 Yes 4494
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94
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95 Using binned distance matrix and pharmacohore atom types, occurrence of
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96 unique pharmacohore atom triplets is counted.
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97
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98 The final pharmacophore atom triples count along with atom pair
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99 identifiers involving all non-hydrogen atoms constitute pharmacophore
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100 topological atom triplets fingerprints of the molecule.
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101
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102 For *ArbitrarySize* value of --AtomTripletsSetSizeToUse option, the
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103 fingerprint vector correspond to only those topological pharmacophore
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104 atom triplets which are present and have non-zero count. However, for
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105 *FixedSize* value of --AtomTripletsSetSizeToUse option, the fingerprint
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106 vector contains all possible valid topological pharmacophore atom
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107 triplets with both zero and non-zero count values.
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108
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109 Example of *SD* file containing topological pharmacophore atom triplets
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110 fingerprints string data:
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111
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112 ... ...
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113 ... ...
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114 $$$$
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115 ... ...
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116 ... ...
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117 ... ...
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118 41 44 0 0 0 0 0 0 0 0999 V2000
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119 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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120 ... ...
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121 2 3 1 0 0 0 0
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122 ... ...
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123 M END
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124 > <CmpdID>
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125 Cmpd1
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126
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127 > <TopologicalPharmacophoreAtomTripletsFingerprints>
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128 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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129 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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130 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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131 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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132 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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133 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
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134 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
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135 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
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136
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137 $$$$
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138 ... ...
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139 ... ...
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140
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141 Example of *FP* file containing topological pharmacophore atom triplets
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142 fingerprints string data:
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143
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144 #
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145 # Package = MayaChemTools 7.4
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146 # Release Date = Oct 21, 2010
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147 #
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148 # TimeStamp = Fri Mar 11 15:38:58 2011
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149 #
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150 # FingerprintsStringType = FingerprintsVector
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151 #
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152 # Description = TopologicalPharmacophoreAtomTriplets:ArbitrarySize:M...
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153 # VectorStringFormat = IDsAndValuesString
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154 # VectorValuesType = NumericalValues
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155 #
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156 Cmpd1 696;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1...;;46 106...
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157 Cmpd2 251;H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-H1-NI1...;4 1 3 1 1 2 2...
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158 ... ...
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159 ... ..
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160
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161 Example of CSV *Text* file containing topological pharmacophore atom
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162 triplets fingerprints string data:
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163
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164 "CompoundID","TopologicalPharmacophoreAtomTripletsFingerprints"
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165 "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomTriplets:Arbitr
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166 arySize:MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesStri
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167 ng;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HB
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168 A1 Ar1-H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA
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169 1 H1-HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 A...;
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170 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
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171 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
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172 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
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173 ... ...
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174 ... ...
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175
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176 The current release of MayaChemTools generates the following types of
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177 topological pharmacophore atom triplets fingerprints vector strings:
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178
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179 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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180 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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181 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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182 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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183 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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184 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
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185 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
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186 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
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187
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188 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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189 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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190 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
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191 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
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192 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
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193 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...
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194
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195 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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196 istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString;
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197 Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-Ar1-NI1 Ar1-Ar1-P
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198 I1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1-H1-HBD1 Ar1-H1-NI1 Ar1-H1-PI1 Ar1-HBA1-HB
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199 A1 Ar1-HBA1-HBD1 Ar1-HBA1-NI1 Ar1-HBA1-PI1 Ar1-HBD1-HBD1 Ar1-HBD1-...;
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200 46 106 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1
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201 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145
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202 132 26 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 ...
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203
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204 OPTIONS
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205 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
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206 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
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207 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
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208 MayaChemToolsAromaticityModel*
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209 Specify aromaticity model to use during detection of aromaticity.
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210 Possible values in the current release are: *MDLAromaticityModel,
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211 TriposAromaticityModel, MMFFAromaticityModel,
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212 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
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213 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
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214 value: *MayaChemToolsAromaticityModel*.
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215
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216 The supported aromaticity model names along with model specific
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217 control parameters are defined in AromaticityModelsData.csv, which
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218 is distributed with the current release and is available under
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219 lib/data directory. Molecule.pm module retrieves data from this file
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220 during class instantiation and makes it available to method
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221 DetectAromaticity for detecting aromaticity corresponding to a
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222 specific model.
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223
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224 --AtomTripletsSetSizeToUse *ArbitrarySize | FixedSize*
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225 Atom triplets set size to use during generation of topological
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226 pharmacophore atom triplets fingerprints.
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227
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228 Possible values: *ArbitrarySize | FixedSize*; Default value:
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229 *ArbitrarySize*.
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230
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231 For *ArbitrarySize* value of --AtomTripletsSetSizeToUse option, the
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232 fingerprint vector correspond to only those topological
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233 pharmacophore atom triplets which are present and have non-zero
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234 count. However, for *FixedSize* value of --AtomTripletsSetSizeToUse
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235 option, the fingerprint vector contains all possible valid
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236 topological pharmacophore atom triplets with both zero and non-zero
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237 count values.
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238
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239 -a, --AtomTypesToUse *"AtomType1,AtomType2,..."*
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240 Pharmacophore atom types to use during generation of topological
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241 phramacophore atom triplets. It's a list of comma separated valid
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242 pharmacophore atom types.
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243
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244 Possible values for pharmacophore atom types are: *Ar, CA, H, HBA,
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245 HBD, Hal, NI, PI, RA*. Default value [ Ref 71 ] :
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246 *HBD,HBA,PI,NI,H,Ar*.
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247
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248 The pharmacophore atom types abbreviations correspond to:
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249
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250 HBD: HydrogenBondDonor
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251 HBA: HydrogenBondAcceptor
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252 PI : PositivelyIonizable
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253 NI : NegativelyIonizable
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254 Ar : Aromatic
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255 Hal : Halogen
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256 H : Hydrophobic
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257 RA : RingAtom
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258 CA : ChainAtom
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259
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260 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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261 pharmacophore atom types. It uses following definitions [ Ref 60-61,
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262 Ref 65-66 ]:
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263
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264 HydrogenBondDonor: NH, NH2, OH
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265 HydrogenBondAcceptor: N[!H], O
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266 PositivelyIonizable: +, NH2
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267 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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268
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269 --CompoundID *DataFieldName or LabelPrefixString*
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270 This value is --CompoundIDMode specific and indicates how compound
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271 ID is generated.
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272
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273 For *DataField* value of --CompoundIDMode option, it corresponds to
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274 datafield label name whose value is used as compound ID; otherwise,
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275 it's a prefix string used for generating compound IDs like
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276 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
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277 IDs which look like Cmpd<Number>.
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278
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279 Examples for *DataField* value of --CompoundIDMode:
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280
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281 MolID
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282 ExtReg
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283
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284 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
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285 --CompoundIDMode:
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286
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287 Compound
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288
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289 The value specified above generates compound IDs which correspond to
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290 Compound<Number> instead of default value of Cmpd<Number>.
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291
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292 --CompoundIDLabel *text*
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293 Specify compound ID column label for CSV/TSV text file(s) used
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294 during *CompoundID* value of --DataFieldsMode option. Default value:
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295 *CompoundID*.
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296
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297 --CompoundIDMode *DataField | MolName | LabelPrefix |
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298 MolNameOrLabelPrefix*
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299 Specify how to generate compound IDs and write to FP or CSV/TSV text
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300 file(s) along with generated fingerprints for *FP | text | all*
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301 values of --output option: use a *SDFile(s)* datafield value; use
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302 molname line from *SDFile(s)*; generate a sequential ID with
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303 specific prefix; use combination of both MolName and LabelPrefix
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304 with usage of LabelPrefix values for empty molname lines.
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305
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306 Possible values: *DataField | MolName | LabelPrefix |
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307 MolNameOrLabelPrefix*. Default value: *LabelPrefix*.
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308
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309 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
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310 in *SDFile(s)* takes precedence over sequential compound IDs
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311 generated using *LabelPrefix* and only empty molname values are
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312 replaced with sequential compound IDs.
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313
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314 This is only used for *CompoundID* value of --DataFieldsMode option.
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315
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316 --DataFields *"FieldLabel1,FieldLabel2,..."*
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317 Comma delimited list of *SDFiles(s)* data fields to extract and
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318 write to CSV/TSV text file(s) along with generated fingerprints for
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319 *text | all* values of --output option.
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320
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321 This is only used for *Specify* value of --DataFieldsMode option.
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322
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323 Examples:
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324
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325 Extreg
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326 MolID,CompoundName
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327
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328 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
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329 Specify how data fields in *SDFile(s)* are transferred to output
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330 CSV/TSV text file(s) along with generated fingerprints for *text |
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331 all* values of --output option: transfer all SD data field; transfer
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332 SD data files common to all compounds; extract specified data
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333 fields; generate a compound ID using molname line, a compound
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334 prefix, or a combination of both. Possible values: *All | Common |
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335 specify | CompoundID*. Default value: *CompoundID*.
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336
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337 --DistanceBinSize *number*
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338 Distance bin size used to bin distances between atom pairs in atom
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339 triplets. Default value: *2*. Valid values: positive integers.
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340
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341 For default --MinDistance and --MaxDistance values of 1 and 10 with
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342 --DistanceBinSize of 2 [ Ref 70 ], the following 5 distance bins are
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343 generated:
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344
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345 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]
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346
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347 The lower distance bound on the distance bin is uses to bin the
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348 distance between atom pairs in atom triplets. So in the previous
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349 example, atom pairs with distances 1 and 2 fall in first distance
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350 bin, atom pairs with distances 3 and 4 fall in second distance bin
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351 and so on.
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352
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353 In order to distribute distance bins of equal size, the last bin is
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354 allowed to go past --MaxDistance by up to distance bin size. For
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355 example, --MinDistance and --MaxDistance values of 2 and 10 with
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356 --DistanceBinSize of 2 generates the following 6 distance bins:
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357
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358 [2, 3] [4, 5] [6, 7] [8, 9] [10 11]
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359
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360 -f, --Filter *Yes | No*
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361 Specify whether to check and filter compound data in SDFile(s).
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362 Possible values: *Yes or No*. Default value: *Yes*.
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363
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364 By default, compound data is checked before calculating fingerprints
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365 and compounds containing atom data corresponding to non-element
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366 symbols or no atom data are ignored.
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367
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368 --FingerprintsLabelMode *FingerprintsLabelOnly |
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369 FingerprintsLabelWithIDs*
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370 Specify how fingerprints label is generated in conjunction with
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371 --FingerprintsLabel option value: use fingerprints label generated
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372 only by --FingerprintsLabel option value or append topological atom
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373 pair count value IDs to --FingerprintsLabel option value.
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374
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375 Possible values: *FingerprintsLabelOnly | FingerprintsLabelWithIDs*.
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376 Default value: *FingerprintsLabelOnly*.
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377
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378 Topological atom pairs IDs appended to --FingerprintsLabel value
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379 during *FingerprintsLabelWithIDs* values of --FingerprintsLabelMode
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380 correspond to atom pair count values in fingerprint vector string.
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381
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382 *FingerprintsLabelWithIDs* value of --FingerprintsLabelMode is
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383 ignored during *ArbitrarySize* value of --AtomTripletsSetSizeToUse
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384 option and topological atom triplets IDs not appended to the label.
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385
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386 --FingerprintsLabel *text*
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387 SD data label or text file column label to use for fingerprints
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388 string in output SD or CSV/TSV text file(s) specified by --output.
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389 Default value: *TopologicalPharmacophoreAtomTripletsFingerprints*.
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390
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391 -h, --help
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392 Print this help message.
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393
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394 -k, --KeepLargestComponent *Yes | No*
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395 Generate fingerprints for only the largest component in molecule.
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396 Possible values: *Yes or No*. Default value: *Yes*.
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397
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398 For molecules containing multiple connected components, fingerprints
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399 can be generated in two different ways: use all connected components
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400 or just the largest connected component. By default, all atoms
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401 except for the largest connected component are deleted before
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402 generation of fingerprints.
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403
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404 --MinDistance *number*
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405 Minimum bond distance between atom pairs corresponding to atom
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406 triplets for generating topological pharmacophore atom triplets.
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407 Default value: *1*. Valid values: positive integers and less than
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408 --MaxDistance.
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409
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410 --MaxDistance *number*
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411 Maximum bond distance between atom pairs corresponding to atom
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412 triplets for generating topological pharmacophore atom triplets.
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413 Default value: *10*. Valid values: positive integers and greater
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414 than --MinDistance.
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415
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416 --OutDelim *comma | tab | semicolon*
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417 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
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418 tab, or semicolon* Default value: *comma*.
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419
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420 --output *SD | FP | text | all*
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421 Type of output files to generate. Possible values: *SD, FP, text, or
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422 all*. Default value: *text*.
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423
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424 -o, --overwrite
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425 Overwrite existing files.
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426
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427 -q, --quote *Yes | No*
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428 Put quote around column values in output CSV/TSV text file(s).
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429 Possible values: *Yes or No*. Default value: *Yes*.
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430
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431 -r, --root *RootName*
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432 New file name is generated using the root: <Root>.<Ext>. Default for
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433 new file names:
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434 <SDFileName><TopologicalPharmacophoreAtomTripletsFP>.<Ext>. The file
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435 type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values
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436 are used for SD, FP, comma/semicolon, and tab delimited text files,
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437 respectively.This option is ignored for multiple input files.
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438
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439 -u, --UseTriangleInequality *Yes | No*
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440 Specify whether to imply triangle distance inequality test to
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441 distances between atom pairs in atom triplets during generation of
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442 atom triplets basis set generation. Possible values: *Yes or No*.
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443 Default value: *Yes*.
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444
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445 Triangle distance inequality test implies that distance or binned
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446 distance between any two atom pairs in an atom triplet must be less
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447 than the sum of distances or binned distances between other two
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448 atoms pairs and greater than the difference of their distances.
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449
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450 For atom triplet PxDyz-PyDxz-PzDxy to satisfy triangle inequality:
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451
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452 Dyz > |Dxz - Dxy| and Dyz < Dxz + Dxy
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453 Dxz > |Dyz - Dxy| and Dyz < Dyz + Dxy
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454 Dxy > |Dyz - Dxz| and Dxy < Dyz + Dxz
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455
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456 -v, --VectorStringFormat *ValuesString, IDsAndValuesString |
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457 IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*
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458 Format of fingerprints vector string data in output SD, FP or
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459 CSV/TSV text file(s) specified by --output option. Possible values:
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460 *ValuesString, IDsAndValuesString | IDsAndValuesPairsString |
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|
461 ValuesAndIDsString | ValuesAndIDsPairsString*. Defaultvalue:
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462 *ValuesString*.
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463
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464 Default value during *FixedSize* value of --AtomTripletsSetSizeToUse
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465 option: *ValuesString*. Default value during *ArbitrarySize* value
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466 of --AtomTripletsSetSizeToUse option: *IDsAndValuesString*.
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467
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468 *ValuesString* option value is not allowed for *ArbitrarySize* value
|
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|
469 of --AtomTripletsSetSizeToUse option.
|
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470
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471 Examples:
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472
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473 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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474 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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|
475 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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|
476 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
|
|
|
477 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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|
478 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
|
|
|
479 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
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480 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
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481
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482 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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|
483 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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|
484 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
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|
485 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
|
|
|
486 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
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|
487 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...
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|
488
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|
489 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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|
490 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesAndIDsPairsSt
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|
|
491 ring;46 Ar1-Ar1-Ar1 106 Ar1-Ar1-H1 8 Ar1-Ar1-HBA1 3 Ar1-Ar1-HBD1 0 Ar1
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|
492 -Ar1-NI1 0 Ar1-Ar1-PI1 83 Ar1-H1-H1 11 Ar1-H1-HBA1 4 Ar1-H1-HBD1 0 Ar1
|
|
|
493 -H1-NI1 0 Ar1-H1-PI1 0 Ar1-HBA1-HBA1 1 Ar1-HBA1-HBD1 0 Ar1-HBA1-NI1 0
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|
|
494 Ar1-HBA1-PI1 0 Ar1-HBD1-HBD1 0 Ar1-HBD1-NI1 0 Ar1-HBD1-PI1 0 Ar1-NI...
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495
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|
|
496 -w, --WorkingDir *DirName*
|
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497 Location of working directory. Default value: current directory.
|
|
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498
|
|
|
499 EXAMPLES
|
|
|
500 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
501 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
502 1 through 10 using default atoms with distances satisfying triangle
|
|
|
503 inequality and create a SampleTPATFP.csv file containing sequential
|
|
|
504 compound IDs along with fingerprints vector strings data in ValuesString
|
|
|
505 format, type:
|
|
|
506
|
|
|
507 % TopologicalPharmacophoreAtomTripletsFingerprints.pl -r SampleTPATFP
|
|
|
508 -o Sample.sdf
|
|
|
509
|
|
|
510 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
511 fixed size corresponding to 5 distance bins spanning distances from 1
|
|
|
512 through 10 using default atoms with distances satisfying triangle
|
|
|
513 inequality and create a SampleTPATFP.csv file containing sequential
|
|
|
514 compound IDs along with fingerprints vector strings data in ValuesString
|
|
|
515 format, type:
|
|
|
516
|
|
|
517 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
518 --AtomTripletsSetSizeToUse FixedSize -r SampleTPATFP -o Sample.sdf
|
|
|
519
|
|
|
520 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
521 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
522 1 through 10 using default atoms with distances satisfying triangle
|
|
|
523 inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and
|
|
|
524 SampleTPATFP.csv files with CSV file containing sequential compound IDs
|
|
|
525 along with fingerprints vector strings data in ValuesString format,
|
|
|
526 type:
|
|
|
527
|
|
|
528 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --output all
|
|
|
529 -r SampleTPATFP -o Sample.sdf
|
|
|
530
|
|
|
531 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
532 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
533 1 through 10 using default atoms with distances satisfying triangle
|
|
|
534 inequality and create a SampleTPATFP.csv file containing sequential
|
|
|
535 compound IDs along with fingerprints vector strings data in ValuesString
|
|
|
536 format and atom triplets IDs in the fingerprint data column label
|
|
|
537 starting with Fingerprints, type:
|
|
|
538
|
|
|
539 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
540 --FingerprintsLabelMode FingerprintsLabelWithIDs --FingerprintsLabel
|
|
|
541 Fingerprints -r SampleTPATFP -o Sample.sdf
|
|
|
542
|
|
|
543 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
544 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
545 1 through 10 using default atoms with distances not satisfying triangle
|
|
|
546 inequality and create a SampleTPATFP.csv file containing sequential
|
|
|
547 compound IDs along with fingerprints vector strings data in ValuesString
|
|
|
548 format, type:
|
|
|
549
|
|
|
550 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
551 --UseTriangleInequality No -r SampleTPATFP -o Sample.sdf
|
|
|
552
|
|
|
553 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
554 arbitrary size corresponding to 6 distance bins spanning distances from
|
|
|
555 1 through 12 using default atoms with distances satisfying triangle
|
|
|
556 inequality and create a SampleTPATFP.csv file containing sequential
|
|
|
557 compound IDs along with fingerprints vector strings data in ValuesString
|
|
|
558 format, type:
|
|
|
559
|
|
|
560 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
561 --UseTriangleInequality Yes --MinDistance 1 --MaxDistance 12
|
|
|
562 --DistanceBinSIze 2 -r SampleTPATFP -o Sample.sdf
|
|
|
563
|
|
|
564 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
565 arbitrary size corresponding to 6 distance bins spanning distances from
|
|
|
566 1 through 12 using "HBD,HBA,PI, NI, H, Ar" atoms with distances
|
|
|
567 satisfying triangle inequality and create a SampleTPATFP.csv file
|
|
|
568 containing sequential compound IDs along with fingerprints vector
|
|
|
569 strings data in ValuesString format, type:
|
|
|
570
|
|
|
571 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
572 --AtomTypesToUse "HBD,HBA,PI,NI,H,Ar" --UseTriangleInequality Yes
|
|
|
573 --MinDistance 1 --MaxDistance 12 --DistanceBinSIze 2
|
|
|
574 --VectorStringFormat ValuesString -r SampleTPATFP -o Sample.sdf
|
|
|
575
|
|
|
576 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
577 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
578 1 through 10 using default atoms with distances satisfying triangle
|
|
|
579 inequality and create a SampleTPATFP.csv file containing sequential
|
|
|
580 compound IDs from molecule name line along with fingerprints vector
|
|
|
581 strings data in ValuesString format, type:
|
|
|
582
|
|
|
583 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
|
|
|
584 CompoundID -CompoundIDMode MolName -r SampleTPATFP -o Sample.sdf
|
|
|
585
|
|
|
586 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
587 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
588 1 through 10 using default atoms with distances satisfying triangle
|
|
|
589 inequality and create a SampleTPATFP.csv file containing sequential
|
|
|
590 compound IDs using specified data field along with fingerprints vector
|
|
|
591 strings data in ValuesString format, type:
|
|
|
592
|
|
|
593 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
|
|
|
594 CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
|
|
|
595 -r SampleTPATFP -o Sample.sdf
|
|
|
596
|
|
|
597 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
598 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
599 1 through 10 using default atoms with distances satisfying triangle
|
|
|
600 inequality and create a SampleTPATFP.csv file containing sequential
|
|
|
601 compound IDs using combination of molecule name line and an explicit
|
|
|
602 compound prefix along with fingerprints vector strings data, type:
|
|
|
603
|
|
|
604 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
|
|
|
605 CompoundID -CompoundIDMode MolnameOrLabelPrefix
|
|
|
606 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleSampleTPATFP
|
|
|
607 -o Sample.sdf
|
|
|
608
|
|
|
609 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
610 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
611 1 through 10 using default atoms with distances satisfying triangle
|
|
|
612 inequality and create a SampleTPATFP.csv file containing specific data
|
|
|
613 fields columns along with fingerprints vector strings data, type:
|
|
|
614
|
|
|
615 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
|
|
|
616 Specify --DataFields Mol_ID -r SampleTPATFP -o Sample.sdf
|
|
|
617
|
|
|
618 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
619 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
620 1 through 10 using default atoms with distances satisfying triangle
|
|
|
621 inequality and create a SampleTPATFP.csv file containing common data
|
|
|
622 fields columns along with fingerprints vector strings data, type:
|
|
|
623
|
|
|
624 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
|
|
|
625 Common -r SampleTPATFP -o Sample.sdf
|
|
|
626
|
|
|
627 To generate topological pharmacophore atom triplets fingerprints of
|
|
|
628 arbitrary size corresponding to 5 distance bins spanning distances from
|
|
|
629 1 through 10 using default atoms with distances satisfying triangle
|
|
|
630 inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and
|
|
|
631 SampleTPATFP.csv files containing all data fields columns in CSV file
|
|
|
632 along with fingerprints data, type:
|
|
|
633
|
|
|
634 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
|
|
|
635 All --output all -r SampleTPATFP -o Sample.sdf
|
|
|
636
|
|
|
637 AUTHOR
|
|
|
638 Manish Sud <msud@san.rr.com>
|
|
|
639
|
|
|
640 SEE ALSO
|
|
|
641 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
|
|
|
642 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
|
|
|
643 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
644 TopologicalAtomPairsFingerprints.pl,
|
|
|
645 TopologicalAtomTorsionsFingerprints.pl,
|
|
|
646 TopologicalPharmacophoreAtomPairsFingerprints.pl
|
|
|
647
|
|
|
648 COPYRIGHT
|
|
|
649 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
650
|
|
|
651 This file is part of MayaChemTools.
|
|
|
652
|
|
|
653 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
654 under the terms of the GNU Lesser General Public License as published by
|
|
|
655 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
656 your option) any later version.
|
|
|
657
|
