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1 NAME
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2 TopologicalPharmacophoreAtomPairsFingerprints.pl - Generate topological
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3 pharmacophore atom pairs fingerprints for SD files
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4
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5 SYNOPSIS
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6 TopologicalPharmacophoreAtomPairsFingerprints.pl SDFile(s)...
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7
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8 TopologicalPharmacophoreAtomPairsFingerprints.pl [--AromaticityModel
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9 *AromaticityModelType*] [--AtomPairsSetSizeToUse *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*] [-f, --Filter *Yes | No*] [--FingerprintsLabelMode
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16 *FingerprintsLabelOnly | FingerprintsLabelWithIDs*] [--FingerprintsLabel
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17 *text*] [--FuzzifyAtomPairsCount *Yes | No*] [--FuzzificationMode
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18 *FuzzyBinning | FuzzyBinSmoothing*] [--FuzzificationMethodology
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19 *FuzzyBinning | FuzzyBinSmoothing*] [--FuzzFactor *number*] [-h, --help]
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20 [-k, --KeepLargestComponent *Yes | No*] [--MinDistance *number*]
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21 [--MaxDistance *number*] [-n, --NormalizationMethodology *None |
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22 ByHeavyAtomsCount | ByAtomTypesCount*] [--OutDelim *comma | tab |
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23 semicolon*] [--output *SD | FP | text | all*] [-o, --overwrite] [-q,
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24 --quote *Yes | No*] [-r, --root *RootName*] [--ValuesPrecision *number*]
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25 [-v, --VectorStringFormat *ValuesString, IDsAndValuesString |
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26 IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*]
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27 [-w, --WorkingDir dirname] SDFile(s)...
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28
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29 DESCRIPTION
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30 Generate topological pharmacophore atom pairs fingerprints [ Ref 60-62,
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31 Ref 65, Ref 68 ] for *SDFile(s)* and create appropriate SD, FP or
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32 CSV/TSV text file(s) containing fingerprints vector strings
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33 corresponding to molecular fingerprints.
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34
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35 Multiple SDFile names are separated by spaces. The valid file extensions
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36 are *.sdf* and *.sd*. All other file names are ignored. All the SD files
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37 in a current directory can be specified either by **.sdf* or the current
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38 directory name.
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39
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40 Based on the values specified for --AtomTypesToUse, pharmacophore atom
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41 types are assigned to all non-hydrogen atoms in a molecule and a
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42 distance matrix is generated. A pharmacophore atom pairs basis set is
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43 initialized for all unique possible pairs within --MinDistance and
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44 --MaxDistance range.
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45
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46 Let:
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47
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48 P = Valid pharmacophore atom type
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49
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50 Px = Pharmacophore atom type x
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51 Py = Pharmacophore atom type y
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52
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53 Dmin = Minimum distance corresponding to number of bonds between
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54 two atoms
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55 Dmax = Maximum distance corresponding to number of bonds between
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56 two atoms
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57 D = Distance corresponding to number of bonds between two atoms
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58
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59 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at
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60 distance Dn
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61
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62 P = Number of pharmacophore atom types to consider
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63 PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn
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64
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65 PPT = Total number of possible pharmacophore atom pairs at all distances
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66 between Dmin and Dmax
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67
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68 Then:
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69
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70 PPD = (P * (P - 1))/2 + P
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71
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72 PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)
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73 = ((Dmax - Dmin) + 1) * PPD
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74
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75 So for default values of Dmin = 1, Dmax = 10 and P = 5,
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76
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77 PPD = (5 * (5 - 1))/2 + 5 = 15
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78 PPT = ((10 - 1) + 1) * 15 = 150
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79
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80 The pharmacophore atom pairs bais set includes 150 values.
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81
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82 The atom pair IDs correspond to:
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83
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84 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at
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85 distance Dn
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86
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87 For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on
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88
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89 Using distance matrix and pharmacohore atom types, occurrence of unique
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90 pharmacohore atom pairs is counted. The contribution of each atom type
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91 to atom pair interaction is optionally weighted by specified
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92 --AtomTypesWeight before assigning its count to appropriate distance
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93 bin. Based on --NormalizationMethodology option, pharmacophore atom
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94 pairs count is optionally normalized. Additionally, pharmacohore atom
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95 pairs count is optionally fuzzified before or after the normalization
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96 controlled by values of --FuzzifyAtomPairsCount, --FuzzificationMode,
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97 --FuzzificationMethodology and --FuzzFactor options.
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98
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99 The final pharmacophore atom pairs count along with atom pair
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100 identifiers involving all non-hydrogen atoms, with optional
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101 normalization and fuzzification, constitute pharmacophore topological
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102 atom pairs fingerprints of the molecule.
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103
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104 For *ArbitrarySize* value of --AtomPairsSetSizeToUse option, the
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105 fingerprint vector correspond to only those topological pharmacophore
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106 atom pairs which are present and have non-zero count. However, for
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107 *FixedSize* value of --AtomPairsSetSizeToUse option, the fingerprint
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108 vector contains all possible valid topological pharmacophore atom pairs
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109 with both zero and non-zero count values.
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110
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111 Example of *SD* file containing topological pharmacophore atom pairs
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112 fingerprints string data:
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113
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114 ... ...
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115 ... ...
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116 $$$$
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117 ... ...
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118 ... ...
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119 ... ...
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120 41 44 0 0 0 0 0 0 0 0999 V2000
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121 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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122 ... ...
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123 2 3 1 0 0 0 0
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124 ... ...
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125 M END
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126 > <CmpdID>
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127 Cmpd1
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128
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129 > <TopologicalPharmacophoreAtomPairsFingerprints>
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130 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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131 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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132 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
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133 HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D...;
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134 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
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135 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
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136
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137 $$$$
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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 pairs
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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 15:32:48 2011
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149 #
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150 # FingerprintsStringType = FingerprintsVector
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151 #
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152 # Description = TopologicalPharmacophoreAtomPairs:ArbitrarySize:MinDistance1:MaxDistance10
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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 54;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;18 1 2...
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157 Cmpd2 61;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;5 1 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 pairs fingerprints string data:
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163
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164 "CompoundID","TopologicalPharmacophoreAtomPairsFingerprints"
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165 "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomPairs:Arbitrary
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166 Size:MinDistance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H
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167 -D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA H
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168 BA-D2-HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4...;
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169 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
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170 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1"
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171 ... ...
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172 ... ...
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173
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174 The current release of MayaChemTools generates the following types of
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175 topological pharmacophore atom pairs fingerprints vector strings:
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176
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177 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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178 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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179 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
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180 HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
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181 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
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182 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
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183 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
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184
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185 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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186 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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187 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
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188 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
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189 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
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190 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
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191
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192 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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193 ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
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194 -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
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195 BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
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196 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
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197 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
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198 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
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199 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0
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200
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201 OPTIONS
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202 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
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203 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
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204 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
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205 MayaChemToolsAromaticityModel*
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206 Specify aromaticity model to use during detection of aromaticity.
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207 Possible values in the current release are: *MDLAromaticityModel,
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208 TriposAromaticityModel, MMFFAromaticityModel,
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209 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
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210 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
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211 value: *MayaChemToolsAromaticityModel*.
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212
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213 The supported aromaticity model names along with model specific
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214 control parameters are defined in AromaticityModelsData.csv, which
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215 is distributed with the current release and is available under
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216 lib/data directory. Molecule.pm module retrieves data from this file
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217 during class instantiation and makes it available to method
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218 DetectAromaticity for detecting aromaticity corresponding to a
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219 specific model.
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220
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221 --AtomPairsSetSizeToUse *ArbitrarySize | FixedSize*
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222 Atom pairs set size to use during generation of topological
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223 pharmacophore atom pairs fingerprints.
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224
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225 Possible values: *ArbitrarySize | FixedSize*; Default value:
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226 *ArbitrarySize*.
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227
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228 For *ArbitrarySize* value of --AtomPairsSetSizeToUse option, the
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229 fingerprint vector correspond to only those topological
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230 pharmacophore atom pairs which are present and have non-zero count.
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231 However, for *FixedSize* value of --AtomPairsSetSizeToUse option,
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232 the fingerprint vector contains all possible valid topological
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233 pharmacophore atom pairs with both zero and non-zero count values.
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234
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235 -a, --AtomTypesToUse *"AtomType1,AtomType2,..."*
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236 Pharmacophore atom types to use during generation of topological
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237 phramacophore atom pairs. It's a list of comma separated valid
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238 pharmacophore atom types.
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239
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240 Possible values for pharmacophore atom types are: *Ar, CA, H, HBA,
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241 HBD, Hal, NI, PI, RA*. Default value [ Ref 60-62 ] :
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242 *HBD,HBA,PI,NI,H*.
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243
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244 The pharmacophore atom types abbreviations correspond to:
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245
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246 HBD: HydrogenBondDonor
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247 HBA: HydrogenBondAcceptor
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248 PI : PositivelyIonizable
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249 NI : NegativelyIonizable
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250 Ar : Aromatic
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251 Hal : Halogen
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252 H : Hydrophobic
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253 RA : RingAtom
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254 CA : ChainAtom
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255
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256 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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257 pharmacophore atom types. It uses following definitions [ Ref 60-61,
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258 Ref 65-66 ]:
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259
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260 HydrogenBondDonor: NH, NH2, OH
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261 HydrogenBondAcceptor: N[!H], O
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262 PositivelyIonizable: +, NH2
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263 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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264
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265 --AtomTypesWeight *"AtomType1,Weight1,AtomType2,Weight2..."*
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266 Weights of specified pharmacophore atom types to use during
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267 calculation of their contribution to atom pair count. Default value:
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268 *None*. Valid values: real numbers greater than 0. In general it's
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269 comma delimited list of valid atom type and its weight.
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270
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271 The weight values allow to increase the importance of specific
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272 pharmacophore atom type in the generated fingerprints. A weight
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273 value of 0 for an atom type eliminates its contribution to atom pair
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274 count where as weight value of 2 doubles its contribution.
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275
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276 --CompoundID *DataFieldName or LabelPrefixString*
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277 This value is --CompoundIDMode specific and indicates how compound
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278 ID is generated.
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279
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280 For *DataField* value of --CompoundIDMode option, it corresponds to
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281 datafield label name whose value is used as compound ID; otherwise,
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282 it's a prefix string used for generating compound IDs like
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283 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
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284 IDs which look like Cmpd<Number>.
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285
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286 Examples for *DataField* value of --CompoundIDMode:
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287
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288 MolID
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289 ExtReg
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290
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291 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
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292 --CompoundIDMode:
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293
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294 Compound
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295
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296 The value specified above generates compound IDs which correspond to
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297 Compound<Number> instead of default value of Cmpd<Number>.
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298
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299 --CompoundIDLabel *text*
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300 Specify compound ID column label for CSV/TSV text file(s) used
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301 during *CompoundID* value of --DataFieldsMode option. Default value:
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302 *CompoundID*.
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303
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304 --CompoundIDMode *DataField | MolName | LabelPrefix |
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305 MolNameOrLabelPrefix*
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306 Specify how to generate compound IDs and write to FP or CSV/TSV text
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307 file(s) along with generated fingerprints for *FP | text | all*
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308 values of --output option: use a *SDFile(s)* datafield value; use
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309 molname line from *SDFile(s)*; generate a sequential ID with
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310 specific prefix; use combination of both MolName and LabelPrefix
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311 with usage of LabelPrefix values for empty molname lines.
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312
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313 Possible values: *DataField | MolName | LabelPrefix |
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314 MolNameOrLabelPrefix*. Default value: *LabelPrefix*.
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315
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316 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
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317 in *SDFile(s)* takes precedence over sequential compound IDs
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318 generated using *LabelPrefix* and only empty molname values are
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319 replaced with sequential compound IDs.
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320
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321 This is only used for *CompoundID* value of --DataFieldsMode option.
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322
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323 --DataFields *"FieldLabel1,FieldLabel2,..."*
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324 Comma delimited list of *SDFiles(s)* data fields to extract and
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325 write to CSV/TSV text file(s) along with generated fingerprints for
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326 *text | all* values of --output option.
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327
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328 This is only used for *Specify* value of --DataFieldsMode option.
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329
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330 Examples:
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331
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332 Extreg
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333 MolID,CompoundName
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334
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335 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
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336 Specify how data fields in *SDFile(s)* are transferred to output
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337 CSV/TSV text file(s) along with generated fingerprints for *text |
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338 all* values of --output option: transfer all SD data field; transfer
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339 SD data files common to all compounds; extract specified data
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340 fields; generate a compound ID using molname line, a compound
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341 prefix, or a combination of both. Possible values: *All | Common |
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342 specify | CompoundID*. Default value: *CompoundID*.
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343
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344 -f, --Filter *Yes | No*
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345 Specify whether to check and filter compound data in SDFile(s).
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346 Possible values: *Yes or No*. Default value: *Yes*.
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347
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348 By default, compound data is checked before calculating fingerprints
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349 and compounds containing atom data corresponding to non-element
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350 symbols or no atom data are ignored.
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351
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352 --FingerprintsLabelMode *FingerprintsLabelOnly |
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353 FingerprintsLabelWithIDs*
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354 Specify how fingerprints label is generated in conjunction with
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355 --FingerprintsLabel option value: use fingerprints label generated
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356 only by --FingerprintsLabel option value or append topological atom
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357 pair count value IDs to --FingerprintsLabel option value.
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358
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359 Possible values: *FingerprintsLabelOnly | FingerprintsLabelWithIDs*.
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360 Default value: *FingerprintsLabelOnly*.
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361
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362 Topological atom pairs IDs appended to --FingerprintsLabel value
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363 during *FingerprintsLabelWithIDs* values of --FingerprintsLabelMode
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364 correspond to atom pair count values in fingerprint vector string.
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365
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366 *FingerprintsLabelWithIDs* value of --FingerprintsLabelMode is
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367 ignored during *ArbitrarySize* value of --AtomPairsSetSizeToUse
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368 option and topological atom pairs IDs not appended to the label.
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369
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370 --FingerprintsLabel *text*
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371 SD data label or text file column label to use for fingerprints
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372 string in output SD or CSV/TSV text file(s) specified by --output.
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373 Default value: *TopologicalPharmacophoreAtomPairsFingerprints*.
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374
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375 --FuzzifyAtomPairsCount *Yes | No*
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376 To fuzzify or not to fuzzify atom pairs count. Possible values: *Yes
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377 or No*. Default value: *No*.
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378
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379 --FuzzificationMode *BeforeNormalization | AfterNormalization*
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380 When to fuzzify atom pairs count. Possible values:
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381 *BeforeNormalization | AfterNormalizationYes*. Default value:
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382 *AfterNormalization*.
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383
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384 --FuzzificationMethodology *FuzzyBinning | FuzzyBinSmoothing*
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385 How to fuzzify atom pairs count. Possible values: *FuzzyBinning |
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386 FuzzyBinSmoothing*. Default value: *FuzzyBinning*.
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387
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388 In conjunction with values for options --FuzzifyAtomPairsCount,
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389 --FuzzificationMode and --FuzzFactor, --FuzzificationMethodology
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390 option is used to fuzzify pharmacophore atom pairs count.
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391
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392 Let:
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393
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394 Px = Pharmacophore atom type x
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395 Py = Pharmacophore atom type y
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396 PPxy = Pharmacophore atom pair between atom type Px and Py
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397
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398 PPxyDn = Pharmacophore atom pairs count between atom type Px and Py
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399 at distance Dn
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400 PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py
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401 at distance Dn - 1
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402 PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py
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403 at distance Dn + 1
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404
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405 FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing
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406
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407 Then:
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408
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409 For *FuzzyBinning*:
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410
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411 PPxyDn = PPxyDn (Unchanged)
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412
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413 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
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414 PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
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415
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416 For *FuzzyBinSmoothing*:
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417
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418 PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax
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419 PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax
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420
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421 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
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422 PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
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423
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424 In both fuzzification schemes, a value of 0 for FF implies no
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425 fuzzification of occurrence counts. A value of 1 during
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426 *FuzzyBinning* corresponds to maximum fuzzification of occurrence
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427 counts; however, a value of 1 during *FuzzyBinSmoothing* ends up
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428 completely distributing the value over the previous and next
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429 distance bins.
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430
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431 So for default value of --FuzzFactor (FF) 0.15, the occurrence count
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432 of pharmacohore atom pairs at distance Dn during FuzzyBinning is
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433 left unchanged and the counts at distances Dn -1 and Dn + 1 are
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434 incremented by PPxyDn * 0.15.
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435
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436 And during *FuzzyBinSmoothing* the occurrence counts at Distance Dn
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437 is scaled back using multiplicative factor of (1 - 2*0.15) and the
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438 occurrence counts at distances Dn -1 and Dn + 1 are incremented by
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439 PPxyDn * 0.15. In otherwords, occurrence bin count is smoothed out
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440 by distributing it over the previous and next distance value.
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441
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442 --FuzzFactor *number*
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443 Specify by how much to fuzzify atom pairs count. Default value:
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444 *0.15*. Valid values: For *FuzzyBinning* value of
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445 --FuzzificationMethodology option: *between 0 and 1.0*; For
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446 *FuzzyBinSmoothing* value of --FuzzificationMethodology option:
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447 *between 0 and 0.5*.
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448
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449 -h, --help
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450 Print this help message.
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451
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452 -k, --KeepLargestComponent *Yes | No*
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453 Generate fingerprints for only the largest component in molecule.
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454 Possible values: *Yes or No*. Default value: *Yes*.
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455
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456 For molecules containing multiple connected components, fingerprints
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457 can be generated in two different ways: use all connected components
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458 or just the largest connected component. By default, all atoms
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459 except for the largest connected component are deleted before
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460 generation of fingerprints.
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461
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462 --MinDistance *number*
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463 Minimum bond distance between atom pairs for generating topological
|
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464 pharmacophore atom pairs. Default value: *1*. Valid values: positive
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465 integers including 0 and less than --MaxDistance.
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466
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467 --MaxDistance *number*
|
|
|
468 Maximum bond distance between atom pairs for generating topological
|
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469 pharmacophore atom pairs. Default value: *10*. Valid values:
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470 positive integers and greater than --MinDistance.
|
|
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471
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472 -n, --NormalizationMethodology *None | ByHeavyAtomsCount |
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|
473 ByAtomTypesCount*
|
|
|
474 Normalization methodology to use for scaling the occurrence count of
|
|
|
475 pharmacophore atom pairs within specified distance range. Possible
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|
|
476 values: *None, ByHeavyAtomsCount or ByAtomTypesCount*. Default
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|
|
477 value: *None*.
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478
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|
|
479 --OutDelim *comma | tab | semicolon*
|
|
|
480 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
|
|
|
481 tab, or semicolon* Default value: *comma*.
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|
|
482
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|
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483 --output *SD | FP | text | all*
|
|
|
484 Type of output files to generate. Possible values: *SD, FP, text, or
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|
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485 all*. Default value: *text*.
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|
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486
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|
|
487 -o, --overwrite
|
|
|
488 Overwrite existing files.
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489
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|
490 -q, --quote *Yes | No*
|
|
|
491 Put quote around column values in output CSV/TSV text file(s).
|
|
|
492 Possible values: *Yes or No*. Default value: *Yes*
|
|
|
493
|
|
|
494 -r, --root *RootName*
|
|
|
495 New file name is generated using the root: <Root>.<Ext>. Default for
|
|
|
496 new file names:
|
|
|
497 <SDFileName><TopologicalPharmacophoreAtomPairsFP>.<Ext>. The file
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|
|
498 type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values
|
|
|
499 are used for SD, FP, comma/semicolon, and tab delimited text files,
|
|
|
500 respectively.This option is ignored for multiple input files.
|
|
|
501
|
|
|
502 --ValuesPrecision *number*
|
|
|
503 Precision of atom pairs count real values which might be generated
|
|
|
504 after normalization or fuzzification. Default value: up to *2*
|
|
|
505 decimal places. Valid values: positive integers.
|
|
|
506
|
|
|
507 -v, --VectorStringFormat *ValuesString, IDsAndValuesString |
|
|
|
508 IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*
|
|
|
509 Format of fingerprints vector string data in output SD, FP or
|
|
|
510 CSV/TSV text file(s) specified by --output option. Possible values:
|
|
|
511 *ValuesString, IDsAndValuesString | IDsAndValuesPairsString |
|
|
|
512 ValuesAndIDsString | ValuesAndIDsPairsString*.
|
|
|
513
|
|
|
514 Default value during *FixedSize* value of --AtomPairsSetSizeToUse
|
|
|
515 option: *ValuesString*. Default value during *ArbitrarySize* value
|
|
|
516 of --AtomPairsSetSizeToUse option: *IDsAndValuesString*.
|
|
|
517
|
|
|
518 *ValuesString* option value is not allowed for *ArbitrarySize* value
|
|
|
519 of --AtomPairsSetSizeToUse option.
|
|
|
520
|
|
|
521 Examples:
|
|
|
522
|
|
|
523 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
|
|
|
524 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
|
|
|
525 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
|
|
|
526 HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
|
|
|
527 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
|
|
|
528 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
|
|
|
529 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
|
|
|
530
|
|
|
531 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
532 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
533 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
|
|
|
534 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
|
|
|
535 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
|
|
|
536 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
|
|
|
537
|
|
|
538 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
539 ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
|
|
|
540 -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
|
|
|
541 BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
|
|
|
542 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
|
|
|
543 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
|
|
|
544 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
|
|
|
545 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0
|
|
|
546
|
|
|
547 -w, --WorkingDir *DirName*
|
|
|
548 Location of working directory. Default value: current directory.
|
|
|
549
|
|
|
550 EXAMPLES
|
|
|
551 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
552 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
553 default atom types with no weighting, normalization, and fuzzification
|
|
|
554 of atom pairs count and create a SampleTPAPFP.csv file containing
|
|
|
555 sequential compound IDs along with fingerprints vector strings data in
|
|
|
556 ValuesString format, type:
|
|
|
557
|
|
|
558 % TopologicalPharmacophoreAtomPairsFingerprints.pl -r SampleTPAPFP
|
|
|
559 -o Sample.sdf
|
|
|
560
|
|
|
561 To generate topological pharmacophore atom pairs fingerprints of fixed
|
|
|
562 size corresponding to distances from 1 through 10 using default atom
|
|
|
563 types with no weighting, normalization, and fuzzification of atom pairs
|
|
|
564 count and create a SampleTPAPFP.csv file containing sequential compound
|
|
|
565 IDs along with fingerprints vector strings data in ValuesString format,
|
|
|
566 type:
|
|
|
567
|
|
|
568 % TopologicalPharmacophoreAtomPairsFingerprints.pl
|
|
|
569 --AtomPairsSetSizeToUse FixedSize -r SampleTPAPFP-o Sample.sdf
|
|
|
570
|
|
|
571 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
572 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
573 default atom types with no weighting, normalization, and fuzzification
|
|
|
574 of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf and
|
|
|
575 SampleTPAPFP.csv files containing sequential compound IDs in CSV file
|
|
|
576 along with fingerprints vector strings data in ValuesString format,
|
|
|
577 type:
|
|
|
578
|
|
|
579 % TopologicalPharmacophoreAtomPairsFingerprints.pl --output all
|
|
|
580 -r SampleTPAPFP -o Sample.sdf
|
|
|
581
|
|
|
582 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
583 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
584 default atom types with no weighting, normalization, and fuzzification
|
|
|
585 of atom pairs count and create a SampleTPAPFP.csv file containing
|
|
|
586 sequential compound IDs along with fingerprints vector strings data in
|
|
|
587 IDsAndValuesPairsString format, type:
|
|
|
588
|
|
|
589 % TopologicalPharmacophoreAtomPairsFingerprints.pl --VectorStringFormat
|
|
|
590 IDsAndValuesPairsString -r SampleTPAPFP -o Sample.sdf
|
|
|
591
|
|
|
592 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
593 arbitrary size corresponding to distances from 1 through 6 using default
|
|
|
594 atom types with no weighting, normalization, and fuzzification of atom
|
|
|
595 pairs count and create a SampleTPAPFP.csv file containing sequential
|
|
|
596 compound IDs along with fingerprints vector strings data in ValuesString
|
|
|
597 format, type:
|
|
|
598
|
|
|
599 % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
|
|
|
600 -MaxDistance 6 -r SampleTPAPFP -o Sample.sdf
|
|
|
601
|
|
|
602 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
603 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
604 "HBD,HBA,PI,NI" atom types with double the weighting for "HBD,HBA" and
|
|
|
605 normalization by HeavyAtomCount but no fuzzification of atom pairs count
|
|
|
606 and create a SampleTPAPFP.csv file containing sequential compound IDs
|
|
|
607 along with fingerprints vector strings data in ValuesString format,
|
|
|
608 type:
|
|
|
609
|
|
|
610 % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
|
|
|
611 -MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI" --AtomTypesWeight
|
|
|
612 "HBD,2,HBA,2,PI,1,NI,1" --NormalizationMethodology ByHeavyAtomsCount
|
|
|
613 --FuzzifyAtomPairsCount No -r SampleTPAPFP -o Sample.sdf
|
|
|
614
|
|
|
615 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
616 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
617 "HBD,HBA,PI,NI,H" atom types with no weighting of atom types and
|
|
|
618 normalization but with fuzzification of atom pairs count using
|
|
|
619 FuzzyBinning methodology with FuzzFactor value 0.15 and create a
|
|
|
620 SampleTPAPFP.csv file containing sequential compound IDs along with
|
|
|
621 fingerprints vector strings data in ValuesString format, type:
|
|
|
622
|
|
|
623 % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
|
|
|
624 --MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI,H" --AtomTypesWeight
|
|
|
625 "HBD,1,HBA,1,PI,1,NI,1,H,1" --NormalizationMethodology None
|
|
|
626 --FuzzifyAtomPairsCount Yes --FuzzificationMethodology FuzzyBinning
|
|
|
627 --FuzzFactor 0.5 -r SampleTPAPFP -o Sample.sdf
|
|
|
628
|
|
|
629 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
630 arbitrary size corresponding to distances distances from 1 through 10
|
|
|
631 using default atom types with no weighting, normalization, and
|
|
|
632 fuzzification of atom pairs count and create a SampleTPAPFP.csv file
|
|
|
633 containing compound ID from molecule name line along with fingerprints
|
|
|
634 vector strings data, type:
|
|
|
635
|
|
|
636 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
|
|
|
637 CompoundID -CompoundIDMode MolName -r SampleTPAPFP -o Sample.sdf
|
|
|
638
|
|
|
639 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
640 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
641 default atom types with no weighting, normalization, and fuzzification
|
|
|
642 of atom pairs count and create a SampleTPAPFP.csv file containing
|
|
|
643 compound IDs using specified data field along with fingerprints vector
|
|
|
644 strings data, type:
|
|
|
645
|
|
|
646 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
|
|
|
647 CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
|
|
|
648 -r SampleTPAPFP -o Sample.sdf
|
|
|
649
|
|
|
650 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
651 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
652 default atom types with no weighting, normalization, and fuzzification
|
|
|
653 of atom pairs count and create a SampleTPAPFP.csv file containing
|
|
|
654 compound ID using combination of molecule name line and an explicit
|
|
|
655 compound prefix along with fingerprints vector strings data, type:
|
|
|
656
|
|
|
657 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
|
|
|
658 CompoundID -CompoundIDMode MolnameOrLabelPrefix
|
|
|
659 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTPAPFP -o Sample.sdf
|
|
|
660
|
|
|
661 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
662 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
663 default atom types with no weighting, normalization, and fuzzification
|
|
|
664 of atom pairs count and create a SampleTPAPFP.csv file containing
|
|
|
665 specific data fields columns along with fingerprints vector strings
|
|
|
666 data, type:
|
|
|
667
|
|
|
668 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
|
|
|
669 Specify --DataFields Mol_ID -r SampleTPAPFP -o Sample.sdf
|
|
|
670
|
|
|
671 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
672 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
673 default atom types with no weighting, normalization, and fuzzification
|
|
|
674 of atom pairs count and create a SampleTPAPFP.csv file containing common
|
|
|
675 data fields columns along with fingerprints vector strings data, type:
|
|
|
676
|
|
|
677 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
|
|
|
678 Common -r SampleTPAPFP -o Sample.sdf
|
|
|
679
|
|
|
680 To generate topological pharmacophore atom pairs fingerprints of
|
|
|
681 arbitrary size corresponding to distances from 1 through 10 using
|
|
|
682 default atom types with no weighting, normalization, and fuzzification
|
|
|
683 of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf, and
|
|
|
684 SampleTPAPFP.csv files containing all data fields columns in CSV file
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685 along with fingerprints data, type:
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686
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687 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
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688 All --output all -r SampleTPAPFP -o Sample.sdf
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689
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690 AUTHOR
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691 Manish Sud <msud@san.rr.com>
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692
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693 SEE ALSO
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694 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
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695 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
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696 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
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697 TopologicalAtomPairsFingerprints.pl,
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698 TopologicalAtomTorsionsFingerprints.pl,
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699 TopologicalPharmacophoreAtomTripletsFingerprints.pl
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700
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701 COPYRIGHT
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702 Copyright (C) 2015 Manish Sud. All rights reserved.
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703
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704 This file is part of MayaChemTools.
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705
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706 MayaChemTools is free software; you can redistribute it and/or modify it
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707 under the terms of the GNU Lesser General Public License as published by
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708 the Free Software Foundation; either version 3 of the License, or (at
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709 your option) any later version.
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710
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