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1 NAME
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2 TopologicalAtomPairsFingerprints.pl - Generate topological atom pairs
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3 fingerprints for SD files
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4
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5 SYNOPSIS
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6 TopologicalAtomPairsFingerprints.pl SDFile(s)...
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7
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8 TopologicalAtomPairsFingerprints.pl [--AromaticityModel
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9 *AromaticityModelType*] [-a, --AtomIdentifierType
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10 *AtomicInvariantsAtomTypes*] [--AtomicInvariantsToUse
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11 *"AtomicInvariant,AtomicInvariant..."*] [--FunctionalClassesToUse
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12 *"FunctionalClass1,FunctionalClass2..."*] [--CompoundID *DataFieldName
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13 or LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode]
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14 [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode
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15 *All | Common | Specify | CompoundID*] [-f, --Filter *Yes | No*]
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16 [--FingerprintsLabel *text*] [-h, --help] [-k, --KeepLargestComponent
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17 *Yes | No*] [--MinDistance *number*] [--MaxDistance *number*]
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18 [--OutDelim *comma | tab | semicolon*] [--output *SD | FP | text | all*]
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19 [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root *RootName*] [-v,
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20 --VectorStringFormat *ValuesString, IDsAndValuesString |
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21 IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*]
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22 [-w, --WorkingDir dirname] SDFile(s)...
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23
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24 DESCRIPTION
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25 Generate topological atom pairs fingerprints [ Ref 57, Ref 59, Ref 72 ]
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26 for *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s)
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27 containing fingerprints vector strings corresponding to molecular
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28 fingerprints.
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29
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30 Multiple SDFile names are separated by spaces. The valid file extensions
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31 are *.sdf* and *.sd*. All other file names are ignored. All the SD files
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32 in a current directory can be specified either by **.sdf* or the current
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33 directory name.
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34
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35 The current release of MayaChemTools supports generation of topological
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36 atom pairs corresponding to following -a, --AtomIdentifierTypes:
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37
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38 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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39 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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40 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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41
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42 Based on the values specified for -a, --AtomIdentifierType and
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43 --AtomicInvariantsToUse, initial atom types are assigned to all
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44 non-hydrogen atoms in a molecule. Using the distance matrix for the
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45 molecule and initial atom types assigned to non-hydrogen atoms, all
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46 unique atom pairs within --MinDistance and --MaxDistance are identified
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47 and counted. An atom pair identifier is generated for each unique atom
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48 pair; the format of the atom pair identifier is:
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49
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50 <AtomType1>-D<n>-<AtomType2>
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51
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52 AtomType1, AtomType2: Atom types assigned to atom1 and atom2
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53 D: Distance between atom1 and atom2
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54
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55 where AtomType1 <= AtomType2
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56
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57 The atom pair identifiers for all unique atom pairs corresponding to
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58 non-hydrogen atoms constitute topological atom pairs fingerprints of the
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59 molecule.
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60
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61 Example of *SD* file containing topological atom pairs fingerprints
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62 string data:
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63
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64 ... ...
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65 ... ...
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66 $$$$
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67 ... ...
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68 ... ...
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69 ... ...
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70 41 44 0 0 0 0 0 0 0 0999 V2000
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71 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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72 ... ...
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73 2 3 1 0 0 0 0
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74 ... ...
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75 M END
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76 > <CmpdID>
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77 Cmpd1
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78
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79 > <TopologicalAtomPairsFingerprints>
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80 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi
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81 stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H
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82 3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.H1
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83 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-C.X2...;
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84 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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85 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
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86
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87 $$$$
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88 ... ...
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89 ... ...
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90
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91 Example of *FP* file containing topological atom pairs fingerprints
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92 string data:
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93
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94 #
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95 # Package = MayaChemTools 7.4
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96 # Release Date = Oct 21, 2010
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97 #
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98 # TimeStamp = Fri Mar 11 15:04:36 2011
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99 #
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100 # FingerprintsStringType = FingerprintsVector
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101 #
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102 # Description = TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi...
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103 # VectorStringFormat = IDsAndValuesString
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104 # VectorValuesType = NumericalValues
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105 #
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106 Cmpd1 223;C.X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2...;1 1...
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107 Cmpd2 128;C.X1.BO1.H3-D1-C.X2.BO2.H2 C.X1.BO1.H3-D1-C.X3.BO4...;1 1...
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108 ... ...
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109 ... ..
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110
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111 Example of CSV *Text* file containing topological atom pairs
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112 fingerprints string data:
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113
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114 "CompoundID","TopologicalAtomPairsFingerprints"
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115 "Cmpd1","FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTy
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116 pes:MinDistance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C
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117 .X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X
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118 3.BO3.H1C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1...;
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119 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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120 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
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121 ... ...
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122 ... ...
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123
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124 The current release of MayaChemTools generates the following types of
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125 topological atom pairs fingerprints vector strings:
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126
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127 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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128 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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129 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
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130 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
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131 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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132 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
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133
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134 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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135 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
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136 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
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137 C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
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138 .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
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139 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...
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140
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141 FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
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142 :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D
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143 1-C_R C_2-D1-N_3 C_2-D1-O_2 C_2-D1-O_3 C_3-D1-C_3 C_3-D1-C_R C_3-D1-N_
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144 R C_3-D1-O_3 C_R-D1-C_R C_R-D1-F_ C_R-D1-N_3 C_R-D1-N_R C_2-D2-C_3 C_2
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145 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
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146 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...
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147
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148 FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
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149 axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH-
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150 D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH
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151 aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...;
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152 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
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153 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...
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154
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155 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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156 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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157 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
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158 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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159 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
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160 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
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161
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162 FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
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163 axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2
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164 C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1-
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165 CB 1 C=ON-D1-NC=O 1 C=ON-D1-O=CN 1 CB-D1-CB 18 CB-D1-F 1 CB-D1-NC=O 1
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166 COO-D1-CR 1 COO-D1-O=CO 1 COO-D1-OC=O 1 CR-D1-CR 7 CR-D1-N5 1 CR-D1-OR
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167 2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ...
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168
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169 FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
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170 xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1
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171 -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2
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172 C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D
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173 1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1
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174 C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3...
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175
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176 FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
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177 xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C
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178 .2-D1-C.ar 1 C.2-D1-N.am 1 C.2-D1-O.2 1 C.2-D1-O.co2 2 C.3-D1-C.3 7 C.
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179 3-D1-C.ar 1 C.3-D1-N.ar 1 C.3-D1-O.3 2 C.ar-D1-C.ar 23 C.ar-D1-F 1 C.a
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180 r-D1-N.am 1 C.ar-D1-N.ar 2 C.2-D2-C.3 1 C.2-D2-C.ar 3 C.3-D2-C.3 5 C.3
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181 -D2-C.ar 5 C.3-D2-N.ar 2 C.3-D2-O.3 4 C.3-D2-O.co2 2 C.ar-D2-C.ar 2...
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182
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183 FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
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184 Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7
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185 -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7-
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186 D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O
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187 4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4
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188 5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N...
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189
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190 FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
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191 istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2
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192 -D1-C_R 1 C_2-D1-N_3 1 C_2-D1-O_2 2 C_2-D1-O_3 1 C_3-D1-C_3 7 C_3-D1-C
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193 _R 1 C_3-D1-N_R 1 C_3-D1-O_3 2 C_R-D1-C_R 23 C_R-D1-F_ 1 C_R-D1-N_3 1
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194 C_R-D1-N_R 2 C_2-D2-C_3 1 C_2-D2-C_R 3 C_3-D2-C_3 5 C_3-D2-C_R 5 C_3-D
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195 2-N_R 2 C_3-D2-O_2 1 C_3-D2-O_3 5 C_R-D2-C_R 28 C_R-D2-F_ 2 C_R-D2-...
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196
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197 OPTIONS
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198 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
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199 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
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200 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
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201 MayaChemToolsAromaticityModel*
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202 Specify aromaticity model to use during detection of aromaticity.
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203 Possible values in the current release are: *MDLAromaticityModel,
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204 TriposAromaticityModel, MMFFAromaticityModel,
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205 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
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206 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
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207 value: *MayaChemToolsAromaticityModel*.
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208
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209 The supported aromaticity model names along with model specific
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210 control parameters are defined in AromaticityModelsData.csv, which
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211 is distributed with the current release and is available under
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212 lib/data directory. Molecule.pm module retrieves data from this file
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213 during class instantiation and makes it available to method
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214 DetectAromaticity for detecting aromaticity corresponding to a
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215 specific model.
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216
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217 -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes
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218 | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes |
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219 SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes*
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220 Specify atom identifier type to use for assignment of initial atom
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221 identifier to non-hydrogen atoms during calculation of topological
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222 atom pairs fingerprints. Possible values in the current release are:
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223 *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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224 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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225 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value:
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226 *AtomicInvariantsAtomTypes*.
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227
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228 --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."*
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229 This value is used during *AtomicInvariantsAtomTypes* value of a,
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230 --AtomIdentifierType option. It's a list of comma separated valid
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231 atomic invariant atom types.
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232
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233 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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234 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
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235
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236 The atomic invariants abbreviations correspond to:
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237
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238 AS = Atom symbol corresponding to element symbol
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239
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240 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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241 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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242 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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243 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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244 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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245 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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246 H<n> = Number of implicit and explicit hydrogens for atom
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247 Ar = Aromatic annotation indicating whether atom is aromatic
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248 RA = Ring atom annotation indicating whether atom is a ring
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249 FC<+n/-n> = Formal charge assigned to atom
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250 MN<n> = Mass number indicating isotope other than most abundant isotope
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251 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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252 3 (triplet)
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253
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254 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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255 corresponds to:
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256
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257 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
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258
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259 Except for AS which is a required atomic invariant in atom types,
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260 all other atomic invariants are optional. Atom type specification
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261 doesn't include atomic invariants with zero or undefined values.
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262
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263 In addition to usage of abbreviations for specifying atomic
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264 invariants, the following descriptive words are also allowed:
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265
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266 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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267 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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268 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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269 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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270 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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271 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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272 H : NumOfImplicitAndExplicitHydrogens
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273 Ar : Aromatic
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274 RA : RingAtom
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275 FC : FormalCharge
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276 MN : MassNumber
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277 SM : SpinMultiplicity
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278
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279 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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280 atomic invariant atom types.
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281
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282 --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."*
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283 This value is used during *FunctionalClassAtomTypes* value of a,
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284 --AtomIdentifierType option. It's a list of comma separated valid
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285 functional classes.
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286
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287 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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288 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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289 *HBD,HBA,PI,NI,Ar,Hal*.
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290
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291 The functional class abbreviations correspond to:
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292
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293 HBD: HydrogenBondDonor
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294 HBA: HydrogenBondAcceptor
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295 PI : PositivelyIonizable
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296 NI : NegativelyIonizable
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297 Ar : Aromatic
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298 Hal : Halogen
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299 H : Hydrophobic
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300 RA : RingAtom
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301 CA : ChainAtom
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302
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303 Functional class atom type specification for an atom corresponds to:
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304
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305 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
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306
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307 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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308 functional class atom types. It uses following definitions [ Ref
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309 60-61, Ref 65-66 ]:
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310
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311 HydrogenBondDonor: NH, NH2, OH
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312 HydrogenBondAcceptor: N[!H], O
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313 PositivelyIonizable: +, NH2
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314 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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315
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316 --CompoundID *DataFieldName or LabelPrefixString*
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317 This value is --CompoundIDMode specific and indicates how compound
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318 ID is generated.
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319
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320 For *DataField* value of --CompoundIDMode option, it corresponds to
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321 datafield label name whose value is used as compound ID; otherwise,
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322 it's a prefix string used for generating compound IDs like
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323 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
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324 IDs which look like Cmpd<Number>.
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325
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326 Examples for *DataField* value of --CompoundIDMode:
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327
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328 MolID
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329 ExtReg
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330
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331 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
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332 --CompoundIDMode:
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333
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334 Compound
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335
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336 The value specified above generates compound IDs which correspond to
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337 Compound<Number> instead of default value of Cmpd<Number>.
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338
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339 --CompoundIDLabel *text*
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340 Specify compound ID column label for CSV/TSV text file(s) used
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341 during *CompoundID* value of --DataFieldsMode option. Default value:
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342 *CompoundID*.
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343
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344 --CompoundIDMode *DataField | MolName | LabelPrefix |
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345 MolNameOrLabelPrefix*
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346 Specify how to generate compound IDs and write to FP or CSV/TSV text
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347 file(s) along with generated fingerprints for *FP | text | all*
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348 values of --output option: use a *SDFile(s)* datafield value; use
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349 molname line from *SDFile(s)*; generate a sequential ID with
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350 specific prefix; use combination of both MolName and LabelPrefix
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351 with usage of LabelPrefix values for empty molname lines.
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352
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353 Possible values: *DataField | MolName | LabelPrefix |
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354 MolNameOrLabelPrefix*. Default value: *LabelPrefix*.
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355
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356 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
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357 in *SDFile(s)* takes precedence over sequential compound IDs
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358 generated using *LabelPrefix* and only empty molname values are
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359 replaced with sequential compound IDs.
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360
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361 This is only used for *CompoundID* value of --DataFieldsMode option.
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362
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363 --DataFields *"FieldLabel1,FieldLabel2,..."*
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364 Comma delimited list of *SDFiles(s)* data fields to extract and
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|
365 write to CSV/TSV text file(s) along with generated fingerprints for
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366 *text | both* values of --output option.
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367
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368 This is only used for *Specify* value of --DataFieldsMode option.
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369
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370 Examples:
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371
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372 Extreg
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373 MolID,CompoundName
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374
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375 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
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376 Specify how data fields in *SDFile(s)* are transferred to output
|
|
|
377 CSV/TSV text file(s) along with generated fingerprints for *text |
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378 both* values of --output option: transfer all SD data field;
|
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|
379 transfer SD data files common to all compounds; extract specified
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380 data fields; generate a compound ID using molname line, a compound
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381 prefix, or a combination of both. Possible values: *All | Common |
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|
382 specify | CompoundID*. Default value: *CompoundID*.
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383
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384 -f, --Filter *Yes | No*
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385 Specify whether to check and filter compound data in SDFile(s).
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|
386 Possible values: *Yes or No*. Default value: *Yes*.
|
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387
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388 By default, compound data is checked before calculating fingerprints
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|
|
389 and compounds containing atom data corresponding to non-element
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|
390 symbols or no atom data are ignored.
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391
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392 --FingerprintsLabel *text*
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|
|
393 SD data label or text file column label to use for fingerprints
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|
394 string in output SD or CSV/TSV text file(s) specified by --output.
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|
|
395 Default value: *TopologicalAtomPairsFingerprints*.
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396
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397 -h, --help
|
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|
398 Print this help message.
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|
|
399
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|
|
400 -k, --KeepLargestComponent *Yes | No*
|
|
|
401 Generate fingerprints for only the largest component in molecule.
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|
|
402 Possible values: *Yes or No*. Default value: *Yes*.
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|
403
|
|
|
404 For molecules containing multiple connected components, fingerprints
|
|
|
405 can be generated in two different ways: use all connected components
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|
|
406 or just the largest connected component. By default, all atoms
|
|
|
407 except for the largest connected component are deleted before
|
|
|
408 generation of fingerprints.
|
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|
409
|
|
|
410 --MinDistance *number*
|
|
|
411 Minimum bond distance between atom pairs for generating topological
|
|
|
412 atom pairs. Default value: *1*. Valid values: positive integers and
|
|
|
413 less than --MaxDistance.
|
|
|
414
|
|
|
415 --MaxDistance *number*
|
|
|
416 Maximum bond distance between atom pairs for generating topological
|
|
|
417 atom pairs. Default value: *10*. Valid values: positive integers and
|
|
|
418 greater than --MinDistance.
|
|
|
419
|
|
|
420 --OutDelim *comma | tab | semicolon*
|
|
|
421 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
|
|
|
422 tab, or semicolon* Default value: *comma*
|
|
|
423
|
|
|
424 --output *SD | FP | text | all*
|
|
|
425 Type of output files to generate. Possible values: *SD, FP, text, or
|
|
|
426 all*. Default value: *text*.
|
|
|
427
|
|
|
428 -o, --overwrite
|
|
|
429 Overwrite existing files.
|
|
|
430
|
|
|
431 -q, --quote *Yes | No*
|
|
|
432 Put quote around column values in output CSV/TSV text file(s).
|
|
|
433 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
434
|
|
|
435 -r, --root *RootName*
|
|
|
436 New file name is generated using the root: <Root>.<Ext>. Default for
|
|
|
437 new file names: <SDFileName><TopologicalAtomPairsFP>.<Ext>. The file
|
|
|
438 type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values
|
|
|
439 are used for SD, FP, comma/semicolon, and tab delimited text files,
|
|
|
440 respectively.This option is ignored for multiple input files.
|
|
|
441
|
|
|
442 -v, --VectorStringFormat *IDsAndValuesString | IDsAndValuesPairsString |
|
|
|
443 ValuesAndIDsString | ValuesAndIDsPairsString*
|
|
|
444 Format of fingerprints vector string data in output SD, FP or
|
|
|
445 CSV/TSV text file(s) specified by --output option. Possible values:
|
|
|
446 *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
447 ValuesAndIDsPairsString*. Default value: *IDsAndValuesString*.
|
|
|
448
|
|
|
449 Examples:
|
|
|
450
|
|
|
451 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
452 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
453 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
|
|
|
454 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
|
|
|
455 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
456 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
|
|
|
457
|
|
|
458 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
459 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
|
|
|
460 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
|
|
|
461 C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
|
|
|
462 .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
|
|
|
463 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...
|
|
|
464
|
|
|
465 -w, --WorkingDir *DirName*
|
|
|
466 Location of working directory. Default value: current directory.
|
|
|
467
|
|
|
468 EXAMPLES
|
|
|
469 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
470 distances from 1 through 10 using atomic invariants atom types in
|
|
|
471 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
472 sequential compound IDs along with fingerprints vector strings data,
|
|
|
473 type:
|
|
|
474
|
|
|
475 % TopologicalAtomPairsFingerprints.pl -r SampleTAPFP -o Sample.sdf
|
|
|
476
|
|
|
477 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
478 distances from 1 through 10 using atomic invariants atom types in
|
|
|
479 IDsAndValuesString format and create SampleTAPFP.sdf, SampleTAPFP.fpf
|
|
|
480 and SampleTAPFP.csv files containing sequential compound IDs in CSV file
|
|
|
481 along with fingerprints vector strings data, type:
|
|
|
482
|
|
|
483 % TopologicalAtomPairsFingerprints.pl --output all -r SampleTAPFP
|
|
|
484 -o Sample.sdf
|
|
|
485
|
|
|
486 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
487 distances from 1 through 10 using DREIDING atom types in
|
|
|
488 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
489 sequential compound IDs along with fingerprints vector strings data,
|
|
|
490 type:
|
|
|
491
|
|
|
492 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
493 -r SampleTAPFP -o Sample.sdf
|
|
|
494
|
|
|
495 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
496 distances from 1 through 10 using E-state types in IDsAndValuesString
|
|
|
497 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
498 IDs along with fingerprints vector strings data, type:
|
|
|
499
|
|
|
500 % TopologicalAtomPairsFingerprints.pl -a EStateAtomTypes
|
|
|
501 -r SampleTAPFP -o Sample.sdf
|
|
|
502
|
|
|
503 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
504 distances from 1 through 10 using DREIDING atom types in
|
|
|
505 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
506 sequential compound IDs along with fingerprints vector strings data,
|
|
|
507 type:
|
|
|
508
|
|
|
509 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
510 -r SampleTAPFP -o Sample.sdf
|
|
|
511
|
|
|
512 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
513 distances from 1 through 10 using functional class atom types in
|
|
|
514 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
515 sequential compound IDs along with fingerprints vector strings data,
|
|
|
516 type:
|
|
|
517
|
|
|
518 % TopologicalAtomPairsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
519 -r SampleTAPFP -o Sample.sdf
|
|
|
520
|
|
|
521 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
522 distances from 1 through 10 using MMFF94 atom types in
|
|
|
523 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
524 sequential compound IDs along with fingerprints vector strings data,
|
|
|
525 type:
|
|
|
526
|
|
|
527 % TopologicalAtomPairsFingerprints.pl -a MMFF94AtomTypes
|
|
|
528 -r SampleTAPFP -o Sample.sdf
|
|
|
529
|
|
|
530 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
531 distances from 1 through 10 using SLogP atom types in IDsAndValuesString
|
|
|
532 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
533 IDs along with fingerprints vector strings data, type:
|
|
|
534
|
|
|
535 % TopologicalAtomPairsFingerprints.pl -a SLogPAtomTypes
|
|
|
536 -r SampleTAPFP -o Sample.sdf
|
|
|
537
|
|
|
538 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
539 distances from 1 through 10 using SYBYL atom types in IDsAndValuesString
|
|
|
540 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
541 IDs along with fingerprints vector strings data, type:
|
|
|
542
|
|
|
543 % TopologicalAtomPairsFingerprints.pl -a SYBYLAtomTypes
|
|
|
544 -r SampleTAPFP -o Sample.sdf
|
|
|
545
|
|
|
546 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
547 distances from 1 through 10 using TPSA atom types in IDsAndValuesString
|
|
|
548 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
549 IDs along with fingerprints vector strings data, type:
|
|
|
550
|
|
|
551 % TopologicalAtomPairsFingerprints.pl -a TPSAAtomTypes
|
|
|
552 -r SampleTAPFP -o Sample.sdf
|
|
|
553
|
|
|
554 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
555 distances from 1 through 10 using UFF atom types in IDsAndValuesString
|
|
|
556 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
557 IDs along with fingerprints vector strings data, type:
|
|
|
558
|
|
|
559 % TopologicalAtomPairsFingerprints.pl -a UFFAtomTypes
|
|
|
560 -r SampleTAPFP -o Sample.sdf
|
|
|
561
|
|
|
562 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
563 distances from 1 through 10 using atomic invariants atom types in
|
|
|
564 IDsAndValuesPairsString format and create a SampleTAPFP.csv file
|
|
|
565 containing sequential compound IDs along with fingerprints vector
|
|
|
566 strings data, type:
|
|
|
567
|
|
|
568 % TopologicalAtomPairsFingerprints.pl --VectorStringFormat
|
|
|
569 IDsAndValuesPairsString -r SampleTAPFP -o Sample.sdf
|
|
|
570
|
|
|
571 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
572 distances from 1 through 6 using atomic invariants atom types in
|
|
|
573 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
574 sequential compound IDs along with fingerprints vector strings data,
|
|
|
575 type:
|
|
|
576
|
|
|
577 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
578 --MinDistance 1 --MaxDistance 6 -r SampleTAPFP -o Sample.sdf
|
|
|
579
|
|
|
580 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
581 distances from 1 through 10 using only AS,X atomic invariants atom types
|
|
|
582 in IDsAndValuesString format and create a SampleTAPFP.csv file
|
|
|
583 containing sequential compound IDs along with fingerprints vector
|
|
|
584 strings data, type:
|
|
|
585
|
|
|
586 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
587 --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6
|
|
|
588 -r SampleTAPFP -o Sample.sdf
|
|
|
589
|
|
|
590 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
591 distances from 1 through 10 using atomic invariants atom types in
|
|
|
592 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
593 compound ID from molecule name line along with fingerprints vector
|
|
|
594 strings data, type:
|
|
|
595
|
|
|
596 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
597 --DataFieldsMode CompoundID -CompoundIDMode MolName
|
|
|
598 -r SampleTAPFP -o Sample.sdf
|
|
|
599
|
|
|
600 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
601 distances from 1 through 10 using atomic invariants atom types in
|
|
|
602 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
603 compound IDs using specified data field along with fingerprints vector
|
|
|
604 strings data, type:
|
|
|
605
|
|
|
606 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
607 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
|
|
|
608 Mol_ID -r SampleTAPFP -o Sample.sdf
|
|
|
609
|
|
|
610 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
611 distances from 1 through 10 using atomic invariants atom types in
|
|
|
612 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
613 compound ID using combination of molecule name line and an explicit
|
|
|
614 compound prefix along with fingerprints vector strings data, type:
|
|
|
615
|
|
|
616 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
617 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
|
|
|
618 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTAPFP -o Sample.sdf
|
|
|
619
|
|
|
620 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
621 distances from 1 through 10 using atomic invariants atom types in
|
|
|
622 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
623 specific data fields columns along with fingerprints vector strings
|
|
|
624 data, type:
|
|
|
625
|
|
|
626 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
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627 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTAPFP
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628 -o Sample.sdf
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629
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630 To generate topological atom pairs fingerprints corresponding to bond
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631 distances from 1 through 10 using atomic invariants atom types in
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632 IDsAndValuesString format and create a SampleTAPFP.csv file containing
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633 common data fields columns along with fingerprints vector strings data,
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634 type:
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635
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636 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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637 --DataFieldsMode Common -r SampleTAPFP -o Sample.sdf
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638
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639 To generate topological atom pairs fingerprints corresponding to bond
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640 distances from 1 through 10 using atomic invariants atom types in
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641 IDsAndValuesString format and create SampleTAPFP.sdf, SampleTAPFP.fpf
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642 and SampleTAPFP.csv files containing all data fields columns in CSV file
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643 along with fingerprints data, type:
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644
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645 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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646 --DataFieldsMode All --output all -r SampleTAPFP
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647 -o Sample.sdf
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648
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649 AUTHOR
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650 Manish Sud <msud@san.rr.com>
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651
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652 SEE ALSO
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653 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
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654 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
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655 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
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656 TopologicalAtomTorsionsFingerprints.pl,
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657 TopologicalPharmacophoreAtomPairsFingerprints.pl,
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658 TopologicalPharmacophoreAtomTripletsFingerprints.pl
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659
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660 COPYRIGHT
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661 Copyright (C) 2015 Manish Sud. All rights reserved.
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662
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663 This file is part of MayaChemTools.
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664
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665 MayaChemTools is free software; you can redistribute it and/or modify it
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666 under the terms of the GNU Lesser General Public License as published by
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667 the Free Software Foundation; either version 3 of the License, or (at
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668 your option) any later version.
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669
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