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1 NAME
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2 TopologicalAtomTorsionsFingerprints.pl - Generate topological atom
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3 torsions fingerprints for SD files
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4
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5 SYNOPSIS
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6 TopologicalAtomTorsionsFingerprints.pl SDFile(s)...
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7
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8 TopologicalAtomTorsionsFingerprints.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*] [--OutDelim *comma | tab | semicolon*] [--output *SD | FP |
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18 text | all*] [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root
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19 *RootName*] [-v, --VectorStringFormat] [-w, --WorkingDir dirname]
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20 SDFile(s)...
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21
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22 DESCRIPTION
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23 Generate topological atom torsions fingerprints [ Ref 58, Ref 72 ] for
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24 *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s)
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25 containing fingerprints vector strings corresponding to molecular
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26 fingerprints.
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27
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28 Multiple SDFile names are separated by spaces. The valid file extensions
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29 are *.sdf* and *.sd*. All other file names are ignored. All the SD files
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30 in a current directory can be specified either by **.sdf* or the current
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31 directory name.
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32
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33 The current release of MayaChemTools supports generation of topological
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34 atom torsions fingerprints corresponding to following -a,
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35 --AtomIdentifierTypes:
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36
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37 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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38 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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39 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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40
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41 Based on the values specified for -a, --AtomIdentifierType and
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42 --AtomicInvariantsToUse, initial atom types are assigned to all
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43 non-hydrogen atoms in a molecule. All unique atom torsions are
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44 identified and an atom torsion identifier is generated; the format of
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45 atom torsion identifier is:
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46
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47 <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4>
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48
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49 AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types
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50
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51 where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4
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52
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53 The atom torsion identifiers for all unique atom torsions corresponding
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54 to non-hydrogen atoms constitute topological atom torsions fingerprints
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55 of the molecule.
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56
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57 Example of *SD* file containing topological atom torsions fingerprints
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58 string data:
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59
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60 ... ...
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61 ... ...
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62 $$$$
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63 ... ...
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64 ... ...
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65 ... ...
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66 41 44 0 0 0 0 0 0 0 0999 V2000
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67 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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68 ... ...
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69 2 3 1 0 0 0 0
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70 ... ...
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71 M END
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72 > <CmpdID>
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73 Cmpd1
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74
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75 > <TopologicalAtomTorsionsFingerprints>
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76 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33
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77 ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.
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78 X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO2.H
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79 2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O.X1....;
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80 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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81
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82 $$$$
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83 ... ...
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84 ... ...
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85
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86 Example of *FP* file containing topological atom torsions fingerprints
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87 string data:
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88
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89 #
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90 # Package = MayaChemTools 7.4
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91 # Release Date = Oct 21, 2010
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92 #
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93 # TimeStamp = Fri Mar 11 15:17:20 2011
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94 #
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95 # FingerprintsStringType = FingerprintsVector
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96 #
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97 # Description = TopologicalAtomTorsions:AtomicInvariantsAtomTypes
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98 # VectorStringFormat = IDsAndValuesString
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99 # VectorValuesType = NumericalValues
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100 #
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101 Cmpd1 33;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.X3.BO4...;2 2 1 1 2 2 ...
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102 Cmpd2 23;C.X1.BO1.H3-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2...;2 2 1 5 ...
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103 ... ...
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104 ... ..
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105
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106 Example of CSV *Text* file containing topological atom torsions
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107 fingerprints string data:
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108
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109 "CompoundID","TopologicalAtomTorsionsFingerprints"
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110 "Cmpd1","FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAto
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111 mTypes;33;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.
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112 X3.BO4-C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C
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113 .X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3....;
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114 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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115 ... ...
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116 ... ...
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117
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118 The current release of MayaChemTools generates the following types of
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119 topological atom torsions fingerprints vector strings:
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120
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121 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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122 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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123 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
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124 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
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125 ;2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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126
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127 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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128 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
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129 .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
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130 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
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131 O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
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132 O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...
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133
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134 FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
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135 calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C
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136 _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2
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137 C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...;
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138 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1
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139
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140 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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141 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
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142 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
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143 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
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144 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
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145
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146 FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
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147 ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar-
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148 Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar
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149 -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...;
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150 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3
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151
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152 FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
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153 lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5
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154 B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5
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155 A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...;
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156 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
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157 1 1 2 1 1 3 1 3
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158
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159 FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
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160 Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1
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161 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS
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162 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1
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163 C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20
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164 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...
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165
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166 FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
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167 Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2
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168 -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C.
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169 ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3
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170 -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C.
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171 ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ...
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172
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173 FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
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174 lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4
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175 None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None-
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176 None-None 44 None-None-None-O3 3 None-None-None-O4 5
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177
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178 FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
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179 lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C
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180 _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3
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181 -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C
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182 _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2
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183 C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-...
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184
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185 OPTIONS
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186 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
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187 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
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188 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
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189 MayaChemToolsAromaticityModel*
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190 Specify aromaticity model to use during detection of aromaticity.
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191 Possible values in the current release are: *MDLAromaticityModel,
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192 TriposAromaticityModel, MMFFAromaticityModel,
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193 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
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194 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
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195 value: *MayaChemToolsAromaticityModel*.
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196
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197 The supported aromaticity model names along with model specific
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198 control parameters are defined in AromaticityModelsData.csv, which
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199 is distributed with the current release and is available under
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200 lib/data directory. Molecule.pm module retrieves data from this file
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201 during class instantiation and makes it available to method
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202 DetectAromaticity for detecting aromaticity corresponding to a
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203 specific model.
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204
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205 -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes
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206 | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes |
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207 SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes*
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208 Specify atom identifier type to use for assignment of initial atom
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209 identifier to non-hydrogen atoms during calculation of topological
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210 atom torsions fingerprints. Possible values in the current release
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211 are: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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212 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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213 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value:
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214 *AtomicInvariantsAtomTypes*.
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215
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216 --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."*
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217 This value is used during *AtomicInvariantsAtomTypes* value of a,
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218 --AtomIdentifierType option. It's a list of comma separated valid
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219 atomic invariant atom types.
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220
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221 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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222 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
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223
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224 The atomic invariants abbreviations correspond to:
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225
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226 AS = Atom symbol corresponding to element symbol
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227
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228 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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229 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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230 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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231 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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232 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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233 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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234 H<n> = Number of implicit and explicit hydrogens for atom
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235 Ar = Aromatic annotation indicating whether atom is aromatic
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236 RA = Ring atom annotation indicating whether atom is a ring
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237 FC<+n/-n> = Formal charge assigned to atom
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238 MN<n> = Mass number indicating isotope other than most abundant isotope
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239 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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240 3 (triplet)
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241
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242 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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243 corresponds to:
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244
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245 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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246
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247 Except for AS which is a required atomic invariant in atom types,
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248 all other atomic invariants are optional. Atom type specification
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249 doesn't include atomic invariants with zero or undefined values.
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250
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251 In addition to usage of abbreviations for specifying atomic
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252 invariants, the following descriptive words are also allowed:
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253
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254 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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255 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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256 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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257 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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258 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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259 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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260 H : NumOfImplicitAndExplicitHydrogens
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261 Ar : Aromatic
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262 RA : RingAtom
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263 FC : FormalCharge
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264 MN : MassNumber
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265 SM : SpinMultiplicity
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266
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267 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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268 atomic invariant atom types.
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269
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270 --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."*
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271 This value is used during *FunctionalClassAtomTypes* value of a,
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272 --AtomIdentifierType option. It's a list of comma separated valid
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273 functional classes.
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274
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275 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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276 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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277 *HBD,HBA,PI,NI,Ar,Hal*.
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278
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279 The functional class abbreviations correspond to:
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280
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281 HBD: HydrogenBondDonor
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282 HBA: HydrogenBondAcceptor
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283 PI : PositivelyIonizable
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284 NI : NegativelyIonizable
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285 Ar : Aromatic
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286 Hal : Halogen
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287 H : Hydrophobic
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288 RA : RingAtom
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289 CA : ChainAtom
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290
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291 Functional class atom type specification for an atom corresponds to:
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292
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293 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
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294
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295 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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296 functional class atom types. It uses following definitions [ Ref
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297 60-61, Ref 65-66 ]:
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298
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299 HydrogenBondDonor: NH, NH2, OH
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300 HydrogenBondAcceptor: N[!H], O
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301 PositivelyIonizable: +, NH2
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302 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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303
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304 --CompoundID *DataFieldName or LabelPrefixString*
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305 This value is --CompoundIDMode specific and indicates how compound
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306 ID is generated.
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307
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308 For *DataField* value of --CompoundIDMode option, it corresponds to
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309 datafield label name whose value is used as compound ID; otherwise,
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310 it's a prefix string used for generating compound IDs like
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311 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
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312 IDs which look like Cmpd<Number>.
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313
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314 Examples for *DataField* value of --CompoundIDMode:
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315
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316 MolID
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317 ExtReg
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318
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319 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
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320 --CompoundIDMode:
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321
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322 Compound
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323
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324 The value specified above generates compound IDs which correspond to
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325 Compound<Number> instead of default value of Cmpd<Number>.
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326
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327 --CompoundIDLabel *text*
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328 Specify compound ID column label for CSV/TSV text file(s) used
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329 during *CompoundID* value of --DataFieldsMode option. Default value:
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330 *CompoundID*.
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331
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332 --CompoundIDMode *DataField | MolName | LabelPrefix |
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333 MolNameOrLabelPrefix*
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334 Specify how to generate compound IDs and write to FP or CSV/TSV text
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335 file(s) along with generated fingerprints for *FP | text | all*
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336 values of --output option: use a *SDFile(s)* datafield value; use
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337 molname line from *SDFile(s)*; generate a sequential ID with
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338 specific prefix; use combination of both MolName and LabelPrefix
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339 with usage of LabelPrefix values for empty molname lines.
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340
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341 Possible values: *DataField | MolName | LabelPrefix |
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342 MolNameOrLabelPrefix*. Default value: *LabelPrefix*.
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343
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344 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
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345 in *SDFile(s)* takes precedence over sequential compound IDs
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346 generated using *LabelPrefix* and only empty molname values are
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347 replaced with sequential compound IDs.
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348
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349 This is only used for *CompoundID* value of --DataFieldsMode option.
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350
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351 --DataFields *"FieldLabel1,FieldLabel2,..."*
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352 Comma delimited list of *SDFiles(s)* data fields to extract and
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353 write to CSV/TSV text file(s) along with generated fingerprints for
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354 *text | all* values of --output option.
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355
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356 This is only used for *Specify* value of --DataFieldsMode option.
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357
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358 Examples:
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359
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360 Extreg
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361 MolID,CompoundName
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362
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363 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
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364 Specify how data fields in *SDFile(s)* are transferred to output
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365 CSV/TSV text file(s) along with generated fingerprints for *text |
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366 all* values of --output option: transfer all SD data field; transfer
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367 SD data files common to all compounds; extract specified data
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368 fields; generate a compound ID using molname line, a compound
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369 prefix, or a combination of both. Possible values: *All | Common |
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370 specify | CompoundID*. Default value: *CompoundID*.
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371
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372 -f, --Filter *Yes | No*
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373 Specify whether to check and filter compound data in SDFile(s).
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374 Possible values: *Yes or No*. Default value: *Yes*.
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375
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376 By default, compound data is checked before calculating fingerprints
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377 and compounds containing atom data corresponding to non-element
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378 symbols or no atom data are ignored.
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379
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380 --FingerprintsLabel *text*
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381 SD data label or text file column label to use for fingerprints
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382 string in output SD or CSV/TSV text file(s) specified by --output.
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383 Default value: *TopologicalAtomTorsionsFingerprints*.
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384
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385 -h, --help
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386 Print this help message.
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387
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388 -k, --KeepLargestComponent *Yes | No*
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389 Generate fingerprints for only the largest component in molecule.
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390 Possible values: *Yes or No*. Default value: *Yes*.
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391
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392 For molecules containing multiple connected components, fingerprints
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393 can be generated in two different ways: use all connected components
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394 or just the largest connected component. By default, all atoms
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395 except for the largest connected component are deleted before
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396 generation of fingerprints.
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397
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398 --OutDelim *comma | tab | semicolon*
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399 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
|
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|
400 tab, or semicolon* Default value: *comma*.
|
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|
401
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|
402 --output *SD | FP | text | all*
|
|
|
403 Type of output files to generate. Possible values: *SD, FP, text, or
|
|
|
404 all*. Default value: *text*.
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|
405
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|
|
406 -o, --overwrite
|
|
|
407 Overwrite existing files.
|
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|
408
|
|
|
409 -q, --quote *Yes | No*
|
|
|
410 Put quote around column values in output CSV/TSV text file(s).
|
|
|
411 Possible values: *Yes or No*. Default value: *Yes*
|
|
|
412
|
|
|
413 -r, --root *RootName*
|
|
|
414 New file name is generated using the root: <Root>.<Ext>. Default for
|
|
|
415 new file names: <SDFileName><TopologicalAtomTorsionsFP>.<Ext>. The
|
|
|
416 file type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext>
|
|
|
417 values are used for SD, FP, comma/semicolon, and tab delimited text
|
|
|
418 files, respectively.This option is ignored for multiple input files.
|
|
|
419
|
|
|
420 -v, --VectorStringFormat *IDsAndValuesString | IDsAndValuesPairsString |
|
|
|
421 ValuesAndIDsString | ValuesAndIDsPairsString*
|
|
|
422 Format of fingerprints vector string data in output SD, FP or
|
|
|
423 CSV/TSV text file(s) specified by --output option. Possible values:
|
|
|
424 *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
425 ValuesAndIDsPairsString*. Defaultvalue: *IDsAndValuesString*.
|
|
|
426
|
|
|
427 Examples:
|
|
|
428
|
|
|
429 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
430 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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|
|
431 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
|
|
|
432 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
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|
|
433 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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|
|
434
|
|
|
435 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
436 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
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|
|
437 .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
|
|
|
438 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
|
|
|
439 O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
|
|
|
440 O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...
|
|
|
441
|
|
|
442 -w, --WorkingDir *DirName*
|
|
|
443 Location of working directory. Default value: current directory.
|
|
|
444
|
|
|
445 EXAMPLES
|
|
|
446 To generate topological atom torsions fingerprints using atomic
|
|
|
447 invariants atom types in IDsAndValuesString format and create a
|
|
|
448 SampleTATFP.csv file containing sequential compound IDs along with
|
|
|
449 fingerprints vector strings data, type:
|
|
|
450
|
|
|
451 % TopologicalAtomTorsionsFingerprints.pl -r SampleTATFP -o Sample.sdf
|
|
|
452
|
|
|
453 To generate topological atom torsions fingerprints using atomic
|
|
|
454 invariants atom types in IDsAndValuesString format and create
|
|
|
455 SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv files containing
|
|
|
456 sequential compound IDs in CSV file along with fingerprints vector
|
|
|
457 strings data, type:
|
|
|
458
|
|
|
459 % TopologicalAtomTorsionsFingerprints.pl --output all -r SampleTATFP
|
|
|
460 -o Sample.sdf
|
|
|
461
|
|
|
462 To generate topological atom torsions fingerprints using atomic
|
|
|
463 invariants atom types in IDsAndValuesPairsString format and create a
|
|
|
464 SampleTATFP.csv file containing sequential compound IDs along with
|
|
|
465 fingerprints vector strings data, type:
|
|
|
466
|
|
|
467 % TopologicalAtomTorsionsFingerprints.pl --VectorStringFormat
|
|
|
468 IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf
|
|
|
469
|
|
|
470 To generate topological atom torsions fingerprints using DREIDING atom
|
|
|
471 types in IDsAndValuesString format and create a SampleTATFP.csv file
|
|
|
472 containing sequential compound IDs along with fingerprints vector
|
|
|
473 strings data, type:
|
|
|
474
|
|
|
475 % TopologicalAtomTorsionsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
476 -r SampleTATFP -o Sample.sdf
|
|
|
477
|
|
|
478 To generate topological atom torsions fingerprints using E-state atom
|
|
|
479 types in IDsAndValuesString format and create a SampleTATFP.csv file
|
|
|
480 containing sequential compound IDs along with fingerprints vector
|
|
|
481 strings data, type:
|
|
|
482
|
|
|
483 % TopologicalAtomTorsionsFingerprints.pl -a EStateAtomTypes
|
|
|
484 -r SampleTATFP -o Sample.sdf
|
|
|
485
|
|
|
486 To generate topological atom torsions fingerprints using functional
|
|
|
487 class atom types in IDsAndValuesString format and create a
|
|
|
488 SampleTATFP.csv file containing sequential compound IDs along with
|
|
|
489 fingerprints vector strings data, type:
|
|
|
490
|
|
|
491 % TopologicalAtomTorsionsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
492 -r SampleTATFP -o Sample.sdf
|
|
|
493
|
|
|
494 To generate topological atom torsions fingerprints using MMFF94 atom
|
|
|
495 types in IDsAndValuesString format and create a SampleTATFP.csv file
|
|
|
496 containing sequential compound IDs along with fingerprints vector
|
|
|
497 strings data, type:
|
|
|
498
|
|
|
499 % TopologicalAtomTorsionsFingerprints.pl -a MMFF94AtomTypes
|
|
|
500 -r SampleTATFP -o Sample.sdf
|
|
|
501
|
|
|
502 To generate topological atom torsions fingerprints using SLogP atom
|
|
|
503 types in IDsAndValuesString format and create a SampleTATFP.csv file
|
|
|
504 containing sequential compound IDs along with fingerprints vector
|
|
|
505 strings data, type:
|
|
|
506
|
|
|
507 % TopologicalAtomTorsionsFingerprints.pl -a SLogPAtomTypes
|
|
|
508 -r SampleTATFP -o Sample.sdf
|
|
|
509
|
|
|
510 To generate topological atom torsions fingerprints using SYBYL atom
|
|
|
511 types in IDsAndValuesString format and create a SampleTATFP.csv file
|
|
|
512 containing sequential compound IDs along with fingerprints vector
|
|
|
513 strings data, type:
|
|
|
514
|
|
|
515 % TopologicalAtomTorsionsFingerprints.pl -a SYBYLAtomTypes
|
|
|
516 -r SampleTATFP -o Sample.sdf
|
|
|
517
|
|
|
518 To generate topological atom torsions fingerprints using TPSA atom types
|
|
|
519 in IDsAndValuesString format and create a SampleTATFP.csv file
|
|
|
520 containing sequential compound IDs along with fingerprints vector
|
|
|
521 strings data, type:
|
|
|
522
|
|
|
523 % TopologicalAtomTorsionsFingerprints.pl -a TPSAAtomTypes
|
|
|
524 -r SampleTATFP -o Sample.sdf
|
|
|
525
|
|
|
526 To generate topological atom torsions fingerprints using UFF atom types
|
|
|
527 in IDsAndValuesString format and create a SampleTATFP.csv file
|
|
|
528 containing sequential compound IDs along with fingerprints vector
|
|
|
529 strings data, type:
|
|
|
530
|
|
|
531 % TopologicalAtomTorsionsFingerprints.pl -a UFFAtomTypes
|
|
|
532 -r SampleTATFP -o Sample.sdf
|
|
|
533
|
|
|
534 To generate topological atom torsions fingerprints using only AS,X
|
|
|
535 atomic invariants atom types in IDsAndValuesString format and create a
|
|
|
536 SampleTATFP.csv file containing sequential compound IDs along with
|
|
|
537 fingerprints vector strings data, type:
|
|
|
538
|
|
|
539 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
540 --AtomicInvariantsToUse "AS,X" -r SampleTATFP -o Sample.sdf
|
|
|
541
|
|
|
542 To generate topological atom torsions fingerprints using atomic
|
|
|
543 invariants atom types in IDsAndValuesString format and create a
|
|
|
544 SampleTATFP.csv file containing compoundID from molecule name line along
|
|
|
545 with fingerprints vector strings, type:
|
|
|
546
|
|
|
547 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
548 --DataFieldsMode CompoundID -CompoundIDMode MolName
|
|
|
549 -r SampleTATFP -o Sample.sdf
|
|
|
550
|
|
|
551 To generate topological atom torsions fingerprints using atomic
|
|
|
552 invariants atom types in IDsAndValuesString format and create a
|
|
|
553 SampleTATFP.csv file containing compound IDs using specified data field
|
|
|
554 along with fingerprints vector strings, type:
|
|
|
555
|
|
|
556 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
557 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
|
|
|
558 Mol_ID -r SampleTATFP -o Sample.sdf
|
|
|
559
|
|
|
560 To generate topological atom torsions fingerprints using atomic
|
|
|
561 invariants atom types in IDsAndValuesString format and create a
|
|
|
562 SampleTATFP.csv file containing compound ID using combination of
|
|
|
563 molecule name line and an explicit compound prefix along with
|
|
|
564 fingerprints vector strings data, type:
|
|
|
565
|
|
|
566 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
567 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
|
|
|
568 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf
|
|
|
569
|
|
|
570 To generate topological atom torsions fingerprints using atomic
|
|
|
571 invariants atom types in IDsAndValuesString format and create a
|
|
|
572 SampleTATFP.csv file containing specific data fields columns along with
|
|
|
573 fingerprints vector strings, type:
|
|
|
574
|
|
|
575 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
576 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP
|
|
|
577 -o Sample.sdf
|
|
|
578
|
|
|
579 To generate topological atom torsions fingerprints using atomic
|
|
|
580 invariants atom types in IDsAndValuesString format and create a
|
|
|
581 SampleTATFP.csv file containing common data fields columns along with
|
|
|
582 fingerprints vector strings, type:
|
|
|
583
|
|
|
584 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
585 --DataFieldsMode Common -r SampleTATFP -o Sample.sdf
|
|
|
586
|
|
|
587 To generate topological atom torsions fingerprints using atomic
|
|
|
588 invariants atom types in IDsAndValuesString format and create
|
|
|
589 SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv files containing
|
|
|
590 all data fields columns in CSV file along with fingerprints data, type:
|
|
|
591
|
|
|
592 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
593 --DataFieldsMode All --output all -r SampleTATFP
|
|
|
594 -o Sample.sdf
|
|
|
595
|
|
|
596 AUTHOR
|
|
|
597 Manish Sud <msud@san.rr.com>
|
|
|
598
|
|
|
599 SEE ALSO
|
|
|
600 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
|
|
|
601 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
|
|
|
602 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
603 TopologicalAtomPairsFingerprints.pl,
|
|
|
604 TopologicalPharmacophoreAtomPairsFingerprints.pl,
|
|
|
605 TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
606
|
|
|
607 COPYRIGHT
|
|
|
608 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
609
|
|
|
610 This file is part of MayaChemTools.
|
|
|
611
|
|
|
612 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
613 under the terms of the GNU Lesser General Public License as published by
|
|
|
614 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
615 your option) any later version.
|
|
|
616
|
