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1 NAME
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2 TopologicalAtomTripletsFingerprints.pl - Generate topological atom
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3 triplets fingerprints for SD files
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4
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5 SYNOPSIS
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6 TopologicalAtomTripletsFingerprints.pl SDFile(s)...
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7
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8 TopologicalAtomTripletsFingerprints.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*] [-u,
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20 --UseTriangleInequality *Yes | No*] [-v, --VectorStringFormat
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21 *ValuesString, IDsAndValuesString | IDsAndValuesPairsString |
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22 ValuesAndIDsString | ValuesAndIDsPairsString*] [-w, --WorkingDir
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23 dirname] SDFile(s)...
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24
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25 DESCRIPTION
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26 Generate topological atom triplets fingerprints for *SDFile(s)* and
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27 create appropriate SD, FP or CSV/TSV text file(s) containing
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28 fingerprints vector strings corresponding to molecular 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 triplets fingerprints corresponding to following -a,
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37 --AtomIdentifierTypes:
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38
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39 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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40 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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41 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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42
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43 Based on the values specified for -a, --AtomIdentifierType and
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44 --AtomicInvariantsToUse, initial atom types are assigned to all
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45 non-hydrogen atoms in a molecule. Using the distance matrix for the
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46 molecule and initial atom types assigned to non-hydrogen atoms, all
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47 unique atom pairs within --MinDistance and --MaxDistance are identified
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48 and counted. An atom triplet identifier is generated for each unique
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49 atom triplet; the format of the atom triplet identifier is:
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50
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51 <ATx>-Dyz-<ATy>-Dxz-<ATz>-Dxy
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52
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53 ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
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54 Dxy: Distance between atom x and atom y
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55 Dxz: Distance between atom x and atom z
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56 Dyz: Distance between atom y and atom z
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57
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58 where <AT1>-D23 <= <AT2>-D13 <= <AT3>-D12
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59
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60 The atom triplet identifiers for all unique atom triplets corresponding
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61 to non-hydrogen atoms constitute topological atom triplets fingerprints
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62 of the molecule.
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63
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64 Example of *SD* file containing topological atom triplets fingerprints
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65 string data:
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66
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67 ... ...
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68 ... ...
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69 $$$$
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70 ... ...
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71 ... ...
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72 ... ...
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73 41 44 0 0 0 0 0 0 0 0999 V2000
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74 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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75 ... ...
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76 2 3 1 0 0 0 0
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77 ... ...
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78 M END
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79 > <CmpdID>
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80 Cmpd1
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81
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82 > <TopologicalAtomTripletsFingerprints>
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83 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi
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84 nDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1.B
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85 O1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D10-C
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86 .X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1...;
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87 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
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88 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...
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89
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90 $$$$
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91 ... ...
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92 ... ...
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93
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94 Example of *FP* file containing topological atom triplets fingerprints
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95 string data:
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96
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97 #
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98 # Package = MayaChemTools 7.4
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99 # Release Date = Oct 21, 2010
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100 #
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101 # TimeStamp = Fri Mar 11 15:24:01 2011
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102 #
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103 # FingerprintsStringType = FingerprintsVector
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104 #
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105 # Description = TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi...
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106 # VectorStringFormat = IDsAndValuesString
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107 # VectorValuesType = NumericalValues
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108 #
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109 Cmpd1 3096;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2...;1 2 2 2 2...
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110 Cmpd2 1093;C.X1.BO1.H3-D1-C.X1.BO1.H3-D3-C.X2.BO2.H2-D4...;2 2 2 2 2...
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111 ... ...
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112 ... ..
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113
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114 Example of CSV *Text* file containing topological atom triplets
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115 fingerprints string data:
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116
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117 "CompoundID","TopologicalAtomTripletsFingerprints"
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118 "Cmpd1","FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAto
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119 mTypes:MinDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesStri
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120 ng;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2
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121 .H2-D10-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1....;
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122 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
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123 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...
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124 ... ...
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125 ... ...
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126
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127 The current release of MayaChemTools generates the following types of
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128 topological atom triplets fingerprints vector strings:
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129
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130 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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131 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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132 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
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133 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
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134 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
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135 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
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136 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
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137
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138 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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139 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
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140 ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO
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141 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X
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142 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2
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143 -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...
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144
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145 FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
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146 ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D
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147 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_
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148 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_
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149 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...;
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150 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
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151 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...
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152
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153 FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
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154 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D
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155 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC
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156 H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1-
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157 aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...;
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158 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
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159 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
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160 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...
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161
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162 FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
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163 nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1
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164 -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal
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165 -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar
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166 -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...;
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167 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
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168 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
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169 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...
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170
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171 FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
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172 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1-
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173 N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A
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174 -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B
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175 -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3-
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176 O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-...
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177
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178 FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
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179 :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11
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180 -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D
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181 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C
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182 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1
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183 -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS...
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184
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185 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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186 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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187 .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
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188 D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
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189 -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
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190 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...
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191
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192 FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
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193 MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non
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194 e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D
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195 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5
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196 N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21-
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197 D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-...
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198
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199 FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
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200 axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3
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201 -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9
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202 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1-
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203 C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5-
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204 C_3-D6 C_2-D1-C_3-D5-O_3-D4 C_2-D1-C_3-D6-C_3-D7 C_2-D1-C_3-D7-C_3-...
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205
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206 OPTIONS
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207 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
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208 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
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209 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
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210 MayaChemToolsAromaticityModel*
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211 Specify aromaticity model to use during detection of aromaticity.
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212 Possible values in the current release are: *MDLAromaticityModel,
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213 TriposAromaticityModel, MMFFAromaticityModel,
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214 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
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215 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
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216 value: *MayaChemToolsAromaticityModel*.
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217
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218 The supported aromaticity model names along with model specific
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219 control parameters are defined in AromaticityModelsData.csv, which
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220 is distributed with the current release and is available under
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221 lib/data directory. Molecule.pm module retrieves data from this file
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222 during class instantiation and makes it available to method
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223 DetectAromaticity for detecting aromaticity corresponding to a
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224 specific model.
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225
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226 -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes
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227 | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes |
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228 SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes*
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229 Specify atom identifier type to use for assignment of initial atom
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230 identifier to non-hydrogen atoms during calculation of topological
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231 atom triplets fingerprints. Possible values in the current release
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232 are: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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233 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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234 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value:
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235 *AtomicInvariantsAtomTypes*.
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236
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237 --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."*
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238 This value is used during *AtomicInvariantsAtomTypes* value of a,
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239 --AtomIdentifierType option. It's a list of comma separated valid
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240 atomic invariant atom types.
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241
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242 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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243 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
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244
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245 The atomic invariants abbreviations correspond to:
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246
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247 AS = Atom symbol corresponding to element symbol
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248
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249 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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250 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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251 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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252 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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253 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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254 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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255 H<n> = Number of implicit and explicit hydrogens for atom
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256 Ar = Aromatic annotation indicating whether atom is aromatic
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257 RA = Ring atom annotation indicating whether atom is a ring
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258 FC<+n/-n> = Formal charge assigned to atom
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259 MN<n> = Mass number indicating isotope other than most abundant isotope
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260 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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261 3 (triplet)
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262
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263 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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264 corresponds to:
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265
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266 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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267
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268 Except for AS which is a required atomic invariant in atom types,
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269 all other atomic invariants are optional. Atom type specification
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270 doesn't include atomic invariants with zero or undefined values.
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271
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272 In addition to usage of abbreviations for specifying atomic
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273 invariants, the following descriptive words are also allowed:
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274
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275 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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276 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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277 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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278 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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279 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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280 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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281 H : NumOfImplicitAndExplicitHydrogens
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282 Ar : Aromatic
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283 RA : RingAtom
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284 FC : FormalCharge
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285 MN : MassNumber
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286 SM : SpinMultiplicity
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287
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288 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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289 atomic invariant atom types.
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290
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291 --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."*
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292 This value is used during *FunctionalClassAtomTypes* value of a,
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293 --AtomIdentifierType option. It's a list of comma separated valid
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294 functional classes.
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295
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296 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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297 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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298 *HBD,HBA,PI,NI,Ar,Hal*.
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299
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300 The functional class abbreviations correspond to:
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301
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302 HBD: HydrogenBondDonor
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303 HBA: HydrogenBondAcceptor
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304 PI : PositivelyIonizable
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305 NI : NegativelyIonizable
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306 Ar : Aromatic
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307 Hal : Halogen
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308 H : Hydrophobic
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309 RA : RingAtom
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310 CA : ChainAtom
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311
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312 Functional class atom type specification for an atom corresponds to:
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313
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314 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
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315
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316 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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317 functional class atom types. It uses following definitions [ Ref
|
|
|
318 60-61, Ref 65-66 ]:
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319
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320 HydrogenBondDonor: NH, NH2, OH
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|
321 HydrogenBondAcceptor: N[!H], O
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322 PositivelyIonizable: +, NH2
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323 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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324
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325 --CompoundID *DataFieldName or LabelPrefixString*
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326 This value is --CompoundIDMode specific and indicates how compound
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327 ID is generated.
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328
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329 For *DataField* value of --CompoundIDMode option, it corresponds to
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330 datafield label name whose value is used as compound ID; otherwise,
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331 it's a prefix string used for generating compound IDs like
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332 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
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333 IDs which look like Cmpd<Number>.
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334
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335 Examples for *DataField* value of --CompoundIDMode:
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336
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337 MolID
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338 ExtReg
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339
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340 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
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341 --CompoundIDMode:
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342
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343 Compound
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344
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345 The value specified above generates compound IDs which correspond to
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|
346 Compound<Number> instead of default value of Cmpd<Number>.
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347
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348 --CompoundIDLabel *text*
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|
349 Specify compound ID column label for CSV/TSV text file(s) used
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|
350 during *CompoundID* value of --DataFieldsMode option. Default value:
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351 *CompoundID*.
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352
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353 --CompoundIDMode *DataField | MolName | LabelPrefix |
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|
354 MolNameOrLabelPrefix*
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355 Specify how to generate compound IDs and write to FP or CSV/TSV text
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356 file(s) along with generated fingerprints for *FP | text | all*
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357 values of --output option: use a *SDFile(s)* datafield value; use
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358 molname line from *SDFile(s)*; generate a sequential ID with
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359 specific prefix; use combination of both MolName and LabelPrefix
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|
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360 with usage of LabelPrefix values for empty molname lines.
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361
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|
362 Possible values: *DataField | MolName | LabelPrefix |
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|
363 MolNameOrLabelPrefix*. Default value: *LabelPrefix*.
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364
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|
|
365 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
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|
366 in *SDFile(s)* takes precedence over sequential compound IDs
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|
|
367 generated using *LabelPrefix* and only empty molname values are
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|
368 replaced with sequential compound IDs.
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369
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370 This is only used for *CompoundID* value of --DataFieldsMode option.
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371
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|
372 --DataFields *"FieldLabel1,FieldLabel2,..."*
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|
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373 Comma delimited list of *SDFiles(s)* data fields to extract and
|
|
|
374 write to CSV/TSV text file(s) along with generated fingerprints for
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|
|
375 *text | all* values of --output option.
|
|
|
376
|
|
|
377 This is only used for *Specify* value of --DataFieldsMode option.
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|
|
378
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|
|
379 Examples:
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380
|
|
|
381 Extreg
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|
|
382 MolID,CompoundName
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|
|
383
|
|
|
384 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
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|
|
385 Specify how data fields in *SDFile(s)* are transferred to output
|
|
|
386 CSV/TSV text file(s) along with generated fingerprints for *text |
|
|
|
387 all* values of --output option: transfer all SD data field; transfer
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|
|
388 SD data files common to all compounds; extract specified data
|
|
|
389 fields; generate a compound ID using molname line, a compound
|
|
|
390 prefix, or a combination of both. Possible values: *All | Common |
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|
|
391 specify | CompoundID*. Default value: *CompoundID*.
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392
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|
|
393 -f, --Filter *Yes | No*
|
|
|
394 Specify whether to check and filter compound data in SDFile(s).
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|
|
395 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
396
|
|
|
397 By default, compound data is checked before calculating fingerprints
|
|
|
398 and compounds containing atom data corresponding to non-element
|
|
|
399 symbols or no atom data are ignored.
|
|
|
400
|
|
|
401 --FingerprintsLabel *text*
|
|
|
402 SD data label or text file column label to use for fingerprints
|
|
|
403 string in output SD or CSV/TSV text file(s) specified by --output.
|
|
|
404 Default value: *TopologicalAtomTripletsFingerprints*.
|
|
|
405
|
|
|
406 -h, --help
|
|
|
407 Print this help message.
|
|
|
408
|
|
|
409 -k, --KeepLargestComponent *Yes | No*
|
|
|
410 Generate fingerprints for only the largest component in molecule.
|
|
|
411 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
412
|
|
|
413 For molecules containing multiple connected components, fingerprints
|
|
|
414 can be generated in two different ways: use all connected components
|
|
|
415 or just the largest connected component. By default, all atoms
|
|
|
416 except for the largest connected component are deleted before
|
|
|
417 generation of fingerprints.
|
|
|
418
|
|
|
419 --MinDistance *number*
|
|
|
420 Minimum bond distance between atom triplets for generating
|
|
|
421 topological atom triplets. Default value: *1*. Valid values:
|
|
|
422 positive integers and less than --MaxDistance.
|
|
|
423
|
|
|
424 --MaxDistance *number*
|
|
|
425 Maximum bond distance between atom triplets for generating
|
|
|
426 topological atom triplets. Default value: *10*. Valid values:
|
|
|
427 positive integers and greater than --MinDistance.
|
|
|
428
|
|
|
429 --OutDelim *comma | tab | semicolon*
|
|
|
430 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
|
|
|
431 tab, or semicolon* Default value: *comma*
|
|
|
432
|
|
|
433 --output *SD | FP | text | all*
|
|
|
434 Type of output files to generate. Possible values: *SD, FP, text, or
|
|
|
435 all*. Default value: *text*.
|
|
|
436
|
|
|
437 -o, --overwrite
|
|
|
438 Overwrite existing files.
|
|
|
439
|
|
|
440 -q, --quote *Yes | No*
|
|
|
441 Put quote around column values in output CSV/TSV text file(s).
|
|
|
442 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
443
|
|
|
444 -r, --root *RootName*
|
|
|
445 New file name is generated using the root: <Root>.<Ext>. Default for
|
|
|
446 new file names: <SDFileName><TopologicalAtomTripletsFP>.<Ext>. The
|
|
|
447 file type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext>
|
|
|
448 values are used for SD, FP, comma/semicolon, and tab delimited text
|
|
|
449 files, respectively.This option is ignored for multiple input files.
|
|
|
450
|
|
|
451 -u, --UseTriangleInequality *Yes | No*
|
|
|
452 Specify whether to imply triangle distance inequality test to
|
|
|
453 distances between atom pairs in atom triplets during generation of
|
|
|
454 atom triplets generation. Possible values: *Yes or No*. Default
|
|
|
455 value: *No*.
|
|
|
456
|
|
|
457 Triangle distance inequality test implies that distance or binned
|
|
|
458 distance between any two atom pairs in an atom triplet must be less
|
|
|
459 than the sum of distances or binned distances between other two
|
|
|
460 atoms pairs and greater than the difference of their distances.
|
|
|
461
|
|
|
462 For atom triplet ATx-Dyz-ATy-Dxz-ATz-Dxy to satisfy triangle inequality:
|
|
|
463
|
|
|
464 Dyz > |Dxz - Dxy| and Dyz < Dxz + Dxy
|
|
|
465 Dxz > |Dyz - Dxy| and Dyz < Dyz + Dxy
|
|
|
466 Dxy > |Dyz - Dxz| and Dxy < Dyz + Dxz
|
|
|
467
|
|
|
468 -v, --VectorStringFormat *IDsAndValuesString | IDsAndValuesPairsString |
|
|
|
469 ValuesAndIDsString | ValuesAndIDsPairsString*
|
|
|
470 Format of fingerprints vector string data in output SD, FP or
|
|
|
471 CSV/TSV text file(s) specified by --output option. Possible values:
|
|
|
472 *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
473 ValuesAndIDsPairsString*. Default value: *IDsAndValuesString*.
|
|
|
474
|
|
|
475 Examples:
|
|
|
476
|
|
|
477 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
478 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
|
|
|
479 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
|
|
|
480 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
|
|
|
481 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
|
|
|
482 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
|
|
|
483 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
|
|
|
484
|
|
|
485 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
486 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
|
|
|
487 ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO
|
|
|
488 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X
|
|
|
489 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2
|
|
|
490 -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...
|
|
|
491
|
|
|
492 -w, --WorkingDir *DirName*
|
|
|
493 Location of working directory. Default value: current directory.
|
|
|
494
|
|
|
495 EXAMPLES
|
|
|
496 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
497 distances from 1 through 10 using atomic invariants atom types in
|
|
|
498 IDsAndValuesString format and create a SampleTATFP.csv file containing
|
|
|
499 sequential compound IDs along with fingerprints vector strings data,
|
|
|
500 type:
|
|
|
501
|
|
|
502 % TopologicalAtomTripletsFingerprints.pl -r SampleTATFP -o Sample.sdf
|
|
|
503
|
|
|
504 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
505 distances from 1 through 10 using atomic invariants atom types in
|
|
|
506 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf
|
|
|
507 and SampleTATFP.csv files containing sequential compound IDs in CSV file
|
|
|
508 along with fingerprints vector strings data, type:
|
|
|
509
|
|
|
510 % TopologicalAtomTripletsFingerprints.pl --output all -r SampleTATFP
|
|
|
511 -o Sample.sdf
|
|
|
512
|
|
|
513 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
514 distances from 1 through 10 using atomic invariants atom types in
|
|
|
515 IDsAndValuesPairsString format and create a SampleTATFP.csv file
|
|
|
516 containing sequential compound IDs along with fingerprints vector
|
|
|
517 strings data, type:
|
|
|
518
|
|
|
519 % TopologicalAtomTripletsFingerprints.pl --VectorStringFormat
|
|
|
520 IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf
|
|
|
521
|
|
|
522 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
523 distances from 1 through 10 using DREIDING atom types in
|
|
|
524 IDsAndValuesString format and create a SampleTATFP.csv file containing
|
|
|
525 sequential compound IDs along with fingerprints vector strings data,
|
|
|
526 type:
|
|
|
527
|
|
|
528 % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
529 -r SampleTATFP -o Sample.sdf
|
|
|
530
|
|
|
531 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
532 distances from 1 through 10 using E-state atom types in
|
|
|
533 IDsAndValuesString format and create a SampleTATFP.csv file containing
|
|
|
534 sequential compound IDs along with fingerprints vector strings data,
|
|
|
535 type:
|
|
|
536
|
|
|
537 % TopologicalAtomTripletsFingerprints.pl -a EStateAtomTypes
|
|
|
538 -r SampleTATFP -o Sample.sdf
|
|
|
539
|
|
|
540 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
541 distances from 1 through 10 using functional class atom types in
|
|
|
542 IDsAndValuesString format and create a SampleTATFP.csv file containing
|
|
|
543 sequential compound IDs along with fingerprints vector strings data,
|
|
|
544 type:
|
|
|
545
|
|
|
546 % TopologicalAtomTripletsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
547 -r SampleTATFP -o Sample.sdf
|
|
|
548
|
|
|
549 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
550 distances from 1 through 10 using DREIDING atom types in
|
|
|
551 IDsAndValuesString format and create a SampleTATFP.csv file containing
|
|
|
552 sequential compound IDs along with fingerprints vector strings data,
|
|
|
553 type:
|
|
|
554
|
|
|
555 % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
556 -r SampleTATFP -o Sample.sdf
|
|
|
557
|
|
|
558 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
559 distances from 1 through 10 using MM94 atom types in IDsAndValuesString
|
|
|
560 format and create a SampleTATFP.csv file containing sequential compound
|
|
|
561 IDs along with fingerprints vector strings data, type:
|
|
|
562
|
|
|
563 % TopologicalAtomTripletsFingerprints.pl -a MMFF94AtomTypes
|
|
|
564 -r SampleTATFP -o Sample.sdf
|
|
|
565
|
|
|
566 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
567 distances from 1 through 10 using SLogP atom types in IDsAndValuesString
|
|
|
568 format and create a SampleTATFP.csv file containing sequential compound
|
|
|
569 IDs along with fingerprints vector strings data, type:
|
|
|
570
|
|
|
571 % TopologicalAtomTripletsFingerprints.pl -a SLogPAtomTypes
|
|
|
572 -r SampleTATFP -o Sample.sdf
|
|
|
573
|
|
|
574 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
575 distances from 1 through 10 using SYBYL atom types in IDsAndValuesString
|
|
|
576 format and create a SampleTATFP.csv file containing sequential compound
|
|
|
577 IDs along with fingerprints vector strings data, type:
|
|
|
578
|
|
|
579 % TopologicalAtomTripletsFingerprints.pl -a SYBYLAtomTypes
|
|
|
580 -r SampleTATFP -o Sample.sdf
|
|
|
581
|
|
|
582 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
583 distances from 1 through 10 using TPSA atom types in IDsAndValuesString
|
|
|
584 format and create a SampleTATFP.csv file containing sequential compound
|
|
|
585 IDs along with fingerprints vector strings data, type:
|
|
|
586
|
|
|
587 % TopologicalAtomTripletsFingerprints.pl -a TPSAAtomTypes
|
|
|
588 -r SampleTATFP -o Sample.sdf
|
|
|
589
|
|
|
590 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
591 distances from 1 through 10 using UFF atom types in IDsAndValuesString
|
|
|
592 format and create a SampleTATFP.csv file containing sequential compound
|
|
|
593 IDs along with fingerprints vector strings data, type:
|
|
|
594
|
|
|
595 % TopologicalAtomTripletsFingerprints.pl -a UFFAtomTypes
|
|
|
596 -r SampleTATFP -o Sample.sdf
|
|
|
597
|
|
|
598 To generate topological atom triplets fingerprints corresponding to bond
|
|
|
599 distances from 1 through 6 using atomic invariants atom types in
|
|
|
600 IDsAndValuesString format and create a SampleTATFP.csv file containing
|
|
|
601 sequential compound IDs along with fingerprints vector strings data,
|
|
|
602 type:
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603
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604 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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605 --MinDistance 1 --MaxDistance 6 -r SampleTATFP -o Sample.sdf
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606
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607 To generate topological atom triplets fingerprints corresponding to bond
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608 distances from 1 through 10 using only AS,X atomic invariants atom types
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609 in IDsAndValuesString format and create a SampleTATFP.csv file
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610 containing sequential compound IDs along with fingerprints vector
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611 strings data, type:
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612
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613 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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614 --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6
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615 -r SampleTATFP -o Sample.sdf
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616
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617 To generate topological atom triplets fingerprints corresponding to bond
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618 distances from 1 through 10 using atomic invariants atom types in
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619 IDsAndValuesString format and create a SampleTATFP.csv file containing
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620 compound ID from molecule name line along with fingerprints vector
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621 strings data, type:
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622
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623 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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624 --DataFieldsMode CompoundID -CompoundIDMode MolName
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625 -r SampleTATFP -o Sample.sdf
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626
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627 To generate topological atom triplets fingerprints corresponding to bond
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628 distances from 1 through 10 using atomic invariants atom types in
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629 IDsAndValuesString format and create a SampleTATFP.csv file containing
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630 compound IDs using specified data field along with fingerprints vector
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631 strings data, type:
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632
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633 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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634 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
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635 Mol_ID -r SampleTATFP -o Sample.sdf
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636
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637 To generate topological atom triplets fingerprints corresponding to bond
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638 distances from 1 through 10 using atomic invariants atom types in
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639 IDsAndValuesString format and create a SampleTATFP.csv file containing
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640 compound ID using combination of molecule name line and an explicit
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641 compound prefix along with fingerprints vector strings data, type:
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642
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643 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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644 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
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645 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf
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646
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647 To generate topological atom triplets fingerprints corresponding to bond
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648 distances from 1 through 10 using atomic invariants atom types in
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649 IDsAndValuesString format and create a SampleTATFP.csv file containing
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650 specific data fields columns along with fingerprints vector strings
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651 data, type:
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652
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653 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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654 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP
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655 -o Sample.sdf
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656
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657 To generate topological atom triplets fingerprints corresponding to bond
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658 distances from 1 through 10 using atomic invariants atom types in
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659 IDsAndValuesString format and create a SampleTATFP.csv file containing
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660 common data fields columns along with fingerprints vector strings data,
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661 type:
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662
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663 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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664 --DataFieldsMode Common -r SampleTATFP -o Sample.sdf
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665
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666 To generate topological atom triplets fingerprints corresponding to bond
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667 distances from 1 through 10 using atomic invariants atom types in
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668 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf
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669 and SampleTATFP.csv files containing all data fields columns in CSV file
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670 along with fingerprints data, type:
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671
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672 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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673 --DataFieldsMode All --output all -r SampleTATFP
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674 -o Sample.sdf
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675
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676 AUTHOR
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677 Manish Sud <msud@san.rr.com>
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678
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679 SEE ALSO
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680 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
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681 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
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682 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
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683 TopologicalAtomTorsionsFingerprints.pl,
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684 TopologicalPharmacophoreAtomPairsFingerprints.pl,
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685 TopologicalPharmacophoreAtomTripletsFingerprints.pl
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686
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687 COPYRIGHT
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688 Copyright (C) 2015 Manish Sud. All rights reserved.
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689
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690 This file is part of MayaChemTools.
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691
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692 MayaChemTools is free software; you can redistribute it and/or modify it
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693 under the terms of the GNU Lesser General Public License as published by
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694 the Free Software Foundation; either version 3 of the License, or (at
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695 your option) any later version.
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696
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