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1 NAME
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2 AtomNeighborhoodsFingerprints.pl - Generate atom neighborhoods
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3 fingerprints for SD files
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4
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5 SYNOPSIS
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6 AtomNeighborhoodsFingerprints.pl SDFile(s)...
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7
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8 AtomNeighborhoodsFingerprints.pl [--AromaticityModel
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9 *AromaticityModelType*] [-a, --AtomIdentifierType
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10 *AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes |
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11 MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes |
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12 UFFAtomTypes*] [--AtomicInvariantsToUse
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13 *"AtomicInvariant,AtomicInvariant..."*] [--FunctionalClassesToUse
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14 *"FunctionalClass1,FunctionalClass2..."*] [--CompoundID *DataFieldName
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15 or LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode]
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16 [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode
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17 *All | Common | Specify | CompoundID*] [-f, --Filter *Yes | No*]
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18 [--FingerprintsLabel *text*] [-h, --help] [-k, --KeepLargestComponent
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19 *Yes | No*] [--MinNeighborhoodRadius *number*] [--MaxNeighborhoodRadius
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20 *number*] [--OutDelim *comma | tab | semicolon*] [--output *SD | FP |
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21 text | all*] [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root
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22 *RootName*] [-w, --WorkingDir dirname] SDFile(s)...
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23
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24 DESCRIPTION
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25 Generate atom neighborhoods fingerprints [ Ref 53-56, Ref 73 ] for
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26 *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s)
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27 containing fingerprints vector strings corresponding to molecular
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28 fingerprints.
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29
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30 Multiple SDFile names are separated by spaces. The valid file extensions
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31 are *.sdf* and *.sd*. All other file names are ignored. All the SD files
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32 in a current directory can be specified either by **.sdf* or the current
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33 directory name.
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34
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35 The current release of MayaChemTools supports generation of atom
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36 neighborhoods 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 atom neighborhoods around each
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46 non-hydrogen central atom corresponding to radii between specified
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47 values --MinNeighborhoodRadius and --MaxNeighborhoodRadius, unique atom
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48 types at each radii level are counted and an atom neighborhood
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49 identifier is generated.
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50
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51 The format of an atom neighborhood identifier around a central
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52 non-hydrogen atom at a specific radius is:
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53
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54 NR<n>-<AtomType>-ATC<n>
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55
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56 NR: Neighborhood radius
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57 AtomType: Assigned atom type
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58 ATC: Atom type count
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59
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60 The atom neighborhood identifier for a non-hydrogen central atom
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61 corresponding to all specified radii is generated by concatenating
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62 neighborhood identifiers at each radii by colon as a delimiter:
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63
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64 NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...
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65
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66 The atom neighborhood identifiers for all non-hydrogen central atoms at
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67 all specified radii are concatenated using space as a delimiter and
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68 constitute atom neighborhood fingerprint of the molecule.
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69
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70 Example of *SD* file containing atom neighborhood fingerprints string
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71 data:
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72
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73 ... ...
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74 ... ...
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75 $$$$
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76 ... ...
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77 ... ...
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78 ... ...
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79 41 44 0 0 0 0 0 0 0 0999 V2000
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80 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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81 ... ...
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82 2 3 1 0 0 0 0
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83 ... ...
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84 M END
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85 > <CmpdID>
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86 Cmpd1
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87
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88 > <AtomNeighborhoodsFingerprints>
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89 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu
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90 s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-ATC1
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91 :NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X1.B
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92 O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
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93 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C...
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94
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95 $$$$
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96 ... ...
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97 ... ...
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98
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99 Example of *FP* file containing atom neighborhood fingerprints string
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100 data:
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101
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102 #
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103 # Package = MayaChemTools 7.4
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104 # Release Date = Oct 21, 2010
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105 #
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106 # TimeStamp = Fri Mar 11 14:15:27 2011
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107 #
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108 # FingerprintsStringType = FingerprintsVector
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109 #
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110 # Description = AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu...
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111 # VectorStringFormat = ValuesString
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112 # VectorValuesType = AlphaNumericalValues
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113 #
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114 Cmpd1 41;NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-A...
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115 Cmpd2 23;NR0-C.X1.BO1.H3-ATC1:NR1-C.X2.BO2.H2-ATC1:NR2-C.X3.BO3.H1-A...
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116 ... ...
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117 ... ..
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118
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119 Example of CSV *Text* file containing atom neighborhood fingerprints
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120 string data:
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121
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122 "CompoundID","AtomNeighborhoodsFingerprints"
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123 "Cmpd1","FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes
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124 :MinRadius0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.B
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125 O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
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126 NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3
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127 .BO4-ATC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1..."
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128 ... ...
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129 ... ...
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130
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131 The current release of MayaChemTools generates the following types of
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132 atom neighborhoods fingerprints vector strings:
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133
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134 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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135 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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136 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
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137 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
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138 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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139 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
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140
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141 FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
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142 adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
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143 NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
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144 _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
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145 C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
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146 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...
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147
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148 FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
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149 ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
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150 NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
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151 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
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152 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
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153 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...
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154
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155 FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
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156 s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
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157 ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
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158 C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
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159 R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
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160 TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...
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161
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162 FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
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163 ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
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164 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
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165 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
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166 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
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167 C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...
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168
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169 FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
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170 us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
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171 CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
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172 NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
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173 ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
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174 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...
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175
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176 FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
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177 us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
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178 -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
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179 O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
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180 ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
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181 C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...
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182
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183 FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
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184 s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
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185 -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
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186 e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
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187 ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
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188 TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...
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189
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190 FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
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191 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
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192 _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
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193 C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
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194 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
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195 -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...
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196
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197 OPTIONS
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198 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
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199 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
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200 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
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201 MayaChemToolsAromaticityModel*
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202 Specify aromaticity model to use during detection of aromaticity.
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203 Possible values in the current release are: *MDLAromaticityModel,
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204 TriposAromaticityModel, MMFFAromaticityModel,
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205 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
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206 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
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207 value: *MayaChemToolsAromaticityModel*.
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208
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209 The supported aromaticity model names along with model specific
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210 control parameters are defined in AromaticityModelsData.csv, which
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211 is distributed with the current release and is available under
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212 lib/data directory. Molecule.pm module retrieves data from this file
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213 during class instantiation and makes it available to method
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214 DetectAromaticity for detecting aromaticity corresponding to a
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215 specific model.
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216
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217 -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes
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218 | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes |
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219 SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes*
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220 Specify atom identifier type to use for assignment of initial atom
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221 identifier to non-hydrogen atoms during calculation of atom
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222 neighborhoods fingerprints. Possible values in the current release
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223 are: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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224 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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225 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value:
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226 *AtomicInvariantsAtomTypes*.
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227
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228 --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."*
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229 This value is used during *AtomicInvariantsAtomTypes* value of a,
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230 --AtomIdentifierType option. It's a list of comma separated valid
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231 atomic invariant atom types.
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232
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233 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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234 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
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235
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236 The atomic invariants abbreviations correspond to:
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237
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238 AS = Atom symbol corresponding to element symbol
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239
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240 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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241 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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242 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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243 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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244 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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245 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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246 H<n> = Number of implicit and explicit hydrogens for atom
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247 Ar = Aromatic annotation indicating whether atom is aromatic
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248 RA = Ring atom annotation indicating whether atom is a ring
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249 FC<+n/-n> = Formal charge assigned to atom
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250 MN<n> = Mass number indicating isotope other than most abundant isotope
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251 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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252 3 (triplet)
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253
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254 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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255 corresponds to:
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256
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257 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
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258
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259 Except for AS which is a required atomic invariant in atom types,
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260 all other atomic invariants are optional. Atom type specification
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261 doesn't include atomic invariants with zero or undefined values.
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262
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263 In addition to usage of abbreviations for specifying atomic
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264 invariants, the following descriptive words are also allowed:
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265
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266 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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267 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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268 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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269 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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270 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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271 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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272 H : NumOfImplicitAndExplicitHydrogens
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273 Ar : Aromatic
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274 RA : RingAtom
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275 FC : FormalCharge
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276 MN : MassNumber
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277 SM : SpinMultiplicity
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278
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279 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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280 atomic invariant atom types.
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281
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282 --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."*
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283 This value is used during *FunctionalClassAtomTypes* value of a,
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284 --AtomIdentifierType option. It's a list of comma separated valid
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285 functional classes.
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286
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287 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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288 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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289 *HBD,HBA,PI,NI,Ar,Hal*.
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290
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291 The functional class abbreviations correspond to:
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292
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293 HBD: HydrogenBondDonor
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294 HBA: HydrogenBondAcceptor
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295 PI : PositivelyIonizable
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296 NI : NegativelyIonizable
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297 Ar : Aromatic
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298 Hal : Halogen
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299 H : Hydrophobic
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300 RA : RingAtom
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301 CA : ChainAtom
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302
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303 Functional class atom type specification for an atom corresponds to:
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304
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305 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
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306
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307 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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308 functional class atom types. It uses following definitions [ Ref
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309 60-61, Ref 65-66 ]:
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310
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311 HydrogenBondDonor: NH, NH2, OH
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312 HydrogenBondAcceptor: N[!H], O
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313 PositivelyIonizable: +, NH2
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314 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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315
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316 --CompoundID *DataFieldName or LabelPrefixString*
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317 This value is --CompoundIDMode specific and indicates how compound
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318 ID is generated.
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319
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320 For *DataField* value of --CompoundIDMode option, it corresponds to
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321 datafield label name whose value is used as compound ID; otherwise,
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322 it's a prefix string used for generating compound IDs like
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323 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
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324 IDs which look like Cmpd<Number>.
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325
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326 Examples for *DataField* value of --CompoundIDMode:
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327
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328 MolID
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329 ExtReg
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330
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331 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
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332 --CompoundIDMode:
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333
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334 Compound
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335
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336 The value specified above generates compound IDs which correspond to
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337 Compound<Number> instead of default value of Cmpd<Number>.
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338
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339 --CompoundIDLabel *text*
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340 Specify compound ID column label for FP or CSV/TSV text file(s) used
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341 during *CompoundID* value of --DataFieldsMode option. Default:
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342 *CompoundID*.
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343
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344 --CompoundIDMode *DataField | MolName | LabelPrefix |
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345 MolNameOrLabelPrefix*
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346 Specify how to generate compound IDs and write to FP or CSV/TSV text
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347 file(s) along with generated fingerprints for *FP | text | all*
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348 values of --output option: use a *SDFile(s)* datafield value; use
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|
349 molname line from *SDFile(s)*; generate a sequential ID with
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350 specific prefix; use combination of both MolName and LabelPrefix
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351 with usage of LabelPrefix values for empty molname lines.
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352
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353 Possible values: *DataField | MolName | LabelPrefix |
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354 MolNameOrLabelPrefix*. Default: *LabelPrefix*.
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355
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356 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
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357 in *SDFile(s)* takes precedence over sequential compound IDs
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358 generated using *LabelPrefix* and only empty molname values are
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359 replaced with sequential compound IDs.
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360
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361 This is only used for *CompoundID* value of --DataFieldsMode option.
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362
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363 --DataFields *"FieldLabel1,FieldLabel2,..."*
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|
364 Comma delimited list of *SDFiles(s)* data fields to extract and
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|
365 write to CSV/TSV text file(s) along with generated fingerprints for
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366 *text | all* values of --output option.
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367
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368 This is only used for *Specify* value of --DataFieldsMode option.
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369
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370 Examples:
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371
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372 Extreg
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373 MolID,CompoundName
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374
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|
375 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
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376 Specify how data fields in *SDFile(s)* are transferred to output
|
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|
377 CSV/TSV text file(s) along with generated fingerprints for *text |
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378 all* values of --output option: transfer all SD data field; transfer
|
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|
379 SD data files common to all compounds; extract specified data
|
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|
380 fields; generate a compound ID using molname line, a compound
|
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|
381 prefix, or a combination of both. Possible values: *All | Common |
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|
382 specify | CompoundID*. Default value: *CompoundID*.
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|
383
|
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384 -f, --Filter *Yes | No*
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385 Specify whether to check and filter compound data in SDFile(s).
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|
386 Possible values: *Yes or No*. Default value: *Yes*.
|
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387
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|
388 By default, compound data is checked before calculating fingerprints
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|
|
389 and compounds containing atom data corresponding to non-element
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|
390 symbols or no atom data are ignored.
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|
391
|
|
|
392 --FingerprintsLabel *text*
|
|
|
393 SD data label or text file column label to use for fingerprints
|
|
|
394 string in output SD or CSV/TSV text file(s) specified by --output.
|
|
|
395 Default value: *AtomNeighborhoodsFingerprints*.
|
|
|
396
|
|
|
397 -h, --help
|
|
|
398 Print this help message.
|
|
|
399
|
|
|
400 -k, --KeepLargestComponent *Yes | No*
|
|
|
401 Generate fingerprints for only the largest component in molecule.
|
|
|
402 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
403
|
|
|
404 For molecules containing multiple connected components, fingerprints
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|
|
405 can be generated in two different ways: use all connected components
|
|
|
406 or just the largest connected component. By default, all atoms
|
|
|
407 except for the largest connected component are deleted before
|
|
|
408 generation of fingerprints.
|
|
|
409
|
|
|
410 --MinNeighborhoodRadius *number*
|
|
|
411 Minimum atom neighborhood radius for generating atom neighborhoods.
|
|
|
412 Default value: *0*. Valid values: positive integers and less than
|
|
|
413 --MaxNeighborhoodRadius. Neighborhood radius of zero corresponds to
|
|
|
414 list of non-hydrogen atoms.
|
|
|
415
|
|
|
416 --MaxNeighborhoodRadius *number*
|
|
|
417 Maximum atom neighborhood radius for generating atom neighborhoods.
|
|
|
418 Default value: *2*. Valid values: positive integers and greater than
|
|
|
419 --MineighborhoodRadius.
|
|
|
420
|
|
|
421 --OutDelim *comma | tab | semicolon*
|
|
|
422 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
|
|
|
423 tab, or semicolon* Default value: *comma*.
|
|
|
424
|
|
|
425 --output *SD | FP | text | all*
|
|
|
426 Type of output files to generate. Possible values: *SD, FP, text, or
|
|
|
427 all*. Default value: *text*.
|
|
|
428
|
|
|
429 -o, --overwrite
|
|
|
430 Overwrite existing files.
|
|
|
431
|
|
|
432 -q, --quote *Yes | No*
|
|
|
433 Put quote around column values in output CSV/TSV text file(s).
|
|
|
434 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
435
|
|
|
436 -r, --root *RootName*
|
|
|
437 New file name is generated using the root: <Root>.<Ext>. Default for
|
|
|
438 new file names: <SDFileName><AtomNeighborhoodsFP>.<Ext>. The file
|
|
|
439 type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values
|
|
|
440 are used for SD, comma/semicolon, and tab delimited text files,
|
|
|
441 respectively.This option is ignored for multiple input files.
|
|
|
442
|
|
|
443 -w, --WorkingDir *DirName*
|
|
|
444 Location of working directory. Default: current directory.
|
|
|
445
|
|
|
446 EXAMPLES
|
|
|
447 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
448 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
449 vector string format and create a SampleANFP.csv file containing
|
|
|
450 sequential compound IDs along with fingerprints vector strings data,
|
|
|
451 type:
|
|
|
452
|
|
|
453 % AtomNeighborhoodsFingerprints.pl -r SampleANFP -o Sample.sdf
|
|
|
454
|
|
|
455 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
456 neighborhood radii from 0 to 2 using DREIDING atom types in vector
|
|
|
457 string format and create a SampleANFP.csv file containing sequential
|
|
|
458 compound IDs along with fingerprints vector strings data, type:
|
|
|
459
|
|
|
460 % AtomNeighborhoodsFingerprints.pl -a DREIDINGAtomTypes -r SampleANFP
|
|
|
461 -o Sample.sdf
|
|
|
462
|
|
|
463 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
464 neighborhood radii from 0 to 2 using EStateAtomTypes types in vector
|
|
|
465 string format and create a SampleANFP.csv file containing sequential
|
|
|
466 compound IDs along with fingerprints vector strings data, type:
|
|
|
467
|
|
|
468 % AtomNeighborhoodsFingerprints.pl -a EStateAtomTypes -r SampleANFP
|
|
|
469 -o Sample.sdf
|
|
|
470
|
|
|
471 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
472 neighborhood radii from 0 to 2 using SYBYL atom types in vector string
|
|
|
473 format and create a SampleANFP.csv file containing sequential compound
|
|
|
474 IDs along with fingerprints vector strings data, type:
|
|
|
475
|
|
|
476 % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
|
|
|
477 -o Sample.sdf
|
|
|
478
|
|
|
479 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
480 neighborhood radii from 0 to 2 using FunctionalClass atom types in
|
|
|
481 vector string format and create a SampleANFP.csv file containing
|
|
|
482 sequential compound IDs along with fingerprints vector strings data,
|
|
|
483 type:
|
|
|
484
|
|
|
485 % AtomNeighborhoodsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
486 -r SampleANFP -o Sample.sdf
|
|
|
487
|
|
|
488 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
489 neighborhood radii from 0 to 2 using MMFF94 atom types in vector string
|
|
|
490 format and create a SampleANFP.csv file containing sequential compound
|
|
|
491 IDs along with fingerprints vector strings data, type:
|
|
|
492
|
|
|
493 % AtomNeighborhoodsFingerprints.pl -a MMFF94AtomTypes -r SampleANFP
|
|
|
494 -o Sample.sdf
|
|
|
495
|
|
|
496 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
497 neighborhood radii from 0 to 2 using SLogP atom types in vector string
|
|
|
498 format and create a SampleANFP.csv file containing sequential compound
|
|
|
499 IDs along with fingerprints vector strings data, type:
|
|
|
500
|
|
|
501 % AtomNeighborhoodsFingerprints.pl -a SLogPAtomTypes -r SampleANFP
|
|
|
502 -o Sample.sdf
|
|
|
503
|
|
|
504 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
505 neighborhood radii from 0 to 2 using SYBYL atom types in vector string
|
|
|
506 format and create a SampleANFP.csv file containing sequential compound
|
|
|
507 IDs along with fingerprints vector strings data, type:
|
|
|
508
|
|
|
509 % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
|
|
|
510 -o Sample.sdf
|
|
|
511
|
|
|
512 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
513 neighborhood radii from 0 to 2 using TPSA atom types in vector string
|
|
|
514 format and create a SampleANFP.csv file containing sequential compound
|
|
|
515 IDs along with fingerprints vector strings data, type:
|
|
|
516
|
|
|
517 % AtomNeighborhoodsFingerprints.pl -a TPSAAtomTypes -r SampleANFP
|
|
|
518 -o Sample.sdf
|
|
|
519
|
|
|
520 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
521 neighborhood radii from 0 to 2 using UFF atom types in vector string
|
|
|
522 format and create a SampleANFP.csv file containing sequential compound
|
|
|
523 IDs along with fingerprints vector strings data, type:
|
|
|
524
|
|
|
525 % AtomNeighborhoodsFingerprints.pl -a UFFAtomTypes -r SampleANFP
|
|
|
526 -o Sample.sdf
|
|
|
527
|
|
|
528 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
529 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
530 vector string format and create SampleANFP.sdf, SampleANFP.fpf and
|
|
|
531 SampleANFP.csv files containing sequential compound IDs in CSV file
|
|
|
532 along with fingerprints vector strings data, type:
|
|
|
533
|
|
|
534 % AtomNeighborhoodsFingerprints.pl --output all -r SampleANFP
|
|
|
535 -o Sample.sdf
|
|
|
536
|
|
|
537 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
538 neighborhood radii from 1 to 3 using atomic invariants atom types in
|
|
|
539 vector string format and create a SampleANFP.csv file containing
|
|
|
540 sequential compound IDs along with fingerprints vector strings data,
|
|
|
541 type:
|
|
|
542
|
|
|
543 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
544 --MinNeighborhoodRadius 1 --MaxNeighborhoodRadius 3 -r SampleANFP
|
|
|
545 -o Sample.sdf
|
|
|
546
|
|
|
547 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
548 neighborhood radii from 0 to 2 using only AS,X atomic invariants atom
|
|
|
549 types in vector string format and create a SampleANFP.csv file
|
|
|
550 containing sequential compound IDs along with fingerprints vector
|
|
|
551 strings data, type:
|
|
|
552
|
|
|
553 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
554 --AtomicInvariantsToUse "AS,X" --MinNeighborhoodRadius 0
|
|
|
555 --MaxNeighborhoodRadius 3 -r SampleANFP -o Sample.sdf
|
|
|
556
|
|
|
557 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
558 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
559 vector string format and create a SampleANFP.csv file containing
|
|
|
560 compound ID from molecule name line along with fingerprints vector
|
|
|
561 strings data, type:
|
|
|
562
|
|
|
563 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
564 --DataFieldsMode CompoundID --CompoundIDMode MolName
|
|
|
565 -r SampleANFP -o Sample.sdf
|
|
|
566
|
|
|
567 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
568 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
569 vector string format and create a SampleANFP.csv file containing
|
|
|
570 compound IDs using specified data field along with fingerprints vector
|
|
|
571 strings data, type:
|
|
|
572
|
|
|
573 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
574 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
|
|
|
575 Mol_ID -r SampleANFP -o Sample.sdf
|
|
|
576
|
|
|
577 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
578 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
579 vector string format and create a SampleANFP.csv file containing
|
|
|
580 compound ID using combination of molecule name line and an explicit
|
|
|
581 compound prefix along with fingerprints vector strings data, type:
|
|
|
582
|
|
|
583 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
584 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
|
|
|
585 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleANFP -o Sample.sdf
|
|
|
586
|
|
|
587 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
588 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
589 vector string format and create a SampleANFP.csv file containing
|
|
|
590 specific data fields columns along with fingerprints vector strings
|
|
|
591 data, type:
|
|
|
592
|
|
|
593 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
594 --DataFieldsMode Specify --DataFields Mol_ID -r SampleANFP
|
|
|
595 -o Sample.sdf
|
|
|
596
|
|
|
597 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
598 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
599 vector string format and create a SampleANFP.csv file containing common
|
|
|
600 data fields columns along with fingerprints vector strings data, type:
|
|
|
601
|
|
|
602 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
603 --DataFieldsMode Common -r SampleANFP -o Sample.sdf
|
|
|
604
|
|
|
605 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
606 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
607 vector string format and create SampleANFP.sdf, SampleANFP.fpf and
|
|
|
608 SampleANFP.csv files containing all data fields columns in CSV file
|
|
|
609 along with fingerprints data, type:
|
|
|
610
|
|
|
611 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
612 --DataFieldsMode All --output all -r SampleANFP
|
|
|
613 -o Sample.sdf
|
|
|
614
|
|
|
615 AUTHOR
|
|
|
616 Manish Sud <msud@san.rr.com>
|
|
|
617
|
|
|
618 SEE ALSO
|
|
|
619 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
|
|
|
620 SimilaritySearchingFingerprints.pl, ExtendedConnectivityFingerprints.pl,
|
|
|
621 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
622 TopologicalAtomPairsFingerprints.pl,
|
|
|
623 TopologicalAtomTorsionsFingerprints.pl,
|
|
|
624 TopologicalPharmacophoreAtomPairsFingerprints.pl,
|
|
|
625 TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
626
|
|
|
627 COPYRIGHT
|
|
|
628 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
629
|
|
|
630 This file is part of MayaChemTools.
|
|
|
631
|
|
|
632 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
633 under the terms of the GNU Lesser General Public License as published by
|
|
|
634 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
635 your option) any later version.
|
|
|
636
|
