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EStateIndiciesFingerprints.pl - Generate E-state indicies fingerprints for SD files
EStateIndiciesFingerprints.pl SDFile(s)...
EStateIndiciesFingerprints.pl [--CompoundID DataFieldName or LabelPrefixString] [--CompoundIDLabel text] [--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix] [--DataFields ''FieldLabel1,FieldLabel2,...''] [-d, --DataFieldsMode All | Common | Specify | CompoundID] [-e, --EStateAtomTypesSetToUse ArbitrarySize or FixedSize] [-f, --Filter Yes | No] [--FingerprintsLabelMode FingerprintsLabelOnly | FingerprintsLabelWithIDs] [--FingerprintsLabel text] [-h, --help] [-k, --KeepLargestComponent Yes | No] [--OutDelim comma | tab | semicolon] [--output SD | FP | text | all] [-o, --overwrite] [-q, --quote Yes | No] [-r, --root RootName] [-s, --size number] [--ValuesPrecision number] [-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString] [-w, --WorkingDir DirName]
Generate E-state indicies fingerprints [ Ref 75-78 ] for SDFile(s) and create appropriate SD, FP, or CSV/TSV text file(s) containing fingerprints bit-vector or vector strings corresponding to molecular fingerprints.
Multiple SDFile names are separated by spaces. The valid file extensions are .sdf and .sd. All other file names are ignored. All the SD files in a current directory can be specified either by *.sdf or the current directory name.
E-state atom types are assigned to all non-hydrogen atoms in a molecule using module AtomTypes::EStateAtomTypes.pm and E-state values are calculated using module AtomicDescriptors::EStateValues.pm. Using E-state atom types and E-state values, EStateIndiciesFingerprints constituting sum of E-state values for E-sate atom types is generated.
Two types of E-state atom types set size are allowed:
Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types to non-hydrogen atoms in the molecule, is able to assign atom types to any valid atom group. However, for FixedSize value of EStateAtomTypesSetToUse, only a fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in Ref 77 ] are used for fingerprints.
The fixed size E-state atom type set size used during generation of fingerprints contains 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with MayaChemTools.
Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of E-state indicies fingerprints:
Example of SD file containing E-state indicies fingerprints string data:
Example of FP file containing E-state indicies fingerprints string data:
Example of CSV Text file containing E-state indicies fingerprints string data:
The current release of MayaChemTools generates the following types of E-state fingerprints vector strings:
For DataField value of --CompoundIDMode option, it corresponds to datafield label name whose value is used as compound ID; otherwise, it's a prefix string used for generating compound IDs like LabelPrefixString<Number>. Default value, Cmpd, generates compound IDs which look like Cmpd<Number>.
Examples for DataField value of --CompoundIDMode:
Examples for LabelPrefix or MolNameOrLabelPrefix value of --CompoundIDMode:
The value specified above generates compound IDs which correspond to Compound<Number> instead of default value of Cmpd<Number>.
Possible values: DataField | MolName | LabelPrefix | MolNameOrLabelPrefix. Default: LabelPrefix.
For MolNameAndLabelPrefix value of --CompoundIDMode, molname line in SDFile(s) takes precedence over sequential compound IDs generated using LabelPrefix and only empty molname values are replaced with sequential compound IDs.
This is only used for CompoundID value of --DataFieldsMode option.
This is only used for Specify value of --DataFieldsMode option.
Examples:
ArbitrarySize corrresponds to only E-state atom types detected in molecule; FixedSize corresponds to fixed number of previously defined E-state atom types.
For EStateIndicies, a fingerprint vector string is generated. The vector string corresponding to EStateIndicies contains sum of E-state values for E-state atom types.
Module AtomTypes::EStateAtomTypes.pm is used to assign E-state atom types to non-hydrogen atoms in the molecule which is able to assign atom types to any valid atom group. However, for FixedSize value of EStateAtomTypesSetToUse, only a fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in Ref 77 ] are used for fingerprints.
The fixed size E-state atom type set size used during generation of fingerprints contains 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with MayaChemTools.
By default, compound data is checked before calculating fingerprints and compounds containing atom data corresponding to non-element symbols or no atom data are ignored.
Possible values: FingerprintsLabelOnly | FingerprintsLabelWithIDs. Default value: FingerprintsLabelOnly.
This option is only used for FixedSize value of -e, --EStateAtomTypesSetToUse option during generation of EStateIndicies E-state fingerprints.
E-state atom type IDs appended to --FingerprintsLabel value during FingerprintsLabelWithIDs values of --FingerprintsLabelMode correspond to fixed number of previously defined E-state atom types.
For molecules containing multiple connected components, fingerprints can be generated in two different ways: use all connected components or just the largest connected component. By default, all atoms except for the largest connected component are deleted before generation of fingerprints.
Default value during ArbitrarySize value of -e, --EStateAtomTypesSetToUse option: IDsAndValuesString. Default value during FixedSize value of -e, --EStateAtomTypesSetToUse option: ValuesString.
Examples:
To generate E-state fingerprints of arbitrary size in vector string format and create a SampleESFP.csv file containing sequential compound IDs along with fingerprints vector strings data, type:
To generate E-state fingerprints of fixed size in vector string format and create a SampleESFP.csv file containing sequential compound IDs along with fingerprints vector strings data, type:
To generate E-state fingerprints of fixed size in vector string with IDsAndValues format and create a SampleESFP.csv file containing sequential compound IDs along with fingerprints vector strings data, type:
To generate E-state fingerprints of fixed size in vector string format and create a SampleESFP.csv file containing compound ID from molecule name line along with fingerprints vector strings data, type
To generate E-state fingerprints of fixed size in vector string format and create a SampleESFP.csv file containing compound IDs using specified data field along with fingerprints vector strings data, type:
To generate E-state fingerprints of fixed size in vector string format and create a SampleESFP.csv file containing compound ID using combination of molecule name line and an explicit compound prefix along with fingerprints vector strings data, type:
To generate E-state fingerprints of fixed size in vector string format and create a SampleESFP.csv file containing specific data fields columns along with fingerprints vector strings data, type:
To generate E-state fingerprints of fixed size in vector string format and create a SampleESFP.csv file containing common data fields columns along with fingerprints vector strings data, type:
To generate E-state fingerprints of fixed size in vector string format and create SampleESFP.sdf, SampleESFP.fpf, and SampleESFP.csv files containing all data fields columns in CSV file along with fingerprints vector strings data, type:
InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl, MACCSKeysFingeprints.pl, PathLengthFingerprints.pl, TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
Copyright (C) 2004-2012 Manish Sud. All rights reserved.
This file is part of MayaChemTools.
MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
