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TopologicalPharmacophoreAtomTripletsFingerprints.pl - Generate topological pharmacophore atom triplets fingerprints for SD files
TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)...
TopologicalPharmacophoreAtomTripletsFingerprints.pl [--AromaticityModel AromaticityModelType] [--AtomTripletsSetSizeToUse ArbitrarySize | FixedSize] [-a, --AtomTypesToUse "AtomType1, AtomType2..."] [--AtomTypesWeight "AtomType1, Weight1, AtomType2, Weight2..."] [--CompoundID DataFieldName or LabelPrefixString] [--CompoundIDLabel text] [--CompoundIDMode] [--DataFields "FieldLabel1, FieldLabel2,..."] [-d, --DataFieldsMode All | Common | Specify | CompoundID] [--DistanceBinSize number] [-f, --Filter Yes | No] [--FingerprintsLabelMode FingerprintsLabelOnly | FingerprintsLabelWithIDs] [--FingerprintsLabel text] [-h, --help] [-k, --KeepLargestComponent Yes | No] [--MinDistance number] [--MaxDistance number] [--OutDelim comma | tab | semicolon] [--output SD | FP | text | all] [-o, --overwrite] [-q, --quote Yes | No] [-r, --root RootName] [-u, --UseTriangleInequality Yes | No] [-v, --VectorStringFormat ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString] [-w, --WorkingDir dirname] SDFile(s)...
Generate topological pharmacophore atom triplets fingerprints [ Ref 66, Ref 68-71 ] for SDFile(s) and create appropriate SD, FP or CSV/TSV text file(s) containing fingerprints 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.
Based on the values specified for --AtomTypesToUse, pharmacophore atom types are assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated. Using --MinDistance, --MaxDistance, and --DistanceBinSize values, a binned distance matrix is generated with lower bound on the distance bin as the distance in distance matrix; the lower bound on the distance bin is also used as the distance between atom pairs for generation of atom triplet identifiers.
A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting atom pairs binned distances between --MinDistance and --MaxDistance. The value of --UseTriangleInequality determines whether the triangle inequality test is applied during generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore types, is used during generation of atom triplet IDs.
Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom triplets is counted.
The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen atoms constitute pharmacophore topological atom triplets fingerprints of the molecule.
For ArbitrarySize value of --AtomTripletsSetSizeToUse option, the fingerprint vector correspond to only those topological pharmacophore atom triplets which are present and have non-zero count. However, for FixedSize value of --AtomTripletsSetSizeToUse option, the fingerprint vector contains all possible valid topological pharmacophore atom triplets with both zero and non-zero count values.
Example of SD file containing topological pharmacophore atom triplets fingerprints string data:
Example of FP file containing topological pharmacophore atom triplets fingerprints string data:
Example of CSV Text file containing topological pharmacophore atom triplets fingerprints string data:
The current release of MayaChemTools generates the following types of topological pharmacophore atom triplets fingerprints vector strings:
Specify aromaticity model to use during detection of aromaticity. Possible values in the current release are: MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel or MayaChemToolsAromaticityModel. Default value: MayaChemToolsAromaticityModel.
The supported aromaticity model names along with model specific control parameters are defined in AromaticityModelsData.csv, which is distributed with the current release and is available under lib/data directory. Molecule.pm module retrieves data from this file during class instantiation and makes it available to method DetectAromaticity for detecting aromaticity corresponding to a specific model.
Atom triplets set size to use during generation of topological pharmacophore atom triplets fingerprints.
Possible values: ArbitrarySize | FixedSize; Default value: ArbitrarySize.
For ArbitrarySize value of --AtomTripletsSetSizeToUse option, the fingerprint vector correspond to only those topological pharmacophore atom triplets which are present and have non-zero count. However, for FixedSize value of --AtomTripletsSetSizeToUse option, the fingerprint vector contains all possible valid topological pharmacophore atom triplets with both zero and non-zero count values.
Pharmacophore atom types to use during generation of topological phramacophore atom triplets. It's a list of comma separated valid pharmacophore atom types.
Possible values for pharmacophore atom types are: Ar, CA, H, HBA, HBD, Hal, NI, PI, RA. Default value [ Ref 71 ] : HBD,HBA,PI,NI,H,Ar.
The pharmacophore atom types abbreviations correspond to:
AtomTypes::FunctionalClassAtomTypes module is used to assign pharmacophore atom types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
This value is --CompoundIDMode specific and indicates how compound ID is generated.
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>.
Specify compound ID column label for CSV/TSV text file(s) used during CompoundID value of --DataFieldsMode option. Default value: CompoundID.
Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated fingerprints for FP | text | all values of --output option: use a SDFile(s) datafield value; use molname line from SDFile(s); generate a sequential ID with specific prefix; use combination of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
Possible values: DataField | MolName | LabelPrefix | MolNameOrLabelPrefix. Default value: 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.
Comma delimited list of SDFiles(s) data fields to extract and write to CSV/TSV text file(s) along with generated fingerprints for text | all values of --output option.
This is only used for Specify value of --DataFieldsMode option.
Examples:
Specify how data fields in SDFile(s) are transferred to output CSV/TSV text file(s) along with generated fingerprints for text | all values of --output option: transfer all SD data field; transfer SD data files common to all compounds; extract specified data fields; generate a compound ID using molname line, a compound prefix, or a combination of both. Possible values: All | Common | specify | CompoundID. Default value: CompoundID.
Distance bin size used to bin distances between atom pairs in atom triplets. Default value: 2. Valid values: positive integers.
For default --MinDistance and --MaxDistance values of 1 and 10 with --DistanceBinSize of 2 [ Ref 70 ], the following 5 distance bins are generated:
The lower distance bound on the distance bin is uses to bin the distance between atom pairs in atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance bin, atom pairs with distances 3 and 4 fall in second distance bin and so on.
In order to distribute distance bins of equal size, the last bin is allowed to go past --MaxDistance by up to distance bin size. For example, --MinDistance and --MaxDistance values of 2 and 10 with --DistanceBinSize of 2 generates the following 6 distance bins:
Specify whether to check and filter compound data in SDFile(s). Possible values: Yes or No. Default value: Yes.
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.
Specify how fingerprints label is generated in conjunction with --FingerprintsLabel option value: use fingerprints label generated only by --FingerprintsLabel option value or append topological atom pair count value IDs to --FingerprintsLabel option value.
Possible values: FingerprintsLabelOnly | FingerprintsLabelWithIDs. Default value: FingerprintsLabelOnly.
Topological atom pairs IDs appended to --FingerprintsLabel value during FingerprintsLabelWithIDs values of --FingerprintsLabelMode correspond to atom pair count values in fingerprint vector string.
FingerprintsLabelWithIDs value of --FingerprintsLabelMode is ignored during ArbitrarySize value of --AtomTripletsSetSizeToUse option and topological atom triplets IDs not appended to the label.
SD data label or text file column label to use for fingerprints string in output SD or CSV/TSV text file(s) specified by --output. Default value: TopologicalPharmacophoreAtomTripletsFingerprints.
Print this help message.
Generate fingerprints for only the largest component in molecule. Possible values: Yes or No. Default value: Yes.
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.
Minimum bond distance between atom pairs corresponding to atom triplets for generating topological pharmacophore atom triplets. Default value: 1. Valid values: positive integers and less than --MaxDistance.
Maximum bond distance between atom pairs corresponding to atom triplets for generating topological pharmacophore atom triplets. Default value: 10. Valid values: positive integers and greater than --MinDistance.
Delimiter for output CSV/TSV text file(s). Possible values: comma, tab, or semicolon Default value: comma.
Type of output files to generate. Possible values: SD, FP, text, or all. Default value: text.
Overwrite existing files.
Put quote around column values in output CSV/TSV text file(s). Possible values: Yes or No. Default value: Yes.
New file name is generated using the root: <Root>.<Ext>. Default for new file names: <SDFileName><TopologicalPharmacophoreAtomTripletsFP>.<Ext>. The file type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab delimited text files, respectively.This option is ignored for multiple input files.
Specify whether to imply triangle distance inequality test to distances between atom pairs in atom triplets during generation of atom triplets basis set generation. Possible values: Yes or No. Default value: Yes.
Triangle distance inequality test implies that distance or binned distance between any two atom pairs in an atom triplet must be less than the sum of distances or binned distances between other two atoms pairs and greater than the difference of their distances.
Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by --output option. Possible values: ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString. Defaultvalue: ValuesString.
Default value during FixedSize value of --AtomTripletsSetSizeToUse option: ValuesString. Default value during ArbitrarySize value of --AtomTripletsSetSizeToUse option: IDsAndValuesString.
ValuesString option value is not allowed for ArbitrarySize value of --AtomTripletsSetSizeToUse option.
Examples:
Location of working directory. Default value: current directory.
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:
To generate topological pharmacophore atom triplets fingerprints of fixed size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files with CSV file containing sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound IDs along with fingerprints vector strings data in ValuesString format and atom triplets IDs in the fingerprint data column label starting with Fingerprints, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances not satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6 distance bins spanning distances from 1 through 12 using default atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6 distance bins spanning distances from 1 through 12 using "HBD,HBA,PI, NI, H, Ar" atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound IDs from molecule name line along with fingerprints vector strings data in ValuesString format, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound IDs using specified data field along with fingerprints vector strings data in ValuesString format, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound IDs using combination of molecule name line and an explicit compound prefix along with fingerprints vector strings data, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing specific data fields columns along with fingerprints vector strings data, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create a SampleTPATFP.csv file containing common data fields columns along with fingerprints vector strings data, type:
To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files containing all data fields columns in CSV file along with fingerprints data, type:
InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, TopologicalPharmacophoreAtomPairsFingerprints.pl
Copyright (C) 2024 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.
