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NAME

PathLengthFingerprints.pl - Generate atom path length based fingerprints for SD files

SYNOPSIS

PathLengthFingerprints.pl SDFile(s)...

PathLengthFingerprints.pl [--CompoundID DataFieldName or LabelPrefixString] [--CompoundIDLabel text] [--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix] [--DataFields FieldLabel1,FieldLabel2,... ] [-d, --DataFieldsMode All | Common | Specify | CompoundID] [--DetectAromaticity Yes | No] [--FingerprintsLabel text] [-f, --FingerprintsOutput BinaryString | HexadecimalString | RawBinaryString] [--fold Yes | No] [--FoldedSize number] [-h, --help] [-i, --IgnoreHydrogens Yes | No] [-k, --KeepLargestComponent Yes | No] [-m, --mode AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings] [--MinPathLength number] [--MaxPathLength number] [--OutDelim comma | tab | semicolon] [--output SD | text | both] [-q, --quote Yes | No] [-r, --root RootName] [-s, --size number] [-u, --UseBondSymbols Yes | No] [-w, --WorkingDir dirname] SDFile(s)...

DESCRIPTION

Generate atom path length based fingerprints for SDFile(s) and create appropriate SD or CSV/TSV text containing bit-strings corresponding to molecular fingerprints.

Based on values specified for -m, --mode, --MinPathLength and --MaxPathLength, all appropriate atom paths are generated for each atom in the molecule and collected in a list. For each atom path in the atom paths list, an atom path string is created using atom symbol and bond order and collected in an atom path string list. Duplicate atom path strings are removed from the list. For each unique atom path string, a 32 bit unsigned integer hash key is generated using TextUtil::HashCode function. Using the hash key as a seed for a random number generator, a random integer value between 0 and --Size is used to set corresponding bits in the fingerprint bit-string.

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.

OPTIONS

--CompoundID DataFieldName or LabelPrefixString

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:

MolID
ExtReg

Examples for LabelPrefix or MolNameOrLabelPrefix value of --CompoundIDMode:

Compound

The value specified above generates compound IDs which correspond to Compound<Number> instead of default value of Cmpd<Number>.

--CompoundIDLabel text

Specify compound ID column label for CSV/TSV text file(s) used during CompoundID value of --DataFieldsMode option. Default: CompoundID.

--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix

Specify how to generate compound IDs and write to CSV/TSV text file(s) along with generated fingerprints for text | both 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: 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.

--DataFields FieldLabel1,FieldLabel2,...

Comma delimited list of SDFiles(s) data fields to extract and write to CSV/TSV text file(s) along with generated fingerprints for text | both values of --output option.

This is only used for Specify value of --DataFieldsMode option.

Examples:

Extreg
MolID,CompoundName

-d, --DataFieldsMode All | Common | Specify | CompoundID

Specify how data fields in SDFile(s) are transferred to output CSV/TSV text file(s) along with generated fingerprints for text | both 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.

--DetectAromaticity Yes | No

Detect aromaticity before generating fingerprints. Possible values: Yes or No. Default value: Yes.

no --DetectAromaticity forces usage of atom and bond aromaticity values from SDFile(s) and skips the step which detects and assigns aromaticity.

--FingerprintsLabel text

SD data label or text file column label to use for fingerprints bit-string in output SD or CSV/TSV text file(s) specified by --output. Default value: PathLenghFingerprints.

-f, --FingerprintsOutput BinaryString | HexadecimalString | RawBinaryString

Format of fingerprints bit-string data in output SD or CSV/TSV text file(s) specified by --output. Possible values: BinaryString, HexadecimalString, RawBinary. Default value: HexadecimalString.

BinaryString corresponds to an ASCII string containing 1s and 0s. HexadecimalString contains bit values in ASCII hexadecimal format and it's more compact than BinaryString. RawBinary contains unpacked byte data.

--fold Yes | No

Fold fingerprints to increase bit density. Possible values: Yes or No. Default value: No.

--FoldedSize number

Size of folded fingerprint. Default value: 256. Valid values correspond to any positive integer which is less than -s, --size and meets the criteria for its value.

Examples:

128 512

-h, --help

Print this help message

-i, --IgnoreHydrogens Yes | No

Ignore hydrogens during fingerprints generation. Possible values: Yes or No. Default value: Yes.

For yes value of -i, --IgnoreHydrogens, any explicit hydrogens are also used for generation of atoms path lengths and fingerprints; implicit hydrogens are still ignored.

-k, --KeepLargestComponent Yes | No

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.

-m, --mode AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings

Specify type of path length fingerprints to generate for molecules in SDFile(s). Possible values:AtomPathsWithoutRings, AtomPathsWithRings, AllAtomPathsWithoutRings, AllAtomPathsWithRings. Default value: AllAtomPathsWithRings.

For molecules with no rings, first two and last two options are equivalent and generate same set of atom paths starting from each atom with length between --MinPathLength and --MaxPathLength. However, all these four options can result in the same set of final atom paths for molecules containing fused, bridged or spiro rings.

For molecules containing rings, atom paths starting from each atom can be traversed in four different ways:

AtomPathsWithoutRings - Atom paths containing no rings and without sharing of bonds in traversed paths.

AtomPathsWithRings - Atom paths containing rings and without any sharing of bonds in traversed paths.

AllAtomPathsWithoutRings - All possible atom paths containing no rings and without any sharing of bonds in traversed paths.

AllAtomPathsWithRings - All possible atom paths containing rings and with sharing of bonds in traversed paths.

Atom path traversal is terminated at the ring atom.

In addition to atom symbols, bond symbols are also used to generate a string for atom paths. These atom paths strings are hashed to a 32 bit integer key which in turn is used as a seed for a random number generation in range of 1 to fingerprint size for setting corresponding bit in bit vector.

Based on values specified for for -m, --mode, --MinPathLength and --MaxPathLength, all appropriate atom paths are generated for each atom in the molecule and collected in a list. For each atom path in the atom paths list, an atom path string is created using atom symbol and bond order and collected in an atom path string list. Atom symbol corresponds to element symbol and characters used to represent bond order are: 1 - None; 2 - '='; 3 - '#'; 1.5 or aromatic - ':'; others: bond order value.

Atom path strings corresponding purely to atom symbols can also be generated using --UseBondSymbols option. By default, bond symbols are included in atom path strings. Exclusion of bond symbols in atom path strings results in fingerprints which correspond purely to atom paths without considering bonds.

Duplicate atom path strings are removed from the list. For each unique atom path string, a 32 bit unsigned integer hash key is produced. Using hash key as a seed for a random number generator, a random integer value between 0 and --Size is used to set corresponding bit in the fingerprint bit-string.

For molecule containing rings, combination of -m, --mode and --UseBondSymbols allows generation of up to 8 different types of fingerprints:

Default atom path length fingerprints generation for molecules containing rings with AllAtomPathsWithRings value for -m, --mode, Yes value for --UseBondSymbols, 2 value for --MinPathLength and 8 value for --MaxPathLength is the most time consuming. Combinations of other options can substantially speed up fingerprint generation for molecules containing complex ring systems.

--MinPathLength number

Minimum atom path length to include in fingerprints. Default value: 1. Valid values: positive integers and less than --MaxPathLength. Path length of 1 correspond to a path containing only one atom.

--MaxPathLength number

Maximum atom path length to include in fingerprints. Default value: 8. Valid values: positive integers and greater than --MinPathLength.

--OutDelim comma | tab | semicolon

Delimiter for output CSV/TSV text file(s). Possible values: comma, tab, or semicolon Default value: comma

--output SD | text | both

Type of output files to generate. Possible values: SD, text, or both. Default value: text

-o, --overwrite

Overwrite existing files

-q, --quote Yes | No

Put quote around column values in output CSV/TSV text file(s). Possible values: Yes or No. Default value: Yes

-r, --root RootName

New file name is generated using the root: <Root>.<Ext>. Default for new file names: <SDFileName><PathLengthFP>.<Ext>. The file type determines <Ext> value. The sdf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab delimited text files, respectively.This option is ignored for multiple input files.

-s, --size number

Size of fingerprints. Default value: 1024. Valid values correspond to any positive interger which satisfies the following criteria: power of 2, >= 32 and <= 2 ** 32.

Examples:

256 512 2048

-u, --UseBondSymbols Yes | No

Specify whether to use bond symbols for atom paths during generation of atom path strings. Possible values: Yes or No. Default value: Yes.

No value option for -u, --UseBondSymbols allows the generation of fingerprints corresponding purely to atoms disregarding all bonds.

-w, --WorkingDir DirName

Location of working directory. Default: current directory

EXAMPLES

To generate path length fingerprints in hexadecimal bit-string format of size 1024 and create a SampleHexPLFP.csv file containing sequential compound IDs along with fingerprint bit-string data, type

To generate path length fingerprints in binary bit-string format of size 512 and create a SampleBinPLFP.csv file containing sequential compound IDs along with fingerprint bit-string data , type

To generate folded path length fingerprints in hexadecimal bit-string format and create SampleHexPLFP.sdf and SampleHexPLFP.csv files containing sequential compound IDs along with fingerprint bit-string data, type

To generate path length fingerprints corresponding to atom paths containing no rings and without sharing of bonds in hexadecimal bit-string format and create a SampleHexPLFP.csv file containing all data fields along with fingerprint bit-string data, type

To generate path length fingerprints corresponding to atom paths containing rings and without sharing of bonds in hexadecimal bit-string format and create a SampleHexPLFP.tsv file containing compound IDs derived from combination of molecule name line and an explicit compound prefix and fingerprints column name along with fingerprint bit-string data, type

To generate path length fingerprints in hexadecimal bit-string format and create a SampleHexPLFP.csv file containing sequential compounds ID along with fingerprint bit-string data using aromaticity specified in SD file, type

To generate path length fingerprints in hexadecimal bit-string format corresponding purely to atoms without any consideration of bonds between the atoms, path lengths between 2 and 6, and create a SampleHexPLFP.csv file containing sequential compound IDs along with fingerprint bit-string data, type

AUTHOR

Manish Sud

SEE ALSO

InfoFingerprintsSDFiles.pl, InfoFingerprintsTextFiles.pl, SimilarityMatrixSDFiles.pl, SimilarityMatrixTextFiles.pl

COPYRIGHT

Copyright (C) 2004-2008 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.