rdkit2fps - Online in the Cloud

PROGRAM:

NAME

rdkit2fps - rdkit2fps

DESCRIPTION

usage: rdkit2fps [-h] [--fpSize INT] [--RDK] [--minPath INT] [--maxPath INT]

[--nBitsPerHash INT] [--useHs 0|1] [--morgan] [--radius INT] [--useFeatures 0|1]
[--useChirality 0|1] [--useBondTypes 0|1] [--torsions] [--targetSize INT] [--pairs]
[--minLength INT] [--maxLength INT] [--maccs166] [--substruct] [--rdmaccs]
[--id-tag NAME] [--in FORMAT] [-o FILENAME] [--errors {strict,report,ignore}]
[filenames [filenames ...]]

Generate FPS fingerprints from a structure file using RDKit

positional arguments:
filenames
input structure files (default is stdin)

optional arguments:
-h, --help
show this help message and exit

--fpSize INT
number of bits in the fingerprint (applies to RDK, Morgan, topological torsion, and
atom pair fingerprints (default=2048)

--id-tag NAME
tag name containing the record id (SD files only)

--in FORMAT
input structure format (default guesses from filename)

-o FILENAME, --output FILENAME
save the fingerprints to FILENAME (default=stdout)

--errors {strict,report,ignore}
how should structure parse errors be handled? (default=strict)

RDKit topological fingerprints:
--RDK generate RDK fingerprints (default)

--minPath INT
minimum number of bonds to include in the subgraph (default=1)

--maxPath INT
maximum number of bonds to include in the subgraph (default=7)

--nBitsPerHash INT
number of bits to set per path (default=4)

--useHs 0|1
include information about the number of hydrogens on each atom (default=1)

RDKit Morgan fingerprints:
--morgan
generate Morgan fingerprints

--radius INT
radius for the Morgan algorithm (default=2)

--useFeatures 0|1
use chemical-feature invariants (default=0)

--useChirality 0|1
include chirality information (default=0)

--useBondTypes 0|1
include bond type information (default=1)

RDKit Topological Torsion fingerprints:
--torsions
generate Topological Torsion fingerprints

--targetSize INT
number of bits in the fingerprint (default=4)

RDKit Atom Pair fingerprints:
--pairs
generate Atom Pair fingerprints

--minLength INT
minimum bond count for a pair (default=1)

--maxLength INT
maximum bond count for a pair (default=30)

166 bit MACCS substructure keys:
--maccs166
generate MACCS fingerprints

881 bit substructure keys:
--substruct
generate ChemFP substructure fingerprints

ChemFP version of the 166 bit RDKit/MACCS keys:
--rdmaccs
generate 166 bit RDKit/MACCS fingerprints

This program guesses the input structure format based on the filename extension. If the
data comes from stdin, or the extension name us unknown, then use "--in" to change the
default input format. The supported format extensions are:

File Type
Valid FORMATs (use gz if compressed)

--------- ------------------------------------

SMILES
smi, ism, can, smi.gz, ism.gz, can.gz

SDF sdf, mol, sd, mdl, sdf.gz, mol.gz, sd.gz, mdl.gz

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