rdkit2fps(1) rdkit2fps


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:

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)
input structure format (default guesses from filename)
save the fingerprints to FILENAME (default=stdout)
--errors {strict,report,ignore}
how should structure parse errors be handled? (default=strict)

RDKit topological fingerprints:

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:

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:

generate Topological Torsion fingerprints
--targetSize INT
number of bits in the fingerprint (default=4)

RDKit Atom Pair fingerprints:

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:

generate MACCS fingerprints

881 bit substructure keys:

generate ChemFP substructure fingerprints

ChemFP version of the 166 bit RDKit/MACCS keys:

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)
--------- ------------------------------------
smi, ism, can, smi.gz, ism.gz, can.gz
sdf, mol, sd, mdl, sdf.gz, mol.gz, sd.gz, mdl.gz