chemfp command¶
Chemfp 4.0 added the chemfp
command. New chemfp command-line
functionality will be added as subcommands of chemfp
rather than
through new command-line programs.
The subcommands are:
butina - Cluster using the Butina/leader-follower algorithm.
cdk2fps - Generate fingerprints using CDK.
csv2fps - Generate fingerprints from an SDF tag.
fpb_text - Show the TEXT sections of an FPB file.
fpc2fps - Convert count fingerprints to binary.
fpcat - Combine multiple fingerprint files into a single file.
fps2fpc - Convert binary fingerprints to count.
heapsweep -Diversity selection using the heapsweep algorithm.
license - Show the chemfp license status.
maxmin - Diversity selection using the MaxMin algorithm.
ob2fps - Generate fingerprints using Open Babel.
oe2fps - Generate fingerprints using OEChem and OEGraphSim.
rdkit2fps - Generate fingerprints using RDKit.
rdkit2fpc - Generate count fingerprints using RDKit.
report - Report chemfp similarity search implementation details.
sdf2fps - Extract fingerprints from an SDF file.
shardsearch - Similarity search of multiple target files.
simarray - Generate the full matrix of query and target scores.
simhistogram - Generate histograms from the similarity scores.
simsearch - Search an FPS or FPB file for similar fingerprints.
spherex -Diversity selection using the sphere exclusion algorithm.
toolkits - Show underlying cheminformatics toolkit availability.
translate - Translate between two structure file formats
chemfp command-line options¶
The following comes from chemfp --help
:
Usage: chemfp [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
--traceback Print the traceback on KeyboardInterrupt
--license-file FILENAME Specify a chemfp license file
--help Show this message and exit.
Generation commands:
cdk2fps Generate fingerprints using CDK.
ob2fps Generate fingerprints using Open Babel.
oe2fps Generate fingerprints using OEChem and OEGraphSim.
rdkit2fps Generate fingerprints using RDKit.
rdkit2fpc Generate count fingerprints using RDKit.
sdf2fps Extract fingerprints from an SDF file.
csv2fps Generate fingerprints from an SDF tag.
Algorithms:
simsearch Search an FPS or FPB file for similar fingerprints.
shardsearch Similarity search across multiple fingerprint files.
simarray Generate the full matrix of query and target scores.
simhistogram Generate a histogram from full or sampled Tanimoto scores.
spherex Diversity selection using the sphere exclusion algorithm.
maxmin Diversity selection using the MaxMin algorithm.
heapsweep Diversity selection using the heapsweep algorithm.
butina Cluster using the Butina/leader-follower algorithm.
Fingerprint file commands:
fpcat Combine multiple fingerprint files into a single file.
fpb_text Show the TEXT sections of an FPB file.
fpc2fps Convert count fingerprints to binary.
fps2fpc Convert binary fingerprint to count.
Structure file commmand:
translate Translate between two structure file formats
Other commands:
license Show the chemfp license status.
report Report chemfp similarity search implementation details.
toolkits Show underlying cheminformatics toolkit availability.