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.