.. _chemfp_command:

chemfp command-line options
====================================

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 following comes from ``chemfp --help``:

.. code-block:: none

  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.
    sdf2fps    Extract fingerprints from an SDF file.
  
  Algorithms:
    simsearch  Search an FPS or FPB file for similar fingerprints.
    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.
  
  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.