.. _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 [--help] [--license-file FILENAME] [--traceback] [--version]
                [command] ...
  
  chemfp tools for cheminformatics fingerprints and structure I/O
  
  positional arguments:
    command
    rest
  
  options:
    --help, -h
    --license-file FILENAME
    --traceback           print the traceback on KeyboardInterrupt
    --version             show program's version number and exit
  
  Summary of the available commands.
  
  Fingerprint generation
  
    cdk2fps               Generate RDKit fingerprints
    ob2fps                Generate Open Babel fingerprints
    oe2fps                Generate OpenEye fingerprints
    rdkit2fps             Generate RDKit fingerprints
    sdf2fps               Extract a fingerprint tag from an SD file and generate
                           FPS or FPB fingerprints
  
  Fingerprint search
  
    simsearch             Search an FPS or FPB file for similar fingerprints
  
  Fingerprint format conversion
  
    fpcat                 Combine multiple fingerprint files into a single file
  
  Fingerprint file tools
  
    fpb_text              Show the TEXT sections of an FPB file
  
  Diversity selection
  
    heapsweep             Select diverse fingerprints using the heapsweep
                           algorithm
    maxmin                Select diverse fingerprints using the MaxMin algorithm
    spherex               Select diverse fingerprints using the sphere exclusion
                           algorithm
  
  Configuration
  
    license               Show the chemfp license status
    report                Report chemfp similarity search implementation details
    toolkits              Show underlying cheminformatics toolkit availability