.. _tool_help:

Help for the command-line tools
===================================

See :ref:`"Working with the command-line tools" <using_tools>` for an
introduction.

The chemfp command-line tools are:

  * :ref:`fpcat <fpcat>` - merge multiple fingerprint files into one
  * :ref:`cdk2fps <cdk2fps>` - use CDK to generate fingerprints 
  * :ref:`ob2fps <ob2fps>` - use Open Babel to generate fingerprints
  * :ref:`oe2fps <oe2fps>` - use OEChem/OEGraphSim to generate fingerprints
  * :ref:`rdkit2fps <rdkit2fps>` - use RDKit to generate fingerprints
  * :ref:`sdf2fps <sdf2fps>` - extract fingerprints from an SD file
  * :ref:`simsearch <simsearch>` - search a fingerprint file for similar fingerprints
  * :ref:`chemfp <chemfp_command>` - top-level command for additional chemfp commands

The ``chemfp`` command implements many subcommands:
    
  * :ref:`chemfp butina <chemfp_butina>` - cluster using the Butina algorithm 
  * :ref:`chemfp csv2fps <chemfp_csv2fps>` - generate fingerprints from a CSV file
  * :ref:`chemfp fpb_text <chemfp_fpb_text>` - show the TEXT sections of an FPB file  
  * :ref:`chemfp heapsweep <chemfp_heapsweep>` -- heapsweep diversity picking
  * :ref:`chemfp license <chemfp_license>` - show the chemfp license status
  * :ref:`chemfp maxmin <chemfp_maxmin>` - MaxMin diversity picking 
  * :ref:`chemfp report <chemfp_report>` - report chemfp configuration details
  * :ref:`chemfp spherex <chemfp_spherex>` - spherical exclusion diversity picking
  * :ref:`chemfp toolkits <chemfp_toolkits>` - list the available cheminformatics toolkits
  * :ref:`chemfp translate <chemfp_translate>` - translate between two structure formats

.. toctree::
  :maxdepth: 2
  :hidden:

  fpcat <fpcat_command>
  cdk2fps <cdk2fps_command>
  ob2fps <ob2fps_command>
  oe2fps <oe2fps_command>
  rdkit2fps <rdkit2fps_command>
  sdf2fps <sdf2fps_command>
  simsearch <simsearch_command>
  chemfp <chemfp_command>
  chemfp butina <chemfp_butina_command>
  chemfp csv2fps <chemfp_csv2fps_command>
  chemfp fpb_text <chemfp_fpb_text_command>
  chemfp heapsweep <chemfp_heapsweep_command>
  chemfp license <chemfp_license_command>
  chemfp maxmin <chemfp_maxmin_command>
  chemfp report <chemfp_report_command>
  chemfp spherex <chemfp_spherex_command>
  chemfp toolkits <chemfp_toolkits_command>
  chemfp translate <chemfp_translate_command>