.. _chemfp_maxmin:

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

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

.. code-block:: none
                
  usage: chemfp maxmin [-h] [--num-picks N] [-t FLOAT] [--all-equal]
                       [--pick-id PICK_ID] [--pick-index PICK_INDEX]
                       [--in CANDIDATES_FORMAT] [--references FILENAME]
                       [--references-format FORMAT]
                       [--randomize | --no-randomize] [--seed N]
                       [--neighbors FILENAME] [--neighbors-format FILENAME]
                       [--mmap | --no-mmap] [--output FILENAME]
                       [--out OUTPUT_FORMAT] [--precision N]
                       [--save-picks FILENAME] [--save-picks-format FILENAME]
                       [--save-candidates FILENAME]
                       [--save-candidates-format FILENAME]
                       [--pick-time | --no-pick-time] [--no-date] [--date STR]
                       [--times] [--progress | --no-progress]
                       candidates
  
  Select diverse fingerprints using the MaxMin algorithm
  
  positional arguments:
    candidates            fingerprint file containing candidates (fingerprints
                          to pick from)
  
  options:
    -h, --help            show this help message and exit
    --num-picks N, -n N   Number of picks (default: 'all')
    -t FLOAT, --threshold FLOAT
                          Maximum similarity (default: 1.0)
    --all-equal           Continue picking past --num-picks if the pick score is
                          unchanged
    --pick-id PICK_ID     Candidate id to use for the initial pick (default: use
                          heapsweep)
    --pick-index PICK_INDEX
                          Candidate index to use for the initial pick (default:
                          use heapsweep)
    --in CANDIDATES_FORMAT, --candidates-format CANDIDATES_FORMAT
                          Format of the candidates file (default uses filename
                          extension, or 'fps')
    --references FILENAME
                          Fingerprint file containing reference fingerprints to
                          avoid (the fingerprints you have)
    --references-format FORMAT
                          Format of the references file (default uses filename
                          extension, or 'fps')
    --randomize, --no-randomize
                          Use --randomize (the default) to shuffle the
                          candidates before starting MaxMin (default: True)
    --seed N              Specify the random number generator seed between 0 and
                          2**64-1, inclusive, or use -1 to have one picked at
                          random (default: -1)
    --neighbors FILENAME  For each pick, includes the nearest neighbor and score
                          from FILENAME
    --neighbors-format FILENAME
                          Format of the neighbors file (default uses filename
                          extension, or 'fps')
    --mmap, --no-mmap     Don't use mmap to read uncompressed FPB files. May
                          give better performance on networked file systems, at
                          the expense of higher memory use. (default: True)
    --output FILENAME, -o FILENAME
                          Write output to the named file instead of stdout.
    --out OUTPUT_FORMAT   Output format. Must be one of 'chemfp' (the default),
                          'csv', 'tsv', or 'excel-tab', with optional
                          compression
    --precision N         Number of digits in Tanimoto score (default: based on
                          the fingerprint size)
    --save-picks FILENAME
                          Write picked fingerprints to the named file.
    --save-picks-format FILENAME
                          Specify the format for the picked fingerprints.
    --save-candidates FILENAME
                          Write remaining candidate fingerprints to the named
                          file.
    --save-candidates-format FILENAME
                          Specify the format for the remaining candidate
                          fingerprints.
    --pick-time, --no-pick-time
                          include the elapsed time for each pick (default:
                          False)
    --no-date             Do not include the 'date' metadata in the output
                          header
    --date STR            An ISO 8601 date (like '2022-02-07T11:10:15') to use
                          for the 'date' metadata in the output header
    --times               Write timing information to stderr
    --progress, --no-progress
                          Show a progress bar (default: show unless the output
                          is a terminal)