.. _chemfp_heapsweep:

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

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

.. code-block:: none
                
  Usage: chemfp heapsweep [OPTIONS] CANDIDATES
  
    Diversity selection using the heapsweep algorithm.
  
  Options:
    -t, --threshold FLOAT           Maximum similarity (default: 1.0)
    -n, --num-picks N               Number of picks (default: 'all')
    --all-equal                     Continue picking past --num-picks if the
                                    pick score is unchanged
    --in, --candidates-format TEXT  Format of the candidates file (default uses
                                    filename extension, or 'fps')
    --randomize / --no-randomize    Use --randomize (the default) to shuffle the
                                    candidates before starting MaxMin
    --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)
    --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.
    --neighbors FILENAME            For each pick, includes the nearest neighbor
                                    and score from fingerprints in FILENAME
    --neighbors-format FORMAT       Format of the neighbors file (default uses
                                    filename extension, or 'fps')
    --save-picks-format PATH        Specify the format for the picked
                                    fingerprints.
    --save-candidates PATH          Write remaining candidate fingerprints to
                                    the named file.
    --save-candidates-format FORMAT
                                    Specify the format for the remaining
                                    candidate fingerprints.
    --save-picks PATH               Write picked fingerprints to the named file.
    --precision [1|2|3|4|5|6|7|8|9|10]
                                    Number of digits in Tanimoto score (default:
                                    based on the fingerprint size)
    -o, --output PATH               Write output to the named file instead of
                                    stdout.
    --out TEXT                      Output format. Must be one of 'chemfp' (the
                                    default), 'csv', or 'tsv' with optional
                                    compression
    --pick-time / --no-pick-time    Include the elapsed time for each pick
    --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 / --no-times            Write timing information to stderr
    --progress / --no-progress      Show a progress bar (default: show unless
                                    the output is a terminal)
    --help                          Show this message and exit.