.. _chemfp_spherex:

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

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

.. code-block:: none
                
  usage: chemfp spherex [-h] [-t FLOAT] [--num-picks N] [--dise]
                        [--dise-references FILENAME] [--dise-format FORMAT]
                        [--ranks FILENAME] [--ranks-default N]
                        [--ranks-format FORMAT] [--ranks-has-header]
                        [--in CANDIDATES_FORMAT] [--references FILENAME]
                        [--references-format FORMAT] [--pick-id PICK_ID]
                        [--pick-id-file FILENAME] [--randomize | --no-randomize]
                        [--seed N] [--mmap | --no-mmap] [--include-hits]
                        [--output FILENAME] [--out OUTPUT_FORMAT]
                        [--precision N] [--save-picks FILENAME]
                        [--save-picks-format FILENAME]
                        [--save-candidates FILENAME]
                        [--save-candidates-format FILENAME]
                        [--include-empty | --no-include-empty]
                        [--empty-score EMPTY_SCORE]
                        [--empty-hit-id EMPTY_HIT_ID]
                        [--pick-time | --no-pick-time] [--no-date] [--date STR]
                        [--times] [--progress | --no-progress]
                        candidates
  
  Select diverse fingerprints using the sphere exclusion algorithm
  
  positional arguments:
    candidates            fingerprint file containing candidates (fingerprints
                          to pick from)
  
  options:
    -h, --help            show this help message and exit
    -t FLOAT, --threshold FLOAT
                          Maximum similarity (default: 1.0)
    --num-picks N, -n N   Number of picks (default: 'all')
    --dise                Use directed sphere exclusion
    --dise-references FILENAME
                          DISE reference structures or fingerprints (default
                          uses the Gobbi & Lee structures)
    --dise-format FORMAT  format of the DISE reference file (default uses the
                          file extension, else 'fps')
    --ranks FILENAME      file containing fingerprint rank values
    --ranks-default N     default rank value if candidate id not found in the
                          ranks file (default: 2**32-1)
    --ranks-format FORMAT
                          format for the ranks file (only 'tsv' is supported)
    --ranks-has-header    skip the first line of the ranks file
    --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')
    --pick-id PICK_ID     Initial candidate id (if no reference file). Can be
                          used more than once.
    --pick-id-file FILENAME
                          File containing initial candidate ids, one per line
    --randomize, --no-randomize
                          Use --randomize (default for undirected picking) to
                          randomly pick from the available candidates, or --no-
                          random (default for directed picking) to pick the
                          candidate with the smallest arena index.
    --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. (default: True)
    --include-hits        include ids and scores for fingerprints in each sphere
    --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.
    --include-empty, --no-include-empty
                          In csv and tsv format with --include-hits, include
                          picks with no hits (the default) (default: True)
    --empty-score EMPTY_SCORE
                          The score if --include-empty outputs a pick with no
                          hits (default: 'NaN')
    --empty-hit-id EMPTY_HIT_ID
                          The hit id if --include-empty outputs a pick with no
                          hits (default: '*')
    --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)