.. _sdf2fps:

sdf2fps command-line options
====================================

The following comes from ``sdf2fps --help``:

.. code-block:: none

  Usage: sdf2fps [OPTIONS] [FILENAMES]...
  
    Extract fingerprints from an SDF tag.
  
  Options:
    --id-tag TAG                    Get the record it from the tag TAG instead
                                    of the first line of the record.
    --fp-tag TEXT                   Get the fingerprint from tag TAG (required)
    --in FORMAT                     The input format (one of "sdf", "sdf.gz", or
                                    "sdf.zst")
    --num-bits INT                  Use the first INT bits of the input. Use
                                    only when the last 1-7 bits of the last byte
                                    are not part of the fingerprint. Unexpected
                                    errors will occur if these bits are not all
                                    zero.  [x>=1]
    --errors [strict|report|ignore]
                                    How should structure parse errors be
                                    handled? (default=strict)
    --software TEXT                 Use TEXT as the software description
    --type TEXT                     Use TEXT as the fingerprint type description
    --binary                        Encoded with the characters '0' and '1'. Bit
                                    #0 comes first. Example: 00100000 encodes
                                    the value 4
    --binary-msb                    Encoded with the characters '0' and '1'. Bit
                                    #0 comes last. Example: 00000100 encodes the
                                    value 4
    --hex                           Hex encoded. Bit #0 is the first bit (1<<0)
                                    of the first byte. Example: 01f2 encodes the
                                    value \x01\xf2 = 498
    --hex-lsb                       Hex encoded. Bit #0 is the eigth bit (1<<7)
                                    of the first byte. Example: 804f encodes the
                                    value \x01\xf2 = 498
    --hex-msb                       Hex encoded. Bit #0 is the first bit (1<<0)
                                    of the last byte. Example: f201 encodes the
                                    value \x01\xf2 = 498
    --base64                        Base-64 encoded. Bit #0 is first bit (1<<0)
                                    of first byte. Example: AfI= encodes value
                                    \x01\xf2 = 498
    --cactvs                        CACTVS encoding, based on base64 and
                                    includes a version and bit length
    --daylight                      Daylight encoding, which is a base64 variant
    --decoder DECODER               Import and use the DECODER function to
                                    decode the fingerprint
    --pubchem                       decode CACTVS substructure keys used in
                                    PubChem. Same as --software=CACTVS/unknown
                                    --type 'CACTVS-E_SCREEN/1.0 extended=2'
                                    --fp-tag=PUBCHEM_CACTVS_SUBSKEYS --cactvs
    -o, --output FILENAME           Save the fingerprints to FILENAME
                                    (default=stdout)
    --out FORMAT                    Output format, one of 'fps', 'fps.gz',
                                    'fps.zst', 'fpb', or 'flush' (default
                                    guesses from output filename, or is 'fps')
    --include-metadata / --no-metadata
                                    With --no-metadata, do not include the
                                    header metadata for FPS output.
    --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
    --progress / --no-progress      Show a progress bar (default: show unless
                                    the output is a terminal)
    --license-check                 Check the license and report results to
                                    stdout.
    --version                       Show the version and exit.
    --license-file FILENAME         Specify a chemfp license file
    --traceback                     Print the traceback on KeyboardInterrupt
    --version                       Show the version and exit.
    --help                          Show this message and exit.