.. _sdf2fps:

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

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

.. code-block:: none

  usage: sdf2fps [-h] [--id-tag TAG] [--fp-tag TAG] [--in FORMAT]
                 [--num-bits INT] [--errors {strict,report,ignore}]
                 [-o FILENAME] [--out FORMAT] [--software TEXT] [--type TEXT]
                 [--progress | --no-progress] [--version] [--license-check]
                 [--binary] [--binary-msb] [--hex] [--hex-lsb] [--hex-msb]
                 [--base64] [--cactvs] [--daylight] [--decoder DECODER]
                 [--pubchem]
                 [filenames ...]
  
  Extract a fingerprint tag from an SD file and generate FPS or FPB fingerprints
  
  positional arguments:
    filenames             input SD files (default is stdin)
  
  options:
    -h, --help            show this help message and exit
    --id-tag TAG          get the record id from TAG instead of the first line
                          of the record
    --fp-tag TAG          get the fingerprint from tag TAG (required)
    --in FORMAT           Specify 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.
    --errors {strict,report,ignore}
                          how should structure parse errors be handled?
                          (default=strict)
    -o FILENAME, --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')
    --software TEXT       use TEXT as the software description
    --type TEXT           use TEXT as the fingerprint type description
    --progress, --no-progress
                          Show a progress bar (default: show unless the output
                          is a terminal)
    --version             show program's version number and exit
    --license-check       Check the license and report results to stdout.
  
  Fingerprint decoding options:
    --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
  
  shortcuts:
    --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