chemfp fps2fpc

The “chemfp fps2fpc” command-line tools converts FPS or FPB files containing binary fingerprints into FPC files containing sparse count fingerprints.

This conversion is exact, because the sparse count fingerprint in FPC format is the comma-separated list of on-bit indices in the binary fingerprints, or “*” for the empty fingerprint.

The rest of this chapter contains the output from chemfp fps2fpc --help.

chemfp fps2fpc command-line options

The following comes from chemfp fps2fpc --help:

Usage: chemfp fps2fpc [OPTIONS] [FILENAMES]...

  Convert binary fingerprint to count.

Options:
  --in FORMAT                     Input structure format (default guesses from
                                  filename)
  -o, --output FILENAME           Save the fingerprints to FILENAME
                                  (default=stdout)
  --out FORMAT                    Output structure format (default guesses
                                  from output filename, or is 'fpc')
  --include-metadata / --no-metadata
                                  With --no-metadata, do not include the
                                  header metadata for FPS output.
  --progress / --no-progress      Show a progress bar (default: show unless
                                  the output is a terminal)
  --help                          Show this message and exit.

  Convert binary fingerprints into count fingerprints. Each count fingerprint
  contain the list of on-bit indices.

  For example, the FPS line:

    0C3A7105 record1

  converts to:

    2,3,9,11,12,13,16,20,21,22,24,26      record1

  because "0C" sets bits 2 and 3; "3A" sets bits 9, 11, 12, and 13; "71" sets
  bits 16, 20, 21, and 22; and "05" sets bits 24 and 26.

  Example:

    chemfp fps2fps chembl_35.fps.gz -o chembl_35.fpc.gz