sdf2fps command-line options¶
The following comes from sdf2fps --help
:
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