chemfp spherex command-line options¶
The following comes from chemfp spherex --help
:
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)