Module to run the phaser rotation search
PhaserRotationSearch
(mtz, mr_program, tmp_dir, work_dir, max_to_keep=20, skip_mr=False, **kwargs)[source]¶Bases: object
A class to perform the phaser rotation search Attributes ———- mtz : str
The path to the input MTZ
>>> from simbad.rotsearch.phaser_search import PhaserRotationSearch
>>> rotation_search = PhaserRotationSearch('<mtz>', '<mr_program>', '<tmp_dir>', '<work_dir>', '<max_to_keep>',
... '<skip_mr>')
>>> rotation_search.run(
... '<models_dir>', '<nproc>', '<min_solvent_content>', '<submit_qtype>',
... '<submit_queue>', '<monitor>', '<chunk_size>'
... )
>>> rotation_search.summarize()
>>> search_results = rotation_search.search_results
If any results are found, an object is returned containing the pdb_code, and the various associated scores
from phaser.
Attributes
search_results |
Methods
rot_succeeded_log (log) |
Check a rotation search job for it’s success |
run (models_dir[, nproc, …]) |
Run phaser rotation function on a directory of models |
summarize (csv_file) |
Summarize the search results |
rot_succeeded_log
(log)[source]¶Check a rotation search job for it’s success
Parameters: | log : str
|
---|---|
Returns: | bool
|
run
(models_dir, nproc=2, min_solvent_content=20, submit_qtype=None, submit_queue=None, monitor=None, chunk_size=0, **kwargs)[source]¶Run phaser rotation function on a directory of models Parameters ———- models_dir : str
The directory containing the models to run the rotation search on
monitor chunk_size : int, optional
The number of jobs to submit at the same time
search_results
¶