Module to run the amore rotation search
AmoreRotationSearch
(mtz, mr_program, tmp_dir, work_dir, amore_exe=None, max_to_keep=20, skip_mr=False, **kwargs)[source]¶Bases: object
A class to perform the amore rotation search
Examples
>>> from simbad.rotsearch.amore_search import AmoreRotationSearch
>>> rotation_search = AmoreRotationSearch('<amore_exe>', '<mtz>', '<mr_program>', '<tmp_dir>', '<work_dir>',
... '<max_to_keep>')
>>> rotation_search.run(
... '<models_dir>', '<output_dir>', '<nproc>', '<shres>', '<pklim>', '<npic>', '<rotastep>',
... '<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 amore.
Attributes
amore_exe | (str) The path to the amore executable |
mtz | (str) The path to the input MTZ |
work_dir | (str) The path to the working directory |
max_to_keep | (int) The maximum number of results to keep [default: 20] |
search_results | (list) The search results |
Methods
rot_succeeded_log (log) |
Check a rotation search job for it’s success |
run (models_dir[, nproc, shres, pklim, npic, …]) |
Run amore 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
|
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Returns: | bool
|
rotfun_stdin_template
¶run
(models_dir, nproc=2, shres=3.0, pklim=0.5, npic=50, rotastep=1.0, min_solvent_content=20, submit_qtype=None, submit_queue=None, monitor=None, chunk_size=0, **kwargs)[source]¶Run amore rotation function on a directory of models
Parameters: | models_dir : str
nproc : int, optional
shres : int, float, optional
pklim : int, float, optional
npic : int, optional
rotastep : int, float, optional
min_solvent_content : int, float, optional
submit_qtype : str
submit_queue : str
monitor chunk_size : int, optional
|
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Returns: | file
|
search_results
¶sortfun_stdin_template
¶summarize
(csv_file)[source]¶Summarize the search results
Parameters: | csv_file : str
|
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Raises: | No results found |
tabfun_stdin_template
¶