Class to run MR on SIMBAD results
MrSubmit
(mtz, mr_program, refine_program, refine_type, refine_cycles, output_dir, tmp_dir, timeout, sgalternative=None)[source]¶Bases: object
Class to run MR on a defined set of models
Examples
>>> from simbad.mr import MrSubmit
>>> MR = MrSubmit('<mtz>', '<mr_program>', '<refine_program>', '<refine_type>', '<output_dir>', '<sgalternative>')
>>> MR.submit_jobs('<results>', '<nproc>', '<submit_cluster>', '<submit_qtype>', '<submit_queue>',
... '<submit_array>', '<submit_max_array>', '<process_all>', '<monitor>')
If a solution is found and process_all is not set, the queued jobs will be terminated.
Attributes
mtz |
The input MTZ file |
mr_program |
The molecular replacement program to use |
refine_program |
The refinement program to use |
refine_type |
The refinement type to use |
refine_cycles |
The number of refinement cycles to use |
output_dir |
The path to the output directory |
sgalternative |
Whether to check for alternative space groups |
results | (obj) Results from :obj: ‘_LatticeParameterScore’ or :obj: ‘_AmoreRotationScore’ |
Methods
fft (hklin, mapout, map_type) |
Function to run fft to generate difference maps for uglymol |
get_mtz_info (mtz) |
Get various information from the input MTZ |
submit_jobs (results[, nproc, process_all, …]) |
Submit jobs to run in serial or on a cluster |
summarize (csv_file) |
Summarize the search results |
cell_parameters
¶The cell parameters of the input MTZ file
f
¶The F column label of the input MTZ file
fft
(hklin, mapout, map_type)[source]¶Function to run fft to generate difference maps for uglymol
Parameters: | hklin : str
mapout : str
map_type : str
|
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Returns: | list
str
|
Raises: | ValueError
|
free
¶The FREE column label of the input MTZ file
get_mtz_info
(mtz)[source]¶Get various information from the input MTZ
Parameters: | mtz : str
|
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Returns: | self._cell_parameters : list
self._resolution : float
self._space_group : str
self._f : str
self._sigf : str
self._free : str
self._solvent : float
|
i
¶The I column label of the input MTZ file
mr_program
¶The molecular replacement program to use
mr_python_module
¶The MR python module
mtz
¶The input MTZ file
output_dir
¶The path to the output directory
refine_cycles
¶The number of refinement cycles to use
refine_program
¶The refinement program to use
refine_python_module
¶The Refinement python module
refine_type
¶The refinement type to use
resolution
¶The resolution of the input MTZ file
search_results
¶The results from the amore rotation search
sgalternative
¶Whether to check for alternative space groups
sigf
¶The SIGF column label of the input MTZ file
sigi
¶The SIGI column label of the input MTZ file
space_group
¶The space group of the input MTZ file
submit_jobs
(results, nproc=1, process_all=False, submit_qtype=None, submit_queue=False, monitor=None)[source]¶Submit jobs to run in serial or on a cluster
Parameters: | results : class
nproc : int, optional
process_all : bool, optional
submit_qtype : str
submit_queue : str
monitor : str |
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Returns: | file
file
file
file
file
file
|
summarize
(csv_file)[source]¶Summarize the search results
Parameters: | csv_file : str
|
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Raises: | No results found |
timeout
¶The time in minutes before phaser is killed