Molecular Replacement subpackage¶

Class to run MR on SIMBAD results

class MrSubmit(mtz, mr_program, refine_program, refine_type, output_dir, tmp_dir, timeout, enant=False)[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>', '<enam>')
>>> 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 : str The input MTZ file mr_program : str The molecular replacement program to use refine_program : str The refinement program to use output_dir : str The path to the output directory enant : bool Flag to decide if enantiomorphic spacegroups should be trialled 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

enant¶

Flag to decide if enantiomorphic spacegroups should be trialled

f¶

The F column label of the input MTZ file

static fft(hklin, mapout, map_type)[source]¶

Function to run fft to generate difference maps for uglymol

Parameters:	hklin : str Path to input HKL file mapout : str Path to output MAP file map_type : str Define type of run, either mfo-dfc or 2mfo-dfc
Returns:	list cmd str stdin
Raises:	ValueError Unknown map type

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 Path to the input MTZ
Returns:	self._cell_parameters : list The parameters that descibe the unit cell self._resolution : float The resolution of the data self._space_group : str The space group of the data self._f : str The column label for F self._sigf : str The column label for SIGF self._free : str The column label for FREE self._solvent : float The predicted solvent content of the protein

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_program¶

The refinement program to use

refine_python_module¶

The Refinement python module

resolution¶

The resolution of the input MTZ file

search_results¶

The results from the amore rotation search

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 Results from :obj: ‘_LatticeParameterScore’ or :obj: ‘_AmoreRotationScore’ nproc : int, optional Number of processors to use [default: 1] process_all : bool, optional Terminate MR after a success [default: True] submit_qtype : str The cluster submission queue type - currently support SGE and LSF submit_queue : str The queue to submit to on the cluster monitor : str
Returns:	file Output pdb from mr file Output hkl from mr - if using phaser file Output log file from mr program file Output pdb from refinement file Output hkl from refinement file Output log file from refinement program

summarize(csv_file)[source]¶

Summarize the search results

Parameters:	csv_file : str The path for a backup CSV file
Raises:	No results found

timeout¶

The time in minutes before phaser is killed

mr_succeeded_csvfile(f)[source]¶

Check a Molecular Replacement job for it’s success

Parameters:	f : str The path to f
Returns:	bool Success status of the MR run

mr_succeeded_log(log)[source]¶

Check a Molecular Replacement job for it’s success

Parameters:	log : str The path to a log file
Returns:	bool Success status of the MR run