simbad.mr.molrep_mr module¶

Module to run molrep on a model

class Molrep(hklin, logfile, nmol, pdbin, pdbout, sgalternative, space_group, work_dir)[source]¶

Bases: object

Class to run Molrep

Attributes

hklin	The input hkl file
logfile	The logfile output
pdbin	The input pdb file
pdbout	The output pdb file
sgalternative	Whether to check for alternative space groups
space_group	The input space group
work_dir	The path to the working directory

Methods

evaluate_results(results)	Function to evaluate molrep results and move the result with the best contrast score to the output pdb
molrep(key, logfile)	Function to run molecular replacement using MOLREP
run()	Function to run molecular replacement using MOLREP

evaluate_results(results)[source]¶

Function to evaluate molrep results and move the result with the best contrast score to the output pdb

Parameters:	results : dict Dictionary containing space group code with the corresponding contrast score
Returns:	file The output pdb for the best result file The output log for the best result

hklin¶

The input hkl file

logfile¶

The logfile output

static molrep(key, logfile)[source]¶

Function to run molecular replacement using MOLREP

Parameters:	key : str MOLREP keywords logfile : Path to output log file
Returns:	file The output pdb from MOLREP file The output log file

nmol¶

The number of molecules to look for

pdbin¶

The input pdb file

pdbout¶

The output pdb file

run()[source]¶

Function to run molecular replacement using MOLREP

Returns:	file The output pdb from MOLREP

sgalternative¶

Whether to check for alternative space groups

space_group¶

The input space group

work_dir¶

The path to the working directory

check_contrast(logfile)[source]¶

Check the logfile of the job for the contrast value

Parameters:	logfile : str Path to the logfile
Returns:	float Contrast score in log file