ample.util.mrbump_util module¶

class NullHandler(level=0)[source]¶

Bases: logging.Handler

Attributes:	name

Methods

`acquire`()	Acquire the I/O thread lock.
`addFilter`(filter)	Add the specified filter to this handler.
`close`()	Tidy up any resources used by the handler.
`createLock`()	Acquire a thread lock for serializing access to the underlying I/O.
`filter`(record)	Determine if a record is loggable by consulting all the filters.
`flush`()	Ensure all logging output has been flushed.
`format`(record)	Format the specified record.
`handle`(record)	Conditionally emit the specified logging record.
`handleError`(record)	Handle errors which occur during an emit() call.
`release`()	Release the I/O thread lock.
`removeFilter`(filter)	Remove the specified filter from this handler.
`setFormatter`(fmt)	Set the formatter for this handler.
`setLevel`(level)	Set the logging level of this handler.

emit
get_name
set_name

emit(record)[source]¶

class ResultsSummary(results=None, results_pkl=None)[source]¶

Bases: object

Summarise the results for a series of MRBUMP runs

Methods

`parseTableDat`(tfile)	Read a resultsTable file and return a list of MrBump results objects
`processMrbumpPkl`(resultsPkl)	Process dictionary
`sortResults`([prioritise])	Sort the results
`summariseResults`(mrbump_dir)	Return a string summarising the results
`summaryString`()	Return a string suitable for printing the sorted results
`topFiles`([num_results])	Return a list of dictionaries listing the top num_results PDB and MTZ files

analyseResult
createDict
extractResults
results_table

analyseResult(result)[source]¶

createDict()[source]¶

extractResults(mrbump_dir, purge=False)[source]¶

parseTableDat(tfile)[source]¶: Read a resultsTable file and return a list of MrBump results objects

processMrbumpPkl(resultsPkl)[source]¶: Process dictionary

results_table(results)[source]¶

sortResults(prioritise=None)[source]¶: Sort the results

summariseResults(mrbump_dir)[source]¶: Return a string summarising the results

summaryString()[source]¶: Return a string suitable for printing the sorted results

topFiles(num_results=3)[source]¶

Return a list of dictionaries listing the top num_results PDB and MTZ files

Parameters:	num_results : int How many of the top results to return
Returns:	topf : list A list of dictionaries, one per result, with xyz, mtz and info keys

checkSuccess(script_path)[source]¶

Check if a job ran successfully.

Parameters:	script_path : str Path to the MrBUMP script
Returns:	bool True if success

Notes

Success is assumed as a SHELX CC score of >= SHELXSUCCESS

finalSummary(amoptd)[source]¶: Print a final summary of the job

jobSucceeded(job_dict)[source]¶

job_unfinished(job_dict)[source]¶

unfinished_scripts(amoptd)[source]¶: See if there are any unfinished mrbump jobs in a mrbump directory and return a list of the scripts

write_jobscript(name, keyword_file, amoptd, directory=None, job_time=86400, extra_options={})[source]¶: Create the script to run MrBump for this PDB.

write_mrbump_files(ensemble_pdbs, amoptd, job_time=172800, ensemble_options=None, directory=None)[source]¶

Write the MRBUMP job files for all the ensembles.

Arguments: ensemble_pdbs – list of the ensembles, each a single pdb file. amoptd – dictionary with job options. job_time – maximum permissible runtime (mainly used for batch queueing systems). ensemble_options – dictionary with ensemble-specific keywords e.g. ensemble_options[ensemble_name] = {‘ncopies’ : ncopies} directory – working directory to write files to.