NullHandler
(level=0)[source]¶Bases: logging.Handler
Attributes: |
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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 |
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 |
checkSuccess
(script_path)[source]¶Check if a job ran successfully.
Parameters: |
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Returns: |
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Notes
Success is assumed as a SHELX CC score of >= SHELXSUCCESS
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.