Util subpackage¶

Various miscellaneous functions

get_mrbump_ensemble(mrbump_dir, final)[source]¶

Output ensemble from mrbump directory to a dat file

get_sequence(input_f, output_s)[source]¶

Output sequence file from input pdb file

output_files(run_dir, result, output_pdb, output_mtz)[source]¶

Return output pdb/mtz from best result in result obj

result_by_score_from_csv(f, score, ascending=True)[source]¶

Return result with the best defined score

submit_chunk(collector, run_dir, nproc, job_name, submit_qtype, submit_queue, permit_nonzero, monitor, success_func)[source]¶

Submit jobs in small chunks to avoid using too much disk space

Parameters:

collector (list) – ScriptCollector containing run scripts nproc (int, optional) – The number of processors to run the job on job_name (str) – The name of the job to submit submit_qtype (str) – The cluster submission queue type - currently support SGE and LSF submit_queue (str) – The queue to submit to on the cluster permit_nonzero (bool) – Permit non-zero return codes from TaskFactory success_func (func) – function to check for success

summarize_result(results, csv_file=None, columns=None)[source]¶

Summarize the search results

tmp_dir(directory=None, prefix='tmp', suffix='')[source]¶

Return a filename for a temporary directory

Parameters:	directory (str, optional) – Path to a directory to write the files to. prefix (str, optional) – A prefix to the temporary filename suffix (str, optional) – A suffix to the temporary filename

tmp_file(delete=False, directory=None, prefix='tmp', stem=None, suffix='')[source]¶

Return a filename for a temporary file The naming convention of scripts will be prefix + stem + suffix.

Parameters:	delete (bool, optional) – Delete the file, thus return name only [default: True] directory (str, optional) – Path to a directory to write the files to prefix (str, optional) – A prefix to the temporary filename stem (str, optional) – The steam part of the script name suffix (str, optional) – A suffix to the temporary filename