swamp.mr.mrrun module

class MrRun(id, workdir, target_fa, target_mtz, phased_mtz=None, threads=1, phaser_sgalternative='NONE', phaser_early_kill=True, silent=False, save_disk_space=False, logger=None, phaser_packcutoff=None, phaser_timeout=1800, extend_solution=False, quiet_start=False, phaser_peaks_rotcutoff=None)

Bases: swamp.mr.mr.Mr

Class to attempt molecular replacement on a given target

This class contains methods to attempt run molecular replacement on a given target structure. The pipeline uses phaser for search model placement, refmac5 for refinement, shelxe for density modification and model building. If scattering data has been recorded into the target’s mtz file.

Parameters:

• id (str) – unique identifier for the instance
• workdir (str) – working directory where the MR task will be executed
• threads (int) – number of threads to be used in the pipeline (only affects phaser) (default 1)
• target_fa (str) – target’s fasta filename
• target_mtz (str) – target’s mtz filename
• phased_mtz (str) – target’s mtz filename containing phases (default: None)
• phaser_sgalternative (str) – parameter to be passed phaser.InputMR_AUTO.SGAL_SELE() (default ‘NONE’)
• phaser_packcutoff (float) – parameter to be passed to phaser.InputMR_AUTO.setPACK_CUTO() (default None)
• phaser_peaks_rotcutoff (float) – parameter to be passed to phaser.InputMR_AUTO.setPEAK_ROTA_CUTO() (default None)
• phaser_early_kill (bool) – if True pipeline will stop execution if phaser scores are low (default False)
• phaser_timeout (int) – parameter to be passed to phaser.InputMR_AUTO.KILL_TIME() (default 360)
• extend_solution (bool) – if True then solutions will be completed with ideal helices (default False)
• save_disk_space (bool) – if True metadata will be removed to save disk space (default False)
• logger (SwampLogger) – logging interface for the MR pipeline (default None)
• silent (bool) – if set to True the logger will not print messages
• quiet_start (bool) – if True the logger will not display the header section and the inital parameters

Variables:

• error (bool) – True if errors have occurred at some point on the pipeline
• is_extended (str) – ‘YES’ if the instance corresponds with an ideal helices extension run, otherwise ‘NO’
• phaser (Phaser) – phaser wrapper used in the pipeline
• refmac (Refmac) – refmac wrapper used in the pipeline
• shelxe (shelxe) – shelxe wrapper used in the pipeline
• search_id (str) – the search model identifier for the ~swamp.mr.mrrun.MrRun instance
• run_id (str) – the run identifier for the ~swamp.mr.mrrun.MrRun instance
• search_model_list (list) – a list of the search models to be used in this MrRun instance
• solution (str) – ‘YES’ if shelxe CC > 25, otherwise ‘NO’
• idealhelix_run – instance of :py:obj:`~swamp.mr.mrrun.MrRun to extend the solution with ideal helices

add_searchmodel(**kwargs)

Add a search model to phaser

Parameters:

• id (str) – unique identifier for the search model to be added
• ensemble_code (str) – the ensemble’s SWAMP library id to be used as search model
• ermsd (float) – the eRMSD to be used with phaser to place the search model (default 0.1)
• nsearch (int) – number of copies to search with phaser
• disable_check (bool) – passed to phaser.InputMR_AUTO.setENSE_DISA_CHEC (default True)
• mod (str) – indicate how to prepare the search model (default ‘unmod’)
• model (str) – indicate if the search model is an ensemble or a centroid (default ‘ensemble’)

append_results()

Method to append the results obtained into results

cleanup_dir_list

Property storing information about directories used in the pipeline that can be removed to save disk space

fit_helices()

Method to extend the solution with ideal helices

This method will create and set running another swamp.mr.mrrun.MrRun instance that will take the placed search model as an existing solution and try to place ideal helices to extend it.

idealhelices_workdir

Directory where the ideal helices solution extension will take place

phaser_info

Dictionary to use as **kwargs for Phaser

refmac_info

Dictionary to use as **kwargs for wRefmac

register_solution(**kwargs)

Register an existing solution information to be used with phaser

run()

Run the MR pipeline using of phaser, refmac5 and shelxe. Extend the possible solution with ideal helices

searchmodel_dir

Directory where the search model preparation will take place

shelxe_info

Dictionary to use as **kwargs for Shelxe