schrodinger.application.phase.packages.hypo_refine.screen_utils module

Module with phase_hypo_refine screening functionality.

Copyright Schrodinger LLC, All Rights Reserved.

schrodinger.application.phase.packages.hypo_refine.screen_utils.compute_score(args, screener)

Computes the weighted BEDROC score from the provded BedrocScreener

Parameters:
Returns:

Weighted BEDROC score

Return type:

float

schrodinger.application.phase.packages.hypo_refine.screen_utils.compute_tol_search_direct(tol_probe_hypo_files)

Returns a pseudo-gradient search direction based on changes in weighted BEDROC score from +/- changes to positional tolerances.

Parameters:tol_probe_hypo_files (list(str)) – Hypotheses with +/- changes in each tolerance
Returns:Tolerance search direction
Return type:list(float)
schrodinger.application.phase.packages.hypo_refine.screen_utils.refine_hypo_sites(args)

Adjust positions/orientations of hypothesis sites to improve fitness scores of actives relative to decoys.

Parameters:args (argparse.Namespace) – Command line arguments
Returns:Adjusted hypothesis
Return type:phase.PhpHypoAdaptor
schrodinger.application.phase.packages.hypo_refine.screen_utils.refine_hypo_xvol(args)

Runs an active/decoy screen with the current hypothesis, adds excluded volumes that clash only with the decoys, reruns the active/decoy screen, and saves the higher scoring hypothesis to args.hypo. Note that excluded volumes will not necessarily yield a higher score if exhaustive matching isn’t used throughout the refinement procedure. Returns the weighted BEDROC score obtained with the excluded volumes (even if lower) and the elapsed time. If excluded volumes could not be added because no decoys were matched, the returned score will be None.

Parameters:args (argparse.Namespace) – Command line arguments
Returns:tuple of xvol weighted BEDROC score and elapsed time
Return type:float, float
schrodinger.application.phase.packages.hypo_refine.screen_utils.run_bedroc_screen(args, hypo_file, actives_proj, decoys_proj, hit_file=None, report_time=True)

Runs an active/decoy screen and returns the weighted BEDROC score and elapsed time.

Parameters:
  • args (argparse.Namespace) – Command line arguments
  • hypo_file (str) – Hypothesis file
  • actives_proj (str) – Zipped actives project
  • decoys_proj (str) – Zipped decoys project
  • hit_file (str) – Maestro file for hits, or None if hits are not needed
  • report_time (bool) – Whether to report elapsed time for screen
Returns:

Weighted BEDROC score

Return type:

float

schrodinger.application.phase.packages.hypo_refine.screen_utils.setup_distributed_mask_screens(args)

Sets up distributed BEDROC screens that do exhaustive exploration of site masks which allow one or more sites to be missed.

Parameters:args (argparser.Namespace) – argparser.Namespace with command line options
Returns:list of subjob commands
Return type:list(list(str))
schrodinger.application.phase.packages.hypo_refine.screen_utils.setup_distributed_tol_direct_screens(args, direct)

Sets up distributed BEDROC screens that vary positional tolerances along the provided direction.

Parameters:
  • args (argparser.Namespace) – argparser.Namespace with command line options
  • direct (list(float)) – Direction of tolerance shift for each site in args.hypo
Returns:

list of subjob commands

Return type:

list(list(str))

schrodinger.application.phase.packages.hypo_refine.screen_utils.setup_distributed_tol_probe_screens(args)

Sets up distributed BEDROC screens that do exploration of +/- changes to each positional tolerance.

Parameters:args (argparser.Namespace) – argparser.Namespace with command line options
Returns:list of subjob commands
Return type:list(list(str))