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
args (argparse.Namespace) – Command line arguments
screener (bedroc_screener.BedrocScreener) – BedrocScreener for which a screen has been run
- 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))