schrodinger.application.phase.packages.hypo_refine.hypo_utils module¶
Module with phase_hypo_refine hypothesis-related functionality.
Copyright Schrodinger LLC, All Rights Reserved.
- schrodinger.application.phase.packages.hypo_refine.hypo_utils.clean_hypo(hypo, to_static)¶
Prepares the hypothesis for refinement by removing attributes that are likely to be invalidated by the refinement process and/or would interfere with refinement. Also converts the reference ligand to static fragments if to_static is True. Returns a string that describes the changes made and a Boolean indicating whether the changes warrant a new active/decoy screen.
- Parameters
hypo (phase.PhpHypoAdaptor) – Hypothesis to be cleaned
to_static (bool) – Whether to convert reference ligand to static fragments
- Returns
Description of changes and Boolean for rerunning screen
- Return type
str, bool
- schrodinger.application.phase.packages.hypo_refine.hypo_utils.get_match_options(hypo_file, exhaustive)¶
Returns matching options that are appropriate for BEDROC screens against the supplied hypothesis.
- Parameters
hypo_file (str) – Hypothesis file
exhaustive (bool) – Whether to do exhaustive partial matching
- Returns
Matching options
- Return type
phase.PhpMatchOptions
- schrodinger.application.phase.packages.hypo_refine.hypo_utils.get_site_mask_summary(hypo_file)¶
Returns a string that contains a summary of the site mask in the provided hypothesis file.
- Parameters
hypo_file (str) – Hypothesis file
- Returns
Site mask summary
- Return type
str
- schrodinger.application.phase.packages.hypo_refine.hypo_utils.get_site_masks(hypo, max_miss)¶
Returns all possible site masks for the provided hypothesis, where the number of sites that may be missed is 1,…,max_miss.
- Parameters
hypo (phase.PhpHypoAdaptor) – Pharmacophore hypothesis
max_miss (int) – Maximum number of sites that need not be matched
- Returns
All possible site masks
- Return type
list(phase.PhpSiteMask)
- schrodinger.application.phase.packages.hypo_refine.hypo_utils.get_site_tol(hypo, step_size, direct)¶
Returns positional tolerances obtained by adding step_size * direct to the tolerances in the provided hypothesis.
- Parameters
hypo (phase.PhpHypoAdaptor) – Pharmacophore hypothesis
step_size (float) – Scalar step size
direct (list(float)) – Direction of tolerance shift for each site in hypo
- Returns
Positional tolerances
- Return type
phase.PhpDeltaHypo
- schrodinger.application.phase.packages.hypo_refine.hypo_utils.get_site_tol_probes(hypo, step_size)¶
Returns a list of hypothesis positional tolerance objects obtained by adding/subtracting step_size to/from each positional tolerance in the provided hypothesis.
- Parameters
hypo (phase.PhpHypoAdaptor) – Pharmacophore hypothesis
step_size (float) – Scalar step size
- Returns
List of hypothesis positional tolerances
- Return type
list(phase.PhpDeltaHypo)
- schrodinger.application.phase.packages.hypo_refine.hypo_utils.get_site_tol_summary(hypo_file)¶
Returns a string that contains a summary of the positional tolerances in the provided hypothesis file.
- Parameters
hypo_file (str) – Hypothesis file
- Returns
Positional tolerances summary
- Return type
str
- schrodinger.application.phase.packages.hypo_refine.hypo_utils.save_hypo_with_score(hypo, score, hypo_file, baseline=False)¶
Stores the provided score in the hypothesis property PHASE_WEIGHTED_BEDROC and saves the hypothesis to disk. If baseline is true, the score will also be stored in the property PHASE_WEIGHTED_BEDROC_BASELINE.
- Parameters
hypo (phase.PhpHypoAdaptor) – Hypothesis
score (float) – Weighted BEDROC score
hypo_file (str) – Destination hypothesis file
baseline (bool) – Whether to store score in baseline property