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