schrodinger.application.phase.packages.hypo_refine.hypo_utils module¶
Module with phase_hypo_refine hypothesis-related functionality.
Copyright Schrodinger LLC, All Rights Reserved.
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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
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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
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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
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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)
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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
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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)
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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
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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