schrodinger.application.phase.create_xvol module¶
Phase driver for the Develop Common Pharmacophore Hypotheses (DHCP) workflow.
Copyright Schrodinger LLC, All Rights Reserved.
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class
schrodinger.application.phase.create_xvol.
ExcludedVolumeGenerator
(base_hypothesis)¶ Bases:
object
Class to create excluded volumes for a given PhaseHypothesis.
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__init__
(base_hypothesis)¶ Initialize by creating a temp copy of the base hypothesis.
Parameters: base_hypothesis (str or PhpHypoAdaptor
) –
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createExcludedVolumeShell
(active_sts, settings)¶ Runs the excluded volume shell creation for given active structures.
create_xvolShell -hypo <hypo> -ref <actives> [options]
Parameters: - active_sts (list of
structure.Structure
) – structures to build excluded volume shell around - settings (
PhaseHypothesisInputConfig
) – calculation settings
Returns: Excluded volume based on active structure shell
Return type: phase.PhpExclVol
- active_sts (list of
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createExcludedVolumeClash
(active_sts, inactive_sts, settings)¶ Runs the excluded volume clash creation for a given set of active and inactive structures.
create_xvolClash -hypo <hypo> -pos <actives> -neg <inactives> [options]
Parameters: - active_sts (list of
structure.Structure
) – active structures - inactive_sts (list of
structure.Structure
) – inactive structures - settings (
PhaseHypothesisInputConfig
) – calculation settings
Returns: Excluded volume based on active/inactive clash
Return type: phase.PhpExclVol
- active_sts (list of
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createExcludedVolumeReceptor
(receptor_st, settings)¶ Runs the excluded volume creation for a given receptor
create_xvolReceptor -hypo <hypo> -receptor <receptor> [options]
Parameters: - receptor_st (
structure.Structure
) – receptor structure - settings (
PhaseHypothesisInputConfig
) – calculation settings
Returns: Excluded volume based on active/inactive clash
Return type: phase.PhpExclVol
- receptor_st (
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