schrodinger.application.phase.create_xvol module

Phase driver for the Develop Common Pharmacophore Hypotheses (DHCP) workflow.

Copyright Schrodinger LLC, All Rights Reserved.

class schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator(base_hypothesis)

Bases: object

Class to create excluded volumes for a given PhaseHypothesis.

__init__(base_hypothesis)

Initialize by creating a temp copy of the base hypothesis.

Parameters

base_hypothesis (str or PhpHypoAdaptor) –

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

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

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