schrodinger.application.phase.create_xvol module¶

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

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`