Package schrodinger :: Package application :: Package phase :: Module create_xvol :: Class ExcludedVolumeGenerator

Class ExcludedVolumeGenerator

object --+
         |
        ExcludedVolumeGenerator

Class to create excluded volumes for a given PhaseHypothesis.

Instance Methods

[hide private]

__init__(self, base_hypothesis)
Initialize by creating a temp copy of the base hypothesis.

_getSettings(self, settings_inputconfig)
Initialize the class, updating the PhaseHypothesisInputConfig mode, validating the settings, and creating a member namedtuple.

str

_createTempMaeFile(self, sts)
Create a temporary file for running create_xvol jobs.

phase.PhpExclVol

createExcludedVolumeShell(self, active_sts, settings)
Runs the excluded volume shell creation for given active structures.

phase.PhpExclVol

createExcludedVolumeClash(self, active_sts, inactive_sts, settings)
Runs the excluded volume clash creation for a given set of active and inactive structures.

phase.PhpExclVol

createExcludedVolumeReceptor(self, receptor_st, settings)
Runs the excluded volume creation for a given receptor

phase.PhpExclVol

_runCreateXvolCommand(self, xvol_driver, args)
Build and run the excluded volume driver.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, base_hypothesis)
(Constructor)

Initialize by creating a temp copy of the base hypothesis.

Parameters:

base_hypothesis (str or PhpHypoAdaptor)

Overrides: object.__init__

_getSettings(self, settings_inputconfig)

Initialize the class, updating the PhaseHypothesisInputConfig mode, validating the settings, and creating a member namedtuple.

Parameters:

settings_inputconfig (PhaseHypothesisInputConfig) - Phase derived InputConfig instance

_createTempMaeFile(self, sts)

Create a temporary file for running create_xvol jobs.

Parameters:

suffix (str) - file suffix

Returns: str

temporary file path

createExcludedVolumeShell(self, 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: phase.PhpExclVol

Excluded volume based on active structure shell

createExcludedVolumeClash(self, 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: phase.PhpExclVol

Excluded volume based on active/inactive clash

createExcludedVolumeReceptor(self, 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: phase.PhpExclVol

Excluded volume based on active/inactive clash

_runCreateXvolCommand(self, xvol_driver, args)

Build and run the excluded volume driver. All excluded volume calculations rquire a hypothesis name to work from.

Parameters:

xvol_driver (str) - excluded volume driver name
args (list) - list of command arguments

Returns: phase.PhpExclVol

a new excluded volume based on a given hypothesis

Class ExcludedVolumeGenerator

__init__(self, base_hypothesis) (Constructor)

_getSettings(self, settings_inputconfig)

_createTempMaeFile(self, sts)

createExcludedVolumeShell(self, active_sts, settings)

createExcludedVolumeClash(self, active_sts, inactive_sts, settings)

createExcludedVolumeReceptor(self, receptor_st, settings)

_runCreateXvolCommand(self, xvol_driver, args)

init(self, base_hypothesis)
(Constructor)