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

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.create_xvol', '__doc__': '\n Class to create excluded volumes for a given PhaseHypothesis.\n ', '__init__': <function ExcludedVolumeGenerator.__init__>, '_getSettings': <function ExcludedVolumeGenerator._getSettings>, 'createExcludedVolumeShell': <function ExcludedVolumeGenerator.createExcludedVolumeShell>, 'createExcludedVolumeClash': <function ExcludedVolumeGenerator.createExcludedVolumeClash>, 'createExcludedVolumeReceptor': <function ExcludedVolumeGenerator.createExcludedVolumeReceptor>, '_runCreateXvolCommand': <function ExcludedVolumeGenerator._runCreateXvolCommand>, '__dict__': <attribute '__dict__' of 'ExcludedVolumeGenerator' objects>, '__weakref__': <attribute '__weakref__' of 'ExcludedVolumeGenerator' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.phase.create_xvol'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)