schrodinger.application.desmond.system_builder_inp module

A script to create a system builder input file.

class schrodinger.application.desmond.system_builder_inp.SystemBuilderInput

Bases: object

__init__()

Initialize self. See help(type(self)) for accurate signature.

reset()

setVdwScalingFactor(value=0)

setOplsaaVersion(value='')

setSoluteAlignment(name='', value=1)

setMMFepioMapModeOption(value=1)

setMMFepioRetainAngleOption(value=1)

setSolute(name)

fixSolute()

setPositiveIon(name='Na.mae')

setNegativeIon(name='Cl.mae')

setSaltPositiveIon(name='Na.mae')

setSaltNegativeIon(name='Cl.mae')

setMembrane(name='DPPC.mae.gz')

setSolvent(name='spc.box.mae')

setMembranize(value=1)

setMembranePatch(x_mem=10.0, y_mem=10.0)

setNeutralize(value=1)

setAddAlchemicalIons(value=1)

setUseAlchemicalWater(value=1)

addIons(ion_type='positive', nion=0)

addSalt(c=0.0)

setExcludeLocation(value, distance)

setIonLocation(value)

setSolvate(value=1)

setBoundaryCondition(**kwargs)

setWriteOneMaeFile(name='-1')

setWriteMaeFile(name='-1')

setWriteMaeffFile(name='-1')

setWriteXyzFile(name='-1')

setWritePdbFile(name='-1')

setWriteTopFile(name='-1')

setWriteG96File(name='-1')

write(name)

read(name)

read_text(l)

extractSolventFromSt(st, asl='')

deleteSolventFromSt(st, asl='')

treatSolventFromSolute(op='separate', asl='')

run(name='desmond_setup', options=[])

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.system_builder_inp', '__init__': <function SystemBuilderInput.__init__>, 'reset': <function SystemBuilderInput.reset>, 'setVdwScalingFactor': <function SystemBuilderInput.setVdwScalingFactor>, 'setOplsaaVersion': <function SystemBuilderInput.setOplsaaVersion>, 'setSoluteAlignment': <function SystemBuilderInput.setSoluteAlignment>, 'setMMFepioMapModeOption': <function SystemBuilderInput.setMMFepioMapModeOption>, 'setMMFepioRetainAngleOption': <function SystemBuilderInput.setMMFepioRetainAngleOption>, 'setSolute': <function SystemBuilderInput.setSolute>, 'fixSolute': <function SystemBuilderInput.fixSolute>, 'setPositiveIon': <function SystemBuilderInput.setPositiveIon>, 'setNegativeIon': <function SystemBuilderInput.setNegativeIon>, 'setSaltPositiveIon': <function SystemBuilderInput.setSaltPositiveIon>, 'setSaltNegativeIon': <function SystemBuilderInput.setSaltNegativeIon>, 'setMembrane': <function SystemBuilderInput.setMembrane>, 'setSolvent': <function SystemBuilderInput.setSolvent>, 'setMembranize': <function SystemBuilderInput.setMembranize>, 'setMembranePatch': <function SystemBuilderInput.setMembranePatch>, 'setNeutralize': <function SystemBuilderInput.setNeutralize>, 'setAddAlchemicalIons': <function SystemBuilderInput.setAddAlchemicalIons>, 'setUseAlchemicalWater': <function SystemBuilderInput.setUseAlchemicalWater>, 'addIons': <function SystemBuilderInput.addIons>, 'addSalt': <function SystemBuilderInput.addSalt>, 'setExcludeLocation': <function SystemBuilderInput.setExcludeLocation>, 'setIonLocation': <function SystemBuilderInput.setIonLocation>, 'setSolvate': <function SystemBuilderInput.setSolvate>, 'setBoundaryCondition': <function SystemBuilderInput.setBoundaryCondition>, 'setWriteOneMaeFile': <function SystemBuilderInput.setWriteOneMaeFile>, 'setWriteMaeFile': <function SystemBuilderInput.setWriteMaeFile>, 'setWriteMaeffFile': <function SystemBuilderInput.setWriteMaeffFile>, 'setWritePdbFile': <function SystemBuilderInput.setWritePdbFile>, 'setWriteXyzFile': <function SystemBuilderInput.setWriteXyzFile>, 'setWriteTopFile': <function SystemBuilderInput.setWriteTopFile>, 'setWriteG96File': <function SystemBuilderInput.setWriteG96File>, 'write': <function SystemBuilderInput.write>, 'read': <function SystemBuilderInput.read>, 'read_text': <function SystemBuilderInput.read_text>, 'extractSolventFromSt': <function SystemBuilderInput.extractSolventFromSt>, 'deleteSolventFromSt': <function SystemBuilderInput.deleteSolventFromSt>, 'treatSolventFromSolute': <function SystemBuilderInput.treatSolventFromSolute>, 'run': <function SystemBuilderInput.run>, '__dict__': <attribute '__dict__' of 'SystemBuilderInput' objects>, '__weakref__': <attribute '__weakref__' of 'SystemBuilderInput' objects>, '__doc__': None})

__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.desmond.system_builder_inp'

__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)