schrodinger.application.desmond.picklejar module

Facilities for pickling objects that are otherwise uneasy to pickle, e.g., class attributes.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.picklejar.PickleJar

Bases: object

jar = {<class 'schrodinger.application.desmond.picklejar.Picklable'>: {}, <class 'schrodinger.application.desmond.cmj.StageBase'>: {'count': None}, <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>: {}, <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>: {}, <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>: {}, <class 'schrodinger.application.desmond.stage.Primer'>: {}, <class 'schrodinger.application.desmond.stage.Concluder'>: {}, <class 'schrodinger.application.desmond.stage.Multisim'>: {}, <class 'schrodinger.application.desmond.stage.FepLauncher'>: {}, <class 'schrodinger.application.desmond.stage.FepJob'>: {'id': None}, <class 'schrodinger.application.desmond.stage.Task'>: {'gid': None}, <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>: {}, <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>: {}, <class 'schrodinger.application.desmond.stage.BuildGeometry'>: {}, <class 'schrodinger.application.desmond.stage.AssignForcefield'>: {}, <class 'schrodinger.application.desmond.stage.SystemBuilder'>: {}, <class 'schrodinger.application.desmond.stage.FepMapping'>: {}, <class 'schrodinger.application.desmond.stage.SimulateBase'>: {}, <class 'schrodinger.application.desmond.stage.SolvatePocketBase'>: {}, <class 'schrodinger.application.desmond.stage.GCMCCapable'>: {}, <class 'schrodinger.application.desmond.stage.Simulate'>: {}, <class 'schrodinger.application.desmond.stage.Minimize'>: {}, <class 'schrodinger.application.desmond.stage.ReplicaExchange'>: {}, <class 'schrodinger.application.desmond.stage.LambdaHopping'>: {}, <class 'schrodinger.application.desmond.stage.DesmondExtend'>: {}, <class 'schrodinger.application.desmond.stage.Vrun'>: {}, <class 'schrodinger.application.desmond.stage.FepVrun'>: {}, <class 'schrodinger.application.desmond.stage.Concatenate'>: {}, <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.PLAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.Analysis'>: {}, <class 'schrodinger.application.desmond.stage.FepanaJob'>: {'id': None}, <class 'schrodinger.application.desmond.stage.FepAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.CalcDdg'>: {}, <class 'schrodinger.application.desmond.stage.FepMapperReport'>: {}, <class 'schrodinger.application.desmond.stage.VacuumReport'>: {}, <class 'schrodinger.application.desmond.stage.WaterMapCluster'>: {}, <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.SolvatePocket'>: {}, <class 'schrodinger.application.desmond.stage.Extern'>: {}, <class 'schrodinger.application.desmond.stage.Trim'>: {}, <class 'schrodinger.application.desmond.stage.Stop'>: {}, <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>: {}, <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>: {}, <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>: {}, <class 'schrodinger.application.desmond.stage.FepMapper'>: {}, <class 'schrodinger.application.desmond.stage.AlignCore'>: {}, <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>: {}, <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>: {}, <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>: {}, <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>: {}, <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>: {}, <class 'schrodinger.application.desmond.stage.ExtractStructures'>: {}, <class 'schrodinger.application.desmond.stage.HashStructureTitle'>: {}, <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>: {}, <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>: {}, <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.AverageCell'>: {}}

static serialize(fh)

static deserialize(fh)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.picklejar', '__doc__': '\n\n ', 'jar': {<class 'schrodinger.application.desmond.picklejar.Picklable'>: {}, <class 'schrodinger.application.desmond.cmj.StageBase'>: {'count': None}, <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>: {}, <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>: {}, <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>: {}, <class 'schrodinger.application.desmond.stage.Primer'>: {}, <class 'schrodinger.application.desmond.stage.Concluder'>: {}, <class 'schrodinger.application.desmond.stage.Multisim'>: {}, <class 'schrodinger.application.desmond.stage.FepLauncher'>: {}, <class 'schrodinger.application.desmond.stage.FepJob'>: {'id': None}, <class 'schrodinger.application.desmond.stage.Task'>: {'gid': None}, <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>: {}, <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>: {}, <class 'schrodinger.application.desmond.stage.BuildGeometry'>: {}, <class 'schrodinger.application.desmond.stage.AssignForcefield'>: {}, <class 'schrodinger.application.desmond.stage.SystemBuilder'>: {}, <class 'schrodinger.application.desmond.stage.FepMapping'>: {}, <class 'schrodinger.application.desmond.stage.SimulateBase'>: {}, <class 'schrodinger.application.desmond.stage.SolvatePocketBase'>: {}, <class 'schrodinger.application.desmond.stage.GCMCCapable'>: {}, <class 'schrodinger.application.desmond.stage.Simulate'>: {}, <class 'schrodinger.application.desmond.stage.Minimize'>: {}, <class 'schrodinger.application.desmond.stage.ReplicaExchange'>: {}, <class 'schrodinger.application.desmond.stage.LambdaHopping'>: {}, <class 'schrodinger.application.desmond.stage.DesmondExtend'>: {}, <class 'schrodinger.application.desmond.stage.Vrun'>: {}, <class 'schrodinger.application.desmond.stage.FepVrun'>: {}, <class 'schrodinger.application.desmond.stage.Concatenate'>: {}, <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.PLAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.Analysis'>: {}, <class 'schrodinger.application.desmond.stage.FepanaJob'>: {'id': None}, <class 'schrodinger.application.desmond.stage.FepAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.CalcDdg'>: {}, <class 'schrodinger.application.desmond.stage.FepMapperReport'>: {}, <class 'schrodinger.application.desmond.stage.VacuumReport'>: {}, <class 'schrodinger.application.desmond.stage.WaterMapCluster'>: {}, <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.SolvatePocket'>: {}, <class 'schrodinger.application.desmond.stage.Extern'>: {}, <class 'schrodinger.application.desmond.stage.Trim'>: {}, <class 'schrodinger.application.desmond.stage.Stop'>: {}, <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>: {}, <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>: {}, <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>: {}, <class 'schrodinger.application.desmond.stage.FepMapper'>: {}, <class 'schrodinger.application.desmond.stage.AlignCore'>: {}, <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>: {}, <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>: {}, <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>: {}, <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>: {}, <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>: {}, <class 'schrodinger.application.desmond.stage.ExtractStructures'>: {}, <class 'schrodinger.application.desmond.stage.HashStructureTitle'>: {}, <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>: {}, <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>: {}, <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.AverageCell'>: {}}, '_update_data': <staticmethod object>, 'serialize': <staticmethod object>, 'deserialize': <staticmethod object>, '__dict__': <attribute '__dict__' of 'PickleJar' objects>, '__weakref__': <attribute '__weakref__' of 'PickleJar' 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__

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

__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.picklejar'

__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)

class schrodinger.application.desmond.picklejar.PicklableMetaClass(name, bases, dict)

Bases: type

__init__(name, bases, dict)

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

__base__

alias of builtins.type

__bases__ = (<class 'type'>,)

__basicsize__ = 864

__call__

Call self as a function.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.picklejar', '__init__': <function PicklableMetaClass.__init__>, '__doc__': None})

__dictoffset__ = 264

__dir__() → list

specialized __dir__ implementation for types

__eq__

Return self==value.

__flags__ = 2148292097

__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.

__instancecheck__() → bool

check if an object is an instance

__itemsize__ = 40

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.picklejar'

__mro__ = (<class 'schrodinger.application.desmond.picklejar.PicklableMetaClass'>, <class 'type'>, <class 'object'>)

__name__ = 'PicklableMetaClass'

__ne__

Return self!=value.

__new__()

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

__prepare__() → dict

used to create the namespace for the class statement

__qualname__ = 'PicklableMetaClass'

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

return memory consumption of the type object

__str__

Return str(self).

__subclasscheck__() → bool

check if a class is a subclass

__subclasses__() → list of immediate subclasses

__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).

__text_signature__ = None

__weakrefoffset__ = 368

mro() → list

return a type’s method resolution order

class schrodinger.application.desmond.picklejar.Picklable

Bases: object

__class__

alias of PicklableMetaClass

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.picklejar', '__dict__': <attribute '__dict__' of 'Picklable' objects>, '__weakref__': <attribute '__weakref__' of 'Picklable' 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__

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

__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.picklejar'

__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)

class schrodinger.application.desmond.picklejar.PickleState

Bases: object

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.picklejar', '__dict__': <attribute '__dict__' of 'PickleState' objects>, '__weakref__': <attribute '__weakref__' of 'PickleState' 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__

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

__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.picklejar'

__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)