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.CustomUnpickler(file, *, fix_imports=True, encoding='ASCII', errors='strict', buffers=())

Bases: _pickle.Unpickler

find_class(module, name)

Return an object from a specified module.

If necessary, the module will be imported. Subclasses may override this method (e.g. to restrict unpickling of arbitrary classes and functions).

This method is called whenever a class or a function object is needed. Both arguments passed are str objects.

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.cmj.StructureStageBase'>: {}, <class 'schrodinger.application.desmond.stage.jobs.FepJob'>: {'id': None}, <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>: {}, <class 'schrodinger.application.desmond.stage.simulate.SimulateBase'>: {}, <class 'schrodinger.application.desmond.stage.simulate.RemovesInitialGCMCSolvent'>: {}, <class 'schrodinger.application.desmond.stage.simulate.GCMCCapable'>: {}, <class 'schrodinger.application.desmond.stage.simulate.Simulate'>: {}, <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>: {}, <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>: {}, <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>: {}, <class 'schrodinger.application.desmond.stage.simulate.VrunBase'>: {}, <class 'schrodinger.application.desmond.stage.simulate.Vrun'>: {}, <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>: {}, <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>: {}, <class 'schrodinger.application.desmond.stage.simulate.ReInit'>: {}, <class 'schrodinger.application.desmond.stage.workflow.Primer'>: {}, <class 'schrodinger.application.desmond.stage.workflow.Concluder'>: {}, <class 'schrodinger.application.desmond.stage.workflow.Task'>: {'gid': None}, <class 'schrodinger.application.desmond.stage.workflow.Extern'>: {}, <class 'schrodinger.application.desmond.stage.workflow.Trim'>: {}, <class 'schrodinger.application.desmond.stage.workflow.Stop'>: {}, <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge'>: {}, <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield'>: {}, <class 'schrodinger.application.desmond.stage.prepare.forcefield.LambdaDynamicsAssignForcefield'>: {}, <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule'>: {}, <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>: {}, <class 'schrodinger.application.desmond.stage.prepare.forcefield.ForcefieldBuilderLauncher'>: {}, <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>: {}, <class 'schrodinger.application.desmond.stage.prepare.structure.LambdaDynamicsBuildGeometry'>: {}, <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>: {}, <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>: {}, <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>: {}, <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>: {}, <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>: {}, <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>: {}, <class 'schrodinger.application.desmond.stage.prepare.structure.GroupWaters'>: {}, <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.analysis.Analysis'>: {}, <class 'schrodinger.application.desmond.stage.analysis.FepanaJob'>: {'id': None}, <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.launcher.Multisim'>: {}, <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>: {}, <class 'schrodinger.application.desmond.stage.launcher.FepMembraneLauncher'>: {}, <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>: {}, <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>: {}, <class 'schrodinger.application.desmond.stage.fep_mapper.CombinedProteinFepMapper'>: {}, <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>: {}, <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>: {}, <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>: {}, <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>: {}, <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>: {}, <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase'>: {}, <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>: {}, <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>: {}, <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>: {}, <class 'schrodinger.application.desmond.stage.app.kinetics.RandomAcceleratedMD'>: {}, <class 'schrodinger.application.desmond.stage.app.kinetics.RamdGenerateUnbindingPath'>: {}, <class 'schrodinger.application.desmond.stage.app.kinetics.ValidateStability'>: {}, <class 'schrodinger.application.desmond.stage.app.kinetics.RamdSetup'>: {}, <class 'schrodinger.application.desmond.stage.app.kinetics.RamdCleanup'>: {}, <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbinding'>: {}, <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup'>: {}, <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsSplitReceptor'>: {}, <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper'>: {}, <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher'>: {}, <class 'schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob'>: {}, <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>: {}, <class 'schrodinger.application.desmond.stage.app.matsci.DeformCell'>: {}, <class 'schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder'>: {}, <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.app.matsci.ScaleEffectiveSolvent'>: {}, <class 'schrodinger.application.desmond.stage.app.matsci.ExtractSubSystem'>: {}, <class 'schrodinger.application.desmond.stage.app.matsci.FrozenPhononCorrection'>: {}, <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>: {}, <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>: {}, <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>: {}, <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>: {}, <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>: {}, <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>: {}, <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>: {}, <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>: {}, <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.app.constant_ph.ConstantpHAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.app.lambda_dynamics_analysis.LambdaDynamicsAnalysis'>: {}, <class 'schrodinger.application.desmond.stage.deprecate.MustSkip'>: {}, <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>: {}, <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>: {}, <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>: {}, <class 'schrodinger.application.desmond.stage.deprecate.VacuumReport'>: {}, <class 'schrodinger.application.desmond.stage.deprecate.FepMapperReport'>: {}}

static serialize(fh)

static deserialize(fh)

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

Bases: type

__init__(name, bases, dict)

class schrodinger.application.desmond.picklejar.Picklable

Bases: object

class schrodinger.application.desmond.picklejar.PickleState

Bases: object