How to use the openpathsampling.netcdfplus.NamedObjectStore function in openpathsampling

To help you get started, we’ve selected a few openpathsampling examples, based on popular ways it is used in public projects.

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openpathsampling / openpathsampling / openpathsampling / storage / storage.py View on Github

self.create_store('topologies', NamedObjectStore(peng.Topology))

        snapshotstore = SnapshotWrapperStore()
        self.create_store('snapshots', snapshotstore)

        self.create_store('samples', paths.storage.SampleStore())
        self.create_store('samplesets', paths.storage.SampleSetStore())
        self.create_store('movechanges',
                          paths.storage.MoveChangeStore())
        self.create_store('steps', paths.storage.MCStepStore())

        # normal objects
        self.create_store('details', ObjectStore(paths.Details))
        self.create_store('pathmovers', NamedObjectStore(paths.PathMover))
        self.create_store('shootingpointselectors',
                          NamedObjectStore(paths.ShootingPointSelector))
        self.create_store('engines', NamedObjectStore(peng.DynamicsEngine))
        self.create_store('pathsimulators',
                          paths.storage.PathSimulatorStore())
        self.create_store('transitions', NamedObjectStore(paths.Transition))
        self.create_store('networks',
                          NamedObjectStore(paths.TransitionNetwork))
        self.create_store('schemes',
                          NamedObjectStore(paths.MoveScheme))
        self.create_store('interfacesets',
                          NamedObjectStore(paths.InterfaceSet))
        self.create_store('msouters',
                          NamedObjectStore(paths.MSOuterTISInterface))

        # stores where nestable could make sense but is disabled

        self.create_store('volumes',

openpathsampling / openpathsampling / openpathsampling / storage / storage.py View on Github

# normal objects
        self.create_store('details', ObjectStore(paths.Details))
        self.create_store('pathmovers', NamedObjectStore(paths.PathMover))
        self.create_store('shootingpointselectors',
                          NamedObjectStore(paths.ShootingPointSelector))
        self.create_store('engines', NamedObjectStore(peng.DynamicsEngine))
        self.create_store('pathsimulators',
                          paths.storage.PathSimulatorStore())
        self.create_store('transitions', NamedObjectStore(paths.Transition))
        self.create_store('networks',
                          NamedObjectStore(paths.TransitionNetwork))
        self.create_store('schemes',
                          NamedObjectStore(paths.MoveScheme))
        self.create_store('interfacesets',
                          NamedObjectStore(paths.InterfaceSet))
        self.create_store('msouters',
                          NamedObjectStore(paths.MSOuterTISInterface))

        # stores where nestable could make sense but is disabled

        self.create_store('volumes',
                          NamedObjectStore(paths.Volume, nestable=True))
        self.create_store('ensembles',
                          NamedObjectStore(paths.Ensemble, nestable=True))

        # special stores

        self.create_store('tag', ImmutableDictStore())

openpathsampling / openpathsampling / openpathsampling / storage / storage.py View on Github

self.create_store('snapshots', SnapshotWrapperStore())

        self.create_store('samples', paths.storage.SampleStore())
        self.create_store('samplesets', paths.storage.SampleSetStore())
        self.create_store(
            'movechanges',
            paths.storage.MoveChangeStore()
        )
        self.create_store('steps', paths.storage.MCStepStore())

        # normal objects
        self.create_store('details', ObjectStore(paths.Details))
        self.create_store('pathmovers', NamedObjectStore(paths.PathMover))
        self.create_store('shootingpointselectors',
                          NamedObjectStore(paths.ShootingPointSelector))
        self.create_store('engines', NamedObjectStore(peng.DynamicsEngine))
        self.create_store('pathsimulators',
                          paths.storage.PathSimulatorStore())
        self.create_store('transitions', NamedObjectStore(paths.Transition))
        self.create_store('networks',
                          NamedObjectStore(paths.TransitionNetwork))
        self.create_store('schemes',
                          NamedObjectStore(paths.MoveScheme))
        self.create_store('interfacesets',
                          NamedObjectStore(paths.InterfaceSet))
        self.create_store('msouters',
                          NamedObjectStore(paths.MSOuterTISInterface))

        # stores where nestable could make sense but is disabled

        self.create_store('volumes',

openpathsampling / openpathsampling / openpathsampling / storage / storage.py View on Github

'movechanges',
            paths.storage.MoveChangeStore()
        )
        self.create_store('steps', paths.storage.MCStepStore())

        # normal objects
        self.create_store('details', ObjectStore(paths.Details))
        self.create_store('pathmovers', NamedObjectStore(paths.PathMover))
        self.create_store('shootingpointselectors',
                          NamedObjectStore(paths.ShootingPointSelector))
        self.create_store('engines', NamedObjectStore(peng.DynamicsEngine))
        self.create_store('pathsimulators',
                          paths.storage.PathSimulatorStore())
        self.create_store('transitions', NamedObjectStore(paths.Transition))
        self.create_store('networks',
                          NamedObjectStore(paths.TransitionNetwork))
        self.create_store('schemes',
                          NamedObjectStore(paths.MoveScheme))
        self.create_store('interfacesets',
                          NamedObjectStore(paths.InterfaceSet))
        self.create_store('msouters',
                          NamedObjectStore(paths.MSOuterTISInterface))

        # stores where nestable could make sense but is disabled

        self.create_store('volumes',
                          NamedObjectStore(paths.Volume, nestable=True))
        self.create_store('ensembles',
                          NamedObjectStore(paths.Ensemble, nestable=True))

        # special stores

openpathsampling / openpathsampling / openpathsampling / storage / storage.py View on Github

self.create_store('transitions', NamedObjectStore(paths.Transition))
        self.create_store('networks',
                          NamedObjectStore(paths.TransitionNetwork))
        self.create_store('schemes',
                          NamedObjectStore(paths.MoveScheme))
        self.create_store('interfacesets',
                          NamedObjectStore(paths.InterfaceSet))
        self.create_store('msouters',
                          NamedObjectStore(paths.MSOuterTISInterface))

        # stores where nestable could make sense but is disabled

        self.create_store('volumes',
                          NamedObjectStore(paths.Volume, nestable=True))
        self.create_store('ensembles',
                          NamedObjectStore(paths.Ensemble, nestable=True))

        # special stores

        self.create_store('tag', ImmutableDictStore())

openpathsampling / openpathsampling / openpathsampling / storage / storage.py View on Github

self.create_store('details', ObjectStore(paths.Details))
        self.create_store('pathmovers', NamedObjectStore(paths.PathMover))
        self.create_store('shootingpointselectors',
                          NamedObjectStore(paths.ShootingPointSelector))
        self.create_store('engines', NamedObjectStore(peng.DynamicsEngine))
        self.create_store('pathsimulators',
                          paths.storage.PathSimulatorStore())
        self.create_store('transitions', NamedObjectStore(paths.Transition))
        self.create_store('networks',
                          NamedObjectStore(paths.TransitionNetwork))
        self.create_store('schemes',
                          NamedObjectStore(paths.MoveScheme))
        self.create_store('interfacesets',
                          NamedObjectStore(paths.InterfaceSet))
        self.create_store('msouters',
                          NamedObjectStore(paths.MSOuterTISInterface))

        # stores where nestable could make sense but is disabled

        self.create_store('volumes',
                          NamedObjectStore(paths.Volume, nestable=True))
        self.create_store('ensembles',
                          NamedObjectStore(paths.Ensemble, nestable=True))

        # special stores

        self.create_store('tag', ImmutableDictStore())

openpathsampling / openpathsampling / openpathsampling / storage / storage.py View on Github

# topologies might be needed fot CVs so put them here
        self.create_store('topologies', NamedObjectStore(peng.Topology))

        snapshotstore = SnapshotWrapperStore()
        self.create_store('snapshots', snapshotstore)

        self.create_store('samples', paths.storage.SampleStore())
        self.create_store('samplesets', paths.storage.SampleSetStore())
        self.create_store('movechanges',
                          paths.storage.MoveChangeStore())
        self.create_store('steps', paths.storage.MCStepStore())

        # normal objects
        self.create_store('details', ObjectStore(paths.Details))
        self.create_store('pathmovers', NamedObjectStore(paths.PathMover))
        self.create_store('shootingpointselectors',
                          NamedObjectStore(paths.ShootingPointSelector))
        self.create_store('engines', NamedObjectStore(peng.DynamicsEngine))
        self.create_store('pathsimulators',
                          paths.storage.PathSimulatorStore())
        self.create_store('transitions', NamedObjectStore(paths.Transition))
        self.create_store('networks',
                          NamedObjectStore(paths.TransitionNetwork))
        self.create_store('schemes',
                          NamedObjectStore(paths.MoveScheme))
        self.create_store('interfacesets',
                          NamedObjectStore(paths.InterfaceSet))
        self.create_store('msouters',
                          NamedObjectStore(paths.MSOuterTISInterface))

        # stores where nestable could make sense but is disabled

openpathsampling / openpathsampling / openpathsampling / storage / storage.py View on Github

# normal objects
        self.create_store('details', ObjectStore(paths.Details))
        self.create_store('pathmovers', NamedObjectStore(paths.PathMover))
        self.create_store('shootingpointselectors',
                          NamedObjectStore(paths.ShootingPointSelector))
        self.create_store('engines', NamedObjectStore(peng.DynamicsEngine))
        self.create_store('pathsimulators',
                          paths.storage.PathSimulatorStore())
        self.create_store('transitions', NamedObjectStore(paths.Transition))
        self.create_store('networks',
                          NamedObjectStore(paths.TransitionNetwork))
        self.create_store('schemes',
                          NamedObjectStore(paths.MoveScheme))
        self.create_store('interfacesets',
                          NamedObjectStore(paths.InterfaceSet))
        self.create_store('msouters',
                          NamedObjectStore(paths.MSOuterTISInterface))

        # stores where nestable could make sense but is disabled

        self.create_store('volumes',
                          NamedObjectStore(paths.Volume, nestable=True))
        self.create_store('ensembles',
                          NamedObjectStore(paths.Ensemble, nestable=True))

        # special stores

        self.create_store('tag', ImmutableDictStore())

openpathsampling / openpathsampling / openpathsampling / storage / storage.py View on Github

def _create_storages(self):
        """
        Register all Stores used in the OpenPathSampling Storage

        """

        # objects with special storages
        self.create_store('trajectories', paths.storage.TrajectoryStore())

        # topologies might be needed fot CVs so put them here
        self.create_store('topologies', NamedObjectStore(peng.Topology))
        self.create_store('cvs', paths.storage.CVStore())

        self.create_store('snapshots', SnapshotWrapperStore())

        self.create_store('samples', paths.storage.SampleStore())
        self.create_store('samplesets', paths.storage.SampleSetStore())
        self.create_store(
            'movechanges',
            paths.storage.MoveChangeStore()
        )
        self.create_store('steps', paths.storage.MCStepStore())

        # normal objects
        self.create_store('details', ObjectStore(paths.Details))
        self.create_store('pathmovers', NamedObjectStore(paths.PathMover))
        self.create_store('shootingpointselectors',

How to use the openpathsampling.netcdfplus.NamedObjectStore function in openpathsampling

To help you get started, we’ve selected a few openpathsampling examples, based on popular ways it is used in public projects.

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