CollectiveVariable Functions

openpathsampling.CollectiveVariable

For an introduction on collective variables, read the user guide topic on Creating collective variables.

Basic CVs

CollectiveVariable(name[, cv_time_reversible])

Wrapper for a function that acts on snapshots or iterables of snapshots

FunctionCV(name, f[, cv_time_reversible, …])

Turn any function into a CollectiveVariable.

CoordinateFunctionCV(name, f[, …])

Turn any function into a CollectiveVariable.

GeneratorCV(name, generator[, …])

Turn a callable class or function generating a callable object into a CV

CoordinateGeneratorCV(name, generator[, …])

Turn a callable class or function generating a callable object into a CV

InVolumeCV(name, volume)

Turn a openpathsampling.volume.Volume into a collective variable

Integrating with other packages

MDTrajFunctionCV(name, f, topology[, …])

Make CollectiveVariable from f that takes mdtraj.Trajectory as input.

PyEMMAFeaturizerCV(name, featurizer, …)

Make a CV from a function that takes mdtraj.trajectory as input.

MSMBFeaturizerCV(**kwargs)

A CollectiveVariable that uses an MSMBuilder3 featurizer