Collective Variables

Here we document the various classes that can wrap functions to make them into OPS collective variables.

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(name, featurizer, topology)	A CollectiveVariable that uses an MSMBuilder3 featurizer
PLUMEDCV(name, plmd, definition[, ...])	Make CollectiveVariable computed by PLUMED [PLU2a] according to the command name: definition, where name is a PLUMED label and definition contains all PLUMED keywords.
PLUMEDInterface(topology[, pathtoplumed, ...])	Interfaces the Cython PLUMED wrapper [PLU2b] located at /path/to/plumed2/python and allows to set and get non-PLUMEDCV commands (i.e., non-outputting).