openpathsampling.collectivevariable.PyEMMAFeaturizerCV

class openpathsampling.collectivevariable.PyEMMAFeaturizerCV(name, featurizer, topology, **kwargs)

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

This is identical to CoordinateGeneratorCV except that the function is called with an mdraj.Trajetory object instead of the openpathsampling.Trajectory one using fnc(traj.to_mdtraj(), **kwargs)

__init__(name, featurizer, topology, **kwargs)

Parameters

• name –

• featurizer (pyemma.coordinates.featurizer) – the pyemma featurizer used as a callable class

• topology (openpathsampling.engines.topology.MDTrajTopology) – the mdtraj topology wrapper from OPS that is used to initialize the featurizer in pyemma.coordinates.featurizer(topology)

• **kwargs (dict) – a dictionary of named arguments which should be given to the featurizer (for example, the atoms which define a specific distance/angle). Finally an instance instance = cls(**kwargs) is created when the CV is created and using the CV will call instance(snapshots)

Notes

All trajectories or snapshots passed in kwargs will be converted to mdtraj objects for convenience

Methods

__init__(name, featurizer, topology, **kwargs)	param name
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableObject
cache_all()	Sync this CV with attached storages
count_weaks()	Return number of objects subclassed from StorableObject still in memory
descendants()	Return a list of all subclassed objects
disable_diskcache()
enable_diskcache()
fix_name()	Set the objects name to be immutable.
from_dict(dct)	Reconstruct an object from a dictionary representaiton
get_uuid()
idx(store)	Return the index which is used for the object in the given store.
named(name)	Name an unnamed object.
objects()	Returns a dictionary of all storable objects
reverse_uuid()
ruuid(uid)
set_cache_store(value_store)	Attach store variables to the collective variables.
set_observer(active)	(De-)Activate observing creation of storable objects
str_chain()	Return a string representation of the chain of dicts called.
sync()	Sync this CV with the attached storages
to_dict()	Convert object into a dictionary representation
with_diskcache([template, chunksize, …])

Attributes

ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
base_cls	Return the base class
base_cls_name	Return the name of the base class
cls	Return the class name as a string
default_name	Return the default name.
featurizer
generator
instance
is_named	True if this object has a custom name.
name	Return the current name of the object.
observe_objects
passing_chain	Return a list of chaindicts in order they will be tried.