openpathsampling.collectivevariables.PyEMMAFeaturizerCV

class openpathsampling.collectivevariables.PyEMMAFeaturizerCV(name, featurizer, topology, **kwargs)[source]

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)[source]
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)

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.