openpathsampling.collectivevariables.MDTrajFunctionCV

class openpathsampling.collectivevariables.MDTrajFunctionCV(name, f, topology, cv_requires_lists=True, cv_wrap_numpy_array=True, cv_scalarize_numpy_singletons=True, **kwargs)[source]

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

This is identical to FunctionCV except that the function is called with an mdtraj.Trajectory object instead of the openpathsampling.Trajectory one using f(traj.to_mdtraj(), **kwargs)

Examples

>>> # To create an order parameter which calculates the dihedral formed
>>> # by atoms [7,9,15,17] (psi in Ala dipeptide):
>>> import mdtraj as md
>>> traj = 'paths.Trajectory()'
>>> psi_atoms = [7,9,15,17]
>>> psi_orderparam = FunctionCV("psi", md.compute_dihedrals,
>>>                              indices=[[2,4,6,8]])
>>> print psi_orderparam( traj )
__init__(name, f, topology, cv_requires_lists=True, cv_wrap_numpy_array=True, cv_scalarize_numpy_singletons=True, **kwargs)[source]
Parameters
  • name (str) –

  • f

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

  • cv_requires_lists

  • cv_wrap_numpy_array

  • cv_scalarize_numpy_singletons

  • scalarize_numpy_singletons (bool, default: True) – If True then arrays of length 1 will be treated as array with one dimension less. e.g. [[1], [2], [3]] will be turned into [1, 2, 3]. This is often useful, when you use en external function from mdtraj to get only a single value.

Methods

__init__(name, f, topology[, ...])

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.

f

is_named

True if this object has a custom name.

mdtraj_function

name

Return the current name of the object.

observe_objects

passing_chain

Return a list of chaindicts in order they will be tried.