openpathsampling.collectivevariable.MDTrajFunctionCV

class openpathsampling.collectivevariable.MDTrajFunctionCV(name, f, topology, cv_requires_lists=True, cv_wrap_numpy_array=True, cv_scalarize_numpy_singletons=True, **kwargs)

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)

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)	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.
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.