openpathsampling.ensemble.MinusInterfaceEnsemble

class openpathsampling.ensemble.MinusInterfaceEnsemble(state_vol, innermost_vols, n_l=2, forbidden=None, greedy=False)[source]

This creates an ensemble for the minus interface.

The specific implementation allows us to use the multiple-segment minus ensemble described by Swenson and Bolhuis. The minus interface was originally developed by van Erp. For more details, see the section “Anatomy of a PathMover: the Minus Move” in the OpenPathSampling Documentation.

Parameters
  • state_vol (Volume) – The Volume which defines the state for this minus interface

  • innermost_vols (list of Volume) – The Volume defining the innermost interface with which this minus interface does its replica exchange.

  • n_l (integer (greater than one)) – The number of segments crossing innermost_vol for this interface.

References

T.S. van Erp. Phys. Rev. Lett.

D.W.H. Swenson and P.G. Bolhuis. J. Chem. Phys. 141, 044101 (2014). doi:10.1063/1.4890037

__init__(state_vol, innermost_vols, n_l=2, forbidden=None, greedy=False)[source]

A path volume defines a set of paths.

Methods

__init__(state_vol, innermost_vols[, n_l, ...])

A path volume defines a set of paths.

args()

Return a list of args of the __init__ function of a class

base()

Return the most parent class actually derived from StorableObject

can_append(trajectory[, trusted])

Returns true, if the trajectory so far can still be in the ensemble if it is appended by a frame.

can_prepend(trajectory[, trusted])

Returns true, if the trajectory so far can still be in the ensemble if it is prepended by a frame.

check(trajectory)

Alias for __call__

check_reverse(trajectory[, trusted])

See __call__; same thing, but potentially in reverse frame order

count_weaks()

Return number of objects subclassed from StorableObject still in memory

descendants()

Return a list of all subclassed objects

extend_sample_from_trajectories(...[, ...])

Generate a sample in the ensemble by extending parts of trajectories

find_first_subtrajectory(trajectory)

Return the first sub-trajectory that matches the ensemble

find_last_subtrajectory(trajectory)

Return the last sub-trajectory that matches the ensemble

fix_name()

Set the objects name to be immutable.

from_dict(dct)

Reconstruct an object from a dictionary representaiton

get_sample_from_trajectories(trajectories[, ...])

Generate a sample in the ensemble by testing trajectories

get_uuid()

idx(store)

Return the index which is used for the object in the given store.

iter_extendable_slices(trajectory[, ...])

Return an iterator over maxiaml slices of extendable subtrajectories

iter_split(trajectory[, max_length, ...])

Return iterator over subtrajectories satisfying the given ensemble.

iter_valid_slices(trajectory[, max_length, ...])

Return an iterator over slices of subtrajectories matching the ensemble

named(name)

Name an unnamed object.

objects()

Returns a dictionary of all storable objects

reverse_uuid()

ruuid(uid)

set_observer(active)

(De-)Activate observing creation of storable objects

split(trajectory[, max_length, min_length, ...])

Return list of subtrajectories satisfying the given ensemble.

split_sample_from_trajectories(trajectories)

Generate a sample in the ensemble by searching for sub-parts

strict_can_append(trajectory[, trusted])

Returns true if the trajectory can be the beginning of a trajectory in the ensemble.

strict_can_prepend(trajectory[, trusted])

Returns true if the trajectory can be the end of a trajectory in the ensemble.

to_dict()

Convert object into a dictionary representation

trajectory_summary(trajectory)

Return dict with info on how this ensemble "sees" the trajectory.

trajectory_summary_str(trajectory)

Returns a string with the results of the trajectory_summary function.

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.

extendable_sub_ensembles

is_named

True if this object has a custom name.

name

Return the current name of the object.

observe_objects