mdentropy.metrics.ContactTransferEntropy

class mdentropy.metrics.ContactTransferEntropy(contacts='all', scheme='closest-heavy', ignore_nonprotein=True, **kwargs)

Transfer entropy calculations for contacts

Methods

partial_transform(traj[, shuffle, verbose])	Transform a single mdtraj.Trajectory into an array of metric scores.
transform(trajs[, shuffle, verbose])	Invokes partial_transform over a list of mdtraj.Trajectory objects

__init__(contacts='all', scheme='closest-heavy', ignore_nonprotein=True, **kwargs)

Methods

__init__([contacts, scheme, ignore_nonprotein])
partial_transform(traj[, shuffle, verbose])	Transform a single mdtraj.Trajectory into an array of metric scores.
transform(trajs[, shuffle, verbose])	Invokes partial_transform over a list of mdtraj.Trajectory objects

partial_transform(traj, shuffle=0, verbose=False)

Transform a single mdtraj.Trajectory into an array of metric scores.

Parameters:

traj : mdtraj.Trajectory

Trajectory to transform

shuffle : int

Number of shuffle iterations (default: 0)

verbose : bool

Whether to display performance

Returns:

result : np.ndarray

Scoring matrix

transform(trajs, shuffle=0, verbose=False)

Invokes partial_transform over a list of mdtraj.Trajectory objects

Parameters:

trajs : list

List of trajectories to transform

shuffle : int

Number of shuffle iterations (default: 0)

verbose : bool

Whether to display performance

Returns:

result : array_like

List of scoring matrices