msmbuilder.featurizer.DihedralFeaturizer¶

class msmbuilder.featurizer.DihedralFeaturizer(types=['phi', 'psi'], sincos=True)¶

Featurizer based on dihedral angles.

This featurizer transforms a dataset containing MD trajectories into a vector dataset by representing each frame in each of the MD trajectories by a vector containing one or more of the backbone or side-chain dihedral angles, or the sin and cosine of these angles.

Parameters:

types : list

One or more of [‘phi’, ‘psi’, ‘omega’, ‘chi1’, ‘chi2’, ‘chi3’, ‘chi4’]

sincos : bool

Instead of outputting the angle, return the sine and cosine of the angle as separate features.

Methods

`describe_features`(traj)	Return a list of dictionaries describing the dihderal features.
`featurize`(traj)
`fit`(traj_list[, y])
`fit_transform`(X[, y])	Fit to data, then transform it.
`get_params`([deep])	Get parameters for this estimator.
`partial_transform`(traj)	Featurize an MD trajectory into a vector space via calculation
`set_params`(**params)	Set the parameters of this estimator.
`summarize`()	Return some diagnostic summary statistics about this Markov model
`transform`(traj_list[, y])	Featurize a several trajectories.

__init__(types=['phi', 'psi'], sincos=True)¶

Methods

`__init__`([types, sincos])
`describe_features`(traj)	Return a list of dictionaries describing the dihderal features.
`featurize`(traj)
`fit`(traj_list[, y])
`fit_transform`(X[, y])	Fit to data, then transform it.
`get_params`([deep])	Get parameters for this estimator.
`partial_transform`(traj)	Featurize an MD trajectory into a vector space via calculation
`set_params`(**params)	Set the parameters of this estimator.
`summarize`()	Return some diagnostic summary statistics about this Markov model
`transform`(traj_list[, y])	Featurize a several trajectories.

describe_features(traj)¶

Return a list of dictionaries describing the dihderal features.

Parameters:

traj : mdtraj.Trajectory

The trajectory to describe

Returns:

feature_descs : list of dict

Dictionary describing each feature with the following information about the atoms participating in each dihedral

resnames: unique names of residues

atominds: the four atom indicies

resseqs: unique residue sequence ids (not necessarily 0-indexed)

resids: unique residue ids (0-indexed)

featurizer: Dihedral

featuregroup: the type of dihedral angle and whether sin or cos has been applied.

fit_transform(X, y=None, **fit_params)¶

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters:

X : numpy array of shape [n_samples, n_features]

Training set.

y : numpy array of shape [n_samples]

Target values.

Returns:

X_new : numpy array of shape [n_samples, n_features_new]

Transformed array.

get_params(deep=True)¶

Get parameters for this estimator.

Parameters:

deep: boolean, optional

If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns:

params : mapping of string to any

Parameter names mapped to their values.

partial_transform(traj)¶

Featurize an MD trajectory into a vector space via calculation of dihedral (torsion) angles

Parameters:

traj : mdtraj.Trajectory

A molecular dynamics trajectory to featurize.

Returns:

features : np.ndarray, dtype=float, shape=(n_samples, n_features)

A featurized trajectory is a 2D array of shape (length_of_trajectory x n_features) where each features[i] vector is computed by applying the featurization function to the `i`th snapshot of the input trajectory.