msmbuilder.featurizer.GaussianSolventFeaturizer¶

class msmbuilder.featurizer.GaussianSolventFeaturizer(solute_indices, solvent_indices, sigma, periodic=False)¶

Featurizer on weighted pairwise distance between solute and solvent.

We apply a Gaussian kernel to each solute-solvent pairwise distance and sum the kernels for each solute atom, resulting in a vector of len(solute_indices).

The values can be physically interpreted as the degree of solvation of each solute atom.

Parameters:

solute_indices : np.ndarray, shape=(n_solute,)

Indices of solute atoms

solvent_indices : np.ndarray, shape=(n_solvent,)

Indices of solvent atoms

sigma : float

Sets the length scale for the gaussian kernel

periodic : bool

Whether to consider a periodic system in distance calculations

References

..[1] Gu, Chen, et al. BMC Bioinformatics 14, no. Suppl 2 (January 21, 2013): S8. doi:10.1186/1471-2105-14-S2-S8.

Methods

`describe_features`(traj)	Generic method for describing 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__(solute_indices, solvent_indices, sigma, periodic=False)¶

Methods

`__init__`(solute_indices, solvent_indices, sigma)
`describe_features`(traj)	Generic method for describing 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)¶

Generic method for describing features.

Parameters:

traj : mdtraj.Trajectory

Trajectory to use

Returns:

feature_descs : list of dict

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

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: Featurizer name

featuregroup: Other information

Notes

Method resorts to returning N/A for everything if describe_features in not implemented in the sub_class

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 solvent fingerprints

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.