MDTraj Utils

MDTraj contains a number of tools to help with development. These are located in mdtraj.utils.

Miscellanies

import_(module)

Import a module, and issue a nice message to stderr if the module isn’t installed.

in_units_of(quantity, units_in, units_out[, …])

Convert a numerical quantity between unit systems.

ilen(iterable)

Length of an iterator.

timing([name])

A timing context manager

Validation

ensure_type(val, dtype, ndim, name[, …])

Typecheck the size, shape and dtype of a numpy array, with optional casting.

check_random_state(seed)

Turn seed into a np.random.RandomState instance

Unit cell and Periodic Boundary Conditions

lengths_and_angles_to_box_vectors(a_length, …)

Convert from the lengths/angles of the unit cell to the box vectors (Bravais vectors).

box_vectors_to_lengths_and_angles(a, b, c)

Convert box vectors into the lengths and angles defining the box.

Rotations

rotation_matrix_from_quaternion(q)

Compute a 3x3 rotation matrix from a given quaternion (4-vector).

uniform_quaternion([size, random_state])

Generate uniform normalized quaternion 4-vectors