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 |