get_positions

qaa.libs.utils.get_positions(topology, trajectory, *, mask='all', stride=None)

Read a molecular dynamics trajectory and retrieve the coordinates.

Parameters

• topology (PathLike) – Topology file

• trajectory (list of str) – Trajectory file

• mask (str) – Selection criterion for coordinates

• stride (int, optional) – Number of steps to read

Returns

The coordinates with shape (n_frames / step, n_atoms, 3)

Return type

NDArray