dynsight.lens.list_neighbours_along_trajectory¶
- dynsight.lens.list_neighbours_along_trajectory(universe, r_cut, centers='all', selection='all', trajslice=None, respect_pbc=True, n_jobs=1)[source]¶
Produce a per-frame list of neighbors.
Warning
The LENS functions only work with orthogonal simulation boxes. We are working to make them compatible with non-orthogonal ones.
- Parameters:
universe (Universe) – MDAnalysis Universe containing the trajectory.
r_cut (float) – r_cut distance (Å) for defining neighbors.
centers (str) – Atom selection string for the centers where LENS is computed.
selection (str) – Atom selection string defining the environment.
trajslice (slice | None) – Frame slicing parameters for trajectory iteration.
respect_pbc (bool) – Whether to apply periodic boundary conditions.
n_jobs (int) – The number of jobs for parallelization with numba.
- Returns:
List of frames, each frame a list of AtomGroups for each atom.
- Return type: