biotite.structure.distance(atoms1, atoms2, box=None)[source]

Measure the euclidian distance between atoms.

atoms1, atoms2 : ndarray or Atom or AtomArray or AtomArrayStack

The atoms to measure the distances between. The dimensions may ary. Alternatively an ndarray containing the coordinates can be provided. Usual NumPy broadcasting rules apply.

box : ndarray, shape=(3,3) or shape=(m,3,3), optional

If this parameter is set, periodic boundary conditions are taken into account (minimum-image convention), based on the box vectors given with this parameter. The shape (m,3,3) is only allowed, when the input coordinates comprise multiple models.

dist : float or ndarray

The atom distances. The shape is equal to the shape of the input atoms with the highest dimensionality minus the last axis.

See also