box

Functions related to simulation boxes and boundary conditions.

Functions

box2cart	Transform box coordinates to Cartesian coordinates.
box_volume	Calculate the volume of a (triclinic) box.
cart2box	Transform Cartesian coordinates to box coordinates.
diagonal	Calculate the length of the diagonal of an orthogonal box.
make_whole	Make compounds of a MDAnalysis AtomGroup whole that are split across periodic boundaries.
triclinic_box	Convert the matrix representation of a simulation box to the length-angle representation.
triclinic_vectors	Convert the length-angle representation of a simulation box to the matrix representation.
unwrap_frame	Unwrap a single trajectory frame.
vdist	Calculate the distance vectors between two position arrays.
volume	Calculate the volume of orthogonal boxes.
wrap	Shift compounds of an MDAnalysis AtomGroup back into the primary unit cell.
wrap_pos	Shift all particle positions into the primary unit cell.