biotite.structure.remove_pbc_from_coord

biotite.structure.remove_pbc_from_coord(coord, box)

Remove segmentation caused by periodic boundary conditions from given coordinates.

In this process the first coordinate is taken as origin and is moved inside the box. All other coordinates are assembled relative to the origin by using the displacement coordinates in adjacent array positions. Basically, this function performs the reverse action of move_inside_box().

Parameters

coordndarray, dtype=float, shape=(m,n,3) or shape=(n,3)

The coordinates of the potentially segmented structure.

boxndarray, dtype=float, shape=(m,3,3) or shape=(3,3)

The simulation box or unit cell that is used as periodic boundary. The amount of dimensions must fit the coord parameter.

Returns

sanitized_coordndarray, dtype=float, shape=(m,n,3) or shape=(n,3)

The reassembled coordinates.

See also

remove_pbc_from_coord

move_inside_box

Notes

This function solves a common problem from MD simulation output: When atoms move over the periodic boundary, they reappear on the other side of the box, segmenting the structure. This function reassembles the given coordinates, removing the segmentation.