remove_pbc

biotite.structure.remove_pbc(atoms, selection=None)

Remove segmentation caused by periodic boundary conditions from each molecule in the given structure.

In this process the centroid of each molecule is moved into the dimensions of the box. To determine the molecules the structure is required to have an associated BondList. Otherwise segmentation removal is performed on a per-chain basis.

Parameters:

atomsAtomArray, shape=(n,) or AtomArrayStack, shape=(m,n)

The potentially segmented structure. The box attribute must be set in the structure. An associated bonds attribute is recommended.

selectionndarray, dtype=bool, shape=(n,)

Specifies which parts of atoms are sanitized, i.e the segmentation is removed.

Returns:

sanitized_atomsAtomArray or AtomArrayStack

The input structure with removed segmentation over periodic boundaries.

See also

remove_pbc_from_coord

Variant that acts directly on coordinates.

Notes

This function ensures that adjacent atoms in the input AtomArray/AtomArrayStack are spatially close to each other, i.e. their distance to each other is be smaller than the half box size.

Gallery

Basic analysis of a MD simulation

Basic analysis of a MD simulation