chemcoord.Cartesian.get_coordination_sphere

Cartesian.get_coordination_sphere(index_of_atom, n_sphere=1, give_only_index=False, only_surface=True, exclude=None, use_lookup=None)

Return a Cartesian of atoms in the n-th coordination sphere.

Connected means that a path along covalent bonds exists.

Parameters:

  • index_of_atom (int)

  • give_only_index (bool) – If True a set of indices is returned. Otherwise a new Cartesian instance.

  • n_sphere (int) – Determines the number of the coordination sphere.

  • only_surface (bool) – Return only the surface of the coordination sphere.

  • exclude (set) – A set of indices that should be ignored for the path finding.

  • use_lookup (bool) – Use a lookup variable for get_bonds(). The default is specified in settings['defaults']['use_lookup']

Returns:

A set of indices or a new Cartesian instance.