Atom Association and Surface Splitting

Molecular and accessible surfaces are created with an atom associated to each vertex. These atom indices can be obtained using the OESurface.GetAtoms and OESurface.GetAtomsElement methods, but the default assignments are not very accurate. Using the OESurfaceToMoleculeDistance function will ensure that each vertex’s atom assignment is to the atom whose van der Waals surface is closest to that vertex. While the associations provide an accurate mapping of individual vertices to atoms, triangles on the surface may have vertices belonging to different atoms. This can make make mapping of atom-based properties onto the surface problematic.

Surface splitting, using the OESplitSurfaceByAtoms function, will divide a surface such that the boundaries between atoms are distinct, with no triangles being shared by multiple atoms. Surfaces are split through a process of moving vertices and subdividing triangles until no triangle edges cross the analytical boundaries between atoms. A comparison of the atom associations of unsplit and split surfaces is shown in Table: Atom Associations.

Atom Associations


Molecular surface of benzene, colored by atom indices assigned during surface construction


Same surface after atom indices are reassigned using OESurfaceToMoleculeDistance


Same surface after splitting with OESplitSurfaceByAtoms

Splitting a surface has some consequences that you should be aware of. A split surface will have significantly more vertices and triangles than the surface it was created from. In addition, it will contain numerous duplicate vertices, having the same coordinates and normals but with different atom associations. Finally, it will contain “zero-area” triangles, generated between duplicated vertices to preserve the connectivity of vertices within the surface.