normalize ( v )

distance ( u,  v )

distance_to_msms_surface ( atoms,  msms_model )

triangle_distance ( xyz,  triangle_vertices )

Returns distance, triangle point, and side (1 or -1) of triangle.

distance_to_surface ( atoms,  smodel )

surface_distance (
        xyz,
        surf_vertex_xyz,
        surf_triangles,
        )

Compute the closest distance from a point to a surface. The surface is represented as a list of triangles. The distance, closest point, and side of the closest triangle that the given point lies on is returned. Side +1 is the right-handed normal clockwise vertex traversal, while -1 indicates the opposite side. This is for determining if the given point is inside or outside the surface.

cross ( u,  v )

add ( u,  v )

write_surface_distances ( atoms,  surfaces )

dot ( u,  v )

multiply ( a,  v )

sign ( x )

subtract ( u,  v )

selection_surface_distance ()