Quick note: One important feature of this extension of the normal PDBFile is that all
indices are shifted so they are consecutive, which is required for betatopologies and
secondary structures to make sense and not crash.
ProGAL is a library containing geometric datastructures and algorithms with special emphasis on supporting
representation and analysis of protein structures.
A simplicial complex is a topological space of a particular kind, constructed by "gluing together" points,
line segments, triangles, and their n-dimensional counterparts.
An alpha complex for a set of d-dimensional points and a real number alpha is a subset of the Delaunay complex
where all simplices that can be enclosed by an alpha-probe (a hypersphere of radius alpha), without the probe
enclosing any points, are removed.
A Delaunay complex for a set of d-dimensional points is a tesselation of the points such that no point is inside
the circumscribing hypersphere of the d-simplices (for the 3D case: Tetrahedra).
Projects the point v onto this plane and returns the parameters of
the projected point (scaling of v1, of v2 and finally the distance or
scaling along n).