CGAL users discussion list

[Nico Kruithof <>]

Then, you should compute the Regular triangulation of the balls and extract the balls that contribute to a dual vertex lying outside the union of balls. To do that, you could iterate over all finite cells of the regular triangulation, check whether the dual point lies outside one (and therefore all) ball defining the cell. In that case all four vertices intersect the union of balls.

You could also use the skin surface package to mesh the union of balls.

Bests,

Nico

On Sun, Dec 26, 2010 at 6:18 PM, Francois Berenger <> wrote:

Nico Kruithof wrote:

Not exactly, the Connolly surface is the surface obtained by rolling a ball of radius r over the union of balls. If r==0, you are right, but not if r>0.

The rolling probe sphere should represent a solvent molecule in my case (water).

The easiest way is to compute the regular triangulation of the balls (weighted points) with the radius increased by r. Then, if a Voronoi cell of a weighted point (ball) is not entirely contained within that ball, the ball contributes to the Connoly surface. This shouldn't be too hard to implement.

I see. In fact, the dot surface should be OK for me, I don't really need the Connoly surface in fact.
I think I will do this outside of CGAL if it does not include such
high level constructs as molecule.get_dot_suface() or molecule.get_Connoly_suface().

Regards,
F.

Bests,
Nico

On Tue, Dec 21, 2010 at 10:27 AM, Laurent Rineau (GeometryFactory) < <mailto:>> wrote:

   On Tuesday 21 December 2010 09:29:41 Francois Berenger wrote:
    > Hi,
    >
    > Using CGAL, is it easy to extract the list of atoms
    > contributing to the Connolly surface for a globular
    > protein?

   Unless I am wrong, the Connolly surface is the skin surface with scale
   factor 1.

   See this chapter if you can find what you need:
    http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Skin_surface_3/Chapter_main.html

   --
   Laurent Rineau, PhD
   R&D Engineer at GeometryFactory              http://www.geometryfactory.com/
   Release Manager of the CGAL Project       http://www.cgal.org/

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