Wednesday, March 16, 2011

Chemkit's VF2 Algorithm in Substructure Benchmark

Asad Rahman posted a benchmark on his blog comparing chemkit's VF2 substructure isomorphism algorithm (which he ported to Java) with two others. As seen from the graph chemkit fares very well against the competition :-).

Tuesday, March 15, 2011

Molecular surface support in chemkit

Today I added support for visualizing molecular surfaces to chemkit. You can see the commit here. The new class is called GraphicsMolecularSurfaceItem and it was added to the chemkit-graphics library.

The rendering is fast due to the underlying O(n log n) alpha-shape based surface algorithm. There is still room for improvement but the new code works well.

Here is a screenshot of the new molecular surface item on top of a guanine molecule:

So far only Van Der Waals and solvent accessible surfaces are supported. Solvent excluded surfaces are coming soon. Stay tuned.