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.
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.
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