Non-polar surface area?

Is there a way to calculate the non-polar surface area of a molecule using Marvin?





Obviously the TPSAPlugin can calculate polar surface area, so if there's a way to calculate the total area, then one can simply subtract. Some old posts on this forum mentioned MarvinSpace's implementation of the Connolly surface area using a triangle mesh approximation. But it wasn't clear to me how (or if) that information is available via public APIs, or if there's a more direct way to calculate the result.





Thanks,


Chris

Hi Chris,





the MarvinSpace surface-mesh based calculation was just an idea, but it appears to be a feasible approach. We plan to implement a Geometry Plugin that provides methods for surface area calculations (among some others).


However, at the moment there is no public method to get these values.





What other values you consider to be interesting/useful? Torsions, volume etc??





Regards,


Miklos

Hi Miklos,





Here's a response from someone else at my company:

Quote:

I would be interested in volume and the solvent accessible surface areas for polar and non-polar surfaces. If they are looking for general ideas I would add atom pairs and topological torsions. There also is a series of papers from Peter Jurs describing methods to calculate some additional 3D descriptors which are useful.

Thanks for considering these requests!





Chris

Hi Chris, thanks for the suggestions.


We will check the relevant papers by prof. Jurs.


Regarding topological torsions, we already have a topology analysis plugin that provides various 2D descriptors, though topological torsion is not yet implemented. We'll consider it.





All suggestions and requests are most welcome.


Miklos