Re: [Cdk-devel] Molecular Cross-Sectional Diameter Calculation with OpenBabel

[Geoffrey H. <ge...@ge...>]

Dear Sebastian,

I am not aware of any descriptors for molecular cross-section. Off the  
top of my head, it seems as if that would require prediction of the 3D  
coordinates, followed by conformational searching, and then a scan of  
coordinates to estimate the cross-section.

Certainly with OB-2.2, you can generate 3D coordinates (e.g., obgen)  
and run conformational searching (e.g., obconformer). You would then  
need to write the code to extract cross-section from the 3D coordinates.

Cheers,
-Geoff

On Jan 20, 2009, at 4:46 AM, Strempel Sebastian wrote:

> Dear Geoffrey,
>
> is there any possibility to approximate the molecular cross- 
> sectional diameter from a 2D SMILES with OpenBabel?
> If not could you point me in the right direction to search? Thank you.
>
> Best regards
>
> Sebastian