On Tue, May 18, 2010 at 2:50 PM, JEAN MARC NUZILLARD <jm.nuzill...@univ-reims.fr> wrote: > Message de Rajarshi Guha <rajarshi.g...@gmail.com>: > >> Aah, this will depend on 3D coordinates. Granted benzene should still >> work since it is flat in 3D - but likely the problem is that is trying >> to call getPoint3d() and that is NULL, since you only have 2D coords. > > The molecule is perceived as 2D because all z coordinates are zero. > Therefore getPoint3d() fails because there are no 3D coordinates > to handle. Is this summary correct?
Yes. > So, what is the solution? > I came to this surface problem because I got NaN values > in the calculation of CPSA descriptors. Aah, OK so this is where it all comes from. CPSA descriptors on non-3d molecules do not make sense You will have to get 3D coordinates > I guess I should work with molecules with 3D coordinates > for all atoms, H included in order to have correct CPSA values. > Is this correct? Correct -- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
