On Apr 14, 2009, at 8:17 PM, Marshall Levesque wrote:
Here is an attempt to try to use OpenBabel's addH functionality and checking stereochemistry with RDKit:
Ooh. Now that's an exciting bug. The hydrogen addition code is designed for 3D molecules... I'll go file that in the bug database. Shouldn't be too hard, since in 2D, you've got the hash/wedge indication there.
My suggestion is the 2D->3D conversion I described to you before (which we do in Avogadro) and *then* add hydrogens. Checking your file, Open Babel always gets the right stereo ('S' for all molecules in your small test set).
Hope that helps, -Geoff
