In an existing workflow that normally works the optimize geometry node throws the following error:
WARN RDKit Optimize Geometry Failed to process data. Generating empty result cells. [All rows]
What could cause this issue? i tired increasing the number of iterations to no avail. The molecules have Hs added and generated coordinates using according RDKit nodes. I also tried UFF instead of MMFF94(s) but issue still there. I assume it's an issue with the molecules (2, but can't post them...)?
I have seen warnings/errors like this when the input molecule doesn't have a 3D conformation.
Could you please check then input to the Optimize Geometry node and make sure that those two molecules actually have 3D coordinates? The easiest way to do this is to look at the input table and change the renderer for the RDKit molecule cell to "SDF String" (you do this by right-clicking on the column header). Check to see that the atoms have z coordinates.
We should probably generate a more informative warning message here.
You're right. The Generate Cooridnates Node does not actually generate 3D cooridnates. All z-values are 0. Ideally the Coordiantes node would fail or give a warning in this case.
Fro now I can use CDK 3D Coodinates node as that works with this specific molecule.
Just as an FYI: I've added a better warning message to the code. This, along with a new version of the RDKit backend (which is a bit more permissive about generating conformers), should be in the nightly build "soon"