Hi
Apologies if I missed a topic on this already.
I wanted to ask whether its necessary to use "molecule to RDKit" before generating conformers with RDKit ? I'm using large SDF files as input and mixing in MOE nodes for cleanup/sanitizing but 5-10% of my molecules still cannot be processed by the conformer generator and I was wondering whether I'm missing some steps.
On a related note, do I need to add explicit hydrogens prior to writing the conformers to disk ? So far, I've simply plugged in an SDF writer directly to the conformer generator but reading the files again and then trying to add hydrogens, tends to give me errors and/or bad geometries.
Thanks in advance,
Adam