RDKit fails to generate 3D coords of certain structures
Hi,
I am attempting to use RDKit to generate 3D coordinates of structures that have been protonated by OpenBabel. RDKit fails to do so for a subset of structures that all seem to have a carbonyl conjugated with a double bond in a cyclic ether (see attached). This only happens when using the ‘-p 7.4’ flag in the preceding OpenBabel node.
An image of the workflow:
OpenBabel settings:
Some examples of failing structures:
SDF file with failing structures (renamed to .txt):