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):
rdkit_fails_3d.txt (636.3 KB)
Well, it may not be what you want, but use the external openbabel. I used your structures to pass through openbabel and then RDkit 3D and the coordinates were generated. A logical explanation for this is the version of openbabel that knime uses, 2.1. While the external openbabel is 3.1.1.
My result was the conversion of all the structures
I hope this helps…
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Will give it a try, thanks for your tip!
BW/Evert
Tried it with an external version 3.1.1 of Openbabel, which does not give any errors.
An update of the bundled version would be in order imo.
BW/Evert
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