RDKit fails to generate 3D coords of certain structures

[evert.homan_scilifelab.se]

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)

[edborba]

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…

[evert.homan_scilifelab.se]

Will give it a try, thanks for your tip!

BW/Evert

[evert.homan_scilifelab.se]

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