Dear KNIME-RDKit friends,
Today I encountered a problem with the RDKit renderer in KNIME and I would like to have your opinion on this. In the attached example workflow you can see the following:
- A compound with a cis/trans double bond is sketched and generated in SD format
- The compound in SDF format is correctly parsed and rendered by RDKit
- The compound is correctly transformed to SMILES format by RDKit
- The compound is NOT correctly rendered by RDKit when it’s in SMILES format. Indeed it is rendered as having a trans double bond.
- The compound is correctly rendered by Marvin renderer.
Why does this happen? Is it a general problem of the RDKit renderer or am I missing something?
Any feedback, comment or suggestion is welcome.
RDKit_renderer_problem.knwf (44.9 KB)