RDKit renderer fails to render cis/trans double bonds when they are in SMILES format

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:

  1. A compound with a cis/trans double bond is sketched and generated in SD format
  2. The compound in SDF format is correctly parsed and rendered by RDKit
  3. The compound is correctly transformed to SMILES format by RDKit
  4. The compound is NOT correctly rendered by RDKit when it’s in SMILES format. Indeed it is rendered as having a trans double bond.
  5. 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)

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