after safely having imported ca. 2Mio compounds I wanted to convert SDF mol field into RDKit for further analysis. I got this error in the table while everything run ok…
this happened after updating to knime 3.6.0 from 3.5.4 (no problem before). W10 used (already patched with latest Microsoft’s patch). The 2D rendering is ok after SDF Reader, but not anymore after RDKit from Molecules and Salt Stripper. Structural content is there though, as I run FPs and similarity searches and got reasonable results after joining back the rendered structures from SDF reader table.
Any idea why this happened? BTW, JAVA = jre1.8.0_172
You need to install the nightly build version of the RDKit nodes in order to use KNIME 3.6. You can install these by adding this update site to KNIME if you don’t have it enabled already:
We are working on a new release of the RDKit nodes so that there is a stable version that works with KNIME 3.6 and hope to have something done within the next week.
everything is fine now.