a new version of the CDK nodes is now available as nightly build (trunk).
Thanks to great work done on the CDK core library (see blog and changelogs), we have moved from CML to SMILES. Beware that this will cause regressions in existing workflows.
The new version of CDK features better overall performance and more accurate descriptors and fingerprints (thanks to improved aromaticity perception, ring detection, etc.).
We have also taken onboard various suggestions from the forum, as promised in the respective posts.
The JChemPaint sketcher and CDK renderers have also seen some improvements.
Any suggestions or bug reports would be greatly appreciated.
Installed and works - I'm happy with the improvement in SMILES handling and speed, I get less problems on large and strangely-shaped molecules (particularly ones with rings within rings and such). :-)
It'd be awesome if SMARTS was handled by the CDKCells and the respective renderer. I'm OK currently using the SMARTS datatype in KNIME, though the AMBIT libraries for SMARTS handling are pretty good now (especially as you can turn a Query Molecule back into SMARTS).
for a start, I have added a SMARTS query node (latest nightly).
There is already a SMARTS cell type. I think it would be advantageous to use the existing type rather than to get the CDK cell type to take QueryAtomContainer into account. What's your use case?
Okies well as I said, it's not a problem as I'm using the SMARTS cell type anyhow. I'll look at the latest nightly build in a few weeks to try out this query node you mentioned.