Suggestion: chemistry - padel descriptor


I would have a suggestion for including the padel descriptor package into the knime. It is free, java application and the source code is avaliable.

best wishes,



I have developed KNIME nodes for PaDEL-Descriptor. Do note that currently it is not possible to use the CDK "Molecule to CDK" node as input to the "PaDEL-Descriptor" node as the CDK extension uses CDK 1.5.x whereas PaDEL-Descriptor uses CDK 1.4.x. Hence, there are some compatibility issues which will only be resolved when PaDEL-Descriptor updates to CDK 1.5.x, which will only happen when CDK 1.5.x becomes the new stable release. So for the time being, I just reimplement (i.e. copied) the CDK "Molecule to CDK" node into a "Molecule to CDK" node that is compatible with the PaDEL-Descriptor node. It also has its own “Compounds Reader” node which can read in chemical files in different formats.

You can add this site ( to your KNIME installation to download the nodes. Please see for more information.

Best regards,

Yap Chun Wei

Nice! Tww suggestions regarding your nodes: instead of using a copy of the CDK library in your plug-in you should use a dependency on the CDK plug-in instead. This would resolve the problem with incompatible CDK version between the two plug-ins (and also lots of other potential issues). Second, what about adding your nodes to the Community Contributions? KNIME user will then find them much easier.

I have tried using a dependency on CDK plug-in but it doesn't work that way. Mainly because the CDK plug-in uses CDK 1.5.x whereas PaDEL-Descriptor uses CDK 1.4.x. So if this plugin depends on the CDK plug-in, this will force PaDEL-Descriptor to use CDK 1.5.x, which will cause it to fail. The failure is caused by the change of IMolecule to IAtomContainer in CDK 1.5.x in some functions. At the current moment, CDK 1.5.x is still considered as unstable so I am not likely to modify PaDEL-Descriptor to use CDK 1.5.x yet until it becomes the stable release.

I don't not fully understand your problem. Why does your node fail, if it uses the new CDK library? If it's a change in the CDK API (leading to a compiler error) then you need to adapt your code and it will work with CDK 1.5. If you are using a different CDK library this will definitely cause problems if nodes from both plug-ins are used in the same workflow. We have seen such issues many times before.