"Timeout while converting molecule"-Error using Molecule to CDK node

KNIME Analytics Platform
1

hello!!

Can anybody Please!! tell me what can I do to avoid the "Timeout while converting molecule Row..."-Error when using the Molecule to CDK Node? Maybe one need to know that the data I handle with is relatively large... I have ~ 50*1500 Rows (in each row there is the sdf-data about the molecule I need to convert)... I already tried write tables to disc but that doesn´t work either and anyway I don´t know whether that has to do with the erreor.

thank you for answering quickly!!!

2

You can set the timeout higher in the node's dialog. The error comes from CDK that took a long time for certain molecules to be parsed in the version the plugin is using. It only affects certain molecules though.

You may also have a look at the new CDK integration, which offers the same functionality but is based on a much more recent version.