The chemistry extensions have changed a lot in version 1.2.0, in particular the molecular parsing nodes, the 2D structure rendering, and the CDK integration. Why?
Ah, right we changed some stuff along those lines. The reasoning behind this was that we wanted to stop to automatically (=hiddenly) convert between formats and leave control over such conversions to the user. Before we converted SMILES automatically into a CDK representation which enabled us to show 2D representations. Now you can read in, for example a SMILES string and explicitly translate it into a CDK representation (or something else using Open Babel). (Note that the FileReader now allows you to choose SMILES directly for columns containing string-like elements.) The reason why you do not see structures in the CDK cell is that we split this functionality. A lot of functions in CDK are somewhat, let’s say “premature”, so we are trying to not combine too much into one node. So the SMILES->CDK converter does not automatically trigger the 2D coordinate generation – you need to use the appropriate node to do this. Afterwards the CDK cell does contain this information and the 2D render
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