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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?

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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?

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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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