The attached patch against CDK master adds functionality to save an IMolecule into a RDF graph and read it back into an IMolecule, using an OWL model reflecting the CDK data model. I believe this is the first format with the potential of roundtripping CDK models without loss of information.
With the Jena libraries, the patch is too large to attach to this report. Instead, you can find it online at my GitHub cdk repository in two versions:
The first has all 32-ish patches separately, and the second collapsed into one patch. Note that the 73-rdf contains two patches files elsewhere in this tracker, which are not present in the f-73-rdf branch (f=final). The collapsed patch must therefore be applied, not the patches from 73-rdf. Those are referred to, to see the history of the patch.
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