No, it wasn't possible. They used different data structures so you could go to/from SMILES and to/from 2D Mol/CML but not from Mol to Smi or Smi to Mol. Please don't use 1.1.5 (I presume as there is no 1.15 version) it's 10+ years old.
John On Tue, 30 Jul 2019 at 08:49, Wehner, Sebastian via Cdk-user < cdk-user@lists.sourceforge.net> wrote: > Hello, > > > > I am trying to produce a smiles string from a molfile, via AtomContainer > as an intermediate. Is it possible to properly resolve stereochemistry in > CDK version 1.15? > > > > In some detail: > > I tried some approaches with known stereo-isotopes for which I both had > the molfile (SDF). The molfile was parsed via MDLV2000Reader to an > AtomContainer which in turn was passed to the SmilesGenerator for parsing > to smiles. Sadly both molfiles resulted in the same smiles string. > > I read the paper for CDK v2.0 ( > https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0220-4) > which states that in this version the stereochemistry is standardized. But > it does not convey whether it wasn’t possible before. So is there a way to > resolve stereochemistry in v1.15? And if so, can anyone provide some code > examples? > > > > Hope someone can shed some light on this, > > Best Regards > > Sebastian > > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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