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
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