Improvements after I believe it was 1.5.4+ https://github.com/cdk/cdk/wiki/1.5.4-Release-Notes#stereochemistry-
On Tue, 30 Jul 2019 at 14:19, John Mayfield <john.wilkinson...@gmail.com> wrote: > Ah okay, in some versions of 1.5 it's supported. Which subversion are you > using? > > On Tue, 30 Jul 2019 at 09:34, Wehner, Sebastian < > sebastian.weh...@bruker.com> wrote: > >> Thanks for the clarification. And sorry, it was a typo I meant version >> 1.5. I assume your explanation still holds true for that as well? >> >> >> >> Sebastian >> >> >> >> *From:* John Mayfield <john.wilkinson...@gmail.com> >> *Sent:* Tuesday, July 30, 2019 10:27 AM >> *To:* Wehner, Sebastian <sebastian.weh...@bruker.com> >> *Cc:* cdk-user@lists.sourceforge.net >> *Subject:* Re: [Cdk-user] Stereochemistry resolution >> >> >> >> 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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