Yes, that explains it. I am using version 1.5.13… Thank you for the explanations.
Basti From: John Mayfield <[email protected]> Sent: Tuesday, July 30, 2019 3:23 PM To: Wehner, Sebastian <[email protected]> Cc: [email protected] Subject: Re: [Cdk-user] Stereochemistry resolution 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> Sent: Tuesday, July 30, 2019 10:27 AM To: Wehner, Sebastian <[email protected]<mailto:[email protected]>> Cc: [email protected]<mailto:[email protected]> 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 <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/cdk-user
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