Hi Sebastian, > I am using CDK version 1.4.17
That is a very old version and does not convert stereochemistry correctly. Essentially there wasn't data structures to represent it so it was store different for 0D (e.g. SMILES) vs 2D vs 3D. This will all fixed about 7 years ago :-). Latest release is 2.2 BTW - https://github.com/cdk/cdk/releases John On Tue, 16 Jul 2019 at 15:04, Wehner, Sebastian via Cdk-user < cdk-user@lists.sourceforge.net> wrote: > Hi, > > > > I could use your help! I am using CDK version 1.4.17 and want to build a > SMILES string from a mol-file (SDF from lipid maps). The molecule has two > isomers, but this information should be included in the mol-file, should it > not? > > > > Anyways, I pass the mol-file as ByteArrayInputStream into MDLV2000Reader and > then create a new AtomContainer from this. Iterating over each atom of > the AtomContainer, using a CDKAtomTypeMatcher to get the IAtomType of the > atom which I then use to configure this atom with via AtomTypeManipulator > .configure(). > > > > Finally adding implicit hydrogens to the AtomContainer, creating a > SmilesGenerator and returning the smiles of the AtomContainer with > smilesGenerator.createSMILES(AtomContainer). > > > > However this produces a SMILES of the molecule which disregards the > stereochemistry. The documentation states, that stereochemistry is taken > into account ( > http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/smiles/SmilesGenerator.html). > Am I missing something? > > > > Would be great I someone could help! Added the link to lipid maps for the > example: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMGL02010378. > > > > > > Best regards, > > Sebastian Wehner > > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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