Why were you using that version? On Wed, 17 Jul 2019 at 06:37, Wehner, Sebastian <sebastian.weh...@bruker.com> wrote:
> Hi John, > > > > That is what I suspected. I had some hope that there was still a way to > properly convert stereochemistry in this version… > > Anyways, thanks for your quick answer and explanations. > > > > Sebastian > > > > *From:* John Mayfield <john.wilkinson...@gmail.com> > *Sent:* Tuesday, July 16, 2019 6:05 PM > *To:* Wehner, Sebastian <sebastian.weh...@bruker.com> > *Cc:* cdk-user@lists.sourceforge.net > *Subject:* Re: [Cdk-user] Stereochemistry is disregarded when creating > SMILES from MOL-File > > > > 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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