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
