Hi, using the latest CDK when I write out a molecule using the
SDFWriter I loose all aromaticity (ie no kekule form or aromatic bonds
in the output). Has anybody seen this?
SmilesParser sp = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = sp.parseSmiles("c1ccccc1CC");
CDKHueckelAromaticityDetector.detectAromaticity(mol);
SDFWriter writer = new SDFWriter(new FileWriter(new File(filename)));
writer.write(mol)
--
Rajarshi Guha
NIH Chemical Genomics Center
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