Dear all
I'm using the following code for the generation of Inchi:
IAtomContainer atomContainer= sp.parseSmiles(SMILES);
CDKHueckelAromaticityDetector.detectAromaticity(atomContainer);
CDKHydrogenAdder hdx.addImplicitHydrogens(atomContainer);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(atomContainer);
Molecule m = builder.newMolecule(atomContainer);
InChIGenerator gen = factory.getInChIGenerator(ac);
String inchi = gen.getInchi();
if the AtomContainer is built from the SMILES "c1ccccc1"
the Inchi is generated
but when I use "c1cc[nH]c1" the Inchi is null. the warning is:
InChI failed: ERROR [Accepted unusual valence(s): C(3); N(4); Cannot
process aromatic bonds]
Can you help me???
Thanks!
Gianfranco
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