The Pyrol is an old problem. Saturation doesn't work, the valences are wrong and inchi fails because of this (lawfully, I would say). Can somebody else comment on the current status of the saturation code? I am not up to date about it.
On Tuesday 01 April 2008 18:13:50 Gianfranco wrote: > 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 > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplac >e _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
