On Wed, Jul 1, 2009 at 6:25 PM, sebi<sebastian.kl...@hispeed.ch> wrote: > On Mit, 2009-07-01 at 18:20 +0200, sebi wrote: >> On Mit, 2009-07-01 at 11:06 +0200, Egon Willighagen wrote: > # these are RCDK methods to build the molecule instance > @mol = Lang.read_molfile(molfile) > # or > @mol = Lang.read_smiles(smiles) > # and im doing this CDK calls > Tools::Manipulator::AtomContainerManipulator.convertImplicitToExplicitHydrogens(@mol) > > Tools::Manipulator::AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(@mol) > Aromaticity::CDKHueckelAromaticityDetector.detectAromaticity(@mol) > desc = XLogPDescriptor.new() > desc.calculate(@mol).getValue().doubleValue() > > I looked at the SmilesParser source and couldn't find something else > that's different
That should do it... OK, can you try the following... save both molecules (read from file, and parsed from SMILES) and save that to CML, and post that here... preferably with the same atom ordering... Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
