On Mit, 2009-07-01 at 18:25 +0200, sebi wrote: > On Mit, 2009-07-01 at 18:20 +0200, sebi wrote: > > On Mit, 2009-07-01 at 11:06 +0200, Egon Willighagen wrote: > > > Hi Seb, > > > > > > On Wed, Jul 1, 2009 at 10:43 AM, sebi<[email protected]> > > wrote: > > > > when calculating xLogP and tPSA descriptors with CDK from SMILES i > > get > > > > values similar to those from PubChem. > > > > When i calculate them from molfile I get different values. > > > > Any idea? Am I doing something wrong? > > > > > > What code are you using? Are you making sure you do the same > > > preprocessing for both? E.g. the SMILES parser will do aromaticity > > > detection, the MDL V2000 molfile reader would not... > > > > Sorry for double post.. > > > > This is the code I'm using now: > > Sorry for triple post, my mailer is buggy :s > the code: > > # 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 > > sebi >
Ok, I figured out. I missed the implicit hydrogens. my fault.. thanks anyway sebi ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
