Hi Egon, Thank you very much for help. I have tried upon your suggestion, unfortunately I got same result as before.
Same issue occurred for a group of non-aromatics compounds I have tried. Kind regards, Xin Egon Willighagen-5 wrote: > > Hi Xin, > > On Fri, Jun 12, 2009 at 7:50 PM, Xin Gong<[email protected]> wrote: >> 1, Here is my rcdk code: >> …. >> mol <- >> parse.smiles("CC(C)C1=C2C(=NC(=NC2=O)CC3=CC=C(C=C3)OCCO)N(N1)C4=C(C=CC=C4Cl)Cl") >> do.aromaticity(mol) >> do.typing(mol) >> convert.implicit.to.explicit(mol) >> alogp = round(get.alogp(mol),2) >> print ("alogp is "%+%alogp) >> …. > > Please try changing the order of typing and aromaticity detection: > > do.typing(mol) > do.aromaticity(mol) > >> The output is 0.02 >> >> 2, Here is my java cdk code: >> >> IteratingMDLReader myiter = new >> IteratingMDLReader(sdfile,DefaultChemObjectBuilder.getInstance()); >> IMolecule mol = null; >> while (myiter.hasNext()) { >> mol = (IMolecule) myiter.next(); >> try { >> CDKAtomTypeMatcher matcher = >> CDKAtomTypeMatcher.getInstance(mol.getBuilder()); >> Iterable<IAtom> atoms = mol.atoms(); >> Iterator a = atoms.iterator(); >> while (a.hasNext()) { >> IAtom atom = (IAtom)a.next(); >> IAtomType type = matcher.findMatchingAtomType(mol, atom); >> AtomTypeManipulator.configure(atom, type); >> } >> CDKHydrogenAdder adder = >> CDKHydrogenAdder.getInstance(mol.getBuilder()); >> adder.addImplicitHydrogens(mol); > > Add here atomaticity detection: > > CDKHueckelAromaticityDetector.detectAromaticity(mol); > >> AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol); >> ALOGPDescriptor descriptor = new ALOGPDescriptor(); >> DescriptorValue value = descriptor.calculate(mol); >> IDescriptorResult theNumbers = (DoubleArrayResult)value.getValue(); >> System.out.println(theNumbers.toString()); >> } catch (Exception e) { >> System.out.println(e.toString()); >> } >> } >> >> The java cdk output is >> 0.01869999999999794,3.4968999999992296E-4,132.36929999999998 >> >> Same issue occurred for non-aromatics compounds. > > What are the CDK values with the updated code? > > Egon > > > -- > Post-doc @ Uppsala University > http://chem-bla-ics.blogspot.com/ > > ------------------------------------------------------------------------------ > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > > -- View this message in context: http://www.nabble.com/cdk-rcdk-alogp-question-tp24003480p24355264.html Sent from the cdk-user mailing list archive at Nabble.com. ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
