Hi everyone, I have a question regarding the alogp computed by cdk (cdk-1.2.3.jar) or rcdk. I would appreciate that if you could share your thoughts.
The alogp number I got from rCDK or CDK is quite different compare to the number obtained from other program, Dragon for example, the online tool (http://www.vcclab.org/lab/alogps/). For example, here is a compound I got from pubchem: 9549301 CC(C)C1=C2C(=NC(=NC2=O)CC3=CC=C(C=C3)OCCO)N(N1)C4=C(C=CC=C4Cl)Cl Alogp given by rcdk 0.02 Alogp given by cdk 0.02 Alogp given by online tool 4.90 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) …. 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); 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. Thanks you very much in advance, Sincerely, Xin Gong -- View this message in context: http://www.nabble.com/cdk-rcdk-alogp-question-tp24003480p24003480.html Sent from the cdk-user mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
