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/
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