Hi,
I am very new on cdk and on java in general so I am struggling a bit
with the syntaxis and construction of commands. I managed to read a .sdf
file and calculate smiles, now I am trying to calculate AlogP values,
however all values return 0.0, I think that I have a problem with
explicit hydrogens. This is what i've done:
IChemObjectBuilder builder =
NoNotificationChemObjectBuilder.getInstance();
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("C"));
molecule.addAtom(builder.newAtom("C"));
molecule.addAtom(builder.newAtom("O"));
molecule.addAtom(builder.newAtom("C"));
CDKAtomTypeMatcher matcher =
CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
for (IAtom atom : molecule.atoms()) {
IAtomType type = matcher.findMatchingAtomType(molecule, atom);
AtomTypeManipulator.configure(atom, type);
}
CDKHydrogenAdder adder =
CDKHydrogenAdder.getInstance(molecule.getBuilder());
adder.addImplicitHydrogens(molecule);
ALOGPDescriptor descriptor = new ALOGPDescriptor();
DescriptorValue value = descriptor.calculate(molecule);
IDescriptorResult theNumbers = value.getValue();
System.out.println(theNumbers);
Also, on using the calculation of Individual Descriptors I have no
problems (except the AlogP) but when using DescriptorEngine how can I
get the numerical values of each descriptor?, so far I have used:
DescriptorEngine engine = new
DescriptorEngine(DescriptorEngine.MOLECULAR);
engine.process(molecule);
but from then I don't know how to get each descriptor separately with
their corresponding names.
I would very much appreciate your reply, many thanks.
Angela
------------------------------------------------------------------------
------------
Dr Angela Beesley
Unilever Research & Development Port Sunlight
Quarry Road East
Bebington
Wirral
CH63 3JW
[email protected] <mailto:[email protected]>
Tel. +44 (0) 151 6411590
Mob. 07811143510
Unilever PLC
Registered in London. Company number: 41424
Registered office: Port Sunlight
Wirral, Merseyside, CH62 4ZD
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