Actually… If you really do want the most abundant isotope replace this with a
call to Istopes.getMajorIsotope()
<http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/config/Isotopes.html>;
J
> On 28 Nov 2014, at 09:29, John May <[email protected]> wrote:
>
> Hi Oscar,
>
> We could add this as a convince function but the following would work:
>
>> for (IAtom atom : container.atoms()) {
>> atom.setAtomicMass(null);
>> }
>
> J
>
>> On 7 Oct 2014, at 12:39, Oscar Mora <[email protected]> wrote:
>>
>> Hi,
>>
>> I use CDK 1.5.8 to read and pre-process a set of molecules (read from an SDF
>> file). Among those molecules there are very specific cases of molecules with
>> Isotopes, typically H isotopes like Deuterium or Tritium. I wonder if is
>> there a mechanism to replace those atoms by the most abundant associated
>> chemical element.
>>
>> For example, if there is an 3H (Tritium) modify this atom in the
>> 'IAtomContainer' java object to transform it to simple H.
>>
>> I am working on some kind of loop over all atoms, to check if an Atom is an
>> Isotope of another chemical element and then replace this atom. My problem
>> is that I cannot see which functionality of the package
>> org.openscience.cdk.Isotope use inside the loop.
>>
>> IAtomContainer molecule = ....
>> for (int i = 0; i < molecule .getAtomCount(); i++)
>> {
>> // molecule.getAtom(i) is an isotope ?
>> // replace molecule.getAtom(i) by the most abundant chemical
>> element
>> }
>>
>> Maybe, another idea could be modify the parameter
>>
>> InterpretHydrogenIsotopes
>>
>> of the object: MDLV2000Reader
>>
>> in this way:
>>
>> final Properties customSettings = new Properties();
>> customSettings.setProperty("InterpretHydrogenIsotopes", "false");
>> final PropertiesListener listener = new PropertiesListener(customSettings);
>>
>> final MDLV2000Reader mdlV2000Reader = new MDLV2000Reader();
>> mdlV2000Reader.addChemObjectIOListener(listener);
>> mdlV2000Reader.setReader(new
>> ByteArrayInputStream(cleanedMolecule.getBytes()));
>> iAtomContainer = mdlV2000Reader.read(new AtomContainer());
>>
>> but it does not works. (and it seems to be designed only of H atoms)
>>
>> Has anybody tried to do this kind of processing ? Any piece of advice is
>> would be most welcome.
>>
>> Thanks in advance.
>>
>> Oscar
>
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