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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