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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