#1158 No mass computed for high atomic number elements

open
nobody
None
5
2012-10-08
2011-06-28
No

The file isotopes.xml does not contain information about relativeAbundance for some isotopes (ex. those of Tc, probably because that information is not available or there is no 'natural' abundance to measure). As a result, when it comes to calculate the mass we get NaN (division by zero).
For those cases, might relativeAbundances be defined as a function of the isotope stability?

Discussion

  • What method are you using?

     
  • Hi, Egon!

    org.openscience.cdk.tools.manipulator.AtomContainerManipulator.getNaturalExactMass(IAtomContainer)

        IMolecule mol = builder.newInstance(IMolecule.class);
        mol.addAtom(new Atom("Tc"));
        System.out.println(AtomContainerManipulator.getNaturalExactMass(mol)); // NaN
    
     
  • OK. just wanted to make sure about that. This problem has been reported, and we need some functionality to calculate the mass for non-natural elements.