Hi Noel,
> I see that MFAnalyser is gone from trunk, to be replaced by
> MolecularFormulaManipulator. Using MolecularFormulaManipulator and the
> jar at http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/,
> I have the following results...
>
> For the molecule represented by the SMILES string "C", I get a
> molecular formula of "C1" (getString)
How Egon commented you have to make explicit the hydrogens
using CDKHydrogenAdded before calling the MolecularFormulaGenerator.
> and a molecular weight of -1
> (getTotalExactMass).
>
The other problem with calculating the exact mass is that you have to
specify what Isotope is the element with the corresponding exact mass.
Of course, we think automatically C is 12 and H is 1 but could not be.
You have different examples in MolecularFormulaManipulatorTest.
Nevertheless I add one possible solution that it could help you.
IsotopeFactory ifac = IsotopeFactory.getInstance(builder);
MolecularFormula formula = new MolecularFormula();
formula.addIsotope(ifac.getMajorIsotope("C"),2);
formula.addIsotope(ifac.getMajorIsotope("H"),6);
For this case you will obtain the correctly exact mass.
Best regards,
Miquel
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