Hi Philippe,
On 8/29/07, Philippe Vaglio <[EMAIL PROTECTED]> wrote:
> I am parsing a sdf file and calculating the molw using
> MFAnalyzer.getMass(). Everything is fine until I get
> to a molecule that contains a Deuterium with the D symbol.
I guess this now gets read as a PseudoAtom....
> The molw return is then 0.
which has mass 0. In principle deuterium is done via Isotope.getMassNumber().
> Also tried to use the WeightDescriptor but the molw is also 0.
Because of PseudoAtom...
> Here is the code I used
>
> MDLReader reader = new MDLReader();
>
> Molecule cdkMol = new Molecule();
> reader.read(cdkMol);
Add:
for (int i=0; i<cdkMol.getAtomCount(); i++) {
if (cdkMol.atomAt(i) instanceof PseudoAtom) {
PseudoAtom possiblyD = (PseudoAtom)cdkMol.atomAt(i);
if ("D".equals(possiblyD.getLabel()) {
IAtom deuterium = possiblyD.getBuilder().newAtom("H");
deuterium.setMassNumber(2);
AtomContainerManipulator.replaceAtomByAtom(cdkMol, possiblyD, deuterium);
}
}
or something along those lines...
Egon
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