Hi
Yes that did the trick.
Thanks
On 9/9/07, Egon Willighagen <[EMAIL PROTECTED]> wrote:
> 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
>
> --
> ----
> http://chem-bla-ics.blogspot.com/
>
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