Looking at the situation I think indeed that atom 3 should have 1 hydrogen,
since it is positivly charged.
Could one of the chemists comment on this?
If it is indeed 1, the code in SaturationChecker is wrong, which seems hard to
believe. Right now the code is:
missingHydrogen = (int) (defaultAtom.getBondOrderSum() -
bondOrderSum - singleElectronSum +
atom.getFormalCharge());
I think indeed it should be -charge, since, if the charge is negative, we need
extra electrons.
Again, the chemists please.
On Tuesday 22 May 2007 16:32, Daniel Fontaine wrote:
> I admit I am not much of a chemist, I am a programmer, but the program
> that generated the fragment, Mass Frontier, has the first molecule with
> 5 hydrogens rather than 7. I was told this is correct due to the
> positive charge on the carbon? Does CDK not handle this sort of thing?
> Or am I missing something?
>
> thanks for all of your help
> Dan
>
> On Tue, 2007-05-22 at 15:48 +0200, Stefan Kuhn wrote:
> > On Tuesday 22 May 2007 15:23, Daniel Fontaine wrote:
> > > Thanks, but if this reader is working properly, why is the hydrogen
> > > adder not taking charges into consideration? I am getting two
> > > hydrogens too many added to that first fragment I posted.
> >
> > Hm, I get for the first molecule the following implicit Hs after
> > addImplicitHydrogensToSatisfyValency:
> > 1: 2
> > 2: 0
> > 3: 3
> > 4:2
> > For the second one:
> > 1: 1
> > 2: 0
> > 3: 1
> > 4: 2
> > That looks ok, I would say, doesn't it?
> > Stefan
> >
> > > thanks,
> > > Dan
> > >
> > > On Tue, 2007-05-22 at 10:29 +0200, Stefan Kuhn wrote:
> > > > Ok, the problem is you are using the wrong property. You should use
> > > > getFormatCharge, which works and is supposed to give that sort of,
> > > > well,
> > > > formal charge. The getCharge is used by classes assigning partial
> > > > charges and
> > > > will always give 0 if you do not explicitly run one of them.
> > > > Stefan
> > > >
> > > > On Monday 21 May 2007 20:28, Daniel Fontaine wrote:
> > > > > Hello, I am new to CDK and the mailing list.
> > > > >
> > > > > I am reading in a list of compounds from an sdf file that include
> > > > > charges. These charges don't appear on the atoms of the
> > > >
> > > > corresponding
> > > >
> > > > > Molecules, however, when loading with MDLV2000Reader. All atoms
> > > >
> > > > show a
> > > >
> > > > > charge of 0.0.
> > > > >
> > > > > This is a problem because I am trying to add implicit hydrogens
> > > > > with HydrogenAdder. I frequently end up with too many hydrogens and
> > > > > the
> > > >
> > > > wrong
> > > >
> > > > > mass.
> > > > >
> > > > > any help would be appreciated,
> > > > > Dan
> > > >
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IPB Halle
AG Bioinformatik & Massenspektrometrie
Weinberg 3
06120 Halle
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