MassFron05210709212D
4 4 0 0 0 0 0 0 0 0 2 V2000
1.8966 -3.2759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8966 -4.0345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2759 -4.6897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5172 -4.6897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
3 4 1 0 0 0 0
M CHG 1 3 1
M END
$$$$
MassFron05210709212D
4 3 0 0 0 0 0 0 0 0 2 V2000
4.5172 2.7931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5172 3.5517 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.1724 3.9310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1724 4.6897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 3 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
M CHG 1 2 1
M END
$$$$
On Mon, 2007-05-21 at 21:28 +0200, Stefan Kuhn wrote:
> Could you sent a fragment of your sd file with charges? The reader should
> work, but it might well be buggy - I would like to debug this with your
> compounds.
> 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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