Stefan, As I said, I am not a chemist. However, I made the change you suggested and recompiled CDK and all my test cases now run as expected. I believe your suggestion of changing +charge to -charge is correct.
I appreciate all of your help. Dan On Tue, 2007-05-22 at 17:17 +0200, Stefan Kuhn wrote: > 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 > > > > > > > > > > --------------------------------------------------------------------- > > > > >---- > > > > > > > > > > > This SF.net email is sponsored by DB2 Express > > > > > > Download DB2 Express C - the FREE version of DB2 express and take > > > > > > control of your XML. No limits. Just data. Click to get it now. > > > > > > http://sourceforge.net/powerbar/db2/ > > > > > > _______________________________________________ > > > > > > Cdk-user mailing list > > > > > > [email protected] > > > > > > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > > > > > > > > -- > > > > > Stefan Kuhn BSc MA > > > > > IPB Halle > > > > > AG Bioinformatik & Massenspektrometrie > > > > > Weinberg 3 > > > > > 06120 Halle > > > > > http://www.ipb-halle.de http://msbi.bic-gh.de > > > > > [EMAIL PROTECTED] Tel. +49 (0) 345 5582 1474 Fax.+49 (0) 345 5582 > > > > > 1409 > > > > > > > > > > --------------------------------------------------------------------- > > > > >---- This SF.net email is sponsored by DB2 Express > > > > > Download DB2 Express C - the FREE version of DB2 express and take > > > > > control of your XML. No limits. Just data. Click to get it now. > > > > > http://sourceforge.net/powerbar/db2/ > > > > > _______________________________________________ > > > > > Cdk-user mailing list > > > > > [email protected] > > > > > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > > > > > > ----------------------------------------------------------------------- > > > >-- This SF.net email is sponsored by DB2 Express > > > > Download DB2 Express C - the FREE version of DB2 express and take > > > > control of your XML. No limits. Just data. Click to get it now. > > > > http://sourceforge.net/powerbar/db2/ > > > > _______________________________________________ > > > > Cdk-user mailing list > > > > [email protected] > > > > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by DB2 Express > > Download DB2 Express C - the FREE version of DB2 express and take > > control of your XML. No limits. 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