From: Stefan K. <sk...@ip...> - 2007-05-22 15:19:09
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Looking at the situation I think indeed that atom 3 should have 1 hydrogen,= =20 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=20 believe. Right now the code is: missingHydrogen =3D (int) (defaultAtom.getBondOrderSum() - bondOrderSum - singleElectronSum +=20 atom.getFormalCharge()); I think indeed it should be -charge, since, if the charge is negative, we n= eed=20 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 a= nd > > > > > the > > > > > > > > wrong > > > > > > > > > mass. > > > > > > > > > > any help would be appreciated, > > > > > Dan > > > > > > > > -------------------------------------------------------------------= =2D- > > > >---- > > > > > > > > > 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 > > > > > Cdk...@li... > > > > > 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 > > > > sk...@ip... Tel. +49 (0) 345 5582 1474 Fax.+49 (0) 345 5582 > > > > 1409 > > > > > > > > -------------------------------------------------------------------= =2D- > > > >---- 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 > > > > Cdk...@li... > > > > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > > > > ---------------------------------------------------------------------= =2D- > > >-- 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 > > > Cdk...@li... > > > 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 > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user =2D-=20 Stefan Kuhn BSc MA IPB Halle AG Bioinformatik & Massenspektrometrie Weinberg 3 06120 Halle http://www.ipb-halle.de http://msbi.bic-gh.de sk...@ip...=A0Tel. +49 (0) 345 5582 1474=A0Fax.+49 (0) 345 5582 1409 |