From: Stefan K. <sk...@ip...> - 2007-05-22 15:20:12
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Please see this discussion on cdk-user, if you are a chemist. =2D--------- Forwarded Message ---------- Subject: Re: [Cdk-user] MDLV2000Reader Date: Tuesday 22 May 2007 17:17 =46rom: Stefan Kuhn <sk...@ip...> To: cdk...@li... 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 =3D (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 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- 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 =2D------------------------------------------------------ =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 |