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.
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
