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] +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
