On Wed, Sep 15, 2010 at 12:43 PM, Egon Willighagen <[email protected]> wrote: > On Wed, Sep 15, 2010 at 12:30 PM, Thomas G. Kristensen <[email protected]> wrote: >> I'm trying to parse molecules with formal charges from a mol2 file, >> but no matter what I try it seems the formal charges are ignored when >> using the Mol2Reader. Inspecting the source code I discovered that mol >> type, charge type and status bit lines are ignored. Does anybody know >> why, > I guess it was never implemented... Okay, I guess nobody needed it before. I find this a bit strange but they might have been doing something completely different than I am.
>> and are there plans for adding the later? > You can file a feature request... best to add an example file that we > can use as test data, so LGPL licensed... a small demo file will do, > so that we can write a unit test. Hmmm, seems like a lot of work for such a simple feature. Do you mean that the molecular file is supposed to be released under LGPL? I don't think anybody has ever done that. >> Is there an alternative format which does support formal charge in the CDK? > Chemical Markup Language, MDL V2000 molfiles, at least... I've tried converting my files to these two but my converter (openbabel) also ignores charges. Thanks for the info though. Best regards, Thomas ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
