[Cdk-user] problems with calculating partial charge with cdk

Hi, I'm calculating partial charge with cdk using the code below. But for some molecule, it throws some exceptions. I don't know what goes wrong. Can anyone help? A example molecule is attached. Thanks. String path = example.sdf; IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();

Re: [Cdk-user] problems with calculating partial charge with cdk

So do you mean, right now cdk doesn't support for calculating partial charge for molecules with atom of boron? Is it? Thanks. On Mon, Jul 13, 2015 at 3:33 PM, John M john.wilkinson...@gmail.com wrote: Sorry meant to be on-list. Have you got the contents of examples.sdf, specifically the one

Re: [Cdk-user] problems with calculating partial charge with cdk

Sorry meant to be on-list. Have you got the contents of examples.sdf, specifically the one that causes the problem? Not all atoms are represented by MMFF94 (of note is boron - OpenEye have added support) - if the molecule has an atom not typed (by MMFF94) the method will fail. However, there are