[ghemical-devel] Re: Ghemical and "Dummy Atoms"

[Geoffrey Hutchison]

I use Ghemical a lot when I'm developing and debugging Open Babel.  
One of the new formats I added (PCModel) incorporates explicit lone- 
pair electron sites, which translate as dummy atoms. But Ghemical  
currently doesn't know what to do with dummy atoms -- it shows them  
as these brown spheres and it kills geometry optimizations, energies,  
etc. ...

Should I change the Ghemical output code for Open Babel to ignore  
dummy atoms?

Cheers,
-Geoff