Line 208 of molchrg.cpp has:

            if (EQ(atom->GetType(),"Npl") || EQ(atom->GetType(),"Nam"))

Gasteiger charge calculation should always return the same results for the same structure. However, the string returned by GetType() is set to an arbitrary value by an atom typer (or indeed the user), and so the results will change.

Line 208 should be rewritten to avoid using GetType

Bug Description

See #1939 for more details. Whenever we significantly change RMG-database, the comments in the chemkin file need to be updated or else this uncertainty IPython notebook example will be broken. It is not ideal to continually update this file, so we should come up with a better solution. Possibilities include:

1. Only update this file every major release. Add a note in the IP

While Avo2 currently supports writing to POV-Ray and VRML formats, it would be great to support writing to the more common PLY format:

http://paulbourke.net/dataformats/ply/

The key component would be to enable writing spheres and cylinders as vertex / face meshes rather than a sphere or cylinder primitive.