Improve TRIPOS atom type parsing #152
Description
Recently, there was a question in the discussions section about metallic atoms and how they are parsed in Mol2 files.
When an atom type is not part of the tripos atom type enumeration, atomic parameters are extracted from RbtElements.dat file if possible, and some warning messages are displayed.
while the overall behavior is right, the user experience is not good, as the warning messages are not clear enough and most of the times they aren't even relevant and should be ignored.
There are two main improvements we should implement here:
- expand the tripos atom type enum to include common metals
- improve the communication towards the user by not sending unnecessary warnings, and make messages for the actually problematic situations more informative
NOTE: Expanding the enum might cause some retro-compatibility issues if not done carefully. Please pay special attention