stefdoerr
commented
4 years ago I don't see this as a meaningful addition. Molecule is not meant to have any sort of chemical understanding/fixing. This is the job of rdkit and other packages. If we don't read in atom types we should not expect atom types out.
The mol2 writer could offer the possibility of compatibility with chemoinformatics tools (e.g. openbabel, rdkit).
Rdkit expects Corina atom types or Tripos sybyl (not as assured): http://rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html Openbabel uses Tripos sybyl atom types: https://media.readthedocs.org/pdf/open-babel/latest/open-babel.pdf
Tripos sybyl atom types example reference: http://www.cmbi.ru.nl/samsam/tutorials/studs/mopac/force_field3.html
MDAnalysis provides the "official" format, for example: https://www.mdanalysis.org/docs/documentation_pages/coordinates/MOL2.html