Generating connectivity table for structure

Hi all.

I have a library of cif files that do not contain any connectivity information. Is it possible to generate a connectivity table using pymatgen?


Hi @StevenCQC, welcome!

Yes, absolutely; however, pymatgen does not currently have a facility to write out the connectivity information into the CIF file.

What pymatgen does offer is a variety of bonding algorithms (inside pymatgen.analysis.local_env) and a StructureGraph class (inside pymatgen.analysis.graphs), so that you can import your crystal from the CIF and then try to estimate which bonds might be present (e.g. using StructureGraph.with_local_env_strategy(). This task is actually not trivial, and can be ambiguous in some cases, which is why a variety of algorithms are offered – we generally recommend CrystalNN. Hopefully this helps, more info in the docs.