Inquiry: Accessing stoichiometry/oligomeric state in parsed mmCIF objects

[wanghch123]

Hi,

I'm using Atomworks to build a PDB dataset. I need to determine the stoichiometry of the assemblies (e.g., monomer vs. dimer) after parsing the mmCIF files.

I couldn't find a direct way to access this information in the current API. Is this feature supported, or is it not currently considered in the design?

Any guidance would be appreciated.

[nscorley]

Hi! The chain_info dictionary only contains the information for the asymmetric unit. If you're building an assembly, you could grab the stoichiometry from the output AtomArray itself. In the AtomArray you get out, we add an chain_entity annotation to each unique chain entity. E.g., if I had a homodimer, I would have two distinct chains (different chain_id/chain_iid), but the same chain_entity. So you could count distinct (chain_iid , entity_id) combinations which would give you the stoichiometry of each constituent.