ihmwg / python-ihm

Python package for handling IHM mmCIF and BinaryCIF files
MIT License
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Populate atom_type for multi-scale models #96

Open brindakv opened 1 year ago

brindakv commented 1 year ago

atom_type is required and populated for atomic models. For consistency, the table could be populated for multi-scale models as well (perhaps based on the components in chem_comp).

benmwebb commented 1 year ago

I'm not sure if this makes sense though. atom_type according to the docs is intended to "record details about the properties of the atoms that occupy the atom sites" rather than, say, the chemical composition of the modeled system. In a coarse-grained model, we don't have atoms. Compare this with an x-ray structure where the "real" system is approximated by a no-hydrogen model; atom_type doesn't contain H.

An additional complication is that the chemical formula isn't mandatory for chem_comp, so we might not know the atoms in a coarse-grained model anyway.