Protein models without protons get protonated without user input

[IAlibay]

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Reported by an OpenFE partner yesterday - passing a model with only polar hydrogens leads to hydrogens being automatically added.

[IAlibay]

Initial thought here is that OpenMM modeller is adding hydrogens based on the OpenMMFF templates.

Probably would want to check that there are missing hydrogens and throw an error at the ProteinComponent level?

[richardjgowers]

This line will be adding in missing hydrogens from residues according to the built in templates: https://github.com/OpenFreeEnergy/openfe/blob/main/openfe/protocols/openmm_utils/system_creation.py#L196

We should probably not be doing this, and yeah probably failing early when you get a malformed input would be best. The current .from_pdb method is probably too lax in allowing these inputs.