Description

Development branch for including the advanced protonation scheme with H2OAC

Changes

The dictionaries to supply the states information to ProtexTemplates have changed.
To allow for multiple atoms in one molecules an atoms list can now be specified. A new additional information is the mode parameter, which can either be donor or acceptor. I.e.:

OAC_HOAC_H2OAC = {
    "OAC": {"atoms": [{"name": "O2", "mode": "acceptor", "equivalent_atom": "O1"}]},
    "HOAC": {
        "atoms": [{"name": "H", "mode": "donor"}, {"name": "O1", "mode": "acceptor"}]
    },
    "H2OAC": {"atoms": [{"name": "HO1", "mode": "donor", "equivalent_atom:": "H"}]},
}

The NaiveMCUpdate can now be used with include_equivalent_atom=True and reorient=True.
The Residue and ProtexTemplates classes have new methods. See the API docs.

Status

• Ready to go