MDAnalysisWrapper

Code to integrate MDAnalysis utilities in QMzyme.

QMzyme.MDAnalysisWrapper.init_universe(*args, frame=0, **kwargs)

Accepts all argument and key word arguments that Universe can accept to create a Universe instance. Note, you may need to pass the format key word in some cases.

QMzyme.MDAnalysisWrapper.select_atoms(universe, selection)

Parameters:

• universe -- MDAnalysis Universe object.

• selection (str, required) -- Selection of atoms to be made- based on MDAnalysis selection command language.

QMzyme.MDAnalysisWrapper.universe_selection(universe, selection)

QMzyme.MDAnalysisWrapper.get_neighbors(ag1, ag2, radius, remove_duplicates=True)

Returns list of atoms in distance based atom group.