def display_molecule(molecule, highlight=None, **kwargs): topology = { 'atom_types': molecule.type_array, 'bonds': molecule.bonds, 'atom_names': molecule.atom_name, 'secondary_structure': molecule.secondary_structure } mv = MolecularViewer(molecule.r_array.astype('float32'), topology) kind = kwargs.get('kind', 'wireframe') if kind == 'wireframe': if molecule.n_bonds != 0: mv.points(size=0.15, highlight=highlight) mv.lines() else: mv.points(highlight=highlight) elif kind == 'ball_and_sticks': mv.ball_and_sticks() elif kind == 'cartoon': mv.cartoon() else: raise ValueError("kind {} not found".format(kind)) return mv
def display_molecule(molecule): topology = {'atom_types': molecule.type_array, 'bonds': molecule.bonds} mv = MolecularViewer(molecule.r_array, topology) if molecule.n_bonds != 0: mv.points(size=0.15) mv.lines() else: mv.points() return mv
def display_molecule(molecule): topology = { 'atom_types': molecule.type_array, 'bonds': molecule.bonds } mv = MolecularViewer(molecule.r_array, topology) if molecule.n_bonds != 0: mv.points(size=0.15) mv.lines() else: mv.points() return mv