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, 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
