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from ase.data import covalent_radii
from ase.data.colors import jmol_colors
def view_sage_jmol(atoms, repeat=None, *args, **kwargs):
try:
from .sage.plot.plot3d.shapes import ColorCube, Sphere
except Exception: # XXX Which kind of exception exactly?
raise ImportError(
'view_sage_jmol requires sage (http://www.sagemath.org/) ' +
'and is intended to be used directly in the browser')
if repeat is not None:
atoms = atoms.repeat(repeat)
cell = atoms.cell.diagonal() / 2
model = ColorCube(list(cell), ['blue', 'blue', 'blue'], opacity=0.1)
for atom in atoms:
atomic_number = atom.number
color = tuple(jmol_colors[atomic_number])
radius = covalent_radii[atomic_number]
model += Sphere(radius, color=color).translate(
*(atom.position - atoms.cell.diagonal() / 2))
model.show(aspect_ratio=1, frame=False)
view_sage = view_sage_jmol
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