Coverage for /builds/kinetik161/ase/ase/visualize/sage.py: 22.22%

1from ase.data import covalent_radii 

2from ase.data.colors import jmol_colors 

3 

4 

5def view_sage_jmol(atoms, repeat=None, *args, **kwargs): 

6 try: 

7 from .sage.plot.plot3d.shapes import ColorCube, Sphere 

8 except Exception: # XXX Which kind of exception exactly? 

9 raise ImportError( 

10 'view_sage_jmol requires sage (http://www.sagemath.org/) ' + 

11 'and is intended to be used directly in the browser') 

12 

13 if repeat is not None: 

14 atoms = atoms.repeat(repeat) 

15 

16 cell = atoms.cell.diagonal() / 2 

17 model = ColorCube(list(cell), ['blue', 'blue', 'blue'], opacity=0.1) 

18 for atom in atoms: 

19 atomic_number = atom.number 

20 color = tuple(jmol_colors[atomic_number]) 

21 radius = covalent_radii[atomic_number] 

22 model += Sphere(radius, color=color).translate( 

23 *(atom.position - atoms.cell.diagonal() / 2)) 

24 model.show(aspect_ratio=1, frame=False) 

25 

26 

27view_sage = view_sage_jmol