diff --git a/rmgpy/molecule/draw.py b/rmgpy/molecule/draw.py index dc10e58253..c23d11fcfa 100644 --- a/rmgpy/molecule/draw.py +++ b/rmgpy/molecule/draw.py @@ -405,18 +405,6 @@ def _generate_coordinates(self): coordinates[i1, 1] -= 0.2 coordinates[i2, 1] += 0.2 - # If two atoms lie on top of each other, push them apart a bit - # This is ugly, but at least the mess you end up with isn't as misleading - # as leaving everything piled on top of each other at the origin - import itertools - for atom1, atom2 in itertools.combinations(backbone, 2): - i1, i2 = atoms.index(atom1), atoms.index(atom2) - if np.linalg.norm(coordinates[i1, :] - coordinates[i2, :]) < 0.5: - coordinates[i1, 0] -= 0.3 - coordinates[i2, 0] += 0.3 - coordinates[i1, 1] -= 0.2 - coordinates[i2, 1] += 0.2 - # Center backbone at origin xmin = np.min(coordinates[:, 0]) xmax = np.max(coordinates[:, 0])