From 6f5c1c83ad66b0702d6e8c10dc88ecbaa72909f0 Mon Sep 17 00:00:00 2001 From: Bjarne Kreitz Date: Tue, 19 Nov 2024 14:33:44 -0500 Subject: [PATCH] Remove code duplicate --- rmgpy/molecule/draw.py | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/rmgpy/molecule/draw.py b/rmgpy/molecule/draw.py index b7a66cc861..d38c519197 100644 --- a/rmgpy/molecule/draw.py +++ b/rmgpy/molecule/draw.py @@ -418,17 +418,6 @@ def _generate_coordinates(self, fix_surface_sites=True): 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 - 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])