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Commit 6f5c1c8

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bjkreitzrwest
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Remove code duplicate
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rmgpy/molecule/draw.py

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Original file line numberDiff line numberDiff line change
@@ -418,17 +418,6 @@ def _generate_coordinates(self, fix_surface_sites=True):
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coordinates[i1, 1] -= 0.2
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coordinates[i2, 1] += 0.2
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# If two atoms lie on top of each other, push them apart a bit
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# This is ugly, but at least the mess you end up with isn't as misleading
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# as leaving everything piled on top of each other at the origin
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for atom1, atom2 in itertools.combinations(backbone, 2):
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i1, i2 = atoms.index(atom1), atoms.index(atom2)
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if np.linalg.norm(coordinates[i1, :] - coordinates[i2, :]) < 0.5:
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coordinates[i1, 0] -= 0.3
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coordinates[i2, 0] += 0.3
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coordinates[i1, 1] -= 0.2
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coordinates[i2, 1] += 0.2
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# Center backbone at origin
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xmin = np.min(coordinates[:, 0])
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xmax = np.max(coordinates[:, 0])

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