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Fix weighted Kabsch lint failure blocking Testing (3.10) #136

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Fix weighted Kabsch lint failure blocking Testing (3.10) #136

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Copilot Sep 26, 2026
472413f
Fix weighted Kabsch lint failure
Copilot Sep 26, 2026
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3 changes: 1 addition & 2 deletions rmsd/calculate_rmsd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -608,8 +608,7 @@ def kabsch_weighted(
CMP = np.zeros(3)
CMQ = np.zeros(3)
C = np.zeros((3, 3))
if W is None:
W = np.ones(len(P)) / len(P)
W = np.ones(len(P)) / len(P) if W is None else W
W = np.array([W, W, W]).T
iw = 3.0 / W.sum()
n = len(P)
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19 changes: 19 additions & 0 deletions tests/test_kabsch_weighted.py
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Expand Up @@ -32,3 +32,22 @@ def test_kabsch_weighted_fit_pdb() -> None:
new_p_coord = rmsdlib.kabsch_fit(p_coord, q_coord, weights)

np.testing.assert_array_almost_equal(q_coord[300], new_p_coord[300], decimal=2)


def test_kabsch_weighted_defaults_to_uniform_weights() -> None:
filename_1 = RESOURCE_PATH / "ci2_12.pdb"
filename_2 = RESOURCE_PATH / "ci2_2.pdb"

_, p_coord = rmsdlib.get_coordinates_pdb(filename_1)
_, q_coord = rmsdlib.get_coordinates_pdb(filename_2)

uniform_weights = np.ones(len(p_coord)) / len(p_coord)

actual_rotation, actual_translation, actual_rmsd = rmsdlib.kabsch_weighted(p_coord, q_coord)
expected_rotation, expected_translation, expected_rmsd = rmsdlib.kabsch_weighted(
p_coord, q_coord, uniform_weights
)

np.testing.assert_allclose(actual_rotation, expected_rotation)
np.testing.assert_allclose(actual_translation, expected_translation)
np.testing.assert_allclose(actual_rmsd, expected_rmsd)