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Use MDAnalysis principal_axes() for single-UA molecules to prevent complex axes #274

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Merged
jkalayan merged 2 commits into from
Feb 12, 2026
Merged

Use MDAnalysis principal_axes() for single-UA molecules to prevent complex axes #274

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28b8d93
use vanilla PA for molecules that are one UA
jkalayan Feb 12, 2026
513664f
update tests for UA axes
jkalayan Feb 12, 2026
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26 changes: 15 additions & 11 deletions CodeEntropy/axes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,21 +92,25 @@ def get_UA_axes(self, data_container, index):
moment_of_inertia: moment of inertia (3,)
"""

index = int(index)
index = int(index) # bead index

# use the same customPI trans axes as the residue level
UAs = data_container.select_atoms("mass 2 to 999")
UA_masses = self.get_UA_masses(data_container.atoms)
center = data_container.atoms.center_of_mass(unwrap=True)
moment_of_inertia_tensor = self.get_moment_of_inertia_tensor(
center, UAs.positions, UA_masses, data_container.dimensions[:3]
)
trans_axes, _moment_of_inertia = self.get_custom_principal_axes(
moment_of_inertia_tensor
)
heavy_atoms = data_container.select_atoms("prop mass > 1.1")
if len(heavy_atoms) > 1:
UA_masses = self.get_UA_masses(data_container.atoms)
center = data_container.atoms.center_of_mass(unwrap=True)
moment_of_inertia_tensor = self.get_moment_of_inertia_tensor(
center, heavy_atoms.positions, UA_masses, data_container.dimensions[:3]
)
trans_axes, _moment_of_inertia = self.get_custom_principal_axes(
moment_of_inertia_tensor
)
else:
# use standard PA for UA not bonded to anything else
make_whole(data_container.atoms)
trans_axes = data_container.atoms.principal_axes()

# look for heavy atoms in residue of interest
heavy_atoms = data_container.select_atoms("prop mass > 1.1")
heavy_atom_indices = []
for atom in heavy_atoms:
heavy_atom_indices.append(atom.index)
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23 changes: 10 additions & 13 deletions tests/test_CodeEntropy/test_axes.py
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Expand Up @@ -118,7 +118,8 @@ def test_get_residue_axes_bonded_default_axes_branch(self):
np.testing.assert_allclose(center_out, center_expected)
np.testing.assert_allclose(moi_out, np.array([3.0, 2.0, 1.0]))

def test_get_UA_axes_returns_expected_outputs(self):
@patch("CodeEntropy.axes.make_whole", autospec=True)
def test_get_UA_axes_returns_expected_outputs(self, mock_make_whole):
"""
Tests that: `get_UA_axes` returns expected UA axes.
"""
Expand All @@ -129,20 +130,17 @@ def test_get_UA_axes_returns_expected_outputs(self):
dc.dimensions = np.array([1.0, 2.0, 3.0, 90.0, 90.0, 90.0])
dc.atoms.center_of_mass.return_value = np.array([0.0, 0.0, 0.0])

uas = MagicMock()
uas.positions = np.zeros((2, 3))

a0 = MagicMock()
a0.index = 7
a1 = MagicMock()
a1.index = 9
heavy_atoms = [a0, a1]

heavy_ag = MagicMock()
heavy_ag.positions = np.array([[9.9, 8.8, 7.7]])
heavy_ag.__getitem__.return_value = MagicMock()
heavy_atoms = MagicMock()
heavy_atoms.__len__.return_value = 2
heavy_atoms.__iter__.return_value = iter([a0, a1])
heavy_atoms.positions = np.array([[9.9, 8.8, 7.7], [1.1, 2.2, 3.3]])

dc.select_atoms.side_effect = [uas, heavy_atoms, heavy_ag]
dc.select_atoms.side_effect = [heavy_atoms, heavy_atoms]

axes.get_UA_masses = MagicMock(return_value=[1.0, 1.0])
axes.get_moment_of_inertia_tensor = MagicMock(return_value=np.eye(3))
Expand All @@ -160,13 +158,12 @@ def test_get_UA_axes_returns_expected_outputs(self):

np.testing.assert_array_equal(trans_axes, trans_axes_expected)
np.testing.assert_array_equal(rot_axes, rot_axes_expected)
np.testing.assert_array_equal(center, heavy_ag.positions[0])
np.testing.assert_array_equal(center, heavy_atoms.positions[0])
np.testing.assert_array_equal(moi, moi_expected)

calls = [c.args[0] for c in dc.select_atoms.call_args_list]
assert calls[0] == "mass 2 to 999"
assert calls[1] == "prop mass > 1.1"
assert calls[2] == "index 9"
assert calls[0] == "prop mass > 1.1"
assert calls[1] == "index 9"

def test_get_bonded_axes_returns_none_for_light_atom(self):
"""
Expand Down