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Merged
mtessmer merged 4 commits into from
May 2, 2025
Merged

small simplication in bisect_alignment #192

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f9608da
small simplication in bisect_alignment
stestoll May 2, 2025
e60689a
reduce test precision requirement
mtessmer May 2, 2025
1883c91
Update test data
mtessmer May 2, 2025
718be16
Fix test data
mtessmer May 2, 2025
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22 changes: 11 additions & 11 deletions src/chilife/alignment_methods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,9 +63,9 @@ def rosetta_alignment(N, CA, C):

@alignment_method
def bisect_alignment(N, CA, C):
"""Calculates a rotation matrix and translation to transform an amino acid from the local coordinate frame to the
global coordinate frame for a given residue with backbone coordinates (N, C, CA). Principal axis bisects the
N->Ca->C angle.
"""Calculates the rotation matrix and translation to transform an amino acid from the local coordinate frame to the
global coordinate frame for a given residue with backbone coordinates (N, C, CA). The principal z axis bisects the
N-CA-C angle, and y is in the N-CA-C plane perpendicular to z, approximately pointing from C to N.

Parameters
----------
Expand All @@ -78,31 +78,31 @@ def bisect_alignment(N, CA, C):

Returns
-------
rotation_matrix : numpy ndarray (3x3)
Rotation matrix to rotate spin label to achieve the correct orientation.
rotation_matrix : numpy .darray (3x3)
Rotation matrix to rotate spin label to achieve the correct orientation.
origin : numpy.ndarray (1x3)
New origin position in 3-dimensional space.
"""
# Define new Z axis that bisects N<--CA-->C angle
# Define new z axis: bisector of N-CA-C angle
CA_N = N - CA
CA_N /= np.linalg.norm(CA_N)
CA_C = C - CA
CA_C /= np.linalg.norm(CA_C)
zaxis = CA_N + CA_C
zaxis = zaxis / np.linalg.norm(zaxis)

# Define new y-axis
yaxis_plane = N - C
z_comp = yaxis_plane.dot(zaxis)
yaxis = yaxis_plane - z_comp * zaxis
# Define new y axis: perpendicular to z in N-CA-C plane
yaxis = CA_N - CA_C
yaxis = yaxis / np.linalg.norm(yaxis)

# Define new x axis
# Define new x axis: perpendicular to y and z
xaxis = np.cross(yaxis, zaxis)

# Create rotation matrix
rotation_matrix = np.array([xaxis, yaxis, zaxis])

origin = CA

return rotation_matrix, origin


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2 changes: 1 addition & 1 deletion tests/test_SpinLabel.py
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Expand Up @@ -81,7 +81,7 @@ def test_add_protein(label):
lib.protein_setup()

with np.load(f"test_data/{label}_label.npz") as f:
np.testing.assert_almost_equal(f["coords"], lib._coords)
np.testing.assert_almost_equal(f["coords"], lib._coords, decimal=5)
np.testing.assert_almost_equal(f["weights"], lib.weights)


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2 changes: 1 addition & 1 deletion tests/test_chiLife.py
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Expand Up @@ -254,7 +254,7 @@ def test_create_library():
)

SL = chilife.SpinLabel('___', 238, protein)
np.testing.assert_allclose(SL.spin_centers, np.array([[-24.444481, 15.084166, 14.754087]]))
np.testing.assert_allclose(SL.spin_centers, np.array([[-24.444479, 15.084169, 14.754088]]))

struct = mda.Universe('test_data/trt_sorted.pdb')
pos = struct.atoms[:3].positions
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4 changes: 2 additions & 2 deletions tests/test_data/bbdep.pdb
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Expand Up @@ -3143,7 +3143,7 @@ ATOM 3 O R1C A 211 -16.726 2.285 12.253 0.10 1.00 O
ATOM 4 CB R1C A 211 -16.533 -0.969 12.162 0.10 1.00 C
ATOM 5 SG R1C A 211 -18.233 -0.504 12.139 0.10 1.00 S
ATOM 6 SD R1C A 211 -18.780 -0.051 10.270 0.10 1.00 S
ATOM 7 CE R1C A 211 -19.192 -1.537 9.414 0.10 1.00 C
ATOM 7 CE R1C A 211 -19.192 -1.538 9.414 0.10 1.00 C
ATOM 8 C3 R1C A 211 -19.738 -1.350 8.009 0.10 1.00 C
ATOM 9 C4 R1C A 211 -19.861 -0.128 7.484 0.10 1.00 C
ATOM 10 C2 R1C A 211 -20.187 -2.404 7.019 0.10 1.00 C
Expand Down Expand Up @@ -4852,7 +4852,7 @@ ATOM 11 C5 R1C A 211 -16.525 -6.890 16.627 0.00 1.00 C
ATOM 12 N1 R1C A 211 -15.270 -7.373 16.077 0.00 1.00 N
ATOM 13 C8 R1C A 211 -14.566 -7.197 13.730 0.00 1.00 C
ATOM 14 C9 R1C A 211 -13.335 -5.977 15.575 0.00 1.00 C
ATOM 15 C6 R1C A 211 -16.461 -6.620 18.123 0.00 1.00 C
ATOM 15 C6 R1C A 211 -16.460 -6.620 18.123 0.00 1.00 C
ATOM 16 C7 R1C A 211 -17.674 -7.834 16.297 0.00 1.00 C
ATOM 17 O1 R1C A 211 -14.762 -8.425 16.429 0.00 1.00 O
TER
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