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test(python/core/geometry): add tests for alignment
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# | ||
# Project NuriKit - Copyright 2024 SNU Compbio Lab. | ||
# SPDX-License-Identifier: Apache-2.0 | ||
# | ||
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from typing import Tuple | ||
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import numpy as np | ||
import pytest | ||
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from nuri.core import geometry as ngeom | ||
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@pytest.fixture(scope="module") | ||
def points(): | ||
gen = np.random.default_rng(42) | ||
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query = gen.random((10, 3)) * 10 | ||
templ = gen.random((10, 3)) * 10 | ||
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return query, templ | ||
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@pytest.mark.parametrize( | ||
"method", | ||
[ | ||
"qcp", | ||
"kabsch", | ||
pytest.param( | ||
"unknown", | ||
marks=pytest.mark.xfail(raises=ValueError, strict=True), | ||
), | ||
], | ||
) | ||
def test_align(points: Tuple[np.ndarray, np.ndarray], method: str): | ||
q, t = points | ||
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xform, rmsd = ngeom.align_points(q, t, method=method, reflection=False) | ||
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p = ngeom.transform(xform, q) | ||
rmsd_calc = np.sqrt(np.mean(np.sum((p - t) ** 2, axis=1))) | ||
assert np.allclose(rmsd, rmsd_calc, atol=1e-6) | ||
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rmsd2 = ngeom.align_rmsd(q, t, method=method, reflection=False) | ||
assert np.allclose(rmsd, rmsd2, atol=1e-6) | ||
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xform, rmsd = ngeom.align_points(q, t, method=method, reflection=True) | ||
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p = ngeom.transform(xform, q) | ||
rmsd_calc = np.sqrt(np.mean(np.sum((p - t) ** 2, axis=1))) | ||
assert np.allclose(rmsd, rmsd_calc, atol=1e-6) | ||
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rmsd2 = ngeom.align_rmsd(q, t, method=method, reflection=True) | ||
assert np.allclose(rmsd, rmsd2, atol=1e-6) |