test(python/core/geometry): add tests for alignment

python/test/core/geometry_test.py

@@ -0,0 +1,54 @@
+#
+# Project NuriKit - Copyright 2024 SNU Compbio Lab.
+# SPDX-License-Identifier: Apache-2.0
+#
+
+from typing import Tuple
+
+import numpy as np
+import pytest
+
+from nuri.core import geometry as ngeom
+
+
+@pytest.fixture(scope="module")
+def points():
+    gen = np.random.default_rng(42)
+
+    query = gen.random((10, 3)) * 10
+    templ = gen.random((10, 3)) * 10
+
+    return query, templ
+
+
+@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
+
+    xform, rmsd = ngeom.align_points(q, t, method=method, reflection=False)
+
+    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)
+
+    rmsd2 = ngeom.align_rmsd(q, t, method=method, reflection=False)
+    assert np.allclose(rmsd, rmsd2, atol=1e-6)
+
+    xform, rmsd = ngeom.align_points(q, t, method=method, reflection=True)
+
+    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)
+
+    rmsd2 = ngeom.align_rmsd(q, t, method=method, reflection=True)
+    assert np.allclose(rmsd, rmsd2, atol=1e-6)