Add benchmarks

benchmarks/structure/benchmark_superimpose.py

@@ -0,0 +1,28 @@
+from pathlib import Path
+import pytest
+import biotite.structure as struc
+import biotite.structure.io.pdbx as pdbx
+from tests.util import data_dir
+
+
+@pytest.fixture
+def atoms():
+    pdbx_file = pdbx.BinaryCIFFile.read(Path(data_dir("structure")) / "1gya.bcif")
+    return pdbx.get_structure(pdbx_file)
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize(
+    "method",
+    [
+        struc.superimpose,
+        struc.superimpose_without_outliers,
+        struc.superimpose_homologs,
+        struc.superimpose_structural_homologs,
+    ],
+)
+def benchmark_superimpose(method, atoms):
+    """
+    Compute superimposition of two structures with the same number of atoms.
+    """
+    method(atoms[0], atoms[1])