Add benchmark

benchmarks/structure/benchmark_celllist.py

@@ -0,0 +1,19 @@
+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, model=1)
+
+
+def benchmark_cell_list(atoms):
+    """
+    Find all contacts in a structure using a cell list.
+    """
+    cell_list = struc.CellList(atoms, 5.0)
+    cell_list.get_atoms(atoms.coord, 5.0)