Merge pull request #699 from padix-key/lddt

Add support for lDDT computation

benchmarks/structure/benchmark_compare.py

@@ -0,0 +1,32 @@
+import itertools
+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")
+    atoms = pdbx.get_structure(pdbx_file)
+    # Reduce the number of atoms to speed up the benchmark
+    return atoms[..., atoms.element != "H"]
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize(
+    "multi_model, aggregation",
+    itertools.product([False, True], ["all", "chain", "residue", "atom"]),
+)
+def benchmark_lddt(atoms, multi_model, aggregation):
+    """
+    Compute lDDT on different aggregation levels.
+    """
+    reference = atoms[0]
+    if multi_model:
+        subject = atoms
+    else:
+        subject = atoms[0]
+
+    struc.lddt(reference, subject, aggregation=aggregation)

doc/apidoc.json

@@ -321,6 +321,7 @@
             "rmsd",
 	        "rmspd",
             "rmsf",
+            "lddt",
             "tm_score"
         ],
         "General analysis" : [