TST: Add tests for the new dihedral option

tests/test_files/CAT_dihedral.yaml

@@ -0,0 +1,24 @@
+path: .
+
+input_cores:
+    - Cd68Se55.xyz
+
+input_ligands:
+    - 'CC(O)=O'
+
+optional:
+    core:
+        dirname: core
+        anchor: Cl
+
+    ligand:
+        dirname: ligand
+        optimize: True
+        anchor:
+            group: "[H]OC=O"
+            group_idx: [1, 2, 3]
+            remove: 0
+            dihedral: 45
+
+    qd:
+        dirname: QD

tests/test_ligand_attach.py

@@ -1,14 +1,28 @@
 """Tests for :mod:`CAT.attachment.ligand_attach`."""
 
-from os.path import join
+import sys
+import shutil
+from pathlib import Path
+from typing import Generator, NamedTuple, TYPE_CHECKING
 
+import yaml
+import pytest
 import numpy as np
-
 from assertionlib import assertion
+from scm.plams import Settings, Molecule
 
+from CAT.base import prep
 from CAT.attachment.ligand_attach import (_get_rotmat1, _get_rotmat2)
+from CAT.workflows import MOL
+
+if TYPE_CHECKING:
+    import _pytest
 
-PATH = join('tests', 'test_files')
+PATH = Path('tests') / 'test_files'
+
+LIG_PATH = PATH / 'ligand'
+QD_PATH = PATH / 'qd'
+DB_PATH = PATH / 'database'
 
 
 def test_get_rotmat1() -> None:
@@ -50,11 +64,58 @@ def test_get_rotmat2() -> None:
     vec1 = np.array([1, 0, 0], dtype=float)
     vec2 = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype=float)
 
-    ref1 = np.load(join(PATH, 'rotmat2_1.npy'))
-    ref2 = np.load(join(PATH, 'rotmat2_2.npy'))
+    ref1 = np.load(PATH / 'rotmat2_1.npy')
+    ref2 = np.load(PATH / 'rotmat2_2.npy')
 
     rotmat1 = _get_rotmat2(vec1)
     np.testing.assert_allclose(rotmat1, ref1)
 
     rotmat2 = _get_rotmat2(vec2)
     np.testing.assert_allclose(rotmat2, ref2)
+
+
+class DihedTup(NamedTuple):
+    mol: Molecule
+    ref: np.recarray
+
+
+class TestDihedral:
+    PARAMS = {
+        "dihed_45": 45,
+        "dihed_45_deg": "45 deg",
+        "dihed_180": 180.0,
+    }
+
+    @pytest.fixture(scope="class", autouse=True, name="output", params=PARAMS.items(), ids=PARAMS)
+    def run_cat(self, request: "_pytest.fixtures.SubRequest") -> Generator[DihedTup, None, None]:
+        # Setup
+        name, dihed = request.param  # type: str, str | float
+        yaml_path = PATH / 'CAT_dihedral.yaml'
+        with open(yaml_path, 'r') as f:
+            arg = Settings(yaml.load(f, Loader=yaml.FullLoader))
+
+        arg.path = PATH
+        arg.optional.ligand.anchor.dihedral = dihed
+        qd_df, _, _ = prep(arg)
+        qd = qd_df[MOL].iloc[0]
+
+        ref = np.load(PATH / f"test_dihedral_{name}.npy").view(np.recarray)
+        yield DihedTup(qd, ref)
+
+        # Teardown
+        files = [LIG_PATH, QD_PATH, DB_PATH]
+        for f in files:
+            shutil.rmtree(f, ignore_errors=True)
+
+    def test_atoms(self, output: DihedTup) -> None:
+        dtype = [("symbols", "U2"), ("coords", "f8", 3)]
+        atoms = np.fromiter(
+            [(at.symbol, at.coords) for at in output.mol], dtype=dtype
+        ).view(np.recarray)
+
+        assertion.eq(atoms.dtype, output.ref.dtype)
+        np.testing.assert_array_equal(atoms.symbols, output.ref.symbols)
+
+        if sys.version_info >= (3, 9):
+            pytest.xfail("Geometries must be updated for RDKit >2019.09.2")
+        np.testing.assert_allclose(atoms.coords, output.ref.coords)