TST: Add tests for the cone-angle remove_anchor_hydrogens keyword

tests/test_cone_angle.py

@@ -9,15 +9,18 @@
 import numpy as np
 import pytest
 import yaml
-from scm.plams import readpdb, Settings
+from scm.plams import readpdb, Settings, Molecule
 
 from CAT.base import prep
 from CAT.workflows import CONE_ANGLE
 from nanoCAT.cone_angle import get_cone_angle
 
 PATH = Path("tests") / "test_files"
 CONE_ANGLE_PATH = PATH / "cone_angle"
+
 MOL = readpdb(PATH / "CCCC[O-]@O5.pdb")
+MOL_AMMONIUM = Molecule(PATH / "pentyl_ammonium.xyz")
+MOL_AMMONIUM.guess_bonds()
 
 
 class TestConeAngle:
@@ -42,6 +45,24 @@ def test_raise(self, kwargs: dict[str, Any], exc_type: type[Exception]) -> None:
         with pytest.raises(exc_type):
             get_cone_angle(MOL, **kwargs)
 
+    REMOVE_H_PARAMS = {
+        "default": (False, (220, 232)),
+        "remove_hydrogens": (True, 81),
+    }
+
+    @pytest.mark.parametrize("remove_h,ref", REMOVE_H_PARAMS.values(), ids=REMOVE_H_PARAMS)
+    def test_remove_hydrogens(self, remove_h: bool, ref: float | tuple[float, float]) -> None:
+        out = get_cone_angle(MOL_AMMONIUM, 5, remove_anchor_hydrogens=remove_h)
+
+        # NOTE: The pentyl ammonium system seems to converge to one of two cone-angles
+        if isinstance(ref, tuple):
+            try:
+                np.testing.assert_allclose(out, ref[0], rtol=0, atol=1)
+            except AssertionError:
+                np.testing.assert_allclose(out, ref[1], rtol=0, atol=1)
+        else:
+            np.testing.assert_allclose(out, ref, rtol=0, atol=1)
+
 
 class TestWorkflow:
     with open(PATH / "cone_angle_setting.yaml", "r") as f:

tests/test_files/pentyl_ammonium.xyz

@@ -0,0 +1,22 @@
+20
+
+C       1.28630756      -0.77573787      -0.00000000
+C       2.47070405       0.18372642      -0.00000000
+C       3.79013383      -0.60191494      -0.00000000
+C       4.99312868       0.34819422      -0.00000000
+C       6.30623936      -0.43099753      -0.00000000
+N       0.00000000       0.00000000      -0.00000000
+H       1.27610811      -1.40641630       0.89215764
+H       1.27610811      -1.40641630      -0.89215764
+H       2.41877024       0.82374106       0.88651503
+H       2.41877024       0.82374106      -0.88651503
+H       3.82571104      -1.24461252      -0.88535152
+H       3.82571104      -1.24461252       0.88535152
+H       4.94575858       0.99045146       0.88526603
+H       4.94575858       0.99045146      -0.88526603
+H       6.37663529      -1.06240433       0.88601442
+H       7.14484734       0.26410989      -0.00000000
+H       6.37663529      -1.06240433      -0.88601442
+H      -0.04282656       0.58998902      -0.82749495
+H      -0.04282656       0.58998902       0.82749495
+H      -0.79342064      -0.63569277      -0.00000000