Backport fix from PR #540. [ci skip]

src/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py

@@ -1472,9 +1472,7 @@ def translate(self, vector, property_map={}):
             if self._sire_object.has_property(coord_prop):
                 _property_map["coordinates"] = coord_prop
                 mol = (
-                    self._sire_object.move()
-                    .translate(_SireMaths.Vector(vec), _property_map)
-                    .commit()
+                    mol.move().translate(_SireMaths.Vector(vec), _property_map).commit()
                 )
 
         else:

src/BioSimSpace/_SireWrappers/_molecule.py

@@ -1412,9 +1412,7 @@ def translate(self, vector, property_map={}):
             if self._sire_object.has_property(coord_prop):
                 _property_map["coordinates"] = coord_prop
                 mol = (
-                    self._sire_object.move()
-                    .translate(_SireMaths.Vector(vec), _property_map)
-                    .commit()
+                    mol.move().translate(_SireMaths.Vector(vec), _property_map).commit()
                 )
 
         else:

tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py

@@ -173,3 +173,54 @@ def test_makeCompatibleWith_regression():
 
     # Make sure the energies are approximately equal.
     assert nrg_compatible == pytest.approx(nrg_leap, rel=1e-5)
+
+
+def test_translate_custom_coordinates_property(perturbable_system):
+    """
+    Regresson test to ensure that a molecule with a custom
+    coordinates property gets translated correctly.
+    """
+
+    from sire.maths import Vector
+
+    # Extract a copy of the perturbable molecule.
+    mol = perturbable_system.getPerturbableMolecules()[0].copy()
+
+    # Copy the "coordinates0" property to a custom property installed
+    # "test"
+    cursor = mol._sire_object.cursor()
+    cursor["test"] = cursor["coordinates0"]
+    mol._sire_object = cursor.commit()
+
+    # Store the existing coordinates.
+    coords0 = mol._sire_object.property("coordinates0").to_vector()
+    coords1 = mol._sire_object.property("coordinates1").to_vector()
+    coords_test = mol._sire_object.property("test").to_vector()
+
+    # Translate the molecule.
+    mol.translate(3 * [BSS.Units.Length.angstrom], property_map={"coordinates": "test"})
+
+    # Get the new coordinates.
+    new_coords0 = mol._sire_object.property("coordinates0").to_vector()
+    new_coords1 = mol._sire_object.property("coordinates1").to_vector()
+    new_coords_test = mol._sire_object.property("test").to_vector()
+
+    # Create a vector of the displacement.
+    v_ref = Vector(1.0, 1.0, 1.0)
+
+    # Check that the coordinates have been translated correctly.
+    for c_new, c_old in zip(new_coords0, coords0):
+        v = c_new - c_old
+        assert pytest.approx(v.x().value(), abs=1e-5) == v_ref.x().value()
+        assert pytest.approx(v.y().value(), abs=1e-5) == v_ref.y().value()
+        assert pytest.approx(v.z().value(), abs=1e-5) == v_ref.z().value()
+    for c_new, c_old in zip(new_coords1, coords1):
+        v = c_new - c_old
+        assert pytest.approx(v.x().value(), abs=1e-5) == v_ref.x().value()
+        assert pytest.approx(v.y().value(), abs=1e-5) == v_ref.y().value()
+        assert pytest.approx(v.z().value(), abs=1e-5) == v_ref.z().value()
+    for c_new, c_old in zip(new_coords_test, coords_test):
+        v = c_new - c_old
+        assert pytest.approx(v.x().value(), abs=1e-5) == v_ref.x().value()
+        assert pytest.approx(v.y().value(), abs=1e-5) == v_ref.y().value()
+        assert pytest.approx(v.z().value(), abs=1e-5) == v_ref.z().value()

tests/Sandpit/Exscientia/conftest.py

@@ -169,3 +169,14 @@ def merged_benzene_pyrrole(benzene, pyrrole, mapping_benzene_pyrrole):
         allow_ring_breaking=True,
         allow_ring_size_change=True,
     )
+
+
+@pytest.fixture(scope="module")
+def perturbable_system():
+    """A vacuum perturbable system."""
+    return BSS.IO.readPerturbableSystem(
+        f"{url}/perturbable_system0.prm7",
+        f"{url}/perturbable_system0.rst7",
+        f"{url}/perturbable_system1.prm7",
+        f"{url}/perturbable_system1.rst7",
+    )

tests/_SireWrappers/test_molecule.py

@@ -145,3 +145,54 @@ def test_makeCompatibleWith_regression():
 
     # Make sure the energies are approximately equal.
     assert nrg_compatible == pytest.approx(nrg_leap, rel=1e-5)
+
+
+def test_translate_custom_coordinates_property(perturbable_system):
+    """
+    Regresson test to ensure that a molecule with a custom
+    coordinates property gets translated correctly.
+    """
+
+    from sire.maths import Vector
+
+    # Extract a copy of the perturbable molecule.
+    mol = perturbable_system.getPerturbableMolecules()[0].copy()
+
+    # Copy the "coordinates0" property to a custom property installed
+    # "test"
+    cursor = mol._sire_object.cursor()
+    cursor["test"] = cursor["coordinates0"]
+    mol._sire_object = cursor.commit()
+
+    # Store the existing coordinates.
+    coords0 = mol._sire_object.property("coordinates0").to_vector()
+    coords1 = mol._sire_object.property("coordinates1").to_vector()
+    coords_test = mol._sire_object.property("test").to_vector()
+
+    # Translate the molecule.
+    mol.translate(3 * [BSS.Units.Length.angstrom], property_map={"coordinates": "test"})
+
+    # Get the new coordinates.
+    new_coords0 = mol._sire_object.property("coordinates0").to_vector()
+    new_coords1 = mol._sire_object.property("coordinates1").to_vector()
+    new_coords_test = mol._sire_object.property("test").to_vector()
+
+    # Create a vector of the displacement.
+    v_ref = Vector(1.0, 1.0, 1.0)
+
+    # Check that the coordinates have been translated correctly.
+    for c_new, c_old in zip(new_coords0, coords0):
+        v = c_new - c_old
+        assert pytest.approx(v.x().value(), abs=1e-5) == v_ref.x().value()
+        assert pytest.approx(v.y().value(), abs=1e-5) == v_ref.y().value()
+        assert pytest.approx(v.z().value(), abs=1e-5) == v_ref.z().value()
+    for c_new, c_old in zip(new_coords1, coords1):
+        v = c_new - c_old
+        assert pytest.approx(v.x().value(), abs=1e-5) == v_ref.x().value()
+        assert pytest.approx(v.y().value(), abs=1e-5) == v_ref.y().value()
+        assert pytest.approx(v.z().value(), abs=1e-5) == v_ref.z().value()
+    for c_new, c_old in zip(new_coords_test, coords_test):
+        v = c_new - c_old
+        assert pytest.approx(v.x().value(), abs=1e-5) == v_ref.x().value()
+        assert pytest.approx(v.y().value(), abs=1e-5) == v_ref.y().value()
+        assert pytest.approx(v.z().value(), abs=1e-5) == v_ref.z().value()