From b55948c92dcc8a61f919cfda5bc43a852d7ea4c1 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 21 Oct 2026 14:41:16 +0100
Subject: [PATCH 1/2] Fix stale inputs and ignored links file in
 generateNetwork. [closes #557]

---
 src/BioSimSpace/Align/_align.py               | 13 ++++--
 .../Sandpit/Exscientia/Align/_align.py        | 13 ++++--
 tests/Align/test_align.py                     | 46 +++++++++++++++++++
 tests/Sandpit/Exscientia/Align/test_align.py  | 46 +++++++++++++++++++
 4 files changed, 110 insertions(+), 8 deletions(-)

diff --git a/src/BioSimSpace/Align/_align.py b/src/BioSimSpace/Align/_align.py
index 72f0f50d7..884ba3ef7 100644
--- a/src/BioSimSpace/Align/_align.py
+++ b/src/BioSimSpace/Align/_align.py
@@ -111,7 +111,8 @@ def generateNetwork(
         molecule will be used.
 
     work_dir : str
-        The working directory for the LOMAP process.
+        The working directory for the LOMAP process. Any existing 'inputs'
+        and 'outputs' sub-directories are replaced on each call.
 
     plot_network : bool
         Whether to plot the network when running from within a notebook.
@@ -169,6 +170,7 @@ def generateNetwork(
     """
     import csv as _csv
     import os as _os
+    import shutil as _shutil
 
     from .. import IO as _IO
     from .. import _is_notebook, _isVerbose, _Utils
@@ -288,9 +290,11 @@ def generateNetwork(
     # Create the working directory.
     work_dir = _Utils.WorkDir(work_dir)
 
-    # Make the LOMAP input and output directories.
-    _os.makedirs(work_dir + "/inputs", exist_ok=True)
-    _os.makedirs(work_dir + "/outputs", exist_ok=True)
+    # Make fresh LOMAP input and output directories, since LOMAP loads every
+    # file in the input directory.
+    for sub_dir in ["inputs", "outputs"]:
+        _shutil.rmtree(f"{work_dir}/{sub_dir}", ignore_errors=True)
+        _os.makedirs(f"{work_dir}/{sub_dir}")
 
     # Dictionary to map ligand names in the links file to the file names
     # that are used in the working directory.
@@ -386,6 +390,7 @@ def generateNetwork(
                 new_line = f"{links_names[records[0]]} {links_names[records[1]]}"
                 if len(records) > 2:
                     new_line += " " + " ".join(records[2:])
+                new_lines.append(new_line + "\n")
 
         # Store the path to the new file.
         lf = f"{work_dir}/inputs/lomap_links_file.txt"
diff --git a/src/BioSimSpace/Sandpit/Exscientia/Align/_align.py b/src/BioSimSpace/Sandpit/Exscientia/Align/_align.py
index db4675e34..430df2021 100644
--- a/src/BioSimSpace/Sandpit/Exscientia/Align/_align.py
+++ b/src/BioSimSpace/Sandpit/Exscientia/Align/_align.py
@@ -111,7 +111,8 @@ def generateNetwork(
         molecule will be used.
 
     work_dir : str
-        The working directory for the LOMAP process.
+        The working directory for the LOMAP process. Any existing 'inputs'
+        and 'outputs' sub-directories are replaced on each call.
 
     plot_network : bool
         Whether to plot the network when running from within a notebook.
@@ -169,6 +170,7 @@ def generateNetwork(
     """
     import csv as _csv
     import os as _os
+    import shutil as _shutil
 
     from .. import IO as _IO
     from .. import _is_notebook, _isVerbose, _Utils
@@ -288,9 +290,11 @@ def generateNetwork(
     # Create the working directory.
     work_dir = _Utils.WorkDir(work_dir)
 
-    # Make the LOMAP input and output directories.
-    _os.makedirs(work_dir + "/inputs", exist_ok=True)
-    _os.makedirs(work_dir + "/outputs", exist_ok=True)
+    # Make fresh LOMAP input and output directories, since LOMAP loads every
+    # file in the input directory.
+    for sub_dir in ["inputs", "outputs"]:
+        _shutil.rmtree(f"{work_dir}/{sub_dir}", ignore_errors=True)
+        _os.makedirs(f"{work_dir}/{sub_dir}")
 
     # Dictionary to map ligand names in the links file to the file names
     # that are used in the working directory.
@@ -386,6 +390,7 @@ def generateNetwork(
                 new_line = f"{links_names[records[0]]} {links_names[records[1]]}"
                 if len(records) > 2:
                     new_line += " " + " ".join(records[2:])
+                new_lines.append(new_line + "\n")
 
         # Store the path to the new file.
         lf = f"{work_dir}/inputs/lomap_links_file.txt"
diff --git a/tests/Align/test_align.py b/tests/Align/test_align.py
index dca7b31be..36fe93a60 100644
--- a/tests/Align/test_align.py
+++ b/tests/Align/test_align.py
@@ -1643,3 +1643,49 @@ def test_unmapped_attachment_warning_not_swallowed(ejm31, jmc28):
         with warnings.catch_warnings():
             warnings.filterwarnings("error", message=".*ringMatchesRingOnly.*")
             BSS.Align.matchAtoms(ejm31, jmc28)
+
+
+@pytest.fixture(scope="module")
+def network_ligands():
+    from rdkit import Chem
+    from rdkit.Chem import AllChem
+
+    smiles = ["c1ccccc1C", "c1ccccc1CC", "c1ccccc1O", "c1ccccc1N", "C1CCCCC1C(=O)O"]
+    ligands = []
+    for s in smiles:
+        mol = Chem.AddHs(Chem.MolFromSmiles(s))
+        AllChem.EmbedMolecule(mol, randomSeed=42)
+        ligands.append(mol)
+    return ligands
+
+
+def test_network_reused_work_dir(network_ligands, tmp_path):
+    names = [f"lig{x}" for x in range(len(network_ligands))]
+
+    expected = BSS.Align.generateNetwork(
+        network_ligands, names=names, work_dir=str(tmp_path / "fresh")
+    )
+
+    # Run with a subset of ligands, then the full set, in the same directory.
+    work_dir = str(tmp_path / "reused")
+    BSS.Align.generateNetwork(network_ligands[1:], names=names[1:], work_dir=work_dir)
+    result = BSS.Align.generateNetwork(network_ligands, names=names, work_dir=work_dir)
+
+    assert result == expected
+
+
+def test_network_links_file(network_ligands, tmp_path):
+    names = [f"lig{x}" for x in range(len(network_ligands))]
+
+    links_file = tmp_path / "links.txt"
+    links_file.write_text("lig1 lig4 -0.5 force\n")
+
+    edges, scores = BSS.Align.generateNetwork(
+        network_ligands,
+        names=names,
+        links_file=str(links_file),
+        work_dir=str(tmp_path / "lomap"),
+    )
+
+    assert (1, 4) in edges
+    assert scores[edges.index((1, 4))] == pytest.approx(0.5)
diff --git a/tests/Sandpit/Exscientia/Align/test_align.py b/tests/Sandpit/Exscientia/Align/test_align.py
index 6d265a166..24f49c909 100644
--- a/tests/Sandpit/Exscientia/Align/test_align.py
+++ b/tests/Sandpit/Exscientia/Align/test_align.py
@@ -1201,3 +1201,49 @@ def test_unmapped_attachment_warning_not_swallowed(ejm31, jmc28):
         with warnings.catch_warnings():
             warnings.filterwarnings("error", message=".*ringMatchesRingOnly.*")
             BSS.Align.matchAtoms(ejm31, jmc28)
+
+
+@pytest.fixture(scope="module")
+def network_ligands():
+    from rdkit import Chem
+    from rdkit.Chem import AllChem
+
+    smiles = ["c1ccccc1C", "c1ccccc1CC", "c1ccccc1O", "c1ccccc1N", "C1CCCCC1C(=O)O"]
+    ligands = []
+    for s in smiles:
+        mol = Chem.AddHs(Chem.MolFromSmiles(s))
+        AllChem.EmbedMolecule(mol, randomSeed=42)
+        ligands.append(mol)
+    return ligands
+
+
+def test_network_reused_work_dir(network_ligands, tmp_path):
+    names = [f"lig{x}" for x in range(len(network_ligands))]
+
+    expected = BSS.Align.generateNetwork(
+        network_ligands, names=names, work_dir=str(tmp_path / "fresh")
+    )
+
+    # Run with a subset of ligands, then the full set, in the same directory.
+    work_dir = str(tmp_path / "reused")
+    BSS.Align.generateNetwork(network_ligands[1:], names=names[1:], work_dir=work_dir)
+    result = BSS.Align.generateNetwork(network_ligands, names=names, work_dir=work_dir)
+
+    assert result == expected
+
+
+def test_network_links_file(network_ligands, tmp_path):
+    names = [f"lig{x}" for x in range(len(network_ligands))]
+
+    links_file = tmp_path / "links.txt"
+    links_file.write_text("lig1 lig4 -0.5 force\n")
+
+    edges, scores = BSS.Align.generateNetwork(
+        network_ligands,
+        names=names,
+        links_file=str(links_file),
+        work_dir=str(tmp_path / "lomap"),
+    )
+
+    assert (1, 4) in edges
+    assert scores[edges.index((1, 4))] == pytest.approx(0.5)

From efca810765f9542f17953d5ae39137f5e54f6b01 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 21 Oct 2026 15:15:55 +0100
Subject: [PATCH 2/2] Disable NAGL for OpenFF parameterisation in tests.
 [closes #556]

---
 tests/Align/test_align.py                            |  8 ++++----
 tests/IO/test_file_cache.py                          | 10 +++++++---
 tests/IO/test_openff_gromacs.py                      |  8 ++++++--
 tests/Parameters/test_parameters.py                  |  2 +-
 tests/Process/test_gromacs.py                        |  2 +-
 tests/Process/test_openmm.py                         |  2 +-
 tests/Sandpit/Exscientia/Align/test_align.py         |  8 ++++----
 tests/Sandpit/Exscientia/IO/test_file_cache.py       | 10 +++++++---
 tests/Sandpit/Exscientia/IO/test_openff_gromacs.py   |  8 ++++++--
 .../Sandpit/Exscientia/Parameters/test_parameters.py |  2 +-
 tests/Sandpit/Exscientia/Process/test_gromacs.py     |  2 +-
 tests/Sandpit/Exscientia/Process/test_openmm.py      |  2 +-
 .../Exscientia/Process/test_position_restraint.py    |  4 ++--
 tests/Sandpit/Exscientia/Process/test_restart.py     |  4 ++--
 tests/Sandpit/Exscientia/Protocol/test_config.py     | 12 +++++++++---
 .../Exscientia/_SireWrappers/test_molecule.py        |  2 +-
 .../Sandpit/Exscientia/_SireWrappers/test_system.py  | 10 +++++++---
 tests/Sandpit/Exscientia/conftest.py                 |  4 ++--
 tests/_SireWrappers/test_system.py                   | 10 +++++++---
 19 files changed, 70 insertions(+), 40 deletions(-)

diff --git a/tests/Align/test_align.py b/tests/Align/test_align.py
index 36fe93a60..3f9850b7c 100644
--- a/tests/Align/test_align.py
+++ b/tests/Align/test_align.py
@@ -939,8 +939,8 @@ def test_ring_opening_and_size_change(ligands, mapping):
     m0 = BSS.IO.readMolecules(f"{url}/{ligands[0]}.sdf.bz2")[0]
     m1 = BSS.IO.readMolecules(f"{url}/{ligands[1]}.sdf.bz2")[0]
 
-    m0 = BSS.Parameters.openff_unconstrained_2_1_1(m0).getMolecule()
-    m1 = BSS.Parameters.openff_unconstrained_2_1_1(m1).getMolecule()
+    m0 = BSS.Parameters.openff_unconstrained_2_1_1(m0, use_nagl=False).getMolecule()
+    m1 = BSS.Parameters.openff_unconstrained_2_1_1(m1, use_nagl=False).getMolecule()
 
     m0 = BSS.Align.rmsdAlign(m0, m1, mapping)
 
@@ -1237,10 +1237,10 @@ def test_ring_breaking_cross_bond_cleanup():
     }
 
     mol0 = BSS.Parameters.openff_unconstrained_2_2_1(
-        BSS.IO.readMolecules(f"{url}/5033.sdf")[0]
+        BSS.IO.readMolecules(f"{url}/5033.sdf")[0], use_nagl=False
     ).getMolecule()
     mol1 = BSS.Parameters.openff_unconstrained_2_2_1(
-        BSS.IO.readMolecules(f"{url}/5035.sdf")[0]
+        BSS.IO.readMolecules(f"{url}/5035.sdf")[0], use_nagl=False
     ).getMolecule()
 
     mol0_aligned = BSS.Align.rmsdAlign(mol0, mol1, mapping)
diff --git a/tests/IO/test_file_cache.py b/tests/IO/test_file_cache.py
index 0fa9035f9..219bb055f 100644
--- a/tests/IO/test_file_cache.py
+++ b/tests/IO/test_file_cache.py
@@ -115,11 +115,15 @@ def test_file_cache_mol_nums():
     BSS.IO.clearCache()
 
     # Create an initial system.
-    system = BSS.Parameters.openff_unconstrained_2_0_0("CO").getMolecule().toSystem()
+    system = (
+        BSS.Parameters.openff_unconstrained_2_0_0("CO", use_nagl=False)
+        .getMolecule()
+        .toSystem()
+    )
 
     # Create two different 5 atom molecules.
-    mol0 = BSS.Parameters.openff_unconstrained_2_0_0("C").getMolecule()
-    mol1 = BSS.Parameters.openff_unconstrained_2_0_0("CF").getMolecule()
+    mol0 = BSS.Parameters.openff_unconstrained_2_0_0("C", use_nagl=False).getMolecule()
+    mol1 = BSS.Parameters.openff_unconstrained_2_0_0("CF", use_nagl=False).getMolecule()
 
     # Create two new systems by adding the different molecules to the original
     # system. These will have the same UID, but different molecule numbers.
diff --git a/tests/IO/test_openff_gromacs.py b/tests/IO/test_openff_gromacs.py
index b556c430d..97e9b5f92 100644
--- a/tests/IO/test_openff_gromacs.py
+++ b/tests/IO/test_openff_gromacs.py
@@ -19,10 +19,14 @@ def test_molecule_combine():
     # which have different parameters.
 
     # Toluene.
-    m0 = BSS.Parameters.openff_unconstrained_2_0_0("Cc1ccccc1").getMolecule()
+    m0 = BSS.Parameters.openff_unconstrained_2_0_0(
+        "Cc1ccccc1", use_nagl=False
+    ).getMolecule()
 
     # Benzene.
-    m1 = BSS.Parameters.openff_unconstrained_2_0_0("c1ccccc1").getMolecule()
+    m1 = BSS.Parameters.openff_unconstrained_2_0_0(
+        "c1ccccc1", use_nagl=False
+    ).getMolecule()
 
     # Translate m1 such that the molecules don't interact.
     m1.translate(3 * [50 * BSS.Units.Length.angstrom])
diff --git a/tests/Parameters/test_parameters.py b/tests/Parameters/test_parameters.py
index a744cda19..d20343bfc 100644
--- a/tests/Parameters/test_parameters.py
+++ b/tests/Parameters/test_parameters.py
@@ -73,7 +73,7 @@ def test_molecule_rename():
 
     # Create the parameterised molecule.
     mol = BSS.Parameters.openff_unconstrained_2_0_0(
-        "[C@@H](C(F)(F)F)(OC(F)F)Cl"
+        "[C@@H](C(F)(F)F)(OC(F)F)Cl", use_nagl=False
     ).getMolecule()
 
     # Make sure the name is correct.
diff --git a/tests/Process/test_gromacs.py b/tests/Process/test_gromacs.py
index 5a4b59daa..731e1975e 100644
--- a/tests/Process/test_gromacs.py
+++ b/tests/Process/test_gromacs.py
@@ -232,7 +232,7 @@ def test_vacuum_com():
     """
 
     # Create a test molecule.
-    mol = BSS.Parameters.openff_unconstrained_2_0_0("CC").getMolecule()
+    mol = BSS.Parameters.openff_unconstrained_2_0_0("CC", use_nagl=False).getMolecule()
 
     # Create a short minimisation protocol.
     protocol = BSS.Protocol.Minimisation(steps=100)
diff --git a/tests/Process/test_openmm.py b/tests/Process/test_openmm.py
index f57fd1852..7b7815ad9 100644
--- a/tests/Process/test_openmm.py
+++ b/tests/Process/test_openmm.py
@@ -80,7 +80,7 @@ def test_rhombic_dodecahedron():
     """Test that OpenMM can load and run rhombic dodecahedral triclinic spaces."""
 
     # Create a methane molecule.
-    mol = BSS.Parameters.openff_unconstrained_2_0_0("C").getMolecule()
+    mol = BSS.Parameters.openff_unconstrained_2_0_0("C", use_nagl=False).getMolecule()
 
     # Generate box dimensions and angles for a hexagonal rhombic dodecahedron.
     box, angles = BSS.Box.rhombicDodecahedronHexagon(5 * BSS.Units.Length.nanometer)
diff --git a/tests/Sandpit/Exscientia/Align/test_align.py b/tests/Sandpit/Exscientia/Align/test_align.py
index 24f49c909..05a599944 100644
--- a/tests/Sandpit/Exscientia/Align/test_align.py
+++ b/tests/Sandpit/Exscientia/Align/test_align.py
@@ -81,14 +81,14 @@ def test_invalid_prematch(system0, system1, prematch):
 @pytest.fixture()
 def propane():
     return BSS.Parameters.parameterise(
-        "CCC", "openff_unconstrained-2.0.0"
+        "CCC", "openff_unconstrained-2.0.0", use_nagl=False
     ).getMolecule()
 
 
 @pytest.fixture()
 def butane():
     return BSS.Parameters.parameterise(
-        "CCCC", "openff_unconstrained-2.0.0"
+        "CCCC", "openff_unconstrained-2.0.0", use_nagl=False
     ).getMolecule()
 
 
@@ -902,8 +902,8 @@ def test_ring_opening_and_size_change(ligands, mapping):
     m0 = BSS.IO.readMolecules(f"{url}/{ligands[0]}.sdf.bz2")[0]
     m1 = BSS.IO.readMolecules(f"{url}/{ligands[1]}.sdf.bz2")[0]
 
-    m0 = BSS.Parameters.openff_unconstrained_2_1_1(m0).getMolecule()
-    m1 = BSS.Parameters.openff_unconstrained_2_1_1(m1).getMolecule()
+    m0 = BSS.Parameters.openff_unconstrained_2_1_1(m0, use_nagl=False).getMolecule()
+    m1 = BSS.Parameters.openff_unconstrained_2_1_1(m1, use_nagl=False).getMolecule()
 
     m0 = BSS.Align.rmsdAlign(m0, m1, mapping)
 
diff --git a/tests/Sandpit/Exscientia/IO/test_file_cache.py b/tests/Sandpit/Exscientia/IO/test_file_cache.py
index 23fc03446..5f129beef 100644
--- a/tests/Sandpit/Exscientia/IO/test_file_cache.py
+++ b/tests/Sandpit/Exscientia/IO/test_file_cache.py
@@ -116,11 +116,15 @@ def test_file_cache_mol_nums():
     BSS.IO.clearCache()
 
     # Create an initial system.
-    system = BSS.Parameters.openff_unconstrained_2_0_0("CO").getMolecule().toSystem()
+    system = (
+        BSS.Parameters.openff_unconstrained_2_0_0("CO", use_nagl=False)
+        .getMolecule()
+        .toSystem()
+    )
 
     # Create two different 5 atom molecules.
-    mol0 = BSS.Parameters.openff_unconstrained_2_0_0("C").getMolecule()
-    mol1 = BSS.Parameters.openff_unconstrained_2_0_0("CF").getMolecule()
+    mol0 = BSS.Parameters.openff_unconstrained_2_0_0("C", use_nagl=False).getMolecule()
+    mol1 = BSS.Parameters.openff_unconstrained_2_0_0("CF", use_nagl=False).getMolecule()
 
     # Create two new systems by adding the different molecules to the original
     # system. These will have the same UID, but different molecule numbers.
diff --git a/tests/Sandpit/Exscientia/IO/test_openff_gromacs.py b/tests/Sandpit/Exscientia/IO/test_openff_gromacs.py
index 14c9cb659..b8d184584 100644
--- a/tests/Sandpit/Exscientia/IO/test_openff_gromacs.py
+++ b/tests/Sandpit/Exscientia/IO/test_openff_gromacs.py
@@ -27,10 +27,14 @@ def test_molecule_combine():
     # which have different parameters.
 
     # Toluene.
-    m0 = BSS.Parameters.openff_unconstrained_2_0_0("Cc1ccccc1").getMolecule()
+    m0 = BSS.Parameters.openff_unconstrained_2_0_0(
+        "Cc1ccccc1", use_nagl=False
+    ).getMolecule()
 
     # Benzene.
-    m1 = BSS.Parameters.openff_unconstrained_2_0_0("c1ccccc1").getMolecule()
+    m1 = BSS.Parameters.openff_unconstrained_2_0_0(
+        "c1ccccc1", use_nagl=False
+    ).getMolecule()
 
     # Translate m1 such that the molecules don't interact.
     m1.translate(3 * [50 * BSS.Units.Length.angstrom])
diff --git a/tests/Sandpit/Exscientia/Parameters/test_parameters.py b/tests/Sandpit/Exscientia/Parameters/test_parameters.py
index a512ff8d9..b49898ed8 100644
--- a/tests/Sandpit/Exscientia/Parameters/test_parameters.py
+++ b/tests/Sandpit/Exscientia/Parameters/test_parameters.py
@@ -78,7 +78,7 @@ def test_molecule_rename():
 
     # Create the parameterised molecule.
     mol = BSS.Parameters.openff_unconstrained_2_0_0(
-        "[C@@H](C(F)(F)F)(OC(F)F)Cl"
+        "[C@@H](C(F)(F)F)(OC(F)F)Cl", use_nagl=False
     ).getMolecule()
 
     # Make sure the name is correct.
diff --git a/tests/Sandpit/Exscientia/Process/test_gromacs.py b/tests/Sandpit/Exscientia/Process/test_gromacs.py
index d74965de6..325afefe1 100644
--- a/tests/Sandpit/Exscientia/Process/test_gromacs.py
+++ b/tests/Sandpit/Exscientia/Process/test_gromacs.py
@@ -483,7 +483,7 @@ def test_vacuum_com():
     """
 
     # Create a test molecule.
-    mol = BSS.Parameters.openff_unconstrained_2_0_0("CC").getMolecule()
+    mol = BSS.Parameters.openff_unconstrained_2_0_0("CC", use_nagl=False).getMolecule()
 
     # Create a short minimisation protocol.
     protocol = BSS.Protocol.Minimisation(steps=100)
diff --git a/tests/Sandpit/Exscientia/Process/test_openmm.py b/tests/Sandpit/Exscientia/Process/test_openmm.py
index 0a83ee671..c52d57817 100644
--- a/tests/Sandpit/Exscientia/Process/test_openmm.py
+++ b/tests/Sandpit/Exscientia/Process/test_openmm.py
@@ -139,7 +139,7 @@ def test_rhombic_dodecahedron():
     """Test that OpenMM can load and run rhombic dodecahedral triclinic spaces."""
 
     # Create a methane molecule.
-    mol = BSS.Parameters.openff_unconstrained_2_0_0("C").getMolecule()
+    mol = BSS.Parameters.openff_unconstrained_2_0_0("C", use_nagl=False).getMolecule()
 
     # Generate box dimensions and angles for a hexagonal rhombic dodecahedron.
     box, angles = BSS.Box.rhombicDodecahedronHexagon(5 * BSS.Units.Length.nanometer)
diff --git a/tests/Sandpit/Exscientia/Process/test_position_restraint.py b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
index bb5583d14..553fcd6d7 100644
--- a/tests/Sandpit/Exscientia/Process/test_position_restraint.py
+++ b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
@@ -20,8 +20,8 @@
 @pytest.fixture
 def system():
     ff = "openff_unconstrained-2.0.0"
-    mol0 = BSS.Parameters.parameterise("c1ccccc1C", ff).getMolecule()
-    mol1 = BSS.Parameters.parameterise("c1ccccc1", ff).getMolecule()
+    mol0 = BSS.Parameters.parameterise("c1ccccc1C", ff, use_nagl=False).getMolecule()
+    mol1 = BSS.Parameters.parameterise("c1ccccc1", ff, use_nagl=False).getMolecule()
     return BSS.Align.merge(mol0, mol1).toSystem()
 
 
diff --git a/tests/Sandpit/Exscientia/Process/test_restart.py b/tests/Sandpit/Exscientia/Process/test_restart.py
index ec09718b0..f09961c18 100644
--- a/tests/Sandpit/Exscientia/Process/test_restart.py
+++ b/tests/Sandpit/Exscientia/Process/test_restart.py
@@ -16,8 +16,8 @@
 @pytest.fixture
 def system():
     ff = "openff_unconstrained-2.0.0"
-    mol0 = BSS.Parameters.parameterise("c1ccccc1C", ff).getMolecule()
-    mol1 = BSS.Parameters.parameterise("c1ccccc1", ff).getMolecule()
+    mol0 = BSS.Parameters.parameterise("c1ccccc1C", ff, use_nagl=False).getMolecule()
+    mol1 = BSS.Parameters.parameterise("c1ccccc1", ff, use_nagl=False).getMolecule()
     return BSS.Align.merge(mol0, mol1).toSystem()
 
 
diff --git a/tests/Sandpit/Exscientia/Protocol/test_config.py b/tests/Sandpit/Exscientia/Protocol/test_config.py
index 9ecd3ca86..cc39bd1df 100644
--- a/tests/Sandpit/Exscientia/Protocol/test_config.py
+++ b/tests/Sandpit/Exscientia/Protocol/test_config.py
@@ -214,7 +214,9 @@ def test_staged_fep_df(self, system):
 @pytest.fixture(scope="module")
 def system_and_mdr_restraint():
     # Benzene.
-    m = BSS.Parameters.openff_unconstrained_2_0_0("c1ccccc1").getMolecule()
+    m = BSS.Parameters.openff_unconstrained_2_0_0(
+        "c1ccccc1", use_nagl=False
+    ).getMolecule()
     m._sire_object = m._sire_object.edit().rename("LIG").molecule().commit()
 
     # Assign atoms for restraint
@@ -271,7 +273,9 @@ class TestGromacsABFE:
     @pytest.fixture(scope="class")
     def system():
         # Benzene.
-        m0 = BSS.Parameters.openff_unconstrained_2_0_0("c1ccccc1").getMolecule()
+        m0 = BSS.Parameters.openff_unconstrained_2_0_0(
+            "c1ccccc1", use_nagl=False
+        ).getMolecule()
         m0._sire_object = m0._sire_object.edit().rename("LIG").molecule().commit()
         protocol = FreeEnergyMinimisation(
             lam=0.0,
@@ -425,7 +429,9 @@ class TestSomdABFE:
     @pytest.fixture(scope="class")
     def system_and_boresch_restraint():
         # Benzene.
-        m = BSS.Parameters.openff_unconstrained_2_0_0("c1ccccc1").getMolecule()
+        m = BSS.Parameters.openff_unconstrained_2_0_0(
+            "c1ccccc1", use_nagl=False
+        ).getMolecule()
 
         # Assign atoms for restraint
         atom_1 = m.getAtoms()[0]
diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py b/tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py
index eef91f38e..43b91814a 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py
@@ -134,7 +134,7 @@ def test_extract(system):
 )
 def test_lipid(lipid):
     ff = "openff_unconstrained-2.0.0"
-    mol = BSS.Parameters.parameterise("c1ccccc1C", ff).getMolecule()
+    mol = BSS.Parameters.parameterise("c1ccccc1C", ff, use_nagl=False).getMolecule()
     if lipid:
         sire_obj = mol._sire_object
         c = sire_obj.cursor()
diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
index c68a9cfe3..29bd54528 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
@@ -380,11 +380,15 @@ def test_isSame_mol_nums():
     # but contain different MolNums.
 
     # Create an initial system.
-    system = BSS.Parameters.openff_unconstrained_2_0_0("CO").getMolecule().toSystem()
+    system = (
+        BSS.Parameters.openff_unconstrained_2_0_0("CO", use_nagl=False)
+        .getMolecule()
+        .toSystem()
+    )
 
     # Create two different 5 atom molecules.
-    mol0 = BSS.Parameters.openff_unconstrained_2_0_0("C").getMolecule()
-    mol1 = BSS.Parameters.openff_unconstrained_2_0_0("CF").getMolecule()
+    mol0 = BSS.Parameters.openff_unconstrained_2_0_0("C", use_nagl=False).getMolecule()
+    mol1 = BSS.Parameters.openff_unconstrained_2_0_0("CF", use_nagl=False).getMolecule()
 
     # Create two new systems by adding the different molecules to the original
     # system. These will have the same UID, but different molecule numbers.
diff --git a/tests/Sandpit/Exscientia/conftest.py b/tests/Sandpit/Exscientia/conftest.py
index 82268b3b3..e98e7ce94 100644
--- a/tests/Sandpit/Exscientia/conftest.py
+++ b/tests/Sandpit/Exscientia/conftest.py
@@ -144,14 +144,14 @@ def get_energy(
 @pytest.fixture
 def benzene():
     return BSS.Parameters.parameterise(
-        "c1ccccc1", "openff_unconstrained-2.0.0"
+        "c1ccccc1", "openff_unconstrained-2.0.0", use_nagl=False
     ).getMolecule()
 
 
 @pytest.fixture
 def pyrrole():
     return BSS.Parameters.parameterise(
-        "C1=CNC=C1", "openff_unconstrained-2.0.0"
+        "C1=CNC=C1", "openff_unconstrained-2.0.0", use_nagl=False
     ).getMolecule()
 
 
diff --git a/tests/_SireWrappers/test_system.py b/tests/_SireWrappers/test_system.py
index ba7d225ee..18a89ed0d 100644
--- a/tests/_SireWrappers/test_system.py
+++ b/tests/_SireWrappers/test_system.py
@@ -371,11 +371,15 @@ def test_isSame_mol_nums():
     # but contain different MolNums.
 
     # Create an initial system.
-    system = BSS.Parameters.openff_unconstrained_2_0_0("CO").getMolecule().toSystem()
+    system = (
+        BSS.Parameters.openff_unconstrained_2_0_0("CO", use_nagl=False)
+        .getMolecule()
+        .toSystem()
+    )
 
     # Create two different 5 atom molecules.
-    mol0 = BSS.Parameters.openff_unconstrained_2_0_0("C").getMolecule()
-    mol1 = BSS.Parameters.openff_unconstrained_2_0_0("CF").getMolecule()
+    mol0 = BSS.Parameters.openff_unconstrained_2_0_0("C", use_nagl=False).getMolecule()
+    mol1 = BSS.Parameters.openff_unconstrained_2_0_0("CF", use_nagl=False).getMolecule()
 
     # Create two new systems by adding the different molecules to the original
     # system. These will have the same UID, but different molecule numbers.