Short protein-ligand complex test implemented

feflow/tests/conftest.py

@@ -74,13 +74,13 @@ def ty2_protein():
 @pytest.fixture(scope="session")
 def tyk2_ligand_ejm_54():
  filepath = files("feflow.tests.data").joinpath("tyk2_lig_ejm_54.sdf")
- return gufe.SmallMoleculeComponent.from_pdb_file(str(filepath))
+ return gufe.SmallMoleculeComponent.from_sdf_file(str(filepath))
 
 
 @pytest.fixture(scope="session")
 def tyk2_ligand_ejm_46():
  filepath = files("feflow.tests.data").joinpath("tyk2_lig_ejm_46.sdf")
- return gufe.SmallMoleculeComponent.from_pdb_file(str(filepath))
+ return gufe.SmallMoleculeComponent.from_sdf_file(str(filepath))
 
 
 # Systems fixtures
@@ -105,6 +105,23 @@ def toluene_vacuum_system(toluene):
 def toluene_solvent_system(toluene, solvent_comp):
  return gufe.ChemicalSystem({"ligand": toluene, "solvent": solvent_comp})
 
+@pytest.fixture
+def tyk2_lig_ejm_46_complex(tyk2_protein, tyk2_ligand_ejm_46, solvent_comp):
+ return gufe.ChemicalSystem({
+ "protein": tyk2_protein,
+ "ligand": tyk2_ligand_ejm_46,
+ "solvent": solvent_comp
+ })
+
+
+@pytest.fixture
+def tyk2_lig_ejm_54_complex(tyk2_protein, tyk2_ligand_ejm_54):
+ return gufe.ChemicalSystem({
+ "protein": tyk2_protein,
+ "ligand": tyk2_ligand_ejm_54,
+ "solvent": solvent_comp
+ })
+
 
 # Settings fixtures
 
@@ -243,5 +260,12 @@ def broken_mapping(benzene, toluene):
 def mapping_tyk2_54_to_46(tyk2_ligand_ejm_54, tyk2_ligand_ejm_46):
  """
  Mapping object from ligand ejm_54 to ejm_46 for the Tyk2 dataset.
+
+ It generates the mapping on runtime using the Kartograf mapper.
  """
- return NotImplementedError
+ from kartograf import KartografAtomMapper
+
+ atom_mapper = KartografAtomMapper()
+ mapping_obj = next(atom_mapper.suggest_mappings(tyk2_ligand_ejm_54, tyk2_ligand_ejm_46))
+
+ return mapping_obj

feflow/tests/test_nonequilibrium_cycling.py

@@ -374,12 +374,30 @@ def test_create_execute_gather_toluene_to_toluene(
  # TODO: We could also generate a plot with the forward and reverse works and visually check the results.
  # TODO: Potentially setup (not run) a protein-ligand system
 
- def test_tyk2_complex (self, protocol_short, tyk2_protein, tyk2_ligand_ejm_54, tyk2_ligand_ejm_46, mapping_tyk2_54_to_46 , tmpdir):
+ def test_tyk2_complex(self, protocol_short, tyk2_lig_ejm_54_complex, tyk2_lig_ejm_46_complex, mapping_tyk2_54_to_46, tmpdir):
  """
  Run the protocol with single transformation between ligands ejm_54 and ejm_46
  from the tyk2 dataset.
  """
- return NotImplementedError
+ dag = protocol_short.create(
+ stateA=tyk2_lig_ejm_54_complex,
+ stateB=tyk2_lig_ejm_46_complex,
+ name="Short protein-ligand complex transformation",
+ mapping=mapping_tyk2_54_to_46,
+ )
+
+ with tmpdir.as_cwd():
+ shared = Path("shared")
+ shared.mkdir()
+ scratch = Path("scratch")
+ scratch.mkdir()
+
+ dagresult = execute_DAG(
+ dag, shared_basedir=shared, scratch_basedir=scratch,
+ )
+
+ # Check that the dag was executed correctly
+ assert dagresult.ok(), f"DAG was not executed correctly."
 
  @pytest.mark.parametrize("method, backend", partial_charges_config())
  def test_partial_charge_assignation(