Test cofactor networks generated with the CLI

openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py

@@ -90,16 +90,16 @@ def __call__(
 
         if self.do_vacuum:
             chem_sys = ChemicalSystem(
-                components={RFEComponentLabels.LIGAND: component},
+                components={RFEComponentLabels.LIGAND.value: component},
                 name=component.name + "_vacuum",
             )
             yield chem_sys
 
         if self.solvent is not None:
             chem_sys = ChemicalSystem(
                 components={
-                    RFEComponentLabels.LIGAND: component,
-                    RFEComponentLabels.SOLVENT: self.solvent,
+                    RFEComponentLabels.LIGAND.value: component,
+                    RFEComponentLabels.SOLVENT.value: self.solvent,
                 },
                 name=component.name + "_solvent",
             )
@@ -108,13 +108,13 @@ def __call__(
         components: dict[str, Component]
         if self.protein is not None:
             components = {
-                RFEComponentLabels.LIGAND: component,
-                RFEComponentLabels.PROTEIN: self.protein,
+                RFEComponentLabels.LIGAND.value: component,
+                RFEComponentLabels.PROTEIN.value: self.protein,
             }
             for i, c in enumerate(self.cofactors):
-                components.update({f'{RFEComponentLabels.COFACTOR}{i+1}': c})
+                components.update({f'{RFEComponentLabels.COFACTOR.value}{i+1}': c})
             if self.solvent is not None:
-                components.update({RFEComponentLabels.SOLVENT: self.solvent})
+                components.update({RFEComponentLabels.SOLVENT.value: self.solvent})
             chem_sys = ChemicalSystem(
                 components=components, name=component.name + "_complex"
             )

openfe/tests/setup/chemicalsystem_generator/component_checks.py

@@ -14,3 +14,7 @@ def solventC_in_chem_sys(chemical_system: ChemicalSystem) -> bool:
 
 def proteinC_in_chem_sys(chemical_system: ChemicalSystem) -> bool:
     return RFEComponentLabels.PROTEIN in chemical_system.components
+
+def cofactorC_in_chem_sys(chemical_system: ChemicalSystem) -> bool:
+    # cofactors are numbered from 1
+    return f"{RFEComponentLabels.COFACTOR.value}1" in chemical_system.components

openfe/tests/setup/chemicalsystem_generator/test_easy_chemicalsystem_generator.py

@@ -11,7 +11,7 @@
 
 from ...conftest import T4_protein_component
 from gufe import SolventComponent
-from .component_checks import proteinC_in_chem_sys, solventC_in_chem_sys, ligandC_in_chem_sys
+from .component_checks import proteinC_in_chem_sys, solventC_in_chem_sys, ligandC_in_chem_sys, cofactorC_in_chem_sys
 
 
 def test_easy_chemical_system_generator_init(T4_protein_component):
@@ -55,7 +55,6 @@ def test_build_solvent_chemical_system(ethane):
 
 
 def test_build_protein_chemical_system(ethane, T4_protein_component):
-    # TODO: cofactors with eg5 system
     chem_sys_generator = EasyChemicalSystemGenerator(
         protein=T4_protein_component,
     )
@@ -66,6 +65,21 @@ def test_build_protein_chemical_system(ethane, T4_protein_component):
     assert proteinC_in_chem_sys(chem_sys)
     assert not solventC_in_chem_sys(chem_sys)
     assert ligandC_in_chem_sys(chem_sys)
+    assert not cofactorC_in_chem_sys(chem_sys)
+
+def test_build_cofactor_chemical_system(eg5_cofactor, eg5_ligands, eg5_protein):
+    chem_sys_generator = EasyChemicalSystemGenerator(
+        cofactors=[eg5_cofactor], protein=eg5_protein
+    )
+    chem_sys = next(chem_sys_generator(eg5_ligands[0]))
+
+    assert chem_sys is not None
+    assert isinstance(chem_sys, ChemicalSystem)
+    assert proteinC_in_chem_sys(chem_sys)
+    assert not solventC_in_chem_sys(chem_sys)
+    assert ligandC_in_chem_sys(chem_sys)
+    assert cofactorC_in_chem_sys(chem_sys)
+
 
 
 def test_build_hydr_scenario_chemical_systems(ethane):
@@ -91,7 +105,6 @@ def test_build_binding_scenario_chemical_systems(ethane, T4_protein_component):
 
     assert len(chem_syss) == 2
     assert all([isinstance(chem_sys, ChemicalSystem) for chem_sys in chem_syss])
-    print(chem_syss)
     assert [proteinC_in_chem_sys(chem_sys) for chem_sys in chem_syss] == [False, True]
     assert [solventC_in_chem_sys(chem_sys) for chem_sys in chem_syss] == [True, True]
     assert [ligandC_in_chem_sys(chem_sys) for chem_sys in chem_syss] == [True, True]

openfecli/tests/commands/test_plan_rbfe_network.py

@@ -2,7 +2,6 @@
 
 import pytest
 from importlib import resources
-import os
 import shutil
 from click.testing import CliRunner
 
@@ -148,9 +147,18 @@ def test_plan_rbfe_network_cofactors(eg5_files):
     with runner.isolated_filesystem():
         result = runner.invoke(plan_rbfe_network, args)
 
-        print(result.output)
-
         assert result.exit_code == 0
+        # make sure the cofactor is in the transformations
+        network = AlchemicalNetwork.from_dict(
+            json.load(open("alchemicalNetwork/alchemicalNetwork.json"), cls=JSON_HANDLER.decoder)
+        )
+        for edge in network.edges:
+            if "protein" in edge.stateA.components:
+                assert "cofactor1" in edge.stateA.components
+                assert "cofactor1" in edge.stateB.components
+            else:
+                assert "cofactor1" not in edge.stateA.components
+                assert "cofactor1" not in edge.stateB.components
 
 @pytest.fixture
 def cdk8_files():