remove box_vector from ChemicalSystem

was causing trouble in eq situations
OpenFreeEnergy · Apr 11, 2023 · 1a613e4 · 1a613e4
1 parent 2bbaabc
commit 1a613e4
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Showing 4 changed files with 5 additions and 57 deletions.
diff --git a/gufe/chemicalsystem.py b/gufe/chemicalsystem.py
@@ -19,9 +19,6 @@ class ChemicalSystem(GufeTokenizable, abc.Mapping):
         The molecular representation of the chemical state, including
         connectivity and coordinates. This is a frozendict with user-defined
         labels as keys, :class:`.Component`\ s as values.
-    box_vectors
-        Numpy array indicating shape and size of unit cell for the system. May
-        be a partial definition to allow for variability on certain dimensions.
     name
         Optional identifier for the chemical state; used as part of the
         (hashable) graph node itself when the chemical state is added to an
@@ -32,7 +29,6 @@ class ChemicalSystem(GufeTokenizable, abc.Mapping):
     def __init__(
         self,
         components: Dict[str, Component],
-        box_vectors: Optional[np.ndarray] = None,
         name: Optional[str] = "",
     ):
         """Create a node for an alchemical network.
@@ -43,10 +39,6 @@ def __init__(
             The molecular representation of the chemical state, including
             connectivity and coordinates. Given as a dict with user-defined
             labels as keys, :class:`.Component`\ s as values.
-        box_vectors
-            Optional ``numpy`` array indicating shape and size of unit cell for
-            the system. May be a partial definition to allow for variability on
-            certain dimensions.
         name
             Optional identifier for the chemical state; included with the other
             attributes as part of the (hashable) graph node itself when the
@@ -58,11 +50,6 @@ def __init__(
         self._components = components
         self._name = name
 
-        if box_vectors is None:
-            self._box_vectors = np.array([np.nan] * 9)
-        else:
-            self._box_vectors = box_vectors
-
     def __repr__(self):
         return (
             f"{self.__class__.__name__}(name={self.name}, components={self.components})"
@@ -73,7 +60,6 @@ def _to_dict(self):
             "components": {
                 key: value for key, value in sorted(self.components.items())
             },
-            "box_vectors": self.box_vectors.tolist(),
             "name": self.name,
         }
 
@@ -83,18 +69,13 @@ def _from_dict(cls, d):
             components={
                 key: value for key, value in d["components"].items()
             },
-            box_vectors=np.array(d["box_vectors"]),
             name=d["name"],
         )
 
     @property
     def components(self):
         return dict(self._components)
 
-    @property
-    def box_vectors(self):
-        return np.array(self._box_vectors)
-
     @property
     def name(self):
         return self._name

diff --git a/gufe/tests/test_chemicalsystem.py b/gufe/tests/test_chemicalsystem.py
@@ -80,19 +80,6 @@ def test_chemical_system_neq_2(solvated_complex, prot_comp, solv_comp,
     assert hash(solvated_complex) != hash(complex2)
 
 
-def test_chemical_system_neq_3(solvated_complex, prot_comp, solv_comp,
-                               toluene_ligand_comp):
-    # different unit cell size
-    complex2 = ChemicalSystem(
-        {'protein': prot_comp,
-         'solvent': solv_comp,
-         'ligand': toluene_ligand_comp},
-        box_vectors=np.array([10, 0, 0] + [np.nan] * 6),
-    )
-    assert solvated_complex != complex2
-    assert hash(solvated_complex) != hash(complex2)
-
-
 def test_chemical_system_neq_4(solvated_complex, solvated_ligand):
     # different component keys
     assert solvated_complex != solvated_ligand
@@ -131,28 +118,12 @@ def test_sorting(solvated_complex, solvated_ligand):
 class TestChemicalSystem(GufeTokenizableTestsMixin):
 
     cls = ChemicalSystem
-    key = "ChemicalSystem-1f244420be5cf662c0f804b052ef2a1e"
-    repr = "ChemicalSystem(name=, components={'solvent': SolventComponent(name=O, K+, Cl-), 'ligand': SmallMoleculeComponent(name=toluene)})"
-
-    @pytest.fixture
-    def instance(self, solv_comp, toluene_ligand_comp):
-        return ChemicalSystem(
-            {'solvent': solv_comp,
-             'ligand': toluene_ligand_comp},
-            box_vectors=np.array([10, 10, 10, 90, 90, 90.]),
-            )
-
-
-class TestChemicalSystemNanBox(GufeTokenizableTestsMixin):
-
-    cls = ChemicalSystem
-    key = "ChemicalSystem-34f6bd8be97cc184bad334e6f8daa469"
+    key = "ChemicalSystem-92176395ceb86ecd7787ce2585b24218"
     repr = "ChemicalSystem(name=, components={'solvent': SolventComponent(name=O, K+, Cl-), 'ligand': SmallMoleculeComponent(name=toluene)})"
 
     @pytest.fixture
     def instance(self, solv_comp, toluene_ligand_comp):
         return ChemicalSystem(
             {'solvent': solv_comp,
              'ligand': toluene_ligand_comp},
-            box_vectors=np.array([np.nan, 10, 10, 90, 90, 90.]),
             )
diff --git a/gufe/tests/test_network.py b/gufe/tests/test_network.py
@@ -13,8 +13,8 @@
 class TestAlchemicalNetwork(GufeTokenizableTestsMixin):
 
     cls = AlchemicalNetwork
-    key = "AlchemicalNetwork-71e52000bd30c7e03857ec8f2abf0f66"
-    repr = "<AlchemicalNetwork-71e52000bd30c7e03857ec8f2abf0f66>"
+    key = "AlchemicalNetwork-8c6df17d7ecf5902e2e338984cc11140"
+    repr = "<AlchemicalNetwork-8c6df17d7ecf5902e2e338984cc11140>"
 
     @pytest.fixture
     def instance(self, benzene_variants_star_map):

diff --git a/gufe/tests/test_transformation.py b/gufe/tests/test_transformation.py
@@ -31,7 +31,7 @@ def complex_equilibrium(solvated_complex):
 class TestTransformation(GufeTokenizableTestsMixin):
 
     cls = Transformation
-    key = "Transformation-0969b1cd6232bf5d78c47216f0200177"
+    key = "Transformation-decb5cda54a4092529bd47a2305c3169"
     repr = "Transformation(stateA=ChemicalSystem(name=, components={'ligand': SmallMoleculeComponent(name=toluene), 'solvent': SolventComponent(name=O, K+, Cl-)}), stateB=ChemicalSystem(name=, components={'protein': ProteinComponent(name=), 'solvent': SolventComponent(name=O, K+, Cl-), 'ligand': SmallMoleculeComponent(name=toluene)}), protocol=<DummyProtocol-84b834e05f8a280c0c26a161010f52c8>)"
 
     @pytest.fixture
@@ -126,7 +126,7 @@ def test_dump_load_roundtrip(self, absolute_transformation):
 class TestNonTransformation(GufeTokenizableTestsMixin):
 
     cls = NonTransformation
-    key = "NonTransformation-a3604da309c4016df7c1bd5340626825"
+    key = "NonTransformation-f82418b1fcc30dc3ec1e8e196a208aa8"
     repr = "NonTransformation(stateA=ChemicalSystem(name=, components={'protein': ProteinComponent(name=), 'solvent': SolventComponent(name=O, K+, Cl-), 'ligand': SmallMoleculeComponent(name=toluene)}), stateB=ChemicalSystem(name=, components={'protein': ProteinComponent(name=), 'solvent': SolventComponent(name=O, K+, Cl-), 'ligand': SmallMoleculeComponent(name=toluene)}), protocol=<DummyProtocol-84b834e05f8a280c0c26a161010f52c8>)"
 
     @pytest.fixture
@@ -203,7 +203,3 @@ def test_equality(self, complex_equilibrium, solvated_ligand, solvated_complex):
             solvated_ligand, protocol=DummyProtocol(settings=DummyProtocol.default_settings())
         )
         assert complex_equilibrium != different_system
-
-    def test_dict_roundtrip(self):
-        # TODO: need registration of `Protocol`s for this to work
-        ...