Merge pull request #51 from openforcefield/str-slots

Store "slot" identifiers as str

examples/smirnoff_argon.ipynb

@@ -122,7 +122,7 @@
     "# SMIRKS pattern as a key connecting the topological data to the\n",
     "# parametrized data\n",
     "sys_out.handlers['vdW'].potentials[\n",
-    "    sys_out.handlers['vdW'].slot_map[(0,)]\n",
+    "    sys_out.handlers['vdW'].slot_map[\"(0,)\"]\n",
     "].parameters['sigma']"
    ]
   }

examples/smirnoff_ethanol.ipynb

@@ -119,7 +119,7 @@
     "# SMIRKS pattern as a key connecting the topological data to the\n",
     "# parametrized data\n",
     "sys_out.handlers['Bonds'].potentials[\n",
-    "    sys_out.handlers['Bonds'].slot_map[(1, 7)]\n",
+    "    sys_out.handlers['Bonds'].slot_map[\"(1, 7)\"]\n",
     "].parameters['k']"
    ]
   }

openff/system/components/potentials.py

@@ -23,7 +23,7 @@ class PotentialHandler(BaseModel):
     name: str
     expression: Union[Expr, str]
     independent_variables: Union[str, Set[Union[Expr, str]]]
-    slot_map: Dict[tuple, str] = dict()
+    slot_map: Dict[str, str] = dict()
     potentials: Dict[str, Potential] = dict()
 
     @validator("expression")

openff/system/components/smirnoff.py

@@ -20,7 +20,7 @@ class SMIRNOFFBondHandler(PotentialHandler):
     name: str = "Bonds"
     expression: str = "1/2 * k * (r - length) ** 2"
     independent_variables: Set[str] = {"r"}
-    slot_map: Dict[tuple, str] = dict()
+    slot_map: Dict[str, str] = dict()
     potentials: Dict[str, Potential] = dict()
 
     def store_matches(self, parameter_handler: BondHandler, topology: Topology) -> None:
@@ -33,6 +33,7 @@ def store_matches(self, parameter_handler: BondHandler, topology: Topology) -> N
             self.slot_map = dict()
         matches = parameter_handler.find_matches(topology)
         for key, val in matches.items():
+            key = str(key)
             self.slot_map[key] = val.parameter_type.smirks
 
     def store_potentials(self, parameter_handler: BondHandler) -> None:
@@ -59,7 +60,7 @@ class SMIRNOFFAngleHandler(PotentialHandler):
     name: str = "Angles"
     expression: str = "1/2 * k * (angle - theta)"
     independent_variables: Set[str] = {"theta"}
-    slot_map: Dict[tuple, str] = dict()
+    slot_map: Dict[str, str] = dict()
     potentials: Dict[str, Potential] = dict()
 
     def store_matches(
@@ -72,6 +73,7 @@ def store_matches(
         """
         matches = parameter_handler.find_matches(topology)
         for key, val in matches.items():
+            key = str(key)
             self.slot_map[key] = val.parameter_type.smirks
 
     def store_potentials(self, parameter_handler: AngleHandler) -> None:
@@ -98,7 +100,7 @@ class SMIRNOFFProperTorsionHandler(PotentialHandler):
     name: str = "ProperTorsions"
     expression: str = "k*(1+cos(periodicity*theta-phase))"
     independent_variables: Set[str] = {"theta"}
-    slot_map: Dict[tuple, str] = dict()
+    slot_map: Dict[str, str] = dict()
     potentials: Dict[str, Potential] = dict()
 
     def store_matches(
@@ -111,6 +113,7 @@ def store_matches(
         """
         matches = parameter_handler.find_matches(topology)
         for key, val in matches.items():
+            key = str(key)
             self.slot_map[key] = val.parameter_type.smirks
 
     def store_potentials(self, parameter_handler: ProperTorsionHandler) -> None:
@@ -138,7 +141,7 @@ class SMIRNOFFvdWHandler(PotentialHandler):
     name: str = "vdW"
     expression: str = "4*epsilon*((sigma/r)**12-(sigma/r)**6)"
     independent_variables: Set[str] = {"r"}
-    slot_map: Dict[tuple, str] = dict()
+    slot_map: Dict[str, str] = dict()
     potentials: Dict[str, Potential] = dict()
 
     def store_matches(
@@ -153,6 +156,7 @@ def store_matches(
         """
         matches = parameter_handler.find_matches(topology)
         for key, val in matches.items():
+            key = str(key)
             self.slot_map[key] = val.parameter_type.smirks
 
     def store_potentials(self, parameter_handler: vdWHandler) -> None:

openff/system/tests/test_potential.py

@@ -25,7 +25,7 @@ def test_bond_parameter_handler(self):
         forcefield.register_parameter_handler(bond_handler)
         bond_potentials = forcefield["Bonds"].create_potential(top)
 
-        pot = bond_potentials.potentials[bond_potentials.slot_map[(0, 1)]]
+        pot = bond_potentials.potentials[bond_potentials.slot_map["(0, 1)"]]
         kcal_ang2_mol = omm_unit.kilocalorie_per_mole / omm_unit.angstrom ** 2
 
         assert pot.parameters["k"] == simtk_to_pint(1.5 * kcal_ang2_mol)
@@ -48,7 +48,7 @@ def test_angle_parameter_handler(self):
         forcefield.register_parameter_handler(angle_handler)
         angle_potentials = forcefield["Angles"].create_potential(top)
 
-        pot = angle_potentials.potentials[angle_potentials.slot_map[(0, 1, 2)]]
+        pot = angle_potentials.potentials[angle_potentials.slot_map["(0, 1, 2)"]]
         kcal_deg2_mol = omm_unit.kilocalorie_per_mole / omm_unit.degree ** 2
 
         assert pot.parameters["k"] == simtk_to_pint(2.5 * kcal_deg2_mol)