Bugfix for atomtyper (#514)

* add back in the type check and change variable name

* revert some variable name change since it broke too many things

foyer/atomtyper.py

@@ -77,14 +77,19 @@ def find_atomtypes(structure, forcefield, max_iter=10):
     elif isinstance(structure, Topology):
         topology_graph = TopologyGraph.from_gmso_topology(structure)
 
-    forcefield = AtomTypingRulesProvider.from_foyer_forcefield(forcefield)
+    if isinstance(forcefield, Forcefield):
+        atomtype_rules = AtomTypingRulesProvider.from_foyer_forcefield(
+            forcefield
+        )
+    elif isinstance(forcefield, AtomTypingRulesProvider):
+        atomtype_rules = forcefield
 
     typemap = {
         atom_index: {"whitelist": set(), "blacklist": set(), "atomtype": None}
         for atom_index in topology_graph.atoms(data=False)
     }
 
-    rules = _load_rules(forcefield, typemap)
+    rules = _load_rules(atomtype_rules, typemap)
 
     # Only consider rules for elements found in topology
     subrules = dict()
@@ -94,7 +99,7 @@ def find_atomtypes(structure, forcefield, max_iter=10):
         # First add non-element types, which are strings, then elements
         name = atom_data.name
         if name.startswith("_"):
-            if name in forcefield.non_element_types:
+            if name in atomtype_rules.non_element_types:
                 system_elements.add(name)
         else:
             atomic_number = atom_data.atomic_number
@@ -143,7 +148,7 @@ def find_atomtypes(structure, forcefield, max_iter=10):
 
 
 def _load_rules(rules_provider, typemap):
-    """Load atomtyping rules from a forcefield into SMARTSGraphs."""
+    """Load atomtyping rules from a AtomTypingRulesProvider into SMARTSGraphs."""
     rules = dict()
     # For every SMARTS string in the force field,
     # create a SMARTSGraph object