Parameterized Parmed Conversions (#721)

* Conversion of parmed structure to GMSO should now properly identify unique potential types

* Clean up legacy functions necessary for mapping types to connections

* Update gmso/external/convert_parmed.py

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

* Update gmso/external/convert_parmed.py

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

* Update gmso/external/convert_parmed.py

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

* Modified ParmEd loading to sort new GMSO topology connections by site appearance in the topology. Copies of connection types are made, which must be filtered using potential filters to get whatever subset is considered unique.

* minor changes/cleanup

* minor change for consistency

---------

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>
Co-authored-by: Co Quach <daico007@gmail.com>

gmso/core/views.py

@@ -31,13 +31,37 @@ def get_name_or_class(potential):
     """Get identifier for a topology potential based on name or membertype/class."""
     if isinstance(potential, AtomType):
         return potential.name
-    if isinstance(potential, (BondType, AngleType, DihedralType, ImproperType)):
+    elif isinstance(
+        potential, (BondType, AngleType, DihedralType, ImproperType)
+    ):
         return potential.member_types or potential.member_classes
 
 
+def get_sorted_names(potential):
+    """Get identifier for a topology potential based on name or membertype/class."""
+    if isinstance(potential, AtomType):
+        return potential.name
+    elif isinstance(potential, BondType):
+        return tuple(sorted(potential.member_types))
+    elif isinstance(potential, AngleType):
+        if potential.member_types[0] > potential.member_types[2]:
+            return tuple(reversed(potential.member_types))
+        else:
+            return potential.member_types
+    elif isinstance(potential, DihedralType):
+        if potential.member_types[1] > potential.member_types[2] or (
+            potential.member_types[1] == potential.member_types[2]
+            and potential.member_types[0] > potential.member_types[3]
+        ):
+            return tuple(reversed(potential.member_types))
+        else:
+            return potential.member_types
+    elif isinstance(potential, ImproperType):
+        return (potential.member_types[0], *sorted(potential.member_types[1:]))
+
+
 def get_parameters(potential):
     """Return hashable version of parameters for a potential."""
-
     return (
         tuple(potential.get_parameters().keys()),
         tuple(map(lambda x: x.to_value(), potential.get_parameters().values())),
@@ -58,6 +82,7 @@ def filtered_potentials(potential_types, identifier):
 
 class PotentialFilters:
     UNIQUE_NAME_CLASS = "unique_name_class"
+    UNIQUE_SORTED_NAMES = "unique_sorted_names"
     UNIQUE_EXPRESSION = "unique_expression"
     UNIQUE_PARAMETERS = "unique_parameters"
     UNIQUE_ID = "unique_id"
@@ -74,6 +99,7 @@ def all():
 
 potential_identifiers = {
     PotentialFilters.UNIQUE_NAME_CLASS: get_name_or_class,
+    PotentialFilters.UNIQUE_SORTED_NAMES: get_sorted_names,
     PotentialFilters.UNIQUE_EXPRESSION: lambda p: str(p.expression),
     PotentialFilters.UNIQUE_PARAMETERS: get_parameters,
     PotentialFilters.UNIQUE_ID: lambda p: id(p),