[DNM] try to vendor bits of openmm code to drop full openmm dependency

gufe/components/proteincomponent.py

@@ -13,6 +13,7 @@
 
 from ..custom_typing import RDKitMol
 from ..molhashing import deserialize_numpy, serialize_numpy
+from ..vendor.openmm.app import topology
 from ..vendor.pdb_file.pdbfile import PDBFile
 from ..vendor.pdb_file.pdbxfile import PDBxFile
 from .explicitmoleculecomponent import ExplicitMoleculeComponent
@@ -24,10 +25,10 @@
     None: BondType.UNSPECIFIED,
 }
 _BONDTYPES_OPENMM_TO_RDKIT = {
-    app.Single: BondType.SINGLE,
-    app.Double: BondType.DOUBLE,
-    app.Triple: BondType.TRIPLE,
-    app.Aromatic: BondType.AROMATIC,
+    topology.Single: BondType.SINGLE,
+    topology.Double: BondType.DOUBLE,
+    topology.Triple: BondType.TRIPLE,
+    topology.Aromatic: BondType.AROMATIC,
     None: BondType.UNSPECIFIED,
 }
 _BONDORDERS_RDKIT_TO_OPENMM = {v: k for k, v in _BONDORDERS_OPENMM_TO_RDKIT.items()}
@@ -395,7 +396,7 @@ def _from_dict(cls, ser_dict: dict, name: str = ""):
 
         return cls(rdkit=rd_mol, name=name)
 
-    def to_openmm_topology(self) -> app.Topology:
+    def to_openmm_topology(self) -> topology.Topology:
         """Convert to an openmm Topology object
 
         Returns
@@ -437,7 +438,7 @@ def chainkey(m):
 
         atom_lookup = {}  # maps rdkit indices to openmm Atoms
 
-        top = app.Topology()
+        top = topology.Topology()
         for atom in self._rdkit.GetAtoms():
             mi = atom.GetMonomerInfo()
             if (new_chainid := chainkey(mi)) != current_chainid:

gufe/vendor/openmm/app/internal/singleton.py

@@ -0,0 +1,14 @@
+"""
+Creates a subclass for all classes intended to be a singleton. This
+maintains the correctness of instance is instance even following
+pickling/unpickling
+"""
+class Singleton(object):
+    _inst = None
+    def __new__(cls):
+        if cls._inst is None:
+            cls._inst = super(Singleton, cls).__new__(cls)
+        return cls._inst
+
+    def __reduce__(self):
+        return repr(self)