VS handler fix for 0.10.6 (#1470)

* allowing to subclass VirtualSiteHandler

* Update openff/toolkit/typing/engines/smirnoff/forcefield.py

Co-authored-by: Matt Thompson <matt.thompson@openforcefield.org>

* PR1470 to pass tests

* qcportal >= 0.15

* Update environments of 0.10.x line

* A test case checking if the _find_matches is treated as a list.

* black

Co-authored-by: Matt Thompson <matt.thompson@openforcefield.org>
Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>

devtools/conda-envs/openeye.yaml

@@ -31,8 +31,8 @@ dependencies:
   - msgpack-python
   - xmltodict
   - qcelemental
-  - qcportal
+  - qcportal >= 0.15
   - qcengine
   - mdtraj
-  - openff-interchange
+  - openff-interchange < 0.2
   - python-constraint

devtools/conda-envs/rdkit.yaml

@@ -30,8 +30,8 @@ dependencies:
   - msgpack-python
   - xmltodict
   - qcelemental
-  - qcportal
+  - qcportal >= 0.15
   - qcengine
   - mdtraj
-  - openff-interchange
+  - openff-interchange < 0.2
   - python-constraint

devtools/conda-envs/test_env.yaml

@@ -32,9 +32,9 @@ dependencies:
   - bson
   - msgpack-python
   - qcelemental
-  - qcportal
+  - qcportal >= 0.15
   - qcengine
-  - openff-interchange
+  - openff-interchange < 0.2
   # Typing
   - mypy
   - typing-extensions

examples/environment.yaml

@@ -9,15 +9,16 @@ dependencies:
   - notebook
   - gromacs
   - qcelemental
-  - qcportal
+  - qcportal >= 0.15
   - qcengine
   - openmmforcefields
   # Below are dependencies of the toolkit; they are listed here as a reference
   - mdtraj
   - numpy
   - openmm
-  - openff-forcefields >=2.0.0
-  - openff-interchange >=0.1.3
+  - openff-forcefields >= 2
+  - openff-interchange < 0.2
   - gromacs
   - lammps
   - ambertools
+  - ipywidgets =7

openff/toolkit/tests/test_forcefield.py

@@ -2224,6 +2224,33 @@ def test_issue_1216(self):
         )
         force_field.label_molecules(Molecule.from_smiles("CF").to_topology())
 
+    def test_issue_1422(self):
+        """Inherited plugin VirtualSite handlers should be detected
+        and treated like VirtualSites
+
+        https://github.com/openforcefield/openff-toolkit/issues/1422
+        """
+
+        class PluginVirtualSites(VirtualSiteHandler):
+            _TAGNAME = "InheritedTestVirtualSites"
+
+            def _find_matches(
+                self,
+                entity: Topology,
+                transformed_dict_cls=dict,
+                unique=False,
+            ) -> Dict[Tuple[int], List[ParameterHandler._Match]]:
+                return {
+                    (0,): [
+                        ParameterHandler._Match(None, None),
+                        ParameterHandler._Match(None, None),
+                    ]
+                }
+
+        force_field = ForceField()
+        force_field.get_parameter_handler("InheritedTestVirtualSites")
+        force_field.label_molecules(Molecule.from_smiles("CO").to_topology())
+
 
 def generate_monatomic_ions():
     return (

openff/toolkit/typing/engines/smirnoff/forcefield.py

@@ -1489,9 +1489,6 @@ def label_molecules(self, topology):
             for tag, parameter_handler in self._parameter_handlers.items():
                 param_is_list = False
 
-                if type(parameter_handler) == VirtualSiteHandler:
-                    param_is_list = True
-
                 matches = parameter_handler.find_matches(top_mol)
                 # Remove the chemical environment matches from the
                 # matched results.
@@ -1506,6 +1503,8 @@ def label_molecules(self, topology):
                 # Now make parameter_matches into a dict mapping
                 # match objects to ParameterTypes
 
+                param_is_list = isinstance(parameter_handler, VirtualSiteHandler)
+
                 if param_is_list:
                     for match in matches:
                         parameter_matches[match] = [