From d25a1a3b401c1241455d099688581b7c7dec741c Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 22 Apr 2025 19:07:54 -0700
Subject: [PATCH 01/27] initial implementation of NAGLChargesHandler

---
 openff/toolkit/_tests/test_nagl.py            |  7 +++-
 openff/toolkit/_tests/test_parameters.py      | 10 +++++
 .../typing/engines/smirnoff/__init__.py       |  1 +
 .../typing/engines/smirnoff/parameters.py     | 39 ++++++++++++++++++-
 openff/toolkit/utils/nagl_wrapper.py          |  2 +-
 openff/toolkit/utils/toolkits.py              |  1 +
 6 files changed, 57 insertions(+), 3 deletions(-)

diff --git a/openff/toolkit/_tests/test_nagl.py b/openff/toolkit/_tests/test_nagl.py
index 9d0bc9a24..c04ecb00a 100644
--- a/openff/toolkit/_tests/test_nagl.py
+++ b/openff/toolkit/_tests/test_nagl.py
@@ -14,6 +14,7 @@
     create_reversed_ethanol,
 )
 from openff.toolkit._tests.utils import requires_openeye
+from openff.toolkit.utils import GLOBAL_TOOLKIT_REGISTRY
 from openff.toolkit.utils.exceptions import (
     ChargeMethodUnavailableError,
     ToolkitUnavailableException,
@@ -38,6 +39,10 @@ def test_version(self):
 
         assert parsed_version == NAGLToolkitWrapper()._toolkit_version
 
+    def test_nagl_in_global_toolkit_registry(self):
+        assert "NAGL" in GLOBAL_TOOLKIT_REGISTRY.__repr__()
+
+
     @requires_openeye
     @pytest.mark.parametrize(
         "molecule_function",
@@ -66,7 +71,7 @@ def test_assign_partial_charges_basic(self, molecule_function, nagl_model):
 
         molecule.assign_partial_charges(
             partial_charge_method=nagl_model,
-            toolkit_registry=NAGLToolkitWrapper(),
+            #toolkit_registry=NAGLToolkitWrapper(),
         )
 
         assert molecule.partial_charges is not None
diff --git a/openff/toolkit/_tests/test_parameters.py b/openff/toolkit/_tests/test_parameters.py
index bd9ae0836..1200d039a 100644
--- a/openff/toolkit/_tests/test_parameters.py
+++ b/openff/toolkit/_tests/test_parameters.py
@@ -2722,6 +2722,16 @@ def test_charge_increment_one_ci_missing(self):
             ],
         )
 
+class TestNAGLChargesHandler:
+    def test_nagl_charges_handler_serialization(self):
+        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
+        handler = NAGLChargesHandler(model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt", skip_version_check=True)
+        assert handler.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
+        handler_dict = handler.to_dict()
+        assert handler_dict["model_file"] == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
+
+        # TODO: test_nagl_charges_handler_are_compatible
+
 
 class TestGBSAHandler:
     def test_create_default_gbsahandler(self):
diff --git a/openff/toolkit/typing/engines/smirnoff/__init__.py b/openff/toolkit/typing/engines/smirnoff/__init__.py
index ae14b1671..d881c950d 100644
--- a/openff/toolkit/typing/engines/smirnoff/__init__.py
+++ b/openff/toolkit/typing/engines/smirnoff/__init__.py
@@ -18,6 +18,7 @@
     IndexedParameterAttribute,
     LibraryChargeHandler,
     MappedParameterAttribute,
+    NAGLChargesHandler,
     ParameterAttribute,
     ParameterHandler,
     ParameterList,
diff --git a/openff/toolkit/typing/engines/smirnoff/parameters.py b/openff/toolkit/typing/engines/smirnoff/parameters.py
index b42fcba8b..7f914c6fe 100644
--- a/openff/toolkit/typing/engines/smirnoff/parameters.py
+++ b/openff/toolkit/typing/engines/smirnoff/parameters.py
@@ -29,6 +29,7 @@
     "LibraryChargeHandler",
     "LibraryChargeType",
     "MappedParameterAttribute",
+    "NAGLChargesHandler",
     "NotEnoughPointsForInterpolationError",
     "ParameterAttribute",
     "ParameterHandler",
@@ -3253,6 +3254,41 @@ def find_matches(self, entity, unique=False):
             unique=unique,
         )
 
+class NAGLChargesHandler(_NonbondedHandler):
+    """ParameterHandler for applying partial charges from a pretrained NAGL model."""
+
+    _TAGNAME = "NAGLCharges"
+    _DEPENDENCIES = [vdWHandler, ElectrostaticsHandler, LibraryChargeHandler]
+    _INFOTYPE = None  # No separate parameter types; just a model path
+    _MAX_SUPPORTED_SECTION_VERSION = Version("0.3")
+    model_file = ParameterAttribute(converter=str)
+
+    def check_handler_compatibility(
+        self,
+        other_handler: "NAGLChargesHandler",
+        assume_missing_is_default: bool = True,
+    ):
+        """
+        Checks whether this ParameterHandler encodes compatible physics as another ParameterHandler. This is
+        called if a second handler is attempted to be initialized for the same tag.
+
+        Parameters
+        ----------
+        other_handler
+            The handler to compare to.
+        assume_missing_is_default
+
+        Raises
+        ------
+        IncompatibleParameterError if handler_kwargs are incompatible with existing parameters.
+        """
+        if self.model_file != other_handler.model_file:
+            raise IncompatibleParameterError("Attempted to initialize two NAGLCharges sections with different "
+                                             "model_files: "
+                                             f"{self.model_file=} is not identical to {other_handler.model_file=}")
+
+
+
 
 class ToolkitAM1BCCHandler(_NonbondedHandler):
     """Handle SMIRNOFF ``<ToolkitAM1BCC>`` tags
@@ -3261,7 +3297,7 @@ class ToolkitAM1BCCHandler(_NonbondedHandler):
     """
 
     _TAGNAME = "ToolkitAM1BCC"  # SMIRNOFF tag name to process
-    _DEPENDENCIES = [vdWHandler, ElectrostaticsHandler, LibraryChargeHandler]
+    _DEPENDENCIES = [vdWHandler, ElectrostaticsHandler, LibraryChargeHandler, NAGLChargesHandler]
     _KWARGS = ["toolkit_registry"]  # Kwargs to catch when create_force is called
 
     def check_handler_compatibility(
@@ -3382,6 +3418,7 @@ def find_matches(self, entity, unique=False):
         return matches
 
 
+
 class GBSAHandler(ParameterHandler):
     """Handle SMIRNOFF ``<GBSA>`` tags
 
diff --git a/openff/toolkit/utils/nagl_wrapper.py b/openff/toolkit/utils/nagl_wrapper.py
index eaec04ebe..76e063eef 100644
--- a/openff/toolkit/utils/nagl_wrapper.py
+++ b/openff/toolkit/utils/nagl_wrapper.py
@@ -135,7 +135,7 @@ def assign_partial_charges(
         except FileNotFoundError as error:
             raise ChargeMethodUnavailableError(
                 f"Charge model {partial_charge_method} not supported by "
-                f"{self.__class__.__name__}."
+                f"{self.__class__.__name__}, or model file can not be found."
             ) from error
 
         model = GNNModel.load(model_path, eval_mode=True)
diff --git a/openff/toolkit/utils/toolkits.py b/openff/toolkit/utils/toolkits.py
index 97875076f..6955b234e 100644
--- a/openff/toolkit/utils/toolkits.py
+++ b/openff/toolkit/utils/toolkits.py
@@ -101,6 +101,7 @@
 # Create global toolkit registry, where all available toolkits are registered
 GLOBAL_TOOLKIT_REGISTRY = ToolkitRegistry(
     toolkit_precedence=[
+        NAGLToolkitWrapper,
         OpenEyeToolkitWrapper,
         RDKitToolkitWrapper,
         AmberToolsToolkitWrapper,

From 10db658bd0c755960dfce8c2666444e51e6c53d9 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 22 Apr 2025 19:24:19 -0700
Subject: [PATCH 02/27] have testing env use naglcharges interchange branch

---
 devtools/conda-envs/openeye-examples.yaml | 2 ++
 devtools/conda-envs/openeye.yaml          | 1 +
 devtools/conda-envs/rdkit-examples.yaml   | 2 ++
 devtools/conda-envs/rdkit.yaml            | 2 ++
 devtools/conda-envs/test_env.yaml         | 2 ++
 5 files changed, 9 insertions(+)

diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml
index 8be786546..c23a6ebd3 100644
--- a/devtools/conda-envs/openeye-examples.yaml
+++ b/devtools/conda-envs/openeye-examples.yaml
@@ -42,3 +42,5 @@ dependencies:
   - pdbfixer
   - openmmforcefields >=0.11.2
   - gromacs >=2023.3
+  - pip:
+      - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
index 2571d5dd2..60fa56b5c 100644
--- a/devtools/conda-envs/openeye.yaml
+++ b/devtools/conda-envs/openeye.yaml
@@ -51,3 +51,4 @@ dependencies:
     - types-xmltodict
     - types-cachetools
     - mongo-types
+    - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
index 40fcec17f..5cbc61eff 100644
--- a/devtools/conda-envs/rdkit-examples.yaml
+++ b/devtools/conda-envs/rdkit-examples.yaml
@@ -43,3 +43,5 @@ dependencies:
   - pdbfixer
   - openmmforcefields >=0.11.2
   - gromacs >=2023.3
+  - pip:
+      - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml
index a180bd066..c996f4f4f 100644
--- a/devtools/conda-envs/rdkit.yaml
+++ b/devtools/conda-envs/rdkit.yaml
@@ -40,3 +40,5 @@ dependencies:
   - qcportal >=0.50
   - qcengine
   - nglview
+  - pip:
+      - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index c2ddad482..676229939 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -49,3 +49,5 @@ dependencies:
   - nbval
   # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
   - nomkl
+  - pip:
+      - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler

From 5f028266a4e7c6cb841346d940b98f838c9f6fe8 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Wed, 9 Jul 2025 17:22:03 -0700
Subject: [PATCH 03/27] implement doi and hash fields

---
 openff/toolkit/typing/engines/smirnoff/parameters.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/openff/toolkit/typing/engines/smirnoff/parameters.py b/openff/toolkit/typing/engines/smirnoff/parameters.py
index 7f914c6fe..d27042279 100644
--- a/openff/toolkit/typing/engines/smirnoff/parameters.py
+++ b/openff/toolkit/typing/engines/smirnoff/parameters.py
@@ -3262,6 +3262,8 @@ class NAGLChargesHandler(_NonbondedHandler):
     _INFOTYPE = None  # No separate parameter types; just a model path
     _MAX_SUPPORTED_SECTION_VERSION = Version("0.3")
     model_file = ParameterAttribute(converter=str)
+    model_file_hash = ParameterAttribute(default=None, converter=str)
+    digital_object_identifier = ParameterAttribute(default=None, converter=str)
 
     def check_handler_compatibility(
         self,

From de0f3df363b652c6baca69e774d05cb1fc4439b0 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Wed, 9 Jul 2025 17:25:01 -0700
Subject: [PATCH 04/27] add tests

---
 openff/toolkit/_tests/test_parameters.py | 91 +++++++++++++++++++++++-
 1 file changed, 90 insertions(+), 1 deletion(-)

diff --git a/openff/toolkit/_tests/test_parameters.py b/openff/toolkit/_tests/test_parameters.py
index 1200d039a..5cc3bf38c 100644
--- a/openff/toolkit/_tests/test_parameters.py
+++ b/openff/toolkit/_tests/test_parameters.py
@@ -2730,7 +2730,96 @@ def test_nagl_charges_handler_serialization(self):
         handler_dict = handler.to_dict()
         assert handler_dict["model_file"] == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
 
-        # TODO: test_nagl_charges_handler_are_compatible
+    def test_nagl_charges_handler_with_optional_fields(self):
+        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
+        
+        # Test with model_file_hash
+        handler = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+            skip_version_check=True
+        )
+        assert handler.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
+        assert handler.model_file_hash == "144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0"
+        assert handler.digital_object_identifier is None
+        
+        # Test with digital_object_identifier
+        handler = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            digital_object_identifier="10.5072/zenodo.203601",
+            skip_version_check=True
+        )
+        assert handler.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
+        assert handler.model_file_hash is None
+        assert handler.digital_object_identifier == "10.5072/zenodo.203601"
+        
+        # Test with both optional fields
+        handler = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+            digital_object_identifier="10.5072/zenodo.203601",
+            skip_version_check=True
+        )
+        assert handler.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
+        assert handler.model_file_hash == "144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0"
+        assert handler.digital_object_identifier == "10.5072/zenodo.203601"
+
+    def test_nagl_charges_handler_serialization_with_optional_fields(self):
+        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
+        
+        # Test serialization with all fields
+        handler = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+            digital_object_identifier="10.5072/zenodo.203601",
+            skip_version_check=True
+        )
+        handler_dict = handler.to_dict()
+        assert handler_dict["model_file"] == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
+        assert handler_dict["model_file_hash"] == "144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0"
+        assert handler_dict["digital_object_identifier"] == "10.5072/zenodo.203601"
+        
+        # Test deserialization
+        handler_from_dict = NAGLChargesHandler.from_dict(handler_dict)
+        assert handler_from_dict.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
+        assert handler_from_dict.model_file_hash == "144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0"
+        assert handler_from_dict.digital_object_identifier == "10.5072/zenodo.203601"
+
+    def test_nagl_charges_handler_compatibility(self):
+        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
+        from openff.toolkit.utils.exceptions import IncompatibleParameterError
+        
+        # Test compatible handlers (same model_file)
+        handler1 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            skip_version_check=True
+        )
+        handler2 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+            skip_version_check=True
+        )
+        # Should not raise exception
+        handler1.check_handler_compatibility(handler2)
+        
+        # Test incompatible handlers (different model_file)
+        handler3 = NAGLChargesHandler(
+            model_file="different-model-file.pt",
+            skip_version_check=True
+        )
+        with pytest.raises(IncompatibleParameterError, match="different model_files"):
+            handler1.check_handler_compatibility(handler3)
+
+    def test_nagl_charges_handler_defaults(self):
+        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
+        
+        # Test that optional fields default to None
+        handler = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            skip_version_check=True
+        )
+        assert handler.model_file_hash is None
+        assert handler.digital_object_identifier is None
 
 
 class TestGBSAHandler:

From 58e33356fdb5d479d3ced5fe5c2831ec64c2cd29 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Wed, 9 Jul 2025 17:48:46 -0700
Subject: [PATCH 05/27] fix tests

---
 openff/toolkit/_tests/test_parameters.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/openff/toolkit/_tests/test_parameters.py b/openff/toolkit/_tests/test_parameters.py
index 5cc3bf38c..34946f937 100644
--- a/openff/toolkit/_tests/test_parameters.py
+++ b/openff/toolkit/_tests/test_parameters.py
@@ -2779,8 +2779,8 @@ def test_nagl_charges_handler_serialization_with_optional_fields(self):
         assert handler_dict["model_file_hash"] == "144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0"
         assert handler_dict["digital_object_identifier"] == "10.5072/zenodo.203601"
         
-        # Test deserialization
-        handler_from_dict = NAGLChargesHandler.from_dict(handler_dict)
+        # Test deserialization via constructor
+        handler_from_dict = NAGLChargesHandler(**handler_dict)
         assert handler_from_dict.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
         assert handler_from_dict.model_file_hash == "144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0"
         assert handler_from_dict.digital_object_identifier == "10.5072/zenodo.203601"

From 37b64173720a51bb7f4c1ea43a6ef278c7179e87 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Wed, 9 Jul 2025 17:51:33 -0700
Subject: [PATCH 06/27] add docstring

---
 .../typing/engines/smirnoff/parameters.py     | 61 ++++++++++++++++++-
 1 file changed, 60 insertions(+), 1 deletion(-)

diff --git a/openff/toolkit/typing/engines/smirnoff/parameters.py b/openff/toolkit/typing/engines/smirnoff/parameters.py
index d27042279..b91a222e2 100644
--- a/openff/toolkit/typing/engines/smirnoff/parameters.py
+++ b/openff/toolkit/typing/engines/smirnoff/parameters.py
@@ -3255,7 +3255,66 @@ def find_matches(self, entity, unique=False):
         )
 
 class NAGLChargesHandler(_NonbondedHandler):
-    """ParameterHandler for applying partial charges from a pretrained NAGL model."""
+    """ParameterHandler for applying partial charges from a pretrained NAGL model.
+    
+    This handler processes the NAGLCharges section of SMIRNOFF force fields, which
+    specifies a pre-trained NAGL model for computing
+    partial charges on molecules.
+    
+    Parameters
+    ----------
+    model_file : str
+        Path to the PyTorch model file (e.g., "openff-gnn-am1bcc-0.1.0-rc.3.pt").
+        This is the model that will be used for charge assignment.
+    model_file_hash : str, optional
+        SHA-256 hash of the model file for integrity verification. When provided,
+        the hash will be validated against the actual model file.
+    digital_object_identifier : str, optional
+        Zenodo DOI that can be used to retrieve the model file if it's not found
+        locally. Must point to a Zenodo record with an attached file matching
+        the model_file name.
+    version : str, optional
+        The version of the NAGLCharges section specification.
+    skip_version_check : bool, optional, default=False
+        If True, skips validation of the version parameter and sets it to the highest
+        supported version.
+    allow_cosmetic_attributes : bool, optional, default=False
+        If True, allows non-specification attributes to be present.
+    
+    Examples
+    --------
+    Create a handler with just the model file:
+    
+    >>> handler = NAGLChargesHandler(
+    ...     model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+    ...     skip_version_check=True
+    ... )
+    
+    Create a handler with hash verification:
+    
+    >>> handler = NAGLChargesHandler(
+    ...     model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+    ...     model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+    ...     skip_version_check=True
+    ... )
+    
+    Create a handler with DOI for model retrieval:
+    
+    >>> handler = NAGLChargesHandler(
+    ...     model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+    ...     digital_object_identifier="10.5072/zenodo.203601",
+    ...     skip_version_check=True
+    ... )
+    
+    Notes
+    -----
+    NAGLChargesHandler compatibility is determined solely by the model_file parameter. Two
+    handlers are compatible if and only if they specify the same model_file,
+    regardless of the values of model_file_hash or digital_object_identifier.
+    
+    The actual model loading, hash verification, and DOI-based retrieval are
+    handled by the openff-nagl-models package, not by this handler directly.
+    """
 
     _TAGNAME = "NAGLCharges"
     _DEPENDENCIES = [vdWHandler, ElectrostaticsHandler, LibraryChargeHandler]

From 47496ae75e6073e311c17ce9e55289d685b6c841 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 10 Jul 2025 00:51:45 +0000
Subject: [PATCH 07/27] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openff/toolkit/_tests/test_parameters.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/openff/toolkit/_tests/test_parameters.py b/openff/toolkit/_tests/test_parameters.py
index 34946f937..95ebf0e76 100644
--- a/openff/toolkit/_tests/test_parameters.py
+++ b/openff/toolkit/_tests/test_parameters.py
@@ -2732,7 +2732,7 @@ def test_nagl_charges_handler_serialization(self):
 
     def test_nagl_charges_handler_with_optional_fields(self):
         from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-        
+
         # Test with model_file_hash
         handler = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2742,7 +2742,7 @@ def test_nagl_charges_handler_with_optional_fields(self):
         assert handler.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
         assert handler.model_file_hash == "144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0"
         assert handler.digital_object_identifier is None
-        
+
         # Test with digital_object_identifier
         handler = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2752,7 +2752,7 @@ def test_nagl_charges_handler_with_optional_fields(self):
         assert handler.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
         assert handler.model_file_hash is None
         assert handler.digital_object_identifier == "10.5072/zenodo.203601"
-        
+
         # Test with both optional fields
         handler = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2766,7 +2766,7 @@ def test_nagl_charges_handler_with_optional_fields(self):
 
     def test_nagl_charges_handler_serialization_with_optional_fields(self):
         from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-        
+
         # Test serialization with all fields
         handler = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2778,7 +2778,7 @@ def test_nagl_charges_handler_serialization_with_optional_fields(self):
         assert handler_dict["model_file"] == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
         assert handler_dict["model_file_hash"] == "144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0"
         assert handler_dict["digital_object_identifier"] == "10.5072/zenodo.203601"
-        
+
         # Test deserialization via constructor
         handler_from_dict = NAGLChargesHandler(**handler_dict)
         assert handler_from_dict.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
@@ -2788,7 +2788,7 @@ def test_nagl_charges_handler_serialization_with_optional_fields(self):
     def test_nagl_charges_handler_compatibility(self):
         from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
         from openff.toolkit.utils.exceptions import IncompatibleParameterError
-        
+
         # Test compatible handlers (same model_file)
         handler1 = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2801,7 +2801,7 @@ def test_nagl_charges_handler_compatibility(self):
         )
         # Should not raise exception
         handler1.check_handler_compatibility(handler2)
-        
+
         # Test incompatible handlers (different model_file)
         handler3 = NAGLChargesHandler(
             model_file="different-model-file.pt",
@@ -2812,7 +2812,7 @@ def test_nagl_charges_handler_compatibility(self):
 
     def test_nagl_charges_handler_defaults(self):
         from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-        
+
         # Test that optional fields default to None
         handler = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",

From 831bc8b24fa0b227d3e238351b75b9ed751f5090 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Wed, 9 Jul 2025 18:07:52 -0700
Subject: [PATCH 08/27] force use of nagl for test

---
 openff/toolkit/_tests/test_nagl.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openff/toolkit/_tests/test_nagl.py b/openff/toolkit/_tests/test_nagl.py
index c04ecb00a..1f347c889 100644
--- a/openff/toolkit/_tests/test_nagl.py
+++ b/openff/toolkit/_tests/test_nagl.py
@@ -71,7 +71,7 @@ def test_assign_partial_charges_basic(self, molecule_function, nagl_model):
 
         molecule.assign_partial_charges(
             partial_charge_method=nagl_model,
-            #toolkit_registry=NAGLToolkitWrapper(),
+            toolkit_registry=NAGLToolkitWrapper(),
         )
 
         assert molecule.partial_charges is not None

From 858d893c7ce514837635c7d35cd5b6153485181b Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Wed, 9 Jul 2025 18:21:10 -0700
Subject: [PATCH 09/27] fix whitespace

---
 .../typing/engines/smirnoff/parameters.py     | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/openff/toolkit/typing/engines/smirnoff/parameters.py b/openff/toolkit/typing/engines/smirnoff/parameters.py
index b91a222e2..351b1bb67 100644
--- a/openff/toolkit/typing/engines/smirnoff/parameters.py
+++ b/openff/toolkit/typing/engines/smirnoff/parameters.py
@@ -3256,11 +3256,11 @@ def find_matches(self, entity, unique=False):
 
 class NAGLChargesHandler(_NonbondedHandler):
     """ParameterHandler for applying partial charges from a pretrained NAGL model.
-    
+
     This handler processes the NAGLCharges section of SMIRNOFF force fields, which
     specifies a pre-trained NAGL model for computing
     partial charges on molecules.
-    
+
     Parameters
     ----------
     model_file : str
@@ -3280,38 +3280,38 @@ class NAGLChargesHandler(_NonbondedHandler):
         supported version.
     allow_cosmetic_attributes : bool, optional, default=False
         If True, allows non-specification attributes to be present.
-    
+
     Examples
     --------
     Create a handler with just the model file:
-    
+
     >>> handler = NAGLChargesHandler(
     ...     model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
     ...     skip_version_check=True
     ... )
-    
+
     Create a handler with hash verification:
-    
+
     >>> handler = NAGLChargesHandler(
     ...     model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
     ...     model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
     ...     skip_version_check=True
     ... )
-    
+
     Create a handler with DOI for model retrieval:
-    
+
     >>> handler = NAGLChargesHandler(
     ...     model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
     ...     digital_object_identifier="10.5072/zenodo.203601",
     ...     skip_version_check=True
     ... )
-    
+
     Notes
     -----
     NAGLChargesHandler compatibility is determined solely by the model_file parameter. Two
     handlers are compatible if and only if they specify the same model_file,
     regardless of the values of model_file_hash or digital_object_identifier.
-    
+
     The actual model loading, hash verification, and DOI-based retrieval are
     handled by the openff-nagl-models package, not by this handler directly.
     """

From 4dfe8e1832795d8bef738d95fcaf9ab85fe82e2c Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 15 Jul 2025 11:49:19 -0700
Subject: [PATCH 10/27] add doi and file_hash to
 nagltoolkitwrapper.assign_partial_charges, switch to use nagl_models'
 get_model method

---
 openff/toolkit/utils/nagl_wrapper.py | 31 +++++++++++++++++++++-------
 1 file changed, 24 insertions(+), 7 deletions(-)

diff --git a/openff/toolkit/utils/nagl_wrapper.py b/openff/toolkit/utils/nagl_wrapper.py
index 76e063eef..4dd167d12 100644
--- a/openff/toolkit/utils/nagl_wrapper.py
+++ b/openff/toolkit/utils/nagl_wrapper.py
@@ -68,6 +68,9 @@ def assign_partial_charges(
         use_conformers: Optional[list["Quantity"]] = None,
         strict_n_conformers: bool = False,
         normalize_partial_charges: bool = True,
+        doi: str = None,
+        file_hash: str = None,
+
         _cls: Optional[type["FrozenMolecule"]] = None,
     ):
         """
@@ -130,13 +133,27 @@ def assign_partial_charges(
                 stacklevel=2,
             )
 
-        try:
-            model_path = validate_nagl_model_path(model=partial_charge_method)
-        except FileNotFoundError as error:
-            raise ChargeMethodUnavailableError(
-                f"Charge model {partial_charge_method} not supported by "
-                f"{self.__class__.__name__}, or model file can not be found."
-            ) from error
+        model_path = get_model(filename=partial_charge_method,
+                               doi=doi,
+                               file_hash=file_hash)
+
+        # try:
+        #     model_path = get_model(filename=partial_charge_method,
+        #                            doi=doi,
+        #                            file_hash=file_hash)
+        # except FileNotFoundError as error:
+        #     raise ChargeMethodUnavailableError(
+        #         f"Charge model {partial_charge_method} not supported by "
+        #         f"{self.__class__.__name__}, or model file can not be found. "
+        #         #f"Note that the NAGLToolkitWrapper.assign_partial_charges method "
+        #         #f"can only use models from the local cache or models fetchable from "
+        #         #f"openff-nagl-models release assets on GitHub. "
+        #         #f"This method does NOT "
+        #         #f"accept custom DOIs to fetch models from other sources. Use "
+        #         #f"NAGLToolkitWrapper.fetch_verify_model_and_assign_partial_charges if "
+        #         #f"you intend to also fetch models from arbitrary Zenodo DOIs and verify "
+        #         #f"their hash."
+        #     ) from error
 
         model = GNNModel.load(model_path, eval_mode=True)
         charges = model.compute_property(

From 8153199c20f9bbe71765bab8a83d5bbb919454b6 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 15 Jul 2025 11:50:03 -0700
Subject: [PATCH 11/27] raise specific error for blank/none model_file values

---
 openff/toolkit/utils/nagl_wrapper.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/openff/toolkit/utils/nagl_wrapper.py b/openff/toolkit/utils/nagl_wrapper.py
index 4dd167d12..042e78ff3 100644
--- a/openff/toolkit/utils/nagl_wrapper.py
+++ b/openff/toolkit/utils/nagl_wrapper.py
@@ -108,7 +108,12 @@ def assign_partial_charges(
             if the charge method is supported by this toolkit, but fails
         """
         from openff.nagl import GNNModel
-        from openff.nagl_models import validate_nagl_model_path
+        from openff.nagl_models._dynamic_fetch import get_model
+
+        if partial_charge_method == "" or partial_charge_method == "None":
+            raise FileNotFoundError("NAGLToolkitWrapper.assign_partial_charges can not accept "
+                                    "a blank model file name. There is no default model, one must be "
+                                    "explicitly defined when being called.")
 
         if _cls is None:
             from openff.toolkit.topology.molecule import Molecule

From d1878fb5d300bc240db952d23a66582e0744ab57 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 15 Jul 2025 12:00:44 -0700
Subject: [PATCH 12/27] improve docstring

---
 openff/toolkit/utils/nagl_wrapper.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/openff/toolkit/utils/nagl_wrapper.py b/openff/toolkit/utils/nagl_wrapper.py
index 042e78ff3..c2def5134 100644
--- a/openff/toolkit/utils/nagl_wrapper.py
+++ b/openff/toolkit/utils/nagl_wrapper.py
@@ -6,7 +6,6 @@
 from openff.toolkit import Quantity, unit
 from openff.toolkit.utils.base_wrapper import ToolkitWrapper
 from openff.toolkit.utils.exceptions import (
-    ChargeMethodUnavailableError,
     ToolkitUnavailableException,
 )
 
@@ -68,9 +67,8 @@ def assign_partial_charges(
         use_conformers: Optional[list["Quantity"]] = None,
         strict_n_conformers: bool = False,
         normalize_partial_charges: bool = True,
-        doi: str = None,
-        file_hash: str = None,
-
+        doi: Optional[str] = None,
+        file_hash: Optional[str] = None,
         _cls: Optional[type["FrozenMolecule"]] = None,
     ):
         """
@@ -96,6 +94,14 @@ def assign_partial_charges(
             formal charge of the molecule. This is used to prevent accumulation
             of rounding errors when the partial charge generation method has
             low precision.
+        doi
+            Zenodo DOI to check if NAGL model file needs to be fetched. Passed
+            directly to openff.nagl_models._dynamic_fetch.get_model, see docs
+            on that method for more details.
+        file_hash
+            sha256 hash to check against NAGL model file. Passed
+            directly to openff.nagl_models._dynamic_fetch.get_model, see docs
+            on that method for more details.
         _cls : class
             Molecule constructor
 

From 787c089d9aef606bdd93309c16776b6fcdced885 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 15 Jul 2025 12:14:05 -0700
Subject: [PATCH 13/27] test with new openff-nagl-models

---
 devtools/conda-envs/openeye-examples.yaml | 1 +
 devtools/conda-envs/openeye.yaml          | 1 +
 devtools/conda-envs/rdkit-examples.yaml   | 1 +
 devtools/conda-envs/rdkit.yaml            | 1 +
 devtools/conda-envs/test_env.yaml         | 1 +
 5 files changed, 5 insertions(+)

diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml
index c23a6ebd3..b9c88be67 100644
--- a/devtools/conda-envs/openeye-examples.yaml
+++ b/devtools/conda-envs/openeye-examples.yaml
@@ -44,3 +44,4 @@ dependencies:
   - gromacs >=2023.3
   - pip:
       - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+      - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
index 60fa56b5c..eaf6217fe 100644
--- a/devtools/conda-envs/openeye.yaml
+++ b/devtools/conda-envs/openeye.yaml
@@ -52,3 +52,4 @@ dependencies:
     - types-cachetools
     - mongo-types
     - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+    - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
index 5cbc61eff..71e21fe65 100644
--- a/devtools/conda-envs/rdkit-examples.yaml
+++ b/devtools/conda-envs/rdkit-examples.yaml
@@ -45,3 +45,4 @@ dependencies:
   - gromacs >=2023.3
   - pip:
       - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+      - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml
index c996f4f4f..1f2e201d4 100644
--- a/devtools/conda-envs/rdkit.yaml
+++ b/devtools/conda-envs/rdkit.yaml
@@ -42,3 +42,4 @@ dependencies:
   - nglview
   - pip:
       - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+      - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 676229939..27b5d538c 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -51,3 +51,4 @@ dependencies:
   - nomkl
   - pip:
       - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+      - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2

From 5981249e73cb57a036bfbabb0b8cb8de37347584 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 17 Jul 2025 14:35:54 -0700
Subject: [PATCH 14/27] update nagl test for bad suffix error

---
 openff/toolkit/_tests/test_nagl.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/openff/toolkit/_tests/test_nagl.py b/openff/toolkit/_tests/test_nagl.py
index 1f347c889..021709c7e 100644
--- a/openff/toolkit/_tests/test_nagl.py
+++ b/openff/toolkit/_tests/test_nagl.py
@@ -23,6 +23,7 @@
 from openff.toolkit.utils.openeye_wrapper import OpenEyeToolkitWrapper
 
 _DEFAULT_MODEL = "openff-gnn-am1bcc-0.1.0-rc.3.pt"
+from openff.nagl_models._dynamic_fetch import BadFileSuffixError
 
 try:
     from openff.nagl_models import list_available_nagl_models
@@ -128,8 +129,8 @@ def test_conformer_argument(self):
 
     def test_unsupported_charge_method(self):
         with pytest.raises(
-            ChargeMethodUnavailableError,
-            match="Charge model hartree_fock not supported",
+            BadFileSuffixError,
+            match="NAGLToolkitWrapper does not recognize file path extension on filename='hartree_fock'",
         ):
             create_ethanol().assign_partial_charges(
                 partial_charge_method="hartree_fock",

From 9b095f9dbbdff171d4dcee4b5b4846460a1b23d5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 17 Jul 2025 21:37:48 +0000
Subject: [PATCH 15/27] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openff/toolkit/_tests/test_nagl.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/openff/toolkit/_tests/test_nagl.py b/openff/toolkit/_tests/test_nagl.py
index 021709c7e..ceef13219 100644
--- a/openff/toolkit/_tests/test_nagl.py
+++ b/openff/toolkit/_tests/test_nagl.py
@@ -16,7 +16,6 @@
 from openff.toolkit._tests.utils import requires_openeye
 from openff.toolkit.utils import GLOBAL_TOOLKIT_REGISTRY
 from openff.toolkit.utils.exceptions import (
-    ChargeMethodUnavailableError,
     ToolkitUnavailableException,
 )
 from openff.toolkit.utils.nagl_wrapper import NAGLToolkitWrapper

From a16a42638a0fdadfc2fa7830d8d42c80d5ccd007 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Fri, 25 Jul 2025 14:52:54 -0700
Subject: [PATCH 16/27] update toolkit registry check to use types rather than
 repr

---
 openff/toolkit/_tests/test_nagl.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/openff/toolkit/_tests/test_nagl.py b/openff/toolkit/_tests/test_nagl.py
index ceef13219..7ca08a126 100644
--- a/openff/toolkit/_tests/test_nagl.py
+++ b/openff/toolkit/_tests/test_nagl.py
@@ -40,8 +40,7 @@ def test_version(self):
         assert parsed_version == NAGLToolkitWrapper()._toolkit_version
 
     def test_nagl_in_global_toolkit_registry(self):
-        assert "NAGL" in GLOBAL_TOOLKIT_REGISTRY.__repr__()
-
+        assert NAGLToolkitWrapper in {type(tk) for tk in GLOBAL_TOOLKIT_REGISTRY.registered_toolkits}
 
     @requires_openeye
     @pytest.mark.parametrize(

From 1788c64b44015cf9f38ab0a53111bea863da6b1f Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 29 Jul 2025 11:18:02 -0700
Subject: [PATCH 17/27] add compatibility checks for doi and hash fields, add
 tests

---
 openff/toolkit/_tests/test_parameters.py      | 115 ++++++++++++++++++
 .../typing/engines/smirnoff/parameters.py     |  11 +-
 2 files changed, 125 insertions(+), 1 deletion(-)

diff --git a/openff/toolkit/_tests/test_parameters.py b/openff/toolkit/_tests/test_parameters.py
index 95ebf0e76..105247a85 100644
--- a/openff/toolkit/_tests/test_parameters.py
+++ b/openff/toolkit/_tests/test_parameters.py
@@ -2821,6 +2821,121 @@ def test_nagl_charges_handler_defaults(self):
         assert handler.model_file_hash is None
         assert handler.digital_object_identifier is None
 
+    def test_nagl_charges_handler_hash_compatibility(self):
+        """Test compatibility checks for model_file_hash"""
+        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
+        from openff.toolkit.utils.exceptions import IncompatibleParameterError
+
+        # Test compatible handlers with same hash
+        handler1 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+            skip_version_check=True
+        )
+        handler2 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+            skip_version_check=True
+        )
+        # Should not raise exception
+        handler1.check_handler_compatibility(handler2)
+
+        # Test incompatible handlers with different hashes
+        handler3 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="different_hash_value",
+            skip_version_check=True
+        )
+        with pytest.raises(IncompatibleParameterError, match="different model_file_hash values"):
+            handler1.check_handler_compatibility(handler3)
+
+        # Test compatibility when only one handler has hash (should be compatible)
+        handler4 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            skip_version_check=True
+        )
+        # Should not raise exception
+        handler1.check_handler_compatibility(handler4)
+        handler4.check_handler_compatibility(handler1)
+
+    def test_nagl_charges_handler_doi_compatibility(self):
+        """Test compatibility checks for digital_object_identifier"""
+        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
+        from openff.toolkit.utils.exceptions import IncompatibleParameterError
+
+        # Test compatible handlers with same DOI
+        handler1 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            digital_object_identifier="10.5072/zenodo.203601",
+            skip_version_check=True
+        )
+        handler2 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            digital_object_identifier="10.5072/zenodo.203601",
+            skip_version_check=True
+        )
+        # Should not raise exception
+        handler1.check_handler_compatibility(handler2)
+
+        # Test incompatible handlers with different DOIs
+        handler3 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            digital_object_identifier="10.5072/zenodo.999999",
+            skip_version_check=True
+        )
+        with pytest.raises(IncompatibleParameterError, match="different digital_object_identifier values"):
+            handler1.check_handler_compatibility(handler3)
+
+        # Test compatibility when only one handler has DOI (should be compatible)
+        handler4 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            skip_version_check=True
+        )
+        # Should not raise exception
+        handler1.check_handler_compatibility(handler4)
+        handler4.check_handler_compatibility(handler1)
+
+    def test_nagl_charges_handler_combined_compatibility(self):
+        """Test compatibility checks with both hash and DOI"""
+        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
+        from openff.toolkit.utils.exceptions import IncompatibleParameterError
+
+        # Test compatible handlers with same hash and DOI
+        handler1 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+            digital_object_identifier="10.5072/zenodo.203601",
+            skip_version_check=True
+        )
+        handler2 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+            digital_object_identifier="10.5072/zenodo.203601",
+            skip_version_check=True
+        )
+        # Should not raise exception
+        handler1.check_handler_compatibility(handler2)
+
+        # Test incompatible with same hash but different DOI
+        handler3 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="144ed56e46c5b3ad80157b342c8c0f8f7340e4d382a678e30dd300c811646bd0",
+            digital_object_identifier="10.5072/zenodo.999999",
+            skip_version_check=True
+        )
+        with pytest.raises(IncompatibleParameterError, match="different digital_object_identifier values"):
+            handler1.check_handler_compatibility(handler3)
+
+        # Test incompatible with different hash but same DOI
+        handler4 = NAGLChargesHandler(
+            model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
+            model_file_hash="different_hash_value",
+            digital_object_identifier="10.5072/zenodo.203601",
+            skip_version_check=True
+        )
+        with pytest.raises(IncompatibleParameterError, match="different model_file_hash values"):
+            handler1.check_handler_compatibility(handler4)
+
 
 class TestGBSAHandler:
     def test_create_default_gbsahandler(self):
diff --git a/openff/toolkit/typing/engines/smirnoff/parameters.py b/openff/toolkit/typing/engines/smirnoff/parameters.py
index 351b1bb67..c8953f25c 100644
--- a/openff/toolkit/typing/engines/smirnoff/parameters.py
+++ b/openff/toolkit/typing/engines/smirnoff/parameters.py
@@ -3348,8 +3348,17 @@ def check_handler_compatibility(
                                              "model_files: "
                                              f"{self.model_file=} is not identical to {other_handler.model_file=}")
 
+        # If both handlers have model_file_hashes defined, ensure they're identical
+        if self.model_file_hash and other_handler.model_file_hash and self.model_file_hash != other_handler.model_file_hash:
+            raise IncompatibleParameterError("Attempted to initialize two NAGLCharges sections with different "
+                                             "model_file_hash values: "
+                                             f"{self.model_file_hash=} is not identical to {other_handler.model_file_hash=}")
 
-
+        # If both handlers have digital_object_identifiers defined, ensure they're identical
+        if self.digital_object_identifier and other_handler.digital_object_identifier and self.digital_object_identifier != other_handler.digital_object_identifier:
+            raise IncompatibleParameterError("Attempted to initialize two NAGLCharges sections with different "
+                                             "digital_object_identifier values: "
+                                             f"{self.digital_object_identifier=} is not identical to {other_handler.digital_object_identifier=}")
 
 class ToolkitAM1BCCHandler(_NonbondedHandler):
     """Handle SMIRNOFF ``<ToolkitAM1BCC>`` tags

From 706c84cbecf96b3df7961dc2847033936432d3b5 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 29 Jul 2025 11:20:42 -0700
Subject: [PATCH 18/27] lint

---
 openff/toolkit/_tests/test_nagl.py                   |  2 +-
 openff/toolkit/typing/engines/smirnoff/parameters.py | 12 ++++++++----
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/openff/toolkit/_tests/test_nagl.py b/openff/toolkit/_tests/test_nagl.py
index 7ca08a126..b51b054c7 100644
--- a/openff/toolkit/_tests/test_nagl.py
+++ b/openff/toolkit/_tests/test_nagl.py
@@ -5,6 +5,7 @@
 import pytest
 from openff.utilities import has_package, skip_if_missing
 
+from openff.nagl_models._dynamic_fetch import BadFileSuffixError
 from openff.toolkit import Molecule, unit
 from openff.toolkit._tests.create_molecules import (
     create_acetaldehyde,
@@ -22,7 +23,6 @@
 from openff.toolkit.utils.openeye_wrapper import OpenEyeToolkitWrapper
 
 _DEFAULT_MODEL = "openff-gnn-am1bcc-0.1.0-rc.3.pt"
-from openff.nagl_models._dynamic_fetch import BadFileSuffixError
 
 try:
     from openff.nagl_models import list_available_nagl_models
diff --git a/openff/toolkit/typing/engines/smirnoff/parameters.py b/openff/toolkit/typing/engines/smirnoff/parameters.py
index c8953f25c..be5f7a7b3 100644
--- a/openff/toolkit/typing/engines/smirnoff/parameters.py
+++ b/openff/toolkit/typing/engines/smirnoff/parameters.py
@@ -3349,16 +3349,20 @@ def check_handler_compatibility(
                                              f"{self.model_file=} is not identical to {other_handler.model_file=}")
 
         # If both handlers have model_file_hashes defined, ensure they're identical
-        if self.model_file_hash and other_handler.model_file_hash and self.model_file_hash != other_handler.model_file_hash:
+        if self.model_file_hash and other_handler.model_file_hash and \
+                self.model_file_hash != other_handler.model_file_hash:
             raise IncompatibleParameterError("Attempted to initialize two NAGLCharges sections with different "
                                              "model_file_hash values: "
-                                             f"{self.model_file_hash=} is not identical to {other_handler.model_file_hash=}")
+                                             f"{self.model_file_hash=} is not identical to "
+                                             f"{other_handler.model_file_hash=}")
 
         # If both handlers have digital_object_identifiers defined, ensure they're identical
-        if self.digital_object_identifier and other_handler.digital_object_identifier and self.digital_object_identifier != other_handler.digital_object_identifier:
+        if self.digital_object_identifier and other_handler.digital_object_identifier and \
+                self.digital_object_identifier != other_handler.digital_object_identifier:
             raise IncompatibleParameterError("Attempted to initialize two NAGLCharges sections with different "
                                              "digital_object_identifier values: "
-                                             f"{self.digital_object_identifier=} is not identical to {other_handler.digital_object_identifier=}")
+                                             f"{self.digital_object_identifier=} is not identical to "
+                                             f"{other_handler.digital_object_identifier=}")
 
 class ToolkitAM1BCCHandler(_NonbondedHandler):
     """Handle SMIRNOFF ``<ToolkitAM1BCC>`` tags

From 3b5687f20b8d850d482f6e2cee97db734d4655ef Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 29 Jul 2025 11:30:00 -0700
Subject: [PATCH 19/27] move imports to top of file

---
 openff/toolkit/_tests/test_parameters.py | 20 +-------------------
 1 file changed, 1 insertion(+), 19 deletions(-)

diff --git a/openff/toolkit/_tests/test_parameters.py b/openff/toolkit/_tests/test_parameters.py
index 105247a85..2a667104e 100644
--- a/openff/toolkit/_tests/test_parameters.py
+++ b/openff/toolkit/_tests/test_parameters.py
@@ -14,6 +14,7 @@
 from openff.toolkit import ForceField, Molecule, Quantity, Topology, unit
 from openff.toolkit._tests.mocking import VirtualSiteMocking
 from openff.toolkit._tests.utils import does_not_raise
+from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
 from openff.toolkit.typing.engines.smirnoff.parameters import (
     AngleHandler,
     BondHandler,
@@ -2724,15 +2725,12 @@ def test_charge_increment_one_ci_missing(self):
 
 class TestNAGLChargesHandler:
     def test_nagl_charges_handler_serialization(self):
-        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
         handler = NAGLChargesHandler(model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt", skip_version_check=True)
         assert handler.model_file == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
         handler_dict = handler.to_dict()
         assert handler_dict["model_file"] == "openff-gnn-am1bcc-0.1.0-rc.3.pt"
 
     def test_nagl_charges_handler_with_optional_fields(self):
-        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-
         # Test with model_file_hash
         handler = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2765,8 +2763,6 @@ def test_nagl_charges_handler_with_optional_fields(self):
         assert handler.digital_object_identifier == "10.5072/zenodo.203601"
 
     def test_nagl_charges_handler_serialization_with_optional_fields(self):
-        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-
         # Test serialization with all fields
         handler = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2786,9 +2782,6 @@ def test_nagl_charges_handler_serialization_with_optional_fields(self):
         assert handler_from_dict.digital_object_identifier == "10.5072/zenodo.203601"
 
     def test_nagl_charges_handler_compatibility(self):
-        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-        from openff.toolkit.utils.exceptions import IncompatibleParameterError
-
         # Test compatible handlers (same model_file)
         handler1 = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2811,8 +2804,6 @@ def test_nagl_charges_handler_compatibility(self):
             handler1.check_handler_compatibility(handler3)
 
     def test_nagl_charges_handler_defaults(self):
-        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-
         # Test that optional fields default to None
         handler = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2823,9 +2814,6 @@ def test_nagl_charges_handler_defaults(self):
 
     def test_nagl_charges_handler_hash_compatibility(self):
         """Test compatibility checks for model_file_hash"""
-        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-        from openff.toolkit.utils.exceptions import IncompatibleParameterError
-
         # Test compatible handlers with same hash
         handler1 = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2860,9 +2848,6 @@ def test_nagl_charges_handler_hash_compatibility(self):
 
     def test_nagl_charges_handler_doi_compatibility(self):
         """Test compatibility checks for digital_object_identifier"""
-        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-        from openff.toolkit.utils.exceptions import IncompatibleParameterError
-
         # Test compatible handlers with same DOI
         handler1 = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",
@@ -2897,9 +2882,6 @@ def test_nagl_charges_handler_doi_compatibility(self):
 
     def test_nagl_charges_handler_combined_compatibility(self):
         """Test compatibility checks with both hash and DOI"""
-        from openff.toolkit.typing.engines.smirnoff import NAGLChargesHandler
-        from openff.toolkit.utils.exceptions import IncompatibleParameterError
-
         # Test compatible handlers with same hash and DOI
         handler1 = NAGLChargesHandler(
             model_file="openff-gnn-am1bcc-0.1.0-rc.3.pt",

From 0df39aab1c8e17f4c6ee60a81219366c2fc321d1 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Tue, 29 Jul 2025 11:38:50 -0700
Subject: [PATCH 20/27] thread naglcharges handler into inits for correct
 import paths and docs

---
 docs/typing.rst            | 1 +
 openff/toolkit/__init__.py | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/docs/typing.rst b/docs/typing.rst
index 7157e4cb5..8c07100df 100644
--- a/docs/typing.rst
+++ b/docs/typing.rst
@@ -75,6 +75,7 @@ During ``System`` creation, each ``ParameterHandler`` registered to a ``ForceFie
     ElectrostaticsHandler
     LibraryChargeHandler
     ToolkitAM1BCCHandler
+    NAGLChargesHandler
     GBSAHandler
     ChargeIncrementModelHandler
     VirtualSiteHandler
diff --git a/openff/toolkit/__init__.py b/openff/toolkit/__init__.py
index 69a3ccf76..cf62c730a 100644
--- a/openff/toolkit/__init__.py
+++ b/openff/toolkit/__init__.py
@@ -21,6 +21,7 @@
         GLOBAL_TOOLKIT_REGISTRY,
         AmberToolsToolkitWrapper,
         BuiltInToolkitWrapper,
+        NAGLToolkitWrapper,
         OpenEyeToolkitWrapper,
         RDKitToolkitWrapper,
         ToolkitRegistry,
@@ -53,6 +54,7 @@
     "GLOBAL_TOOLKIT_REGISTRY": "openff.toolkit.utils.toolkits",
     "AmberToolsToolkitWrapper": "openff.toolkit.utils.toolkits",
     "BuiltInToolkitWrapper": "openff.toolkit.utils.toolkits",
+    "NAGLToolkitWrapper": "openff.toolkit.utils.toolkits",
     "OpenEyeToolkitWrapper": "openff.toolkit.utils.toolkits",
     "RDKitToolkitWrapper": "openff.toolkit.utils.toolkits",
     "ToolkitRegistry": "openff.toolkit.utils.toolkits",

From 800c2f111a751752cf685d2bdbe4fabd50766c31 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 7 Aug 2025 08:31:17 -0700
Subject: [PATCH 21/27] remove commented code

---
 openff/toolkit/utils/nagl_wrapper.py | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/openff/toolkit/utils/nagl_wrapper.py b/openff/toolkit/utils/nagl_wrapper.py
index c2def5134..2fa08e03d 100644
--- a/openff/toolkit/utils/nagl_wrapper.py
+++ b/openff/toolkit/utils/nagl_wrapper.py
@@ -148,24 +148,6 @@ def assign_partial_charges(
                                doi=doi,
                                file_hash=file_hash)
 
-        # try:
-        #     model_path = get_model(filename=partial_charge_method,
-        #                            doi=doi,
-        #                            file_hash=file_hash)
-        # except FileNotFoundError as error:
-        #     raise ChargeMethodUnavailableError(
-        #         f"Charge model {partial_charge_method} not supported by "
-        #         f"{self.__class__.__name__}, or model file can not be found. "
-        #         #f"Note that the NAGLToolkitWrapper.assign_partial_charges method "
-        #         #f"can only use models from the local cache or models fetchable from "
-        #         #f"openff-nagl-models release assets on GitHub. "
-        #         #f"This method does NOT "
-        #         #f"accept custom DOIs to fetch models from other sources. Use "
-        #         #f"NAGLToolkitWrapper.fetch_verify_model_and_assign_partial_charges if "
-        #         #f"you intend to also fetch models from arbitrary Zenodo DOIs and verify "
-        #         #f"their hash."
-        #     ) from error
-
         model = GNNModel.load(model_path, eval_mode=True)
         charges = model.compute_property(
             molecule,

From ec518e70cd2dc94c0354502fac4e79e00d2b0893 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 7 Aug 2025 08:53:12 -0700
Subject: [PATCH 22/27] have tests run without interchange branch

---
 devtools/conda-envs/openeye-examples.yaml | 2 +-
 devtools/conda-envs/openeye.yaml          | 2 +-
 devtools/conda-envs/rdkit-examples.yaml   | 2 +-
 devtools/conda-envs/rdkit.yaml            | 2 +-
 devtools/conda-envs/test_env.yaml         | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml
index b9c88be67..43c842fbb 100644
--- a/devtools/conda-envs/openeye-examples.yaml
+++ b/devtools/conda-envs/openeye-examples.yaml
@@ -43,5 +43,5 @@ dependencies:
   - openmmforcefields >=0.11.2
   - gromacs >=2023.3
   - pip:
-      - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+      #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
       - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
index eaf6217fe..090a0c4d8 100644
--- a/devtools/conda-envs/openeye.yaml
+++ b/devtools/conda-envs/openeye.yaml
@@ -51,5 +51,5 @@ dependencies:
     - types-xmltodict
     - types-cachetools
     - mongo-types
-    - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+    #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
     - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
index 71e21fe65..e6f7721aa 100644
--- a/devtools/conda-envs/rdkit-examples.yaml
+++ b/devtools/conda-envs/rdkit-examples.yaml
@@ -44,5 +44,5 @@ dependencies:
   - openmmforcefields >=0.11.2
   - gromacs >=2023.3
   - pip:
-      - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+      #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
       - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml
index 1f2e201d4..244fbc59c 100644
--- a/devtools/conda-envs/rdkit.yaml
+++ b/devtools/conda-envs/rdkit.yaml
@@ -41,5 +41,5 @@ dependencies:
   - qcengine
   - nglview
   - pip:
-      - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+      #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
       - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 27b5d538c..cbbb50adb 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -50,5 +50,5 @@ dependencies:
   # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
   - nomkl
   - pip:
-      - git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
+      #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
       - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2

From ae283a8548601a1ec257e323b58d84a7b7141c66 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 7 Aug 2025 09:26:03 -0700
Subject: [PATCH 23/27] point to nagl-models main branch for pip installs

---
 devtools/conda-envs/openeye-examples.yaml | 2 +-
 devtools/conda-envs/openeye.yaml          | 2 +-
 devtools/conda-envs/rdkit-examples.yaml   | 2 +-
 devtools/conda-envs/rdkit.yaml            | 2 +-
 devtools/conda-envs/test_env.yaml         | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml
index 43c842fbb..c64879cd8 100644
--- a/devtools/conda-envs/openeye-examples.yaml
+++ b/devtools/conda-envs/openeye-examples.yaml
@@ -44,4 +44,4 @@ dependencies:
   - gromacs >=2023.3
   - pip:
       #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-      - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
+      - git+https://github.com/openforcefield/openff-nagl-models.git@main
diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
index 090a0c4d8..2f4bbac0a 100644
--- a/devtools/conda-envs/openeye.yaml
+++ b/devtools/conda-envs/openeye.yaml
@@ -52,4 +52,4 @@ dependencies:
     - types-cachetools
     - mongo-types
     #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-    - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
+    - git+https://github.com/openforcefield/openff-nagl-models.git@main
diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
index e6f7721aa..7e8974213 100644
--- a/devtools/conda-envs/rdkit-examples.yaml
+++ b/devtools/conda-envs/rdkit-examples.yaml
@@ -45,4 +45,4 @@ dependencies:
   - gromacs >=2023.3
   - pip:
       #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-      - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
+      - git+https://github.com/openforcefield/openff-nagl-models.git@main
diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml
index 244fbc59c..aa67c2b5c 100644
--- a/devtools/conda-envs/rdkit.yaml
+++ b/devtools/conda-envs/rdkit.yaml
@@ -42,4 +42,4 @@ dependencies:
   - nglview
   - pip:
       #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-      - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
+      - git+https://github.com/openforcefield/openff-nagl-models.git@main
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index cbbb50adb..fda2430bd 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -51,4 +51,4 @@ dependencies:
   - nomkl
   - pip:
       #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-      - git+https://github.com/openforcefield/openff-nagl-models.git@fetch-by-doi2
+      - git+https://github.com/openforcefield/openff-nagl-models.git@main

From ad9b5a0aa1191723920eb5a9e2e04fd06bd349b3 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 7 Aug 2025 09:53:00 -0700
Subject: [PATCH 24/27] update expected error message in test

---
 openff/toolkit/_tests/test_nagl.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openff/toolkit/_tests/test_nagl.py b/openff/toolkit/_tests/test_nagl.py
index b51b054c7..3a6779fb9 100644
--- a/openff/toolkit/_tests/test_nagl.py
+++ b/openff/toolkit/_tests/test_nagl.py
@@ -128,7 +128,7 @@ def test_conformer_argument(self):
     def test_unsupported_charge_method(self):
         with pytest.raises(
             BadFileSuffixError,
-            match="NAGLToolkitWrapper does not recognize file path extension on filename='hartree_fock'",
+            match="Found an unrecognized file path extension on filename='hartree_fock'",
         ):
             create_ethanol().assign_partial_charges(
                 partial_charge_method="hartree_fock",

From c4a370c7f0c71e73463bbac8964077778058ecdc Mon Sep 17 00:00:00 2001
From: Jeff Wagner <jwagnerjpl@gmail.com>
Date: Thu, 14 Aug 2025 08:22:15 -0700
Subject: [PATCH 25/27] revert tests to using conda packages

---
 devtools/conda-envs/rdkit.yaml    | 3 ---
 devtools/conda-envs/test_env.yaml | 3 ---
 2 files changed, 6 deletions(-)

diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml
index aa67c2b5c..a180bd066 100644
--- a/devtools/conda-envs/rdkit.yaml
+++ b/devtools/conda-envs/rdkit.yaml
@@ -40,6 +40,3 @@ dependencies:
   - qcportal >=0.50
   - qcengine
   - nglview
-  - pip:
-      #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-      - git+https://github.com/openforcefield/openff-nagl-models.git@main
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index fda2430bd..c2ddad482 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -49,6 +49,3 @@ dependencies:
   - nbval
   # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
   - nomkl
-  - pip:
-      #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-      - git+https://github.com/openforcefield/openff-nagl-models.git@main

From 62c0edbe3c3ac764c65ebb15a2e38e4168719503 Mon Sep 17 00:00:00 2001
From: Jeff Wagner <jwagnerjpl@gmail.com>
Date: Thu, 14 Aug 2025 08:22:57 -0700
Subject: [PATCH 26/27] revert other test envs

---
 devtools/conda-envs/openeye-examples.yaml | 3 ---
 devtools/conda-envs/openeye.yaml          | 2 --
 devtools/conda-envs/rdkit-examples.yaml   | 3 ---
 3 files changed, 8 deletions(-)

diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml
index c64879cd8..8be786546 100644
--- a/devtools/conda-envs/openeye-examples.yaml
+++ b/devtools/conda-envs/openeye-examples.yaml
@@ -42,6 +42,3 @@ dependencies:
   - pdbfixer
   - openmmforcefields >=0.11.2
   - gromacs >=2023.3
-  - pip:
-      #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-      - git+https://github.com/openforcefield/openff-nagl-models.git@main
diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
index 2f4bbac0a..2571d5dd2 100644
--- a/devtools/conda-envs/openeye.yaml
+++ b/devtools/conda-envs/openeye.yaml
@@ -51,5 +51,3 @@ dependencies:
     - types-xmltodict
     - types-cachetools
     - mongo-types
-    #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-    - git+https://github.com/openforcefield/openff-nagl-models.git@main
diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
index 7e8974213..40fcec17f 100644
--- a/devtools/conda-envs/rdkit-examples.yaml
+++ b/devtools/conda-envs/rdkit-examples.yaml
@@ -43,6 +43,3 @@ dependencies:
   - pdbfixer
   - openmmforcefields >=0.11.2
   - gromacs >=2023.3
-  - pip:
-      #- git+https://github.com/openforcefield/openff-interchange.git@naglcharges-handler
-      - git+https://github.com/openforcefield/openff-nagl-models.git@main

From fc431e2744a958e5da031262913533fdb9aa9b35 Mon Sep 17 00:00:00 2001
From: Jeff Wagner <jwagnerjpl@gmail.com>
Date: Thu, 14 Aug 2025 09:32:32 -0700
Subject: [PATCH 27/27] update releasenotes

---
 docs/releasehistory.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/releasehistory.md b/docs/releasehistory.md
index e93f42d87..8bbb9f3cb 100644
--- a/docs/releasehistory.md
+++ b/docs/releasehistory.md
@@ -6,7 +6,7 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 * `minor` increments add features but do not break API compatibility
 * `micro` increments represent bugfix releases or improvements in documentation
 
-## Current development
+## 0.17.0
 
 ### API-breaking changes
 
@@ -15,6 +15,8 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 ### Bugfixes
 
 ### New features
+- [PR #2048](https://github.com/openforcefield/openff-toolkit/pull/2048): Adds NAGLChargesHandler. See [SMIRNOFF EP 11](https://github.com/openforcefield/standards/pull/71) for the new SMIRNOFF specification section and discussion.
+
 
 ### Improved documentation and warnings