Revert some changes for simpler diff

examples/using_smirnoff_with_amber_protein_forcefield/.gitignore

@@ -1,5 +1,4 @@
 complex.*
-complex_pointenergy.mdp
 receptor.*
 ligand.*
 protein.pdb

examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb

@@ -24,11 +24,10 @@
     "repo_url = (\n",
     "    \"https://raw.githubusercontent.com/MobleyLab/benchmarksets/master/input_files/\"\n",
     ")\n",
-    "\n",
     "sources = {\n",
-    "    \"receptor.pdb\": f\"{repo_url}BRD4/pdb/BRD4.pdb\",\n",
-    "    \"ligand.pdb\": f\"{repo_url}BRD4/pdb/ligand-1.pdb\",\n",
-    "    \"ligand.sdf\": f\"{repo_url}BRD4/sdf/ligand-1.sdf\",\n",
+    "    \"receptor.pdb\": repo_url + \"BRD4/pdb/BRD4.pdb\",\n",
+    "    \"ligand.pdb\": repo_url + \"BRD4/pdb/ligand-1.pdb\",\n",
+    "    \"ligand.sdf\": repo_url + \"BRD4/sdf/ligand-1.sdf\",\n",
     "}\n",
     "for filename, url in sources.items():\n",
     "    r = requests.get(url)\n",
@@ -41,20 +40,44 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from openff.toolkit import ForceField, Molecule, Quantity, Topology"
+    "from openff.toolkit import ForceField, Molecule, Topology"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Later we will use `Interchange.__add__`, which is an experimental feature. It needs to be turned on by setting the environment variable below, and by doing so we accept [some stability and accuracy risks](https://docs.openforcefield.org/projects/interchange/en/stable/using/experimental.html)."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "env: INTERCHANGE_EXPERIMENTAL=1\n"
+     ]
+    }
+   ],
+   "source": [
+    "%env INTERCHANGE_EXPERIMENTAL=1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
    "metadata": {
     "tags": []
    },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "48226cb62a2849029c42d579843ef0f7",
+       "model_id": "2f3b86c392c24705b86721395cf43ea4",
        "version_major": 2,
        "version_minor": 0
       },
@@ -67,8 +90,8 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.10/site-packages/openff/interchange/operations/_combine.py:52: InterchangeCombinationWarning: Interchange object combination is complex and likely to produce strange results outside of a limited set of use cases it has been tested in. Any workflow using this method is not guaranteed to be suitable for production or stable between versions. Use with extreme caution and thoroughly validate results!\n",
-      "  warnings.warn(\n"
+      "/Users/jeffreywagner/projects/OpenForceField/openff-interchange/openff/interchange/_experimental.py:35: UserWarning: Interchange object combination is experimental and likely to produce strange results. Any workflow using this method is not guaranteed to be suitable for production. Use with extreme caution and thoroughly validate results!\n",
+      "  return func(*args, **kwargs)\n"
      ]
     }
    ],
@@ -84,32 +107,32 @@
     "\n",
     "receptor = ff14sb.create_interchange(topology=receptor_topology)\n",
     "\n",
-    "# Interchange.combine works nicely for some cases but hasn't been tested for all - use caution\n",
-    "# if adapting this for more novel workflows!\n",
-    "complex_system = receptor.combine(ligand)"
+    "complex_system = receptor.combine(ligand)\n",
+    "\n",
+    "# TODO\n",
+    "# complex.box = pdbfile box vectors ...\n",
+    "# complex.positions = np.vstack([receptor.positions, ligand.positions])"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Export to OpenMM\n",
-    "\n",
-    "See [docs](https://docs.openforcefield.org/projects/interchange/en/stable/using/output.html#openmm) for more options."
+    "### Export to OpenMM"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x14ba376f0> >"
+       "<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x14380adf0> >"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -124,35 +147,31 @@
     "tags": []
    },
    "source": [
-    "### Export to Amber\n",
-    "\n",
-    "See [docs](https://docs.openforcefield.org/projects/interchange/en/stable/using/output.html#amber) for more options."
+    "### Export to Amber"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
-    "complex_system.to_inpcrd(\"complex.inpcrd\")\n",
-    "complex_system.to_prmtop(\"complex.prmtop\")"
+    "# TODO: Fix inferring residue information with mixed topology\n",
+    "if False:\n",
+    "    complex_system.to_inpcrd(\"complex.inpcrd\")\n",
+    "    complex_system.to_prmtop(\"complex.prmtop\")"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Export to GROMACS\n",
-    "\n",
-    "See [docs](https://docs.openforcefield.org/projects/interchange/en/stable/using/output.html#gromacs) for more options.\n",
-    "\n",
-    "GROMACS does not support vacuum simulations. In this example, we didn't add solvent and the original PDB file didn't have box vectors. We'll just arbitrarily add a 4 nm cubic box around the receptor-ligand complex."
+    "### Export to GROMACS"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {
     "tags": []
    },
@@ -161,16 +180,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.10/site-packages/openff/interchange/components/mdconfig.py:471: UserWarning: Ambiguous failure while processing constraints. Constraining h-bonds as a stopgap.\n",
-      "  warnings.warn(\n"
+      "/Users/jeffreywagner/projects/OpenForceField/openff-interchange/openff/interchange/interop/gromacs/export/_export.py:48: UserWarning: WARNING: System defined with no box vectors, which GROMACS does not offically support in versions 2020 or newer (see https://gitlab.com/gromacs/gromacs/-/issues/3526). Setting box vectors to a 5  nm cube.\n",
+      "  self._write_gro(gro, decimal)\n"
      ]
     }
    ],
    "source": [
-    "complex_system.box = Quantity([4, 4, 4], \"nanometer\")\n",
-    "\n",
-    "# This step might be slow, writing some large proteins is not yet optimized\n",
-    "complex_system.to_gromacs(\"complex\")"
+    "complex_system.to_gro(\"complex.gro\")\n",
+    "complex_system.to_top(\"complex.top\")"
    ]
   }
  ],
@@ -191,7 +208,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.10"
   }
  },
  "nbformat": 4,

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

@@ -30,7 +30,7 @@
 
 from packaging.version import Version
 
-from openff.toolkit import Quantity
+from openff.toolkit import Quantity, unit
 from openff.toolkit.typing.engines.smirnoff.io import ParameterIOHandler
 from openff.toolkit.typing.engines.smirnoff.parameters import ParameterHandler
 from openff.toolkit.typing.engines.smirnoff.plugins import load_handler_plugins
@@ -1400,7 +1400,7 @@ def get_partial_charges(self, molecule: "Molecule", **kwargs: Any) -> Quantity:
                     force_field=self, topology=[molecule], **kwargs
                 )["Electrostatics"].charges.values()
             ],
-            "elementary_charge",
+            unit.elementary_charge,
         )
 
     def __getitem__(self, val: Union[str, ParameterHandler]) -> ParameterHandler: