Test against openff-interchange-0.4.0beta1

Updates for Interchange 0.4.0/Pydantic v2 Update BRD4 notebook cosmetic commit to kick CI Revert
openforcefield · Sep 10, 2024 · 4c132f6 · 4c132f6
1 parent c84b321
commit 4c132f6
Show file tree

Hide file tree

Showing 13 changed files with 63 additions and 71 deletions.
diff --git a/devtools/conda-envs/conda.yaml b/devtools/conda-envs/conda.yaml
@@ -1,5 +1,6 @@
 name: latest-deployment
 channels:
+  - conda-forge/label/openff-interchange_rc
   - conda-forge
 dependencies:
     # Base depends

diff --git a/devtools/conda-envs/conda_oe.yaml b/devtools/conda-envs/conda_oe.yaml
@@ -1,5 +1,6 @@
 name: latest-deployment
 channels:
+  - conda-forge/label/openff-interchange_rc
   - conda-forge
   - openeye
 dependencies:

diff --git a/devtools/conda-envs/installer.yaml b/devtools/conda-envs/installer.yaml
@@ -1,6 +1,7 @@
 name: constructor
 
 channels:
+  - conda-forge/label/openff-interchange_rc
   - defaults
   - conda-forge
 

diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml
@@ -1,11 +1,12 @@
 name: openeye-examples
 channels:
+  - conda-forge/label/openff-interchange_rc
   - openeye
   - conda-forge
 dependencies:
     # Base depends
   - python
-  - pydantic =1
+  - pydantic
   - packaging
   - numpy
   - networkx
@@ -19,7 +20,7 @@ dependencies:
   - openff-amber-ff-ports >=0.0.3
   - openff-units =0.2.0
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.19
+  - openff-interchange-base >=0.4.0beta1
   - openff-nagl-base ~=0.4.0
   - openff-nagl-models ==0.3.0
   - typing_extensions

diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
@@ -1,11 +1,12 @@
 name: openff-toolkit-test-openeye
 channels:
+  - conda-forge/label/openff-interchange_rc
   - openeye
   - conda-forge
 dependencies:
     # Base depends
   - python
-  - pydantic =1
+  - pydantic
   - packaging
   - numpy
   - networkx
@@ -19,7 +20,7 @@ dependencies:
   - openff-units =0.2.0
   - openff-amber-ff-ports
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.19
+  - openff-interchange-base >=0.4.0beta1
   - openff-nagl-base ~=0.4.0
   - openff-nagl-models ==0.3.0
   - typing_extensions

diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
@@ -1,10 +1,11 @@
 name: rdkit-examples
 channels:
+  - conda-forge/label/openff-interchange_rc
   - conda-forge
 dependencies:
     # Base depends
   - python
-  - pydantic =1
+  - pydantic
   - packaging
   - numpy
   - networkx
@@ -18,7 +19,7 @@ dependencies:
   - openff-amber-ff-ports >=0.0.3
   - openff-units =0.2.0
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.19
+  - openff-interchange-base >=0.4.0beta1
   - openff-nagl-base ~=0.4.0
   - openff-nagl-models ==0.3.0
   - typing_extensions

diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml
@@ -1,10 +1,11 @@
 name: openff-toolkit-test-rdkit
 channels:
+  - conda-forge/label/openff-interchange_rc
   - conda-forge
 dependencies:
     # Base depends
   - python
-  - pydantic =1
+  - pydantic
   - packaging
   - numpy
   - networkx
@@ -18,7 +19,7 @@ dependencies:
   - openff-units =0.2.0
   - openff-amber-ff-ports
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.19
+  - openff-interchange-base >=0.4.0beta1
   - openff-nagl-base ~=0.4.0
   - openff-nagl-models ==0.3.0
   - typing_extensions

diff --git a/devtools/conda-envs/release-build.yaml b/devtools/conda-envs/release-build.yaml
@@ -1,5 +1,6 @@
 name: release-build
 channels:
+  - conda-forge/label/openff-interchange_rc
   - conda-forge
 
 dependencies:

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -1,5 +1,6 @@
 name: openff-toolkit-test
 channels:
+  - conda-forge/label/openff-interchange_rc
   - openeye
   - conda-forge
 dependencies:
@@ -19,7 +20,7 @@ dependencies:
   - openff-units =0.2.0
   - openff-amber-ff-ports
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.19
+  - openff-interchange-base >=0.4.0beta1
   - openff-nagl-base ~=0.4.0
   - openff-nagl-models ==0.3.0
     # Toolkit-specific
@@ -47,7 +48,7 @@ dependencies:
   - nomkl
   - mypy
   - typing_extensions
-  - pydantic =1
+  - pydantic
   - pip:
     - types-setuptools
     - types-toml

diff --git a/examples/using_smirnoff_with_amber_protein_forcefield/.gitignore b/examples/using_smirnoff_with_amber_protein_forcefield/.gitignore
@@ -1,4 +1,5 @@
 complex.*
+complex_pointenergy.mdp
 receptor.*
 ligand.*
 protein.pdb
diff --git a/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb b/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb
@@ -24,10 +24,11 @@
     "repo_url = (\n",
     "    \"https://raw.githubusercontent.com/MobleyLab/benchmarksets/master/input_files/\"\n",
     ")\n",
+    "\n",
     "sources = {\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",
+    "    \"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",
     "}\n",
     "for filename, url in sources.items():\n",
     "    r = requests.get(url)\n",
@@ -40,44 +41,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "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)."
+    "from openff.toolkit import ForceField, Molecule, Quantity, Topology"
    ]
   },
   {
    "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": "2f3b86c392c24705b86721395cf43ea4",
+       "model_id": "48226cb62a2849029c42d579843ef0f7",
        "version_major": 2,
        "version_minor": 0
       },
@@ -90,8 +67,8 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/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"
+      "/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"
      ]
     }
    ],
@@ -107,32 +84,32 @@
     "\n",
     "receptor = ff14sb.create_interchange(topology=receptor_topology)\n",
     "\n",
-    "complex_system = receptor.combine(ligand)\n",
-    "\n",
-    "# TODO\n",
-    "# complex.box = pdbfile box vectors ...\n",
-    "# complex.positions = np.vstack([receptor.positions, ligand.positions])"
+    "# 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)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Export to OpenMM"
+    "### Export to OpenMM\n",
+    "\n",
+    "See [docs](https://docs.openforcefield.org/projects/interchange/en/stable/using/output.html#openmm) for more options."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x14380adf0> >"
+       "<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x14ba376f0> >"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -147,31 +124,35 @@
     "tags": []
    },
    "source": [
-    "### Export to Amber"
+    "### Export to Amber\n",
+    "\n",
+    "See [docs](https://docs.openforcefield.org/projects/interchange/en/stable/using/output.html#amber) for more options."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
-    "# 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\")"
+    "complex_system.to_inpcrd(\"complex.inpcrd\")\n",
+    "complex_system.to_prmtop(\"complex.prmtop\")"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Export to GROMACS"
+    "### 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."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {
     "tags": []
    },
@@ -180,14 +161,16 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/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"
+      "/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"
      ]
     }
    ],
    "source": [
-    "complex_system.to_gro(\"complex.gro\")\n",
-    "complex_system.to_top(\"complex.top\")"
+    "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\")"
    ]
   }
  ],
@@ -208,7 +191,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

diff --git a/openff/toolkit/_tests/test_forcefield.py b/openff/toolkit/_tests/test_forcefield.py
@@ -15,6 +15,7 @@
 from openff.units.openmm import from_openmm, to_openmm
 from openmm import NonbondedForce, Platform, XmlSerializer, app
 from openmm import unit as openmm_unit
+from pydantic import ValidationError
 
 from openff.toolkit import unit
 from openff.toolkit._tests.create_molecules import (
@@ -4028,15 +4029,11 @@ def test_fractional_bondorder_invalid_interpolation_method(self):
         # This error will be either from v1 of the package (if v1 is installed)
         # or the faked v1 API (if v2 is installed). Ensure the v1 error or a
         # mimick of it is imported
-        try:
-            from pydantic.v1 import ValidationError
-        except ImportError:
-            from pydantic import ValidationError
 
         # If important, this can be a custom exception instead of a verbose ValidationError
         with pytest.raises(
             ValidationError,
-            match="given=invalid method name",
+            match="Input should be 'linear'.*input_value='invalid method name'",
         ):
             forcefield.create_openmm_system(
                 topology,

diff --git a/openff/toolkit/typing/engines/smirnoff/forcefield.py b/openff/toolkit/typing/engines/smirnoff/forcefield.py
@@ -1399,7 +1399,7 @@ def get_partial_charges(self, molecule: "Molecule", **kwargs: Any) -> Quantity:
         """
         from openff.interchange import Interchange
 
-        from openff.toolkit import Molecule, unit
+        from openff.toolkit import Molecule
 
         if not isinstance(molecule, Molecule):
             raise ValueError(
@@ -1412,9 +1412,11 @@ def get_partial_charges(self, molecule: "Molecule", **kwargs: Any) -> Quantity:
                 c.m
                 for c in Interchange.from_smirnoff(
                     force_field=self, topology=[molecule], **kwargs
-                )["Electrostatics"].charges.values()
+                )["Electrostatics"]
+                ._get_charges()
+                .values()
             ],
-            unit.elementary_charge,
+            "elementary_charge",
         )
 
     def __getitem__(self, val: Union[str, ParameterHandler]) -> ParameterHandler: