Add partial charges method (#186)

.github/workflows/tests.yml

@@ -55,7 +55,7 @@ jobs:
       - name: Build environment
         run: |
           conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools
+          conda install -c conda-forge openff-toolkit openmm openmmtools dgl
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools
           python -m pip install -e '.[dev]'
@@ -78,7 +78,7 @@ jobs:
       - name: Build environment
         run: |
           conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools
+          conda install -c conda-forge openff-toolkit openmm openmmtools dgl
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools
           python -m pip install -e '.[dev]'

.gitignore

@@ -18,4 +18,5 @@ docs/build
 tests/failures.txt
 
 /examples/gulp_test_output/
-/examples/gulp_test_output_MD/
+/examples/gulp_test_output_MD/
+/examples/.model.pt

README.rst

@@ -40,6 +40,8 @@ Some optional dependencies are only available through conda:
   mamba install openbabel
   # for mdanalysis
   mamba install mdanalysis
+  # for espaloma charge
+  mamba install dgl
 
 Examples
 ========

docs/source/index.rst

@@ -45,6 +45,8 @@ Some optional dependencies are only available through conda:
   mamba install openbabel
   # for mdanalysis
   mamba install mdanalysis
+  # for espaloma charge
+  mamba install dgl
 
 
 Dependencies

examples/openmm_example.py

@@ -23,7 +23,7 @@ def main() -> None:
         # Load the openff-2.1.0 force field appropriate for
         # vacuum calculations (without constraints)
         force_field=ForceField("openff_unconstrained-2.1.0.offxml"),
-        partial_charges_method="mmff94",
+        partial_charges_method="espaloma-am1bcc",
         max_iterations=10,
     )
     ff_cage = ff_optimizer.optimize(cage)
@@ -32,7 +32,7 @@ def main() -> None:
         "ff_opt_cage",
         stko.OpenMMEnergy(
             force_field=ForceField("openff_unconstrained-2.1.0.offxml"),
-            partial_charges_method="mmff94",
+            partial_charges_method="espaloma-am1bcc",
         ).get_energy(ff_cage),
     )
 
@@ -41,15 +41,15 @@ def main() -> None:
         # vacuum calculations (without constraints)
         force_field=ForceField("openff_unconstrained-2.1.0.offxml"),
         restricted=False,
-        partial_charges_method="mmff94",
+        partial_charges_method="espaloma-am1bcc",
     )
     ff_cage = ff_optimizer.optimize(cage)
     ff_cage.write(output / "ffunrest_opt_cage.mol")
     print(
         "ffunrest_opt_cage",
         stko.OpenMMEnergy(
             force_field=ForceField("openff_unconstrained-2.1.0.offxml"),
-            partial_charges_method="mmff94",
+            partial_charges_method="espaloma-am1bcc",
         ).get_energy(ff_cage),
     )
 
@@ -58,15 +58,15 @@ def main() -> None:
         # vacuum calculations (without constraints)
         force_field=ForceField("openff_unconstrained-2.1.0.offxml"),
         restricted=True,
-        partial_charges_method="mmff94",
+        partial_charges_method="espaloma-am1bcc",
     )
     ff_cage = ff_optimizer.optimize(cage)
     ff_cage.write(output / "ffrest_opt_cage.mol")
     print(
         "ffrest_opt_cage",
         stko.OpenMMEnergy(
             force_field=ForceField("openff_unconstrained-2.1.0.offxml"),
-            partial_charges_method="mmff94",
+            partial_charges_method="espaloma-am1bcc",
         ).get_energy(ff_cage),
     )
 
@@ -80,20 +80,27 @@ def main() -> None:
         output_directory=output / "md_optimisation",
         integrator=integrator,
         random_seed=275,
-        partial_charges_method="mmff94",
+        partial_charges_method="espaloma-am1bcc",
         reporting_freq=5,
         trajectory_freq=5,
         num_steps=10000,
         num_conformers=50,
         platform="CUDA",
+        conformer_optimiser=stko.OpenMMForceField(
+            # Load the openff-2.1.0 force field appropriate for
+            # vacuum calculations (without constraints)
+            force_field=ForceField("openff_unconstrained-2.1.0.offxml"),
+            restricted=False,
+            partial_charges_method="espaloma-am1bcc",
+        ),
     )
     md_cage = md_optimizer.optimize(cage)
     md_cage.write(output / "md_opt_cage.mol")
     print(
         "md_opt_cage",
         stko.OpenMMEnergy(
             force_field=ForceField("openff_unconstrained-2.1.0.offxml"),
-            partial_charges_method="mmff94",
+            partial_charges_method="espaloma-am1bcc",
         ).get_energy(md_cage),
     )