dry test #1

src/pontibus/protocols/solvation/asfe_protocol.py

@@ -33,7 +33,7 @@
     MDOutputSettings,
     InterchangeFFSettings,
     PackmolSolvationSettings,
-    AlchemicalSettings,
+    ExperimentalAlchemicalSettings,
     LambdaSettings,
 )
 from pontibus.protocols.solvation import (
@@ -71,15 +71,17 @@ def _default_settings(cls):
         """
         return ASFESettings(
             protocol_repeats=3,
-            solvent_forcefield_settings=InterchangeFFSettings(),
+            solvent_forcefield_settings=InterchangeFFSettings(
+                nonbonded_method='pme',
+            ),
             vacuum_forcefield_settings=InterchangeFFSettings(
                 nonbonded_method="nocutoff",
             ),
             thermo_settings=ThermoSettings(
                 temperature=298.15 * unit.kelvin,
                 pressure=1 * unit.bar,
             ),
-            alchemical_settings=AlchemicalSettings(),
+            alchemical_settings=ExperimentalAlchemicalSettings(),
             lambda_settings=LambdaSettings(
                 lambda_elec=[
                     0.0,
@@ -355,7 +357,7 @@ def _handle_settings(self) -> dict[str, gufe.settings.SettingsBaseModel]:
             * thermo_settings : ThermoSettings
             * charge_settings : OpenFFPartialChargeSettings
             * solvation_settings : PackmolSolvationSettings
-            * alchemical_settings : AlchemicalSettings
+            * alchemical_settings : ExperimentalAlchemicalSettings
             * lambda_settings : LambdaSettings
             * engine_settings : OpenMMEngineSettings
             * integrator_settings : IntegratorSettings
@@ -437,7 +439,7 @@ def _handle_settings(self) -> dict[str, gufe.settings.SettingsBaseModel]:
             * thermo_settings : ThermoSettings
             * charge_settings : OpenFFPartialChargeSettings
             * solvation_settings : PackmolSolvationSettings
-            * alchemical_settings : AlchemicalSettings
+            * alchemical_settings : ExperimentalAlchemicalSettings
             * lambda_settings : LambdaSettings
             * engine_settings : OpenMMEngineSettings
             * integrator_settings : IntegratorSettings

src/pontibus/protocols/solvation/base.py

@@ -159,7 +159,6 @@ def _get_omm_objects(
         * For now this method solely calls interchange system creation for
           solvation.
         """
-
         if self.verbose:
             self.logger.info("Parameterizing system")
 
@@ -179,12 +178,12 @@ def _get_omm_objects(
         # Create your interchange object
         with without_oechem_backend():
             interchange, comp_resids = interchange_packmol_creation(
-                settings["forcefield_settings"],
-                settings["solvation_settings"],
-                protein_component,
-                solvent_component,
-                solvent_offmol,
-                smc_components,
+                ffsettings=settings["forcefield_settings"],
+                solvation_settings=settings["solvation_settings"],
+                smc_components=smc_components,
+                protein_component=protein_component,
+                solvent_component=solvent_component,
+                solvent_offmol=solvent_offmol,
             )
 
         # Get omm objects back

src/pontibus/protocols/solvation/settings.py

@@ -38,6 +38,13 @@
 from pydantic.v1 import validator
 
 
+class ExperimentalAlchemicalSettings(AlchemicalSettings):
+    experimental: bool = False
+    """
+    Turn on experimental alchemy settings
+    """
+
+
 class InterchangeFFSettings(BaseForceFieldSettings):
     """
     Parameters to set up the force field using Interchange and the
@@ -56,7 +63,7 @@ class InterchangeFFSettings(BaseForceFieldSettings):
     ]
     """List of force field ffxmls to apply"""
 
-    nonbonded_method = "PME", "NoCutoff"
+    nonbonded_method: Literal['pme', 'nocutoff'] = "pme"
     """
     Method for treating nonbonded interactions, currently only PME and
     NoCutoff are allowed. Default PME.

src/pontibus/tests/protocols/solvation/test_dry_run.py

@@ -0,0 +1,51 @@
+# This code is part of OpenFE and is licensed under the MIT license.
+# For details, see https://github.com/OpenFreeEnergy/openfe
+import pytest
+from gufe import ChemicalSystem
+from pontibus.protocols.solvation import ASFEProtocol, ASFESolventUnit, ASFEVacuumUnit
+from pontibus.components import ExtendedSolventComponent
+
+
+@pytest.mark.parametrize("method", ["repex", "sams", "independent", "InDePeNdENT"])
+def test_dry_run_vacuum_benzene(benzene_modifications, method, tmpdir):
+    s = ASFEProtocol.default_settings()
+    s.protocol_repeats = 1
+    s.vacuum_simulation_settings.sampler_method = method
+
+    protocol = ASFEProtocol(
+        settings=s,
+    )
+
+    stateA = ChemicalSystem(
+        {
+            "benzene": benzene_modifications["benzene"],
+            "solvent": ExtendedSolventComponent(),
+        }
+    )
+
+    stateB = ChemicalSystem(
+        {
+            "solvent": ExtendedSolventComponent(),
+        }
+    )
+
+    # Create DAG from protocol, get the vacuum and solvent units
+    # and eventually dry run the first vacuum unit
+    dag = protocol.create(
+        stateA=stateA,
+        stateB=stateB,
+        mapping=None,
+    )
+    prot_units = list(dag.protocol_units)
+
+    assert len(prot_units) == 2
+
+    vac_unit = [u for u in prot_units if isinstance(u, ASFEVacuumUnit)]
+    sol_unit = [u for u in prot_units if isinstance(u, ASFESolventUnit)]
+
+    assert len(vac_unit) == 1
+    assert len(sol_unit) == 1
+
+    with tmpdir.as_cwd():
+        vac_sampler = vac_unit[0].run(dry=True)["debug"]["sampler"]
+        assert not vac_sampler.is_periodic