[WIP] SepTop Protocol

openfe/protocols/openmm_md/plain_md_methods.py

@@ -431,26 +431,29 @@ def _run_MD(simulation: openmm.app.Simulation,
             mc_steps=1,
         )
 
-        simulation.reporters.append(XTCReporter(
-            file=str(shared_basepath / output_settings.production_trajectory_filename),
-            reportInterval=write_interval,
-            atomSubset=selection_indices))
-        simulation.reporters.append(openmm.app.CheckpointReporter(
-            file=str(shared_basepath / output_settings.checkpoint_storage_filename),
-            reportInterval=checkpoint_interval))
-        simulation.reporters.append(openmm.app.StateDataReporter(
-            str(shared_basepath / output_settings.log_output),
-            checkpoint_interval,
-            step=True,
-            time=True,
-            potentialEnergy=True,
-            kineticEnergy=True,
-            totalEnergy=True,
-            temperature=True,
-            volume=True,
-            density=True,
-            speed=True,
-        ))
+        if output_settings.production_trajectory_filename:
+            simulation.reporters.append(XTCReporter(
+                file=str(shared_basepath / output_settings.production_trajectory_filename),
+                reportInterval=write_interval,
+                atomSubset=selection_indices))
+        if output_settings.checkpoint_storage_filename:
+            simulation.reporters.append(openmm.app.CheckpointReporter(
+                file=str(shared_basepath / output_settings.checkpoint_storage_filename),
+                reportInterval=checkpoint_interval))
+        if output_settings.log_output:
+            simulation.reporters.append(openmm.app.StateDataReporter(
+                str(shared_basepath / output_settings.log_output),
+                checkpoint_interval,
+                step=True,
+                time=True,
+                potentialEnergy=True,
+                kineticEnergy=True,
+                totalEnergy=True,
+                temperature=True,
+                volume=True,
+                density=True,
+                speed=True,
+            ))
         t0 = time.time()
         simulation.step(prod_steps)
         t1 = time.time()

openfe/protocols/openmm_septop/__init__.py

@@ -0,0 +1,22 @@
+# This code is part of OpenFE and is licensed under the MIT license.
+# For details, see https://github.com/OpenFreeEnergy/openfe
+"""
+Run SepTop free energy calculations using OpenMM and OpenMMTools.
+
+"""
+
+from .equil_septop_method import (
+    SepTopProtocol,
+    SepTopSettings,
+    SepTopProtocolResult,
+    SepTopComplexSetupUnit,
+    SepTopSolventSetupUnit,
+)
+
+__all__ = [
+    "SepTopProtocol",
+    "SepTopSettings",
+    "SepTopProtocolResult",
+    "SepTopComplexSetupUnit",
+    "SepTopSolventSetupUnit",
+]