[WIP] SepTop Protocol

openfe/protocols/openmm_rfe/equil_rfe_methods.py

@@ -702,7 +702,7 @@ def run(self, *, dry=False, verbose=True,
         # Extract relevant settings
         protocol_settings: RelativeHybridTopologyProtocolSettings = self._inputs['protocol'].settings
         stateA = self._inputs['stateA']
-        stateB = self._inputs['stateB']
+        stateB = self._inputs['stateB']  # TODO: open an issue about this not being used.
         mapping = self._inputs['ligandmapping']
 
         forcefield_settings: settings.OpenMMSystemGeneratorFFSettings = protocol_settings.forcefield_settings

openfe/protocols/openmm_septop/__init__.py

@@ -0,0 +1,24 @@
+# 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,
+    SepTopSolventRunUnit,
+    SepTopComplexRunUnit,
+)
+
+__all__ = [
+    "SepTopProtocol",
+    "SepTopSettings",
+    "SepTopProtocolResult",
+    "SepTopComplexSetupUnit",
+    "SepTopSolventSetupUnit",
+]