Merge branch 'main' into start_septop

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/restraint_utils/geometry/__init__.py

@@ -0,0 +1,4 @@
+from .base import BaseRestraintGeometry
+from .harmonic import DistanceRestraintGeometry
+from .flatbottom import FlatBottomDistanceGeometry
+from .boresch import BoreschRestraintGeometry

openfe/protocols/restraint_utils/geometry/base.py

@@ -0,0 +1,48 @@
+# This code is part of OpenFE and is licensed under the MIT license.
+# For details, see https://github.com/OpenFreeEnergy/openfe
+"""
+Restraint Geometry classes
+
+TODO
+----
+* Add relevant duecredit entries.
+"""
+import abc
+from pydantic.v1 import BaseModel, validator
+
+
+class BaseRestraintGeometry(BaseModel, abc.ABC):
+    """
+    A base class for a restraint geometry.
+    """
+    class Config:
+        arbitrary_types_allowed = True
+
+
+class HostGuestRestraintGeometry(BaseRestraintGeometry):
+    """
+    An ordered list of guest atoms to restrain.
+
+    Note
+    ----
+    The order matters! It will be used to define the underlying
+    force.
+    """
+
+    guest_atoms: list[int]
+    """
+    An ordered list of host atoms to restrain.
+
+    Note
+    ----
+    The order matters! It will be used to define the underlying
+    force.
+    """
+    host_atoms: list[int]
+
+    @validator("guest_atoms", "host_atoms")
+    def positive_idxs(cls, v):
+        if v is not None and any([i < 0 for i in v]):
+            errmsg = "negative indices passed"
+            raise ValueError(errmsg)
+        return v