Move ligand utils to gufe

news/deprecate_alchemical_charge_diff.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated ``openfe.utils.ligand_utils.get_alchemical_charge_difference()``, which is replaced by ``LigandAtomMapping.get_alchemical_charge_difference()`` in ``gufe`` (PR #1479).
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

openfe/protocols/openmm_rfe/equil_rfe_methods.py

@@ -133,14 +133,8 @@ def _get_alchemical_charge_difference(
       The formal charge difference between states A and B.
       This is defined as sum(charge state A) - sum(charge state B)
     """
-    chg_A = Chem.rdmolops.GetFormalCharge(
-        mapping.componentA.to_rdkit()
-    )
-    chg_B = Chem.rdmolops.GetFormalCharge(
-        mapping.componentB.to_rdkit()
-    )
-
-    difference = chg_A - chg_B
+
+    difference = mapping.get_alchemical_charge_difference()
 
     if abs(difference) > 0:
         if explicit_charge_correction:

openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py

@@ -34,7 +34,6 @@
     RFEComponentLabels,
 )
 from ...protocols.openmm_rfe.equil_rfe_methods import RelativeHybridTopologyProtocol
-from ...utils.ligand_utils import get_alchemical_charge_difference
 
 # TODO: move/or find better structure for protocol_generator combinations!
 PROTOCOL_GENERATOR = {
@@ -331,7 +330,7 @@ def _build_transformation(
         protocol_settings = transformation_protocol.settings.unfrozen_copy()
         if "vacuum" in transformation_name:
             protocol_settings.forcefield_settings.nonbonded_method = "nocutoff"
-        elif get_alchemical_charge_difference(ligand_mapping_edge) != 0:
+        elif ligand_mapping_edge.get_alchemical_charge_difference() != 0:
             wmsg = ("Charge changing transformation between ligands "
                     f"{ligand_mapping_edge.componentA.name} and {ligand_mapping_edge.componentB.name}. "
                     "A more expensive protocol with 22 lambda windows, sampled "

openfe/tests/setup/atom_mapping/test_atommapper.py

@@ -1,7 +1,7 @@
 import pytest
 
 from openfe.setup.atom_mapping.ligandatommapper import LigandAtomMapper
-
+from openfe.utils import ligand_utils
 
 class TestAtomMapper:
     def test_abstract_error(self, simple_mapping):
@@ -42,3 +42,8 @@ def _mappings_generator(self, componentA, componentB):
         results = list(mapper.suggest_mappings(molA, molB))
         assert len(results) == 2
         assert results == [simple_mapping, other_mapping]
+
+
+    def test_alchemical_charge_deprecation_warning(self, simple_mapping):
+        with pytest.warns(DeprecationWarning, match=r"Use gufe\.LigandAtomMapping"):
+            ligand_utils.get_alchemical_charge_difference(simple_mapping)

openfe/utils/ligand_utils.py

@@ -1,4 +1,5 @@
 from gufe import LigandAtomMapping
+import warnings
 
 def get_alchemical_charge_difference(mapping: LigandAtomMapping) -> int:
     """
@@ -14,7 +15,5 @@ def get_alchemical_charge_difference(mapping: LigandAtomMapping) -> int:
     int:
         The difference in formal charge between the end states.
     """
-    from rdkit import Chem
-    charge_a = Chem.rdmolops.GetFormalCharge(mapping.componentA.to_rdkit())
-    charge_b = Chem.rdmolops.GetFormalCharge(mapping.componentB.to_rdkit())
-    return charge_a - charge_b
+    warnings.warn("Use gufe.LigandAtomMapping.get_alchemical_charge_difference() instead.", DeprecationWarning)
+    return mapping.get_alchemical_charge_difference()