Add results from the openmm840 qa

devtools/conda-envs/environment.yml

@@ -7,3 +7,4 @@ dependencies:
   - pytest
   - pre-commit
   - pontibus==0.4.0
+  - pint

openfe_benchmarks/data/_benchmark_systems.py

@@ -75,7 +75,7 @@ def reload(self):
 
         logger.debug("Benchmark index successfully reloaded and validated.")
 
-    def list_systems_by_tag(self, tags: list[str]) -> list[tuple[str, str]]:
+    def list_systems_by_tag(self, tags: list[str] = []) -> list[tuple[str, str]]:
         """
         Get all systems that match **all** of the provided tags.
 
@@ -84,6 +84,7 @@ def list_systems_by_tag(self, tags: list[str]) -> list[tuple[str, str]]:
         tags : list[str]
             List of tags to filter by (e.g., ['protein', 'cofactors']).
             Only systems containing every tag in this list will be returned.
+            Defaults to ``[]``.
 
         Returns
         -------

openfe_benchmarks/data/_results_utils.py

@@ -0,0 +1,69 @@
+from cinnabar import FEMap
+from openfe_benchmarks.data._benchmark_systems import get_benchmark_data_system
+from collections import defaultdict
+import json
+from gufe.tokenization import JSON_HANDLER
+from openff.units import unit
+
+def build_femap_from_relative_results(results: list[dict]) -> dict[tuple[str, str], FEMap]:
+    """
+    Build FEMaps for each of the unique combinations of system_group and system_name in the DDG results and add experimental data
+    for each of the ligands present in the DDG results.
+
+    Parameters
+    ----------
+    results: list[dict]
+        A list of relative binding free energy estimates which should include at least the following entries:
+         - ligand_a: str
+         - ligand_b: str
+         - system_group: str
+         - system_name: str
+         - ddg: Quantity
+         - ddg_uncertainty: Quantity
+
+    Returns
+    -------
+    dict[tuple[str, str], FEMap]
+        A dictionary mapping each unique combination of system_group and system_name to an FEMap with calculated and experimental reference data.
+    """
+    # get the unique combinations of system_group and system_name
+    results_by_system_key = defaultdict(list)
+    for result in results:
+        key = (result["system_group"], result["system_name"])
+        results_by_system_key[key].append(result)
+
+    femaps_by_system_key = {}
+    unique_ligands = set()
+    for system_key, system_results in results_by_system_key.items():
+        system_group, system_name = system_key
+        benchmark_data = get_benchmark_data_system(system_group, system_name)
+        femap = FEMap()
+        for result in system_results:
+            ligand_a = result["ligand_a"]
+            ligand_b = result["ligand_b"]
+            # record the ligands added to the femap
+            unique_ligands.update([ligand_a, ligand_b])
+            ddg = result["ddg"]
+            ddg_uncertainty = result["ddg_uncertainty"]
+            femap.add_relative_calculation(
+                labelA=ligand_a,
+                labelB=ligand_b,
+                value=ddg,
+                uncertainty=ddg_uncertainty,
+            )
+
+        # add experimental data for each of the ligands in the results
+        experimental_file = benchmark_data.reference_data["experimental_binding_data"]
+        experimental_data = json.load(open(experimental_file), cls=JSON_HANDLER.decoder)
+
+        for ligand in unique_ligands:
+            exp_data = experimental_data.get(ligand, None)
+            if exp_data is not None:
+                femap.add_experimental_measurement(
+                    label=ligand,
+                    value=exp_data["dg"],
+                    uncertainty=exp_data.get("uncertainty", 0 * unit.kilocalorie_per_mole),
+                )
+
+        femaps_by_system_key[system_key] = femap
+    return femaps_by_system_key