Asfe freesolv

devtools/conda-envs/environment.yml

@@ -1,4 +1,4 @@
-name: openfe-benchmarks-test
+name: openfe-benchmarks-test2
 channels:
   - conda-forge
 dependencies:
@@ -8,3 +8,4 @@ dependencies:
   - pre-commit
   - pontibus==0.4.0
   - pint
+#  - cinnabar >= 0.6.1

openfe_benchmarks/results/2026-02-12_sage_230_jacs/submission.yaml

@@ -14,6 +14,9 @@ summary: |
 # REQUIRED: list of submission tags
 tags: [rbfe, ff14SB, phosaa10, tip3p_HFE_multivalent, tip3p_standard, openff-2.3.0, bace, cdk2, jacs_set, jnk1, mcl1, p38, ptp1b, thrombin, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, openfe, alchemicalarchive]
 
+# REQUIRED: calculation type (asfe, rbfe, etc.)
+calculation_type: rbfe
+
 # REQUIRED: list of contributing authors (name, affiliation; ORCID optional)
 authors:
   - name: Josh Horton

openfe_benchmarks/results/2026-03-18-openmm-840-qa-testing/submission.yaml

@@ -17,6 +17,9 @@ summary: |
 # REQUIRED: list of submission tags
 tags: [rbfe, ff14SB, phosaa10, tip3p_HFE_multivalent, tip3p_standard, charge_annihilation_set, egfr, irak4_s2, irak4_s3, jacs_set, p38, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, charge_change, benchmark, openfe, openmm-840]
 
+# REQUIRED: calculation type (asfe, rbfe, etc.)
+calculation_type: rbfe
+
 # REQUIRED: list of contributing authors (name, affiliation; ORCID optional)
 authors:
   - name: Josh Horton

openfe_benchmarks/results/2026-06-22-tyk2-alchemicalarchive-test/submission.yaml

@@ -16,7 +16,10 @@ summary: |
   resources/submissions/2026_03_17_openff-2.3.0_jacs_tyk2/alchemiscale_submission.ipynb
 
 # REQUIRED: list of submission tags
-tags: [rbfe, ff14SB, phosaa10, tip3p_HFE_multivalent, tip3p_standard, openff-2.3.0, jacs_set, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, benchmark, openfe]
+tags: [rbfe, alchemicalarchive, ff14SB, phosaa10, tip3p_HFE_multivalent, tip3p_standard, openff-2.3.0, jacs_set, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, benchmark, openfe]
+
+# REQUIRED: calculation type (asfe, rbfe, etc.)
+calculation_type: rbfe
 
 # REQUIRED: list of contributing authors (name, affiliation; ORCID optional)
 authors:

openfe_benchmarks/results/2026-08-06-openff-2.3.0-solvation_set_freesolv/submission.yaml

@@ -0,0 +1,73 @@
+# REQUIRED: unique, kebab-case identifier for this submission
+submission_id: 2026-08-06-openff-2.3.0-solvation_set_freesolv
+
+# REQUIRED: short descriptive title
+title: OpenFE ASFE - solvation_set - freesolv - 2026-08-06-openff-2.3.0-solvation_set_freesolv
+
+# REQUIRED: short descriptive summary (1-2 sentences)
+summary: |
+  This submission describes the ASFE benchmark covering the solvation_set benchmark set (freesolv)
+  prepared with openff-2.3.0/tip3p for solvents and nagl_openff-gnn-am1bcc-1.0.0.pt for solutes and
+  cofactors. The archive contains 603 edges across 603 unique solutes and 1 unique solvents. Results
+  are derived from archived Alchemiscale workflow data. This is the full freesolv set that is
+  parametrizable by OpenFF-2.3.0, submitted before the development of OpenFF subsets.
+
+# REQUIRED: list of submission tags
+tags: [alchemicalarchive, asfe, freesolv, nagl_openff-gnn-am1bcc-1.0.0.pt, openff-2.3.0, pontibus, solvation_set, tip3p]
+
+# REQUIRED: calculation type (asfe, rbfe, etc.)
+calculation_type: asfe
+
+# REQUIRED: list of contributing authors (name, affiliation; ORCID optional)
+authors:
+  - name: Jennifer A Clark
+
+# REQUIRED: publication/submission date (ISO 8601)
+date: 2026-08-06
+openfe_version: "1.8.0"
+openmm_version: "8.2.0"
+openff_toolkit_version: "0.18"
+
+forcefield: ["openff-2.3.0", "tip3p"]
+
+partial_charges: "nagl_openff-gnn-am1bcc-1.0.0.pt"
+
+## BenchmarkData Provenance (from openfe-benchmarks planning script) with associated network key 
+benchmark_data:
+  source_repository: https://github.com/OpenFreeEnergy/openfe-benchmarks
+  "solvation_set":
+    "freesolv": AlchemicalNetwork-55961080ba1805b112aff83fca84b15f
+
+
+# REQUIRED: results file
+results: computational_results.json.bz2
+
+# REQUIRED: long-term archive pointer (at least doi or url)
+archive:
+  doi: 10.5281/zenodo.21810272
+  archive_provider: zenodo
+
+# REQUIRED: license for the submission
+license: CC-BY-4.0
+
+# RECOMMENDED / OPTIONAL metadata for protocol settings
+protocol_settings:
+  - protocol: "ASFEProtocol"
+    protocol_library: "pontibus"
+    timestep: "4.0 fs"
+    temperature: "298.15 K"
+    pressure: "1 bar"
+    forcefields: ["openff-2.3.0", "tip3p"]
+    small_molecule_forcefield: ""
+    partial_charges: "nagl_openff-gnn-am1bcc-1.0.0.pt"
+    equilibration_time: 
+    production_time: 
+    vacuum_equilibration_time: "500.00000000000006 ps"
+    vacuum_production_time: "2.0 ns"
+    solvent_equilibration_time: "1.0 ns"
+    solvent_production_time: "10.0 ns"
+    lambda_functions: ""
+    lambda_windows: ""
+    lambda_schedule: ""
+    notes: "Applies to all edges"
+

openfe_benchmarks/results/2026-08_04-openff3.0.0-alpha1b_opc3-jacs/submission.yaml

@@ -15,7 +15,10 @@ summary: |
   resources/submissions/2026_07_15_openff-3.0.0-alpha1b_opc3/alchemiscale_submission.ipynb
 
 # REQUIRED: list of submission tags
-tags: [rbfe, opc3.offxml, openff-3.0.0-alpha1b, bace, cdk2, jacs_set, jnk1, mcl1, p38, ptp1b, thrombin, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, benchmark, openfe]
+tags: [rbfe, "alchemicalarchive", opc3.offxml, openff-3.0.0-alpha1b, bace, cdk2, jacs_set, jnk1, mcl1, p38, ptp1b, thrombin, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, benchmark, openfe]
+
+# REQUIRED: calculation type (asfe, rbfe, etc.)
+calculation_type: rbfe
 
 # REQUIRED: list of contributing authors (name, affiliation; ORCID optional)
 authors:

openfe_benchmarks/scripts/_no_test_example_mutlinetwork_rbfe_submission.py

@@ -24,42 +24,12 @@
     [
         "jacs_set",
         "bace",
-        "AlchemicalNetwork-58ef1baba714145eaddb8f81abf609ce-openff-openff_3_0_0_alpha1b_opc3-rbfe_pontibus_jacs_set_bace",
+        "AlchemicalNetwork-your-key",
     ],
     [
         "jacs_set",
         "cdk2",
-        "AlchemicalNetwork-8b3e6b25fe046924998a1f520c798b19-openff-openff_3_0_0_alpha1b_opc3-rbfe_pontibus_jacs_set_cdk2",
-    ],
-    [
-        "jacs_set",
-        "jnk1",
-        "AlchemicalNetwork-6cea205bc124349b8add8824e2060147-openff-openff_3_0_0_alpha1b_opc3-rbfe_pontibus_jacs_set_jnk1",
-    ],
-    [
-        "jacs_set",
-        "mcl1",
-        "AlchemicalNetwork-ee5422ba932ced782b51da9bb9eb24ff-openff-openff_3_0_0_alpha1b_opc3-rbfe_pontibus_jacs_set_mcl1",
-    ],
-    [
-        "jacs_set",
-        "p38",
-        "AlchemicalNetwork-c613a533bdaa47f92e9a1cf4d58fe6dd-openff-openff_3_0_0_alpha1b_opc3-rbfe_pontibus_jacs_set_p38",
-    ],
-    [
-        "jacs_set",
-        "ptp1b",
-        "AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2-openff-openff_3_0_0_alpha1b_opc3-rbfe_pontibus_jacs_set_ptp1b",
-    ],
-    [
-        "jacs_set",
-        "thrombin",
-        "AlchemicalNetwork-7fcf1d4cb0a6af702747de83fc23af69-openff-openff_3_0_0_alpha1b_opc3-rbfe_pontibus_jacs_set_thrombin",
-    ],
-    [
-        "jacs_set",
-        "tyk2",
-        "AlchemicalNetwork-51caad3a5d3daea240406eb23fa6dad6-openff-openff_3_0_0_alpha1b_opc3-rbfe_pontibus_jacs_set_tyk2",
+        "AlchemicalNetwork-your-key",
     ],
 )
 OUTPUT_DIR = "output"
@@ -71,7 +41,7 @@
     "For scripts to generate this network: "
     "github.com/openforcefield/alchemical-benchmark-resources/submissions/2026_07_15_openff-3.0.0-alpha1b_opc3/alchemiscale_submission.ipynb"
 )
-TAGS = "rbfe,benchmark,openfe"
+TAGS = ""
 SMALL_MOL_FF = "openff-3.0.0-alpha1b"
 WATER_MODEL = "opc3.offxml"
 OPENFE_VER = "1.8.0"

openfe_benchmarks/scripts/_no_test_example_plot_asfe.py

@@ -0,0 +1,72 @@
+"""Plot ASFEs, only for cinnabar >= 0.6.1, which is not compatible with current env"""
+
+import pathlib
+import json
+import bz2
+
+from gufe.tokenization import JSON_HANDLER
+from cinnabar import plotting
+
+from openfe_benchmarks.scripts._results_utils import build_femap_from_absolute_results
+
+RESULTS_FILE = "../results/2026-08-06-openff-2.3.0-solvation_set_freesolv/computational_results.json.bz2"
+OUTPUT_DIR = "outputs"
+
+
+def _load_results(results_file: str) -> dict:
+    results_path = pathlib.Path(results_file)
+    compressed_path = results_path.with_name(results_path.name + ".bz2")
+
+    if results_path.suffix == ".bz2":
+        open_func = bz2.open
+        path_to_open = results_path
+    elif compressed_path.exists():
+        open_func = bz2.open
+        path_to_open = compressed_path
+    elif results_path.exists():
+        open_func = open
+        path_to_open = results_path
+    else:
+        raise FileNotFoundError(
+            f"Could not find results file: {results_path} or {compressed_path}"
+        )
+
+    with open_func(path_to_open, "rt") as handle:
+        return json.load(handle, cls=JSON_HANDLER.decoder)
+
+
+def main():
+    """
+    An example script which can load the calculated DG values from ASFE calculations and plot vs experimental solvation data.
+
+    This script creates plots comparing the computed absolute solvation free energies (DG)
+    to experimental values for each benchmark system.
+    """
+
+    # load the results file, whether compressed or not
+    results = _load_results(RESULTS_FILE)
+    if "dg" not in results:
+        raise ValueError(
+            f"Results file {RESULTS_FILE} does not contain 'dg' values, cannot plot"
+        )
+
+    # build FEMaps and load with experimental data
+    femaps_by_system = build_femap_from_absolute_results(results=results["dg"])
+
+    output_dir = pathlib.Path(OUTPUT_DIR)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # for each system plot the ASFE results compared to experimental data
+    for (system_group, system_name), femap in femaps_by_system.items():
+        plotting.plot_DGs(
+            femap,
+            source="Computational",
+            title=f"{system_group}-{system_name}",
+            figsize=5,
+            scatter_kwargs={"s": 20, "marker": "o"},
+            filename=(output_dir / f"{system_group}_{system_name}_DG.png").as_posix(),
+        )
+
+
+if __name__ == "__main__":
+    main()

openfe_benchmarks/scripts/_no_test_example_rbfe_submission.py → openfe_benchmarks/scripts/_no_test_example_rbfe_asfe_submission.py

@@ -5,6 +5,8 @@
 1. Pull alchemical network from Alchemiscale
 2. Generate computational results
 3. Generate submission metadata
+
+Also works for ASFEs
 """
 
 import logging
@@ -32,7 +34,7 @@
     " and provide an indication of the variability in results. For scripts to generate this network: "
     "github.com/openforcefield/alchemical-benchmark-resources/submissions/2026_03_17_openff-2.3.0_jacs_tyk2/alchemiscale_submission.ipynb"
 )
-TAGS = "rbfe,benchmark,openfe"
+TAGS = ""
 OPENFE_VER = "1.8.0"
 OPENMM_VER = "8.2.0"
 OFFTOOL_VER = "0.18"

openfe_benchmarks/scripts/_results_utils.py

@@ -79,9 +79,100 @@ def build_femap_from_relative_results(
                     label=ligand,
                     value=exp_data["dg"],
                     uncertainty=exp_data.get(
-                        "uncertainty", 0 * unit.kilocalorie_per_mole
+                        "uncertainty", 0 * unit.kilocalories_per_mole
                     ),
                 )
 
         femaps_by_system_key[system_key] = femap
     return femaps_by_system_key
+
+
+def build_femap_from_absolute_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 absolute solvation results
+    and add experimental solvation free energy data.
+
+    Parameters
+    ----------
+    results: list[dict]
+        A list of absolute solvation free energy estimates which should include at least the following entries:
+         - solute: str
+         - system_group: str
+         - system_name: str
+         - dg: Quantity
+         - dg_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 solvation free energy 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 = {}
+    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)
+
+        # Check if all solutes have valid dg_uncertainty (not NaN)
+        solutes_no_uncertainty = [
+            result["solute"]
+            for result in system_results
+            if np.isnan(
+                result["dg_uncertainty"].magnitude
+                if "dg" in result
+                else result["estimate_error"].magnitude
+            )
+        ]
+        if solutes_no_uncertainty:
+            raise ValueError(
+                f"Not all solutes have dg_uncertainty for {system_group} {system_name}: {solutes_no_uncertainty}"
+            )
+
+        femap = FEMap()
+        for result in system_results:
+            value_key = "dg" if "dg" in result else "estimate"
+            err_key = "dg_uncertainty" if value_key == "dg" else "estimate_error"
+            label = f"{result['solute']},{result['solvent']}"
+            femap.add_absolute_calculation(
+                label=label,
+                value=result[value_key],
+                uncertainty=result[err_key],
+                source="Computational",
+            )
+
+        # add experimental solvation data for each of the solutes in the results
+        experimental_file = benchmark_data.reference_data[
+            "experimental_solvation_free_energy_data"
+        ]
+        experimental_data = json.load(open(experimental_file), cls=JSON_HANDLER.decoder)
+        n_experimental_points = 0
+        for result in system_results:
+            label = f"{result['solute']},{result['solvent']}"
+            exp_data = experimental_data.get(label, None)
+            if exp_data is not None:
+                femap.add_experimental_measurement(
+                    label=label,
+                    value=exp_data["dg"],
+                    uncertainty=exp_data.get(
+                        "uncertainty", 0 * unit.kilocalories_per_mole
+                    ),
+                )
+                n_experimental_points += 1
+        if n_experimental_points == 0:
+            raise ValueError("No experimental data points where found")
+        else:
+            print(
+                f"Of the {len(system_results)}, {n_experimental_points} has corresponding exp. data."
+            )
+
+        femaps_by_system_key[system_key] = femap
+
+    return femaps_by_system_key