Asfe freesolv

devtools/conda-envs/environment.yml

@@ -3,8 +3,9 @@ channels:
   - conda-forge
 dependencies:
   - gufe
-  - openfe<1.9
+  - openfe<1.9 # From alchemiscale stack dependence?
   - pytest
   - 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/results/2026-08_05-openff3.0.0-alpha0_opc3-jacs/submission.yaml

@@ -17,6 +17,9 @@ summary: |
 # REQUIRED: list of submission tags
 tags: [rbfe, opc3.offxml, openff-3.0.0-alpha0, 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:
   - name: Jennifer A. Clark

openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha1b_tip3p-jacs/submission.yaml

@@ -17,6 +17,9 @@ summary: |
 # REQUIRED: list of submission tags
 tags: [rbfe, openff-3.0.0-alpha1b, tip3p.offxml, 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:
   - name: Jennifer A. Clark

openfe_benchmarks/results/2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin/submission.yaml

@@ -17,6 +17,9 @@ summary: |
 # REQUIRED: list of submission tags
 tags: [rbfe, ff14SB, lipid17_merged, phosaa10, tip3p_HFE_multivalent, tip3p_standard, openff-3.0.0-alpha1b, jacs_set, 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:
   - name: Jennifer A. Clark

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 +1,63 @@
+"""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)
+
+    if not results_path.exists():
+        raise FileNotFoundError(f"Could not find results file: {results_path}")
+
+    open_func = bz2.open if "bz2" in results_file else open
+
+    with open_func(results_path, "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)
+    dg_records = results.get("dg")
+    if not isinstance(dg_records, list):
+        raise ValueError(
+            f"Results file {RESULTS_FILE} does not contain a valid 'dg' list, cannot plot"
+        )
+
+    # build FEMaps and load with experimental data
+    femaps_by_system = build_femap_from_absolute_results(results=dg_records)
+
+    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"