chore(tools): pin docking 4, mol-props 2, secondary-pharma 3

CONTEXT.md

@@ -12,7 +12,7 @@ As of tool 0.9.3+, toxicity and metabolism endpoints (hERG, CYP, AMES) moved to
 ``deeporigin.admet-properties``. The CLI class ``Molprops`` mutates dedicated
 :class:`~deeporigin.drug_discovery.structures.ligand.Ligand` attributes in place
 (attrs-only; not ``properties``). Default ``props`` is the full tool input enum.
-Tool version pin is major ``"1"``.
+Tool version pin is major ``"2"``.
 _Avoid_: conflating with ``Admet``; calling it "ADMET" when you mean the
 admet-properties tool; storing molprops results only in ``properties``; local
 RDKit ``@property`` methods named like molprops fields

docs/dd/tutorial/abfe.md

@@ -144,7 +144,6 @@ abfe.params
 
     ```
     ABFEParams(
-      annihilate: True
       dt: 0.004
       temperature: 298.15
       cutoff: 0.9
@@ -178,7 +177,6 @@ Parameters modified from the defaults are indicated with an asterisk:
 
 ```{.python notest}
 ABFEParams(
-  annihilate: True
   dt: 0.004
   temperature: 300 *
   cutoff: 0.9

src/drug_discovery/fep_common.py

@@ -20,7 +20,6 @@ class ABFEParams:
     """FEP calculation parameters for absolute binding free energy (ABFE).
 
     Attributes:
-        annihilate: Whether to annihilate the ligand.
         dt: Time step in ps. Used for both emeq_md_options and prod_md_options.
         temperature: Temperature in K. Used for both emeq_md_options and prod_md_options.
         cutoff: Cutoff distance in nm. Used for both emeq_md_options and prod_md_options.
@@ -37,7 +36,6 @@ class ABFEParams:
         solvation_steps: Number of steps for solvation calculation.
     """
 
-    annihilate: bool = True
     dt: float = 0.004
     temperature: float = 298.15
     cutoff: float = 0.9
@@ -181,7 +179,6 @@ def _simulation_blocks(params: ABFEParams) -> dict[str, dict[str, Any]]:
     }
     return {
         "binding": {
-            "annihilate": params.annihilate,
             "emeq_md_options": md_options,
             "n_windows": params.binding_n_windows,
             "npt_reduce_restraints_ns": params.binding_npt_reduce_restraints_ns,
@@ -193,7 +190,6 @@ def _simulation_blocks(params: ABFEParams) -> dict[str, dict[str, Any]]:
             "test_run": params.test_run,
         },
         "solvation": {
-            "annihilate": params.annihilate,
             "emeq_md_options": md_options,
             "n_windows": params.solvation_n_windows,
             "npt_reduce_restraints_ns": params.solvation_npt_reduce_restraints_ns,
@@ -225,7 +221,6 @@ def _fep_params_from_inputs(
     md_options = binding.get("emeq_md_options", {})
 
     binding_key_map = {
-        "annihilate": "annihilate",
         "n_windows": "binding_n_windows",
         "npt_reduce_restraints_ns": "binding_npt_reduce_restraints_ns",
         "nvt_heating_ns": "binding_nvt_heating_ns",

src/platform/constants.py

@@ -113,7 +113,7 @@ def display_platform_status(status: str | None) -> str:
 TOOL_KEYS_AND_VERSIONS: dict[str, dict[str, str]] = {
     "docking": {
         "tool_key": "deeporigin.docking",
-        "tool_version": "3",
+        "tool_version": "4",
     },
     "constrained_docking": {
         "tool_key": "deeporigin.constrained-docking",
@@ -125,7 +125,7 @@ def display_platform_status(status: str | None) -> str:
     },
     "mol_props": {
         "tool_key": "deeporigin.mol-props-combined",
-        "tool_version": "1",
+        "tool_version": "2",
     },
     "protonation": {
         "tool_key": "deeporigin.mol-props-protonation",
@@ -137,11 +137,11 @@ def display_platform_status(status: str | None) -> str:
     },
     "abfe": {
         "tool_key": "deeporigin.abfe-end-to-end",
-        "tool_version": "latest",
+        "tool_version": "2",
     },
     "rbfe": {
         "tool_key": "deeporigin.rbfe",
-        "tool_version": "latest",
+        "tool_version": "2",
     },
     "sysprep": {
         "tool_key": "deeporigin.system-prep",
@@ -181,6 +181,6 @@ def display_platform_status(status: str | None) -> str:
     },
     "secondary_pharma": {
         "tool_key": "deeporigin.secondary-pharma",
-        "tool_version": "2",
+        "tool_version": "3",
     },
 }

tests/test_abfe.py

@@ -284,7 +284,6 @@ def test_abfe_from_dto_rehydrates_prepared_system_lv0(client: DeepOriginClient):
                 "ligand1_id": "lig-xyz",
             },
             "binding": {
-                "annihilate": True,
                 "emeq_md_options": {"T": 300.0, "cutoff": 1.0, "dt": 0.002},
                 "n_windows": 24,
                 "npt_reduce_restraints_ns": 1.0,
@@ -296,7 +295,6 @@ def test_abfe_from_dto_rehydrates_prepared_system_lv0(client: DeepOriginClient):
                 "test_run": 1,
             },
             "solvation": {
-                "annihilate": False,
                 "emeq_md_options": {"T": 300.0, "cutoff": 1.0, "dt": 0.002},
                 "n_windows": 16,
                 "npt_reduce_restraints_ns": 0.1,

tests/test_fep_common.py

@@ -33,7 +33,6 @@ def test_fep_params_from_inputs_round_trip() -> None:
     """_fep_params_from_inputs restores ABFEParams from stored tool inputs."""
     inputs = {
         "binding": {
-            "annihilate": False,
             "emeq_md_options": {"T": 310.0, "cutoff": 1.1, "dt": 0.003},
             "n_windows": 20,
             "npt_reduce_restraints_ns": 1.5,
@@ -45,7 +44,6 @@ def test_fep_params_from_inputs_round_trip() -> None:
             "test_run": 1,
         },
         "solvation": {
-            "annihilate": False,
             "emeq_md_options": {"T": 310.0, "cutoff": 1.1, "dt": 0.003},
             "n_windows": 10,
             "npt_reduce_restraints_ns": 0.2,

tests/test_rbfe.py

@@ -546,7 +546,6 @@ def test_rbfe_from_dto_rehydrates_rbfe_only_steps(client: DeepOriginClient) -> N
                 }
             ],
             "binding": {
-                "annihilate": True,
                 "emeq_md_options": {"T": 310.0, "cutoff": 1.0, "dt": 0.002},
                 "n_windows": 12,
                 "npt_reduce_restraints_ns": 1.0,
@@ -558,7 +557,6 @@ def test_rbfe_from_dto_rehydrates_rbfe_only_steps(client: DeepOriginClient) -> N
                 "test_run": 0,
             },
             "solvation": {
-                "annihilate": True,
                 "emeq_md_options": {"T": 310.0, "cutoff": 1.0, "dt": 0.002},
                 "n_windows": 8,
                 "npt_reduce_restraints_ns": 0.1,

tests/test_secondary_pharma.py

@@ -91,7 +91,7 @@ def test_secondary_pharma_construct_copies_definition_enum(
     job = SecondaryPharmacology(ligands=[ligand], method="docking", client=client)
 
     assert _definition_enum(client) == _PANEL_ACCESSIONS
-    assert job.tool_version == "2"
+    assert job.tool_version == "3"
     assert job.method == "docking"
     assert job.uniprots is None