chore(tools): pin protein-prep 11

CONTEXT.md

@@ -147,7 +147,7 @@ Simulation-ready binding and solvation XML files (and metadata) produced by syst
 _Avoid_: "system" alone when meaning the prepared molecular system artifact
 
 **Protein Prep**:
-Platform tool `deeporigin.protein-prep` (v10) that inventories a caller-supplied
+Platform tool `deeporigin.protein-prep` (v11) that inventories a caller-supplied
 protein, records editable keep/review/skip Decisions, then applies resolved
 keep/skip Decisions and protonation (including loop modelling on the served
 path). CLI class `ProteinPrep` is the sole public preparation session: all

docs/dd/ref/protein_prep.md

@@ -1,6 +1,6 @@
 # `deeporigin.drug_discovery.protein_prep`
 
-`ProteinPrep` drives `deeporigin.protein-prep` v10. Recommend inventories
+`ProteinPrep` drives `deeporigin.protein-prep` v11. Recommend inventories
 components, returns a component table (`pandas.DataFrame`), and updates the same
 object with an editable Selection. Prepare applies resolved keep/skip decisions
 and cleans the structure. ``run()`` blocks on served prepare (including loop

docs/dd/tools/proteinprep.md

@@ -9,7 +9,7 @@ structure via `find_pockets` (`"no"`, `"novel"`, or `"from-crystal-ligand"`).
 Selection-defined pockets require the standalone Pocket Finder tool.
 
 Use standalone [`StructureReport`](structure-report.md) for structure assessment
-(source or prepared). Protein Prep v10 does not bundle Structure Reports in tool
+(source or prepared). Protein Prep v11 does not bundle Structure Reports in tool
 outputs.
 
 ## Recommend and review
@@ -88,7 +88,7 @@ prepared = prep.get_results()
 ## Prepare with loop modelling or pockets
 
 Loop modelling is enabled by default. All prepare paths use
-`deeporigin.protein-prep` v10. Blocking `run()` supports served prepare
+`deeporigin.protein-prep` v11. Blocking `run()` supports served prepare
 (including loops on). `find_pockets="novel"` uses the platform workflow path —
 use `start()` (not `run()`):
 

docs/notebooks/clean/protein-prep.ipynb

@@ -74,7 +74,7 @@
    "source": [
     "## Structure Report \n",
     "\n",
-    "Protein Prep v10 does **not** emit `structure_reports[]`. Run `StructureReport` on the source structure when you need an assessment report before or after prepare.\n"
+    "Protein Prep v11 does **not** emit `structure_reports[]`. Run `StructureReport` on the source structure when you need an assessment report before or after prepare.\n"
    ]
   },
   {

src/drug_discovery/protein_prep.py

@@ -1,7 +1,7 @@
 """Recommend settings and prepare a protein with one mutable configuration.
 
 ``ProteinPrep`` is the sole public preparation session. It uses
-``deeporigin.protein-prep`` v10 for :meth:`recommend` and all :meth:`run` /
+``deeporigin.protein-prep`` v11 for :meth:`recommend` and all :meth:`run` /
 :meth:`start` prepare paths. Extracting a ligand also requests one crystal-ligand
 Pocket per extract (``find_pockets=from-crystal-ligand``). Novel pockets use the
 platform workflow path; use :meth:`start` (not blocking :meth:`run`) for those.
@@ -1042,7 +1042,7 @@ class ProteinPrep(
 ):
     """Recommend settings and prepare a protein.
 
-    All operations use ``deeporigin.protein-prep`` (v10). Blocking :meth:`run`
+    All operations use ``deeporigin.protein-prep`` (v11). Blocking :meth:`run`
     supports served prepare including loop modelling. Novel pocket finding uses
     the platform workflow path — use :meth:`start` (with ``quote`` /
     ``approve_amount`` when pockets are billable). Structure reports are not

src/platform/constants.py

@@ -149,7 +149,7 @@ def display_platform_status(status: str | None) -> str:
     },
     "protein_prep": {
         "tool_key": "deeporigin.protein-prep",
-        "tool_version": "10",
+        "tool_version": "11",
     },
     "patent": {
         "tool_key": "deeporigin.draco",

src/utils/constants.py

@@ -170,7 +170,7 @@
     "Prepare requires a registered protein. Call Protein.sync() or assign "
     "protein.id before run() or start()."
 )
-"""Used when prepare is submitted without ``protein.id`` (protein-prep v10)."""
+"""Used when prepare is submitted without ``protein.id`` (protein-prep v11)."""
 
 PROTEIN_PREP_POCKETS_EXCLUDED_MSG = (
     "This ProteinPrep execution did not request pockets. Configure "

tests/test_protein_prep.py

@@ -653,7 +653,7 @@ def test_run_allows_loops_on(
     client: DeepOriginClient,
     registered_protein: Protein,
 ) -> None:
-    """Blocking prepare supports served loop modelling on protein-prep v10."""
+    """Blocking prepare supports served loop modelling on protein-prep v11."""
     prep = ProteinPrep(
         protein=registered_protein,
         selection=_SAMPLE_SELECTION,
@@ -683,7 +683,7 @@ def test_run_rejects_novel_pockets() -> None:
 
 
 def test_prepare_requires_registered_protein_id() -> None:
-    """Prepare rejects unregistered proteins (protein-prep v10 contract)."""
+    """Prepare rejects unregistered proteins (protein-prep v11 contract)."""
     prep = ProteinPrep(
         protein=_protein_with_remote(),
         selection=_SAMPLE_SELECTION,
@@ -1153,7 +1153,7 @@ def test_loops_off_keep_ligand_sets_find_pockets_no() -> None:
 
 
 def test_loops_on_prepare_uses_protein_prep_payload() -> None:
-    """Loops-on prepare stays on protein-prep with explicit v10 fields."""
+    """Loops-on prepare stays on protein-prep with explicit v11 fields."""
     selection = {
         "analyzer_version": "1.0.0",
         "decisions": {"chain:A": "keep"},
@@ -1239,7 +1239,7 @@ def test_loops_on_start_uses_protein_prep_tool_key(
     client: DeepOriginClient,
     registered_protein: Protein,
 ) -> None:
-    """Loops-on start binds to protein-prep v10."""
+    """Loops-on start binds to protein-prep v11."""
     selection = {
         "analyzer_version": "1.0.0",
         "decisions": {"chain:A": "keep"},
@@ -1259,7 +1259,7 @@ def test_loops_on_start_uses_protein_prep_tool_key(
     assert prep.id is not None
     assert prep.name == "Preparing and loop modelling 1EBY"
     assert prep.tool_key == TOOL_KEYS_AND_VERSIONS["protein_prep"]["tool_key"]
-    assert prep.tool_version == "10"
+    assert prep.tool_version == "11"
     prepared = prep.get_results()
     assert isinstance(prepared, Protein)
     with pytest.raises(ValueError, match="did not request pockets"):