rowan-python 3.2.1__tar.gz → 3.2.2__tar.gz

{rowan_python-3.2.1 → rowan_python-3.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: rowan-python
-Version: 3.2.1
+Version: 3.2.2
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
@@ -12,7 +12,7 @@ Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.275
+Requires-Dist: stjames>=0.0.281
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.2.1 → rowan_python-3.2.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.2.1"
+version = "3.2.2"
 description = "Rowan Python Library"
 readme = "README.md"
 license = "MIT"
@@ -12,7 +12,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
-    "stjames>=0.0.275",
+    "stjames>=0.0.281",
     "setuptools",
     "rdkit",
     "nest-asyncio",

{rowan_python-3.2.1 → rowan_python-3.2.2}/rowan/__init__.py

@@ -67,6 +67,7 @@ from stjames.engine_compatibility import (
     METHOD_ENGINES,
     get_supported_corrections,
 )
+from stjames.pdb import ResidueRef
 from stjames.optimization.band_method import NEBSettings
 from stjames.optimization.interpolation import Interpolation
 from stjames.optimization.string_method import FSMSettings, StringMethodSettings

{rowan_python-3.2.1 → rowan_python-3.2.2}/rowan/project.py

@@ -197,8 +197,15 @@ def default_project() -> Project:
 
     Raises:
         httpx.HTTPStatusError: API request fails
+        ValueError: user has no default project in the API key's organization
     """
     with api_client() as client:
         response = client.get("/user/me/default_project")
         response.raise_for_status()
-        return Project(**response.json())
+        project = response.json()
+    if project is None:
+        raise ValueError(
+            "You have no default project in this organization. "
+            "Set a default project, or pass a folder or project."
+        )
+    return Project(**project)

{rowan_python-3.2.1 → rowan_python-3.2.2}/rowan/workflows/binding_affinity.py

@@ -153,9 +153,15 @@ def submit_binding_affinity_workflow(
         binding_affinity_settings=binding_affinity_settings or SinglePointEnergySettings(),
     )
 
+    workflow_data = workflow.model_dump(serialize_as_any=True, mode="json")
+    if isinstance(workflow.binding_affinity_settings, SinglePointEnergySettings):
+        workflow_data["binding_affinity_settings"]["truncation_radius"] = (
+            workflow.binding_affinity_settings.truncation_radius
+        )
+
     data = {
         "workflow_type": "binding_affinity",
-        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
+        "workflow_data": workflow_data,
         "name": name,
         "folder_uuid": folder_uuid,
         "max_credits": max_credits,

{rowan_python-3.2.1 → rowan_python-3.2.2}/rowan/workflows/protein_md.py

@@ -149,7 +149,7 @@ def submit_protein_md_workflow(
     binder: Binder | None = None,
     protein_restraint_cutoff: float | None = None,
     protein_restraint_constant: float = 100,
-    analysis_interval_ps: float | None = None,
+    analysis_interval_ps: float | None = 100,
     clustering: KMeansClusteringSettings | GreedyClusteringSettings | None = None,
     validate_forcefield: bool = True,
     name: str = "Protein MD Workflow",
@@ -194,8 +194,8 @@ def submit_protein_md_workflow(
         protein_restraint_cutoff: cutoff distance from the binder past which Cα atoms are
             harmonically restrained, in Å; None disables restraints
         protein_restraint_constant: force constant for Cα backbone restraints, in kcal/mol/Ų
-        analysis_interval_ps: interval at which to compute per-frame SASA and polar SASA, in ps.
-            None disables those analyses
+        analysis_interval_ps: interval at which to compute per-frame SASA and polar SASA
+            (default 100), in ps. None disables those analyses
         clustering: how to cluster trajectory frames. None disables clustering; pass a
             KMeansClusteringSettings (num_clusters) or GreedyClusteringSettings (cutoff_angstrom)
         validate_forcefield: validate the protein forcefield

{rowan_python-3.2.1 → rowan_python-3.2.2}/skills/computational-chemistry-and-biology/reference/binding_affinity.md

@@ -57,9 +57,19 @@ for name, score in zip(ligands.keys(), result.scores):
 
 - `rowan.SinglePointEnergySettings` (default):
   - `multistage_opt_settings` (default PM6-D3H4X/COSMO optimization + PM6-D3H4X/COSMO2 single-point in water): a `rowan.MultiStageOptSettings` controlling ligand geometry optimization and energy evaluation.
-  - `truncation_radius` (default `6.0` Å): protein residues beyond this distance from the ligand are excluded from the calculation.
+  - `truncation_radius` (default `6.0` Å): selects whole protein residues with any atom within this distance of any submitted ligand atom.
+  - `truncation_residues`: nonempty list of `rowan.ResidueRef` objects identifying polymer residues by chain and residue keys in the submitted protein. Requires `truncation_radius=None`; a radius and explicit residues cannot be supplied together.
 - `rowan.GninaAffinitySettings`, `rowan.AEVPLIGAffinitySettings`, `rowan.NessoAffinitySettings`: no tunable parameters.
 
+For an explicit pocket, pass settings like these, using keys from your protein:
+
+```python
+rowan.SinglePointEnergySettings(
+    truncation_radius=None,
+    truncation_residues=[rowan.ResidueRef("polymer", "A", "A.182")],
+)
+```
+
 ```python
 # Replace the path, residue name, and SMILES with those of your holo complex.
 holo_protein = rowan.upload_protein("Holo complex", "PATH_TO_HOLO_PDB")

{rowan_python-3.2.1 → rowan_python-3.2.2}/skills/computational-chemistry-and-biology/reference/protein_md.md

@@ -61,7 +61,7 @@ result.download_trajectories([0], path=".")  # save DCD trajectory files
 - `binder` (default `None`): a `rowan.Binder` specifying the binder within the complex — protein/peptide chains (`chain_ids`), small molecules (`small_molecule_residues`, identified by residue-name string or 0-based non-polymer residue index), or both. Enables per-frame MM/GBSA and binder RMSD analyses (see result fields).
 - `protein_restraint_cutoff` (default `None`): distance from the binder past which Cα atoms are harmonically restrained, in angstrom; `None` disables restraints. Useful for keeping the binding site mobile while stabilizing the rest of the protein.
 - `protein_restraint_constant` (default `100`): force constant for the Cα backbone restraints, in kcal/mol/Ų.
-- `analysis_interval_ps` (default `None`): interval at which to compute per-frame SASA and polar SASA, in ps. `None` (the default) disables those analyses.
+- `analysis_interval_ps` (default `100`): interval at which to compute per-frame SASA and polar SASA, in ps. `None` disables those analyses.
 - `clustering` (default `None`): cluster the trajectory frames. `None` disables it; pass `rowan.KMeansClusteringSettings(num_clusters=10)` or `rowan.GreedyClusteringSettings(cutoff_angstrom=2.0)`.
 - `validate_forcefield` (default `True`): validate the protein forcefield before submitting; raises early if the protein cannot be parameterized or has clashing residues. When a `binder` is set, its small molecules are excluded from validation, whether keyed by residue name or by non-polymer index, since they are parameterized from their SMILES. Cofactors, metals, and glycans outside the binder are still validated — set `False` to skip the pre-check entirely.
 

{rowan_python-3.2.1 → rowan_python-3.2.2}/tests/test_binding_affinity.py

@@ -124,3 +124,36 @@ def test_binding_affinity_results_preserve_failed_inputs() -> None:
     )
 
     assert result.scores == [BindingAffinityScore(binding_affinity=-6.5), None]
+
+
+@pytest.mark.parametrize(
+    "settings",
+    [
+        pytest.param(rowan.SinglePointEnergySettings(), id="default-radius"),
+        pytest.param(rowan.SinglePointEnergySettings(truncation_radius=8.0), id="custom-radius"),
+        pytest.param(
+            rowan.SinglePointEnergySettings(
+                truncation_radius=None,
+                truncation_residues=[rowan.ResidueRef("polymer", "A", "A.182")],
+            ),
+            id="explicit-residues",
+        ),
+    ],
+)
+def test_submit_binding_affinity_pocket_roundtrip(
+    monkeypatch: pytest.MonkeyPatch, settings: rowan.SinglePointEnergySettings
+) -> None:
+    """Preserve radius and explicit residue selections through submission JSON."""
+    client = _mock_client(monkeypatch)
+    rowan.submit_binding_affinity_workflow(
+        protein="protein-uuid",
+        ligand_residue_name="LIG",
+        ligand_smiles=["CCO"],
+        binding_affinity_settings=settings,
+    )
+    payload = client.post.call_args.kwargs["json"]["workflow_data"]
+    assert payload["binding_affinity_settings"]["truncation_radius"] == settings.truncation_radius
+    restored = stjames.BindingAffinityWorkflow.model_validate(payload).binding_affinity_settings
+    assert restored.model_dump(mode="json", exclude_none=False) == settings.model_dump(
+        mode="json", exclude_none=False
+    )

{rowan_python-3.2.1 → rowan_python-3.2.2}/tests/test_md_workflow_updates.py

@@ -108,6 +108,7 @@ def test_protein_md_uses_new_defaults_and_forcefields(monkeypatch: pytest.Monkey
     assert payload["timestep_fs"] == 4
     assert payload["hydrogen_mass"] == 3
     assert payload["water_buffer"] == 8
+    assert payload["analysis_interval_ps"] == 100
 
 
 def test_protein_md_exposes_binder_and_representative_structure_results(

rowan_python-3.2.2/tests/test_project.py

@@ -0,0 +1,35 @@
+"""Tests for project retrieval."""
+
+from collections.abc import Iterator
+from contextlib import contextmanager
+from unittest.mock import MagicMock
+
+import pytest
+
+from rowan import project as project_module
+
+
+def _mock_client(monkeypatch: pytest.MonkeyPatch, payload: dict[str, str] | None) -> None:
+    client = MagicMock()
+    client.get.return_value.json.return_value = payload
+
+    @contextmanager
+    def mock_api_client() -> Iterator[MagicMock]:
+        yield client
+
+    monkeypatch.setattr(project_module, "api_client", mock_api_client)
+
+
+def test_default_project_returns_the_project(monkeypatch: pytest.MonkeyPatch) -> None:
+    """Return the default project the API reports."""
+    _mock_client(monkeypatch, {"uuid": "project-uuid", "name": "Default"})
+
+    assert project_module.default_project().uuid == "project-uuid"
+
+
+def test_default_project_without_one_raises_a_clear_error(monkeypatch: pytest.MonkeyPatch) -> None:
+    """Explain a missing default project instead of failing to build one from null."""
+    _mock_client(monkeypatch, None)
+
+    with pytest.raises(ValueError, match="no default project"):
+        project_module.default_project()

{rowan_python-3.2.1 → rowan_python-3.2.2}/uv.lock

@@ -1148,7 +1148,7 @@ wheels = [
 
 [[package]]
 name = "rowan-python"
-version = "3.2.1"
+version = "3.2.2"
 source = { editable = "." }
 dependencies = [
     { name = "httpx" },
@@ -1181,7 +1181,7 @@ requires-dist = [
     { name = "nest-asyncio" },
     { name = "rdkit" },
     { name = "setuptools" },
-    { name = "stjames", specifier = ">=0.0.275" },
+    { name = "stjames", specifier = ">=0.0.281" },
 ]
 
 [package.metadata.requires-dev]
@@ -1275,7 +1275,7 @@ wheels = [
 
 [[package]]
 name = "stjames"
-version = "0.0.275"
+version = "0.0.281"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "more-itertools" },
@@ -1283,9 +1283,9 @@ dependencies = [
     { name = "pydantic" },
     { name = "requests" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/a3/42/749b9b573680d9a072f058f96a0bc711250f739412a05b3713e6f00ce7b0/stjames-0.0.275.tar.gz", hash = "sha256:c99e5d0cc375d964812decec45cf7dd1d9b0abcb9ea0688525b033d7770219d3", size = 158319, upload-time = "2026-09-17T20:02:54.749Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/b9/bf/b834e4016ea17396564674f5b2804580bd4225c1386e095810549fde6f32/stjames-0.0.281.tar.gz", hash = "sha256:ef267c3fe4fe4ddd8bf39edd50334dc78945df171239d1ce73252c5ec0ee9a9f", size = 1437540, upload-time = "2026-10-08T17:51:46.292Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/6b/40/0f4e0e0fc864bc103ec662a283da2a6ab5a90e579400ca1af077ea4ab854/stjames-0.0.275-py3-none-any.whl", hash = "sha256:cb452931a506bf46a7774f8da0122b40c7608d63be2b5252202f67e001f8fb3c", size = 174423, upload-time = "2026-09-17T20:02:53.482Z" },
+    { url = "https://files.pythonhosted.org/packages/d3/05/546152338686aab103ac1813bb65a94ac402c7db0fccb21e5c4e7a39de70/stjames-0.0.281-py3-none-any.whl", hash = "sha256:8e4c4dacc1af87168e38d8aa676a7bc7dfe0f8ed14fcb62f2d9eb56a54fbe471", size = 196578, upload-time = "2026-10-08T17:51:44.751Z" },
 ]
 
 [[package]]