PyPI - rowan-python - Versions diffs - 2.1.5__tar.gz → 2.1.6__tar.gz - Mend

rowan-python 2.1.5tar.gz → 2.1.6tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (52) hide show

{rowan_python-2.1.5 → rowan_python-2.1.6}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.5
+Version: 2.1.6
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
@@ -11,7 +11,7 @@ Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.104
+Requires-Dist: stjames>=0.0.109
 Description-Content-Type: text/markdown
 # Rowan Python Library

{rowan_python-2.1.5 → rowan_python-2.1.6}/examples/protein_cofolding.py RENAMED Viewed

@@ -12,6 +12,8 @@ result = rowan.submit_protein_cofolding_workflow(
     ],
     ligand_binding_affinity_index=0,
     name="Torcetrapib Cofolding",
+    do_pose_refinement=True,
+    compute_strain=True,
 )
 print(result.wait_for_result().fetch_latest(in_place=True))

rowan_python-2.1.6/examples/strain.py ADDED Viewed

@@ -0,0 +1,16 @@
+from stjames import Molecule
+import rowan
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+# ordinarily, we'd try a 3D conformer and see what the strain is.
+# here we'll investigate the strain of the autogenerated hexane conformer
+result = rowan.submit_strain_workflow(
+    initial_molecule=Molecule.from_smiles("CCCCCC"),
+    name="test autogen hexane strain",
+)
+print(result.wait_for_result().fetch_latest(in_place=True))

{rowan_python-2.1.5 → rowan_python-2.1.6}/pixi.lock RENAMED Viewed

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   requires_python: '>=3.8'
 - pypi: https://files.pythonhosted.org/packages/04/11/432f32f8097b03e3cd5fe57e88efb685d964e2e5178a48ed61e841f7fdce/pyyaml_env_tag-1.1-py3-none-any.whl
   name: pyyaml-env-tag
@@ -1468,25 +1467,25 @@ packages:
   requires_python: '>=3.9'
 - pypi: ./
   name: rowan-python
-  version: 2.1.5
-  sha256: 59ef0b1195e9f104c84465182fddecc1ab0606c00f5da8a2f73503c467d65a80
+  version: 2.1.6
+  sha256: 7cd0ec9e2e7b39b21b717eeac596ec082a7beba1b6b36685007b4154bd4aeb34
   requires_dist:
   - httpx
-  - stjames>=0.0.104
+  - stjames>=0.0.109
   - setuptools
   - rdkit
   - nest-asyncio
   requires_python: '>=3.9'
   editable: true
-- pypi: https://files.pythonhosted.org/packages/44/cf/40bc7221a949470307d9c35b4ef5810c294e6cfa3caafb57d882731a9f42/ruff-0.13.0-py3-none-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/64/8b/e87cfca2be6f8b9f41f0bb12dc48c6455e2d66df46fe61bb441a226f1089/ruff-0.13.2-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
   name: ruff
-  version: 0.13.0
-  sha256: 64de45f4ca5441209e41742d527944635a05a6e7c05798904f39c85bafa819e3
+  version: 0.13.2
+  sha256: 5bcb10276b69b3cfea3a102ca119ffe5c6ba3901e20e60cf9efb53fa417633c3
   requires_python: '>=3.7'
-- pypi: https://files.pythonhosted.org/packages/a8/a6/7985ad1778e60922d4bef546688cd8a25822c58873e9ff30189cfe5dc4ab/ruff-0.13.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/c6/15/125a7f76eb295cb34d19c6778e3a82ace33730ad4e6f28d3427e134a02e0/ruff-0.13.2-py3-none-macosx_11_0_arm64.whl
   name: ruff
-  version: 0.13.0
-  sha256: 03447f3d18479df3d24917a92d768a89f873a7181a064858ea90a804a7538991
+  version: 0.13.2
+  sha256: c75e9d2a2fafd1fdd895d0e7e24b44355984affdde1c412a6f6d3f6e16b22d46
   requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl
   name: setuptools
@@ -1568,10 +1567,10 @@ packages:
   - pygments ; extra == 'tests'
   - littleutils ; extra == 'tests'
   - cython ; extra == 'tests'
-- pypi: https://files.pythonhosted.org/packages/00/f0/e816b819334c25a221ac1e10b2d24a8428233364b6511191cd7894f5390f/stjames-0.0.105-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/12/ba/11595ccc9f9cc697349ac66b6227f58140dce7b3e77e433501392e5994f5/stjames-0.0.109-py3-none-any.whl
   name: stjames
-  version: 0.0.105
-  sha256: e9e4a3eb3478e8761855a6274bd79647a965954f2e0ca2490c3b0a2a2441ad25
+  version: 0.0.109
+  sha256: 919dad07e10d64307caddfe367e14c153ed236002dec9d9371c503c134a1c8a9
   requires_dist:
   - pydantic>=2.4
   - numpy
@@ -1691,9 +1690,8 @@ packages:
   requires_dist:
   - pyyaml>=3.10 ; extra == 'watchmedo'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/fd/84/fd2ba7aafacbad3c4201d395674fc6348826569da3c0937e75505ead3528/wcwidth-0.2.13-py2.py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/af/b5/123f13c975e9f27ab9c0770f514345bd406d0e8d3b7a0723af9d43f710af/wcwidth-0.2.14-py2.py3-none-any.whl
   name: wcwidth
-  version: 0.2.13
-  sha256: 3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859
-  requires_dist:
-  - backports-functools-lru-cache>=1.2.1 ; python_full_version < '3.2'
+  version: 0.2.14
+  sha256: a7bb560c8aee30f9957e5f9895805edd20602f2d7f720186dfd906e82b4982e1
+  requires_python: '>=3.6'

{rowan_python-2.1.5 → rowan_python-2.1.6}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.1.5"
+version = "2.1.6"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -9,7 +9,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
-    "stjames>=0.0.104",
+    "stjames>=0.0.109",
     "setuptools",
     "rdkit",
     "nest-asyncio",

{rowan_python-2.1.5 → rowan_python-2.1.6}/rowan/workflow.py RENAMED Viewed

@@ -980,6 +980,8 @@ def submit_protein_cofolding_workflow(
     ligand_binding_affinity_index: int | None = None,
     use_msa_server: bool = True,
     use_potentials: bool = False,
+    compute_strain: bool = False,
+    do_pose_refinement: bool = False,
     name: str = "Cofolding Workflow",
     model: str = stjames.CofoldingModel.BOLTZ_2.value,
     folder_uuid: str | None = None,
@@ -993,6 +995,8 @@ def submit_protein_cofolding_workflow(
     :param ligand_binding_affinity_index: The index of the ligand for which to compute the binding affinity.
     :param use_msa_server: Whether to use the MSA server for the computation.
     :param use_potentials: Whether to use potentials for the computation.
+    :param do_pose_refinement: whether to optimize non-rotatable bonds in output poses
+    :param compute_strain: whether to compute the strain of the pose (if `pose_refinement` is enabled)
     :param name: The name of the workflow.
     :param model: The model to use for the computation.
     :param folder_uuid: The UUID of the folder to store the workflow in.
@@ -1008,7 +1012,10 @@ def submit_protein_cofolding_workflow(
         ligand_binding_affinity_index=ligand_binding_affinity_index,
         initial_smiles_list=initial_smiles_list,
         initial_protein_sequences=initial_protein_sequences,
+        do_pose_refinement=do_pose_refinement,
+        compute_strain=compute_strain,
     )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
@@ -1063,7 +1070,7 @@ def submit_docking_workflow(
         pocket=pocket,
         do_csearch=do_csearch,
         do_optimization=do_optimization,
-        do_pose_refinement=do_pose_refinement
+        do_pose_refinement=do_pose_refinement,
     )
     data = {
@@ -1184,3 +1191,41 @@ def submit_nmr_workflow(
         response = client.post("/workflow", json=data)
         response.raise_for_status()
         return Workflow(**response.json())
+def submit_strain_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    name: str = "Strain Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a strain workflow to the API.
+    :param initial_molecule: The molecule used in the scan.
+    :param name: The name of the workflow.
+    :param folder_uuid: The UUID of the folder to store the workflow in.
+    :param max_credits: The maximum number of credits to use for the workflow.
+    :return: A Workflow object representing the submitted workflow.
+    :raises requests.HTTPError: if the request to the API fails.
+    """
+    if isinstance(initial_molecule, StJamesMolecule):
+        initial_molecule = initial_molecule.model_dump()
+    elif isinstance(initial_molecule, RdkitMol):
+        initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
+    workflow = stjames.StrainWorkflow(initial_molecule=initial_molecule)
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "strain",
+        "workflow_data": workflow.model_dump(serialize_as_any=True),
+        "initial_molecule": initial_molecule,
+        "max_credits": max_credits,
+    }
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())