rowan-python 2.1.11__py3-none-any.whl → 2.1.13__py3-none-any.whl

rowan/folder.py

@@ -58,7 +58,6 @@ class Folder(BaseModel):
 
         return self
 
-
     def update(
         self,
         name: str | None = None,
@@ -121,6 +120,7 @@ class Folder(BaseModel):
         """
         print_folder_tree(self.uuid, max_depth, show_uuids)
 
+
 def retrieve_folder(uuid: str) -> Folder:
     """
     Retrieves a folder from the API by UUID. Folder UUID can be found in the folder's URL.
@@ -208,6 +208,7 @@ def create_folder(
         folder_data = response.json()
     return Folder(**folder_data)
 
+
 def print_folder_tree(uuid: str, max_depth: int = 10, show_uuids: bool = False) -> None:
     """
     Retrieves a folder tree from the API.

rowan/workflow.py

@@ -242,8 +242,9 @@ class Workflow(BaseModel):
         with open(path / f"{self.name}-msa.tar.gz", "wb") as f:
             f.write(response.content)
 
-    def download_dcd_files(self, replicates: list[int],
-                           name: str | None = None, path: Path | None = None) -> None:
+    def download_dcd_files(
+        self, replicates: list[int], name: str | None = None, path: Path | None = None
+    ) -> None:
         """
         Downloads DCD trajectory files for specified replicates
 
@@ -262,9 +263,7 @@ class Workflow(BaseModel):
         path.mkdir(parents=True, exist_ok=True)
 
         with api_client() as client:
-            response = client.post(
-                f"/trajectory/{self.uuid}/trajectory_dcds", json=replicates
-            )
+            response = client.post(f"/trajectory/{self.uuid}/trajectory_dcds", json=replicates)
             response.raise_for_status()
 
         file_path = path / f"{name or self.name}.tar.gz"
@@ -313,11 +312,13 @@ def submit_workflow(
     if initial_smiles is not None:
         data["initial_smiles"] = initial_smiles
     elif isinstance(initial_molecule, StJamesMolecule):
-        data["initial_molecule"] = initial_molecule.model_dump()
+        data["initial_molecule"] = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, dict):
         data["initial_molecule"] = initial_molecule
     elif isinstance(initial_molecule, RdkitMol):
-        data["initial_molecule"] = StJamesMolecule.from_rdkit(initial_molecule, cid=0).model_dump()
+        data["initial_molecule"] = StJamesMolecule.from_rdkit(initial_molecule, cid=0).model_dump(
+            mode="json"
+        )
     else:
         raise ValueError("You must provide either `initial_smiles` or a valid `initial_molecule`.")
 
@@ -423,6 +424,7 @@ def retrieve_workflows(uuids: list[str]) -> list[Workflow]:
         response.raise_for_status()
         return [Workflow(**workflow_data) for workflow_data in response.json()]
 
+
 def batch_poll_status(uuids: list[str]) -> list[Workflow]:
     """
     Polls the status of a list of workflows.
@@ -538,7 +540,7 @@ def submit_basic_calculation_workflow(
         tasks = ["optimize"]
 
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -560,7 +562,7 @@ def submit_basic_calculation_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "basic_calculation",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -601,7 +603,7 @@ def submit_conformer_search_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -639,7 +641,7 @@ def submit_conformer_search_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "conformer_search",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -690,7 +692,7 @@ def submit_solubility_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "solubility",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_smiles": initial_smiles,
         "max_credits": max_credits,
     }
@@ -762,8 +764,10 @@ def submit_pka_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "pka",
-        "workflow_data": workflow.model_dump(),
-        "initial_molecule": initial_stjames_mol.model_dump() if initial_stjames_mol else None,
+        "workflow_data": workflow.model_dump(mode="json"),
+        "initial_molecule": initial_stjames_mol.model_dump(mode="json")
+        if initial_stjames_mol
+        else None,
         "initial_smiles": initial_smiles,
         "max_credits": max_credits,
     }
@@ -799,7 +803,7 @@ def submit_redox_potential_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -814,7 +818,7 @@ def submit_redox_potential_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "redox_potential",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -848,7 +852,7 @@ def submit_fukui_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -862,9 +866,9 @@ def submit_fukui_workflow(
     )
 
     workflow_data = {
-        "opt_settings": optimization_settings.model_dump(),
+        "opt_settings": optimization_settings.model_dump(mode="json"),
         "opt_engine": stjames.Method(optimization_method).default_engine(),
-        "fukui_settings": fukui_settings.model_dump(),
+        "fukui_settings": fukui_settings.model_dump(mode="json"),
         "fukui_engine": stjames.Method(fukui_method).default_engine(),
     }
 
@@ -904,7 +908,7 @@ def submit_tautomer_search_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -917,7 +921,7 @@ def submit_tautomer_search_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "tautomers",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -945,7 +949,7 @@ def submit_descriptors_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -991,7 +995,7 @@ def submit_scan_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -1018,7 +1022,7 @@ def submit_scan_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "scan",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -1072,7 +1076,7 @@ def submit_macropka_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "macropka",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_smiles": initial_smiles,
         "max_credits": max_credits,
     }
@@ -1111,7 +1115,7 @@ def submit_irc_workflow(
     """
 
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -1136,7 +1140,7 @@ def submit_irc_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "irc",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -1193,7 +1197,7 @@ def submit_protein_cofolding_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "protein_cofolding",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "max_credits": max_credits,
     }
 
@@ -1236,7 +1240,7 @@ def submit_docking_workflow(
     """
 
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -1263,7 +1267,7 @@ def submit_docking_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "docking",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -1300,7 +1304,7 @@ def submit_ion_mobility_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -1316,7 +1320,7 @@ def submit_ion_mobility_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "ion_mobility",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -1350,7 +1354,7 @@ def submit_nmr_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -1368,7 +1372,7 @@ def submit_nmr_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "nmr",
-        "workflow_data": workflow.model_dump(serialize_as_any=True),
+        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -1396,7 +1400,7 @@ def submit_strain_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
     if isinstance(initial_molecule, StJamesMolecule):
-        initial_molecule = initial_molecule.model_dump()
+        initial_molecule = initial_molecule.model_dump(mode="json")
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
@@ -1406,7 +1410,7 @@ def submit_strain_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "strain",
-        "workflow_data": workflow.model_dump(serialize_as_any=True),
+        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -1454,8 +1458,10 @@ def submit_double_ended_ts_search_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "double_ended_ts_search",
-        "workflow_data": workflow.model_dump(),
-        "initial_molecule": reactant if isinstance(reactant, dict) else reactant.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
+        "initial_molecule": reactant
+        if isinstance(reactant, dict)
+        else reactant.model_dump(mode="json"),
         "max_credits": max_credits,
     }
 
@@ -1506,7 +1512,7 @@ def submit_pose_analysis_md_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "pose_analysis_md",
-        "workflow_data": workflow.model_dump(serialize_as_any=True),
+        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
         "initial_smiles": initial_smiles,
         "max_credits": max_credits,
     }
@@ -1560,7 +1566,7 @@ def submit_batch_docking_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "batch_docking",
-        "workflow_data": workflow.model_dump(serialize_as_any=True),
+        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
         "max_credits": max_credits,
     }
 
@@ -1598,7 +1604,7 @@ def submit_msa_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "msa",
-        "workflow_data": workflow.model_dump(serialize_as_any=True),
+        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
         "max_credits": max_credits,
     }
 
@@ -1606,3 +1612,101 @@ def submit_msa_workflow(
         response = client.post("/workflow", json=data)
         response.raise_for_status()
         return Workflow(**response.json())
+
+
+def submit_admet_workflow(
+    initial_smiles: str,
+    name: str = "ADMET Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits an ADMET workflow to the API.
+
+    :param initial_smiles: The molecule used in the workflow.
+    :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.
+    """
+
+    workflow = stjames.ADMETWorkflow(initial_smiles=initial_smiles)
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "admet",
+        "workflow_data": workflow.model_dump(mode="json"),
+        "initial_smiles": initial_smiles,
+        "max_credits": max_credits,
+    }
+
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())
+
+
+def submit_membrane_permeability_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | str,
+    method: Literal["gnn-mtl", "pypermm"] = "gnn-mtl",
+    name: str = "ADMET Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a membrane permeability workflow to the API.
+
+    :param initial_molecule: The molecule used in the workflow.
+    :param method: The method used to compute membrane permeability.
+    :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.
+    """
+
+    data: dict[str, Any] = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "membrane_permeability",
+        "max_credits": max_credits,
+    }
+
+    match method:
+        case "gnn-mtl":
+            assert isinstance(initial_molecule, str)
+            workflow = stjames.MembranePermeabilityWorkflow(
+                initial_smiles=initial_molecule,
+                membrane_permeability_method="chemprop_ohlsson2025",
+            )
+
+            data["initial_smiles"] = initial_molecule
+
+        case "pypermm":
+            if isinstance(initial_molecule, str):
+                raise ValueError("Cannot specify molecule as SMILES for PyPermm")
+            elif isinstance(initial_molecule, StJamesMolecule):
+                initial_molecule = initial_molecule.model_dump(mode="json")
+            elif isinstance(initial_molecule, RdkitMol):
+                initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0).model_dump(
+                    mode="json"
+                )
+
+            workflow = stjames.MembranePermeabilityWorkflow(
+                initial_molecule=initial_molecule,
+                membrane_permeability_method="pypermm",
+            )
+
+            data["initial_molecule"] = initial_molecule
+
+        case _:
+            raise ValueError(f"Unexpected {method=}")
+
+    data["workflow_data"] = workflow.model_dump(mode="json")
+
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())

{rowan_python-2.1.11.dist-info → rowan_python-2.1.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.11
+Version: 2.1.13
 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>=0.0.128
+Requires-Dist: stjames>=0.0.144
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-2.1.11.dist-info → rowan_python-2.1.13.dist-info}/RECORD

@@ -1,15 +1,15 @@
 rowan/__init__.py,sha256=2rz6dW0l9DzawiFi6S0WSv8XlZq1CoTBKJrsJ1uesvk,171
 rowan/constants.py,sha256=emCH4m9OL2Hm5E-6mJGM_FgzrK_JrZT-FiKJ6pMNQ4Y,84
-rowan/folder.py,sha256=MF3SU7uG6Hl2SJLFxbPmbhosS-pPEHwbTyummaaRdzM,7509
+rowan/folder.py,sha256=IAda7apRsow_qhausWlAGWKkD9cRvPmt-DkXwqOOM20,7510
 rowan/project.py,sha256=ALPPkMa_cg7w5OkXno1cs6acCofw8AOUYRSeWgr3L0o,3774
 rowan/protein.py,sha256=mFSVCr-08bSikXBUtJtSWzjKcVAuBmTeRckn7JUHYSE,8810
 rowan/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rowan/user.py,sha256=Dl--NPUPATKCs2VmILsW8HnLiunG0Lxr0n6mKuHm21U,3891
 rowan/utils.py,sha256=64II-cPOe_SFJK302Bm8hP62d_3_CgnTVYCbn3zKT7U,3334
-rowan/workflow.py,sha256=5nNhsKCo2AxryyL85vZX2AbDCZju4ENA3DlLaaOT30I,61451
+rowan/workflow.py,sha256=hsRh0J6bdNs78eByuL5G3_k1CrNQg2szR5sPPalWTMA,65376
 rowan/rowan_rdkit/__init__.py,sha256=EATX2VRzywzKxqkpCUMTf7RNQLkWsfi5VcCNDW6EIiw,503
 rowan/rowan_rdkit/chem_utils.py,sha256=sKCzul2e0ldVYTBImhTwso7ddNgPKmvS-OmvCEjVJH0,34788
-rowan_python-2.1.11.dist-info/METADATA,sha256=4Cs9-dQFzabaW1Eemwjqq3absuWc3DNYomL9AQHdbGU,1601
-rowan_python-2.1.11.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-rowan_python-2.1.11.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-2.1.11.dist-info/RECORD,,
+rowan_python-2.1.13.dist-info/METADATA,sha256=3zsPCrGRWTd9snLuYFsleM0iDWkChWQaOEaiGExtLbY,1601
+rowan_python-2.1.13.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rowan_python-2.1.13.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-2.1.13.dist-info/RECORD,,

{rowan_python-2.1.11.dist-info → rowan_python-2.1.13.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any