rowan-python 2.1.12__py3-none-any.whl → 2.1.13__py3-none-any.whl

rowan/workflow.py

@@ -312,11 +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`.")
 
@@ -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,
     }
 
@@ -1631,7 +1637,7 @@ def submit_admet_workflow(
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "admet",
-        "workflow_data": workflow.model_dump(),
+        "workflow_data": workflow.model_dump(mode="json"),
         "initial_smiles": initial_smiles,
         "max_credits": max_credits,
     }
@@ -1643,7 +1649,8 @@ def submit_admet_workflow(
 
 
 def submit_membrane_permeability_workflow(
-    initial_smiles: str,
+    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,
@@ -1651,7 +1658,8 @@ def submit_membrane_permeability_workflow(
     """
     Submits a membrane permeability workflow to the API.
 
-    :param initial_smiles: The molecule used in the workflow.
+    :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.
@@ -1659,17 +1667,45 @@ def submit_membrane_permeability_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
 
-    workflow = stjames.MembranePermeabilityWorkflow(initial_smiles=initial_smiles)
-
-    data = {
+    data: dict[str, Any] = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "membrane_permeability",
-        "workflow_data": workflow.model_dump(),
-        "initial_smiles": initial_smiles,
         "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()

{rowan_python-2.1.12.dist-info → rowan_python-2.1.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.12
+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>=0.0.137
+Requires-Dist: stjames>=0.0.144
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-2.1.12.dist-info → rowan_python-2.1.13.dist-info}/RECORD

@@ -6,10 +6,10 @@ 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=Y9H1qXCjTd-E-LehtlbpEp5l7a0__TKE7nYqY5XwUI8,63669
+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-2.1.12.dist-info/METADATA,sha256=IdwxdzM7GqpuqU9lF9_69NKeGldpBq-FOW00C4tZaqg,1601
-rowan_python-2.1.12.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rowan_python-2.1.12.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-2.1.12.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,,