rowan-python 2.1.2__py3-none-any.whl → 2.1.4__py3-none-any.whl

rowan/workflow.py

@@ -1,6 +1,6 @@
 import time
 from datetime import datetime
-from typing import Any, Self, TypeAlias
+from typing import Any, Literal, Self, TypeAlias
 
 import stjames
 from pydantic import BaseModel, Field
@@ -387,20 +387,21 @@ def submit_basic_calculation_workflow(
     if isinstance(method, str):
         method = stjames.Method(method)
 
-    workflow_data = {
-        "settings": {
-            "method": method.name,
-            "tasks": tasks,
-            "mode": mode,
-        },
-        "engine": engine,
-    }
+    workflow = stjames.BasicCalculationWorkflow(
+        initial_molecule=initial_molecule,
+        settings=stjames.Settings(
+            method=method,
+            tasks=tasks,
+            mode=mode,
+        ),
+        engine=engine,
+    )
 
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "basic_calculation",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -466,19 +467,20 @@ def submit_conformer_search_workflow(
         optimization_settings=[opt_settings],
     )
 
-    workflow_data = {
-        "multistage_opt_settings": msos.model_dump(),
-        "conf_gen_mode": conf_gen_mode,
-        "mso_mode": "manual",
-        "solvent": solvent,
-        "transition_state": transition_state,
-    }
+    workflow = stjames.ConformerSearchWorkflow(
+        initial_molecule=initial_molecule,
+        multistage_opt_settings=msos,
+        conf_gen_mode=conf_gen_mode,
+        mso_mode="manual",
+        solvent=solvent,
+        transition_state=transition_state,
+    )
 
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "conformer_search",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -491,6 +493,7 @@ def submit_conformer_search_workflow(
 
 def submit_solubility_workflow(
     initial_smiles: str,
+    solubility_method: Literal["fastsolv", "kingfisher", "esol"] = "fastsolv",
     solvents: list[str] | None = None,
     temperatures: list[float] | None = None,
     name: str = "Solubility Workflow",
@@ -500,6 +503,7 @@ def submit_solubility_workflow(
     """
     Submits a solubility workflow to the API.
 
+    :param solubility_method: The name of the desired model for solubility prediction.
     :param initial_smiles: The smiles of the molecule to calculate the solubility of.
     :param solvents: The list of solvents to use for the calculation.
     :param temperatures: The list of temperatures to use for the calculation.
@@ -516,13 +520,18 @@ def submit_solubility_workflow(
     if not temperatures:
         temperatures = [273.15, 298.15, 323.15, 348.15, 373.15]
 
-    workflow_data = {"solvents": solvents, "temperatures": temperatures}
+    workflow = stjames.SolubilityWorkflow(
+        initial_smiles=initial_smiles,
+        solubility_method=solubility_method,
+        solvents=solvents,
+        temperatures=temperatures,
+    )
 
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "solubility",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_smiles": initial_smiles,
         "max_credits": max_credits,
     }
@@ -567,18 +576,19 @@ def submit_pka_workflow(
     protonate_elements = protonate_elements or [7]
     deprotonate_elements = deprotonate_elements or [7, 8, 16]
 
-    workflow_data = {
-        "pka_range": pka_range,
-        "deprotonate_elements": deprotonate_elements,
-        "protonate_elements": protonate_elements,
-        "mode": mode,
-    }
+    workflow = stjames.pKaWorkflow(
+        initial_molecule=initial_molecule,
+        pka_range=pka_range,
+        deprotonate_elements=deprotonate_elements,
+        protonate_elements=protonate_elements,
+        mode=mode,
+    )
 
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "pka",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -618,17 +628,18 @@ def submit_redox_potential_workflow(
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
-    workflow_data = {
-        "oxidation": oxidization,
-        "reduction": reduction,
-        "mode": mode,
-    }
+    workflow = stjames.RedoxPotentialWorkflow(
+        initial_molecule=initial_molecule,
+        oxidation=oxidization,
+        reduction=reduction,
+        mode=mode,
+    )
 
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "redox_potential",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -669,6 +680,12 @@ def submit_fukui_workflow(
     optimization_settings = stjames.Settings(method=optimization_method)
     fukui_settings = stjames.Settings(method=fukui_method, solvent_settings=solvent_settings)
 
+    stjames.FukuiIndexWorkflow(
+        initial_molecule=initial_molecule,
+        optimization_settings=optimization_settings,
+        fukui_settings=fukui_settings,
+    )
+
     workflow_data = {
         "opt_settings": optimization_settings.model_dump(),
         "opt_engine": stjames.Method(optimization_method).default_engine(),
@@ -716,15 +733,16 @@ def submit_tautomer_search_workflow(
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
 
-    workflow_data = {
-        "mode": mode,
-    }
+    workflow = stjames.TautomerWorkflow(
+        initial_molecule=initial_molecule,
+        mode=mode,
+    )
 
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "tautomers",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -805,24 +823,27 @@ def submit_scan_workflow(
     if isinstance(calculation_method, str):
         calculation_method = stjames.Method(calculation_method)
 
-    workflow_data = {
-        "wavefront_propagation": wavefront_propagation,
-        "scan_settings": scan_settings,
-        "calc_engine": calculation_engine,
-        "calc_settings": {
-            "method": calculation_method.name,
-            "corrections": [],
-            "tasks": ["optimize"],
-            "mode": "auto",
-            "opt_settings": {"constraints": []},
-        },
-    }
+    calc_settings = stjames.Settings(
+        method=calculation_method,
+        tasks=["optimize"],
+        corrections=[],
+        mode="auto",
+        opt_settings={"constraints": []},
+    )
+
+    workflow = stjames.ScanWorkflow(
+        initial_molecule=initial_molecule,
+        scan_settings=scan_settings,
+        calc_settings=calc_settings,
+        calc_engine=calculation_engine,
+        wavefront_propagation=wavefront_propagation,
+    )
 
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "scan",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -839,6 +860,7 @@ def submit_macropka_workflow(
     max_pH: int = 14,
     min_charge: int = -2,
     max_charge: int = 2,
+    compute_aqueous_solubility: bool = False,
     compute_solvation_energy: bool = True,
     name: str = "Macropka Workflow",
     folder_uuid: str | None = None,
@@ -852,6 +874,7 @@ def submit_macropka_workflow(
     :param max_pH: The maximum pH to use in the macropka workflow.
     :param min_charge: The minimum charge to use in the macropka workflow.
     :param max_charge: The maximum charge to use in the macropka workflow.
+    :param compute_aqueous_solubility: Whether to compute the aqueous solubility for each pH.
     :param compute_solvation_energy: Whether to compute the solvation energy.
     :param name: The name of the workflow.
     :param folder_uuid: The UUID of the folder to store the workflow in.
@@ -860,19 +883,21 @@ def submit_macropka_workflow(
     :raises requests.HTTPError: if the request to the API fails.
     """
 
-    workflow_data = {
-        "min_pH": min_pH,
-        "max_pH": max_pH,
-        "min_charge": min_charge,
-        "max_charge": max_charge,
-        "compute_solvation_energy": compute_solvation_energy,
-    }
+    workflow = stjames.MacropKaWorkflow(
+        initial_smiles=initial_smiles,
+        min_pH=min_pH,
+        max_pH=max_pH,
+        min_charge=min_charge,
+        max_charge=max_charge,
+        compute_solvation_energy=compute_solvation_energy,
+        compute_aqueous_solubility=compute_aqueous_solubility,
+    )
 
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "macropka",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_smiles": initial_smiles,
         "max_credits": max_credits,
     }
@@ -920,25 +945,25 @@ def submit_irc_workflow(
     if isinstance(method, str):
         method = stjames.Method(method)
 
-    workflow_data = {
-        "settings": {
-            "method": method.name,
-            "tasks": [],
-            "corrections": [],
-            "mode": "auto",
-        },
-        "engine": engine,
-        "preopt": preopt,
-        "step_size": step_size,
-        "max_irc_steps": max_irc_steps,
-        "mode": "manual",
-    }
-
+    workflow = stjames.IRCWorkflow(
+        initial_molecule=initial_molecule,
+        settings=stjames.Settings(
+            method=method,
+            tasks=[],
+            corrections=[],
+            mode="auto",
+        ),
+        engine=engine,
+        preopt=preopt,
+        step_size=step_size,
+        max_irc_steps=max_irc_steps,
+        mode="manual",
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "irc",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -975,19 +1000,20 @@ def submit_protein_cofolding_workflow(
     :return: A Workflow object representing the submitted workflow.
     :raises requests.HTTPError: if the request to the API fails.
     """  # noqa: E501
-    workflow_data = {
-        "use_msa_server": use_msa_server,
-        "use_potentials": use_potentials,
-        "model": model,
-        "ligand_binding_affinity_index": ligand_binding_affinity_index,
-        "initial_smiles_list": initial_smiles_list,
-        "initial_protein_sequences": initial_protein_sequences,
-    }
+
+    workflow = stjames.ProteinCofoldingWorkflow(
+        use_msa_server=use_msa_server,
+        use_potentials=use_potentials,
+        model=model,
+        ligand_binding_affinity_index=ligand_binding_affinity_index,
+        initial_smiles_list=initial_smiles_list,
+        initial_protein_sequences=initial_protein_sequences,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "protein_cofolding",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "max_credits": max_credits,
     }
 
@@ -1029,18 +1055,19 @@ def submit_docking_workflow(
     if isinstance(protein, Protein):
         protein = protein.uuid
 
-    workflow_data = {
-        "target_uuid": protein,
-        "pocket": pocket,
-        "do_csearch": do_csearch,
-        "do_optimization": do_optimization,
-    }
+    workflow = stjames.DockingWorkflow(
+        initial_molecule=initial_molecule,
+        target_uuid=protein,
+        pocket=pocket,
+        do_csearch=do_csearch,
+        do_optimization=do_optimization,
+    )
 
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "docking",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }

{rowan_python-2.1.2.dist-info → rowan_python-2.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.2
+Version: 2.1.4
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues

{rowan_python-2.1.2.dist-info → rowan_python-2.1.4.dist-info}/RECORD

@@ -6,10 +6,10 @@ rowan/protein.py,sha256=bMemvLZua_pnTrYOxHFZ4jFlRH9KgpYvtjj5M2__28k,8026
 rowan/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rowan/user.py,sha256=Dl--NPUPATKCs2VmILsW8HnLiunG0Lxr0n6mKuHm21U,3891
 rowan/utils.py,sha256=907lV0fEP6BnjOWyisd3Uh8Mk5JuQMOX9QEjGi_mdew,3314
-rowan/workflow.py,sha256=LwU1iaweXseQENOHYAOQqvjNkwITZn82JHeSr4xZiTc,39505
+rowan/workflow.py,sha256=uFgI-yTSHW6JY5KulpnGPdM3Xrl0UGYtne9OnDIkzz8,40729
 rowan/rowan_rdkit/__init__.py,sha256=EATX2VRzywzKxqkpCUMTf7RNQLkWsfi5VcCNDW6EIiw,503
 rowan/rowan_rdkit/chem_utils.py,sha256=i7-EmAcmvHYtc9NiZblLY_k2DoQKofAZo5KT2qtkUCI,34775
-rowan_python-2.1.2.dist-info/METADATA,sha256=Pj9WxcyKn2jjFIMsew0Ka7GWJ9X0CLElGIsT8agjEME,1598
-rowan_python-2.1.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-rowan_python-2.1.2.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-2.1.2.dist-info/RECORD,,
+rowan_python-2.1.4.dist-info/METADATA,sha256=PJ8hu2ynkYFAQ1hpyKwE0nlKfmtQcAWCQf61NOIkoPU,1598
+rowan_python-2.1.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+rowan_python-2.1.4.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-2.1.4.dist-info/RECORD,,