rowan-python 3.0.4__tar.gz → 3.0.5__tar.gz

{rowan_python-3.0.4 → rowan_python-3.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.4
+Version: 3.0.5
 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-3.0.5/examples/data/Al_FCC.xyz

@@ -0,0 +1,3 @@
+1
+Lattice="0.0 2.0230 2.0230 2.0230 0.0 2.0230 2.0230 2.0230 0.0" Properties=species:S:1:pos:R:3
+Al   0.00000000   0.00000000   0.00000000

rowan_python-3.0.5/examples/periodic_dft.py

@@ -0,0 +1,58 @@
+"""
+Run a periodic DFT energy calculation on bulk aluminium using Quantum ESPRESSO.
+
+Key settings for PBC calculations:
+- ``pw_cutoff``: plane-wave kinetic-energy cutoff in Hartree (higher = more accurate/slower)
+- ``kpoints``: Monkhorst–Pack k-point grid (denser = more accurate/slower)
+- ``smearing``: occupation smearing type — recommended for metals to aid SCF convergence
+- ``degauss``: smearing width in Hartree (typical range: 0.005–0.02)
+
+Periodic molecules are constructed from atomic positions + lattice vectors.
+See documentation at: https://docs.rowansci.com/science/workflows/basic-calculation
+"""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples/periodic_dft")
+
+# Build bulk Al FCC primitive cell.
+# Lattice vectors in Angstrom; Al has 13 electrons so multiplicity=2.
+cell = rowan.PeriodicCell(
+    lattice_vectors=(
+        (0.0,    2.0230, 2.0230),
+        (2.0230, 0.0,    2.0230),
+        (2.0230, 2.0230, 0.0),
+    )
+)
+al_fcc = rowan.Molecule.from_atoms(
+    atoms=[rowan.Atom(atomic_number=13, position=(0.0, 0.0, 0.0))],
+    charge=0,
+    multiplicity=2,
+    cell=cell,
+)
+
+# Marzari–Vanderbilt cold smearing is recommended for metals.
+pbc_settings = rowan.PBCDFTSettings(
+    pw_cutoff=7.5,           # Hartree; SSSP efficiency recommends ~7–9 Ha for Al
+    kpoints=(4, 4, 4),       # Monkhorst–Pack grid; increase for production runs
+    smearing=rowan.PBCDFTSmearing.MV,
+    degauss=0.01,            # Hartree smearing width
+)
+
+workflow = rowan.submit_basic_calculation_workflow(
+    initial_molecule=al_fcc,
+    tasks=["energy"],
+    method="PBE",
+    basis_set="SSSP_efficiency",
+    pbc_dft_settings=pbc_settings,
+    name="Al FCC bulk energy",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/calculation/{workflow.uuid}")
+result = workflow.result()
+print(result)
+# e.g. <BasicCalculationResult energy=-19.725 H>
+print(f"Al FCC energy: {result.energy:.6f} Hartree")

rowan_python-3.0.5/examples/pka.py

@@ -0,0 +1,69 @@
+"""
+Calculate the pKa of phenol using the Rowan API.
+
+Experimental value ≈ 9.99
+
+Four methods are available:
+- aimnet2_wagen2024: AIMNet2-based; requires 3D structure; water only.
+- gxtb_wagen2026: g-xTB-based; requires 3D structure; water only; full periodic table.
+- chemprop_nevolianis2025: Chemprop-based; requires SMILES; several solvents supported.
+- starling: SMILES-based; water only.
+
+See documentation at: https://docs.rowansci.com/science/workflows/pka
+"""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples/pka")
+
+# 3D structure-based methods — pass a Molecule with coordinates
+mol = rowan.Molecule.from_smiles("c1ccccc1O")
+
+workflow = rowan.submit_pka_workflow(
+    initial_molecule=mol,
+    method="aimnet2_wagen2024",
+    name="Phenol pKa (aimnet2_wagen2024)",
+    folder=folder,
+)
+print(f"View at: https://labs.rowansci.com/pka/{workflow.uuid}")
+result = workflow.result()
+print(result)
+# e.g. <pKaResult acid=9.87>
+
+workflow2 = rowan.submit_pka_workflow(
+    initial_molecule=mol,
+    method="gxtb_wagen2026",
+    name="Phenol pKa (gxtb_wagen2026)",
+    folder=folder,
+)
+print(f"View at: https://labs.rowansci.com/pka/{workflow2.uuid}")
+result2 = workflow2.result()
+print(result2)
+# e.g. <pKaResult acid=9.92>
+
+# SMILES-based methods — pass a SMILES string directly
+smiles = "c1ccccc1O"
+
+workflow3 = rowan.submit_pka_workflow(
+    initial_molecule=smiles,
+    method="chemprop_nevolianis2025",
+    name="Phenol pKa (chemprop_nevolianis2025)",
+    folder=folder,
+)
+print(f"View at: https://labs.rowansci.com/pka/{workflow3.uuid}")
+result3 = workflow3.result()
+print(result3)
+# e.g. <pKaResult acid=9.75>
+
+workflow4 = rowan.submit_pka_workflow(
+    initial_molecule=smiles,
+    method="starling",
+    name="Phenol pKa (starling)",
+    folder=folder,
+)
+print(f"View at: https://labs.rowansci.com/pka/{workflow4.uuid}")
+result4 = workflow4.result()
+print(result4)
+# e.g. <pKaResult acid=9.81>

{rowan_python-3.0.4 → rowan_python-3.0.5}/pixi.lock

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-  sha256: e561593fccf61e8a20fc46dfc2dfe075b8be7d0188df33f221ad1f0139180f9d
+  version: 2.13.0
+  sha256: ab0078b90da5f3e2fd2e71e3d9b457ddcb35d0350854fbda93b451e28d56baaf
   requires_dist:
   - annotated-types>=0.6.0
-  - pydantic-core==2.41.5
+  - pydantic-core==2.46.0
   - typing-extensions>=4.14.1
   - typing-inspection>=0.4.2
   - email-validator>=2.0.0 ; extra == 'email'
   - tzdata ; python_full_version >= '3.9' and sys_platform == 'win32' and extra == 'timezone'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/4c/d2/ef2074dc020dd6e109611a8be4449b98cd25e1b9b8a303c2f0fca2f2bcf7/pydantic_core-2.41.5-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/35/95/3a0c6f65e231709fb3463e32943c69d10285cb50203a2130a4732053a06d/pydantic_core-2.46.0-cp314-cp314-macosx_11_0_arm64.whl
   name: pydantic-core
-  version: 2.41.5
-  sha256: 22f0fb8c1c583a3b6f24df2470833b40207e907b90c928cc8d3594b76f874375
+  version: 2.46.0
+  sha256: 0a36f2cc88170cc177930afcc633a8c15907ea68b59ac16bd180c2999d714940
   requires_dist:
   - typing-extensions>=4.14.1
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/74/1a/145646e5687e8d9a1e8d09acb278c8535ebe9e972e1f162ed338a622f193/pydantic_core-2.41.5-cp314-cp314-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/cb/e4/566101a561492ce8454f0844ca29c3b675a6b3a7b3ff577db85ed05c8c50/pydantic_core-2.46.0-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
   name: pydantic-core
-  version: 2.41.5
-  sha256: 1d1d9764366c73f996edd17abb6d9d7649a7eb690006ab6adbda117717099b14
+  version: 2.46.0
+  sha256: 67e2c2e171b78db8154da602de72ffdc473c6ee51de8a9d80c0f1cd4051abfc7
   requires_dist:
   - typing-extensions>=4.14.1
   requires_python: '>=3.9'
@@ -1531,8 +1531,8 @@ packages:
   requires_python: '>=3.10'
 - pypi: ./
   name: rowan-python
-  version: 3.0.4
-  sha256: 68bb5250327c5075096e931e0f397030cdb0a64fec9cb12c901fc97caba6f01d
+  version: 3.0.5
+  sha256: 0edb360654d940882164004a70b7a68baea296fd2ab32bd1e2ddab8a3e84fcf9
   requires_dist:
   - httpx
   - stjames>=0.0.174

{rowan_python-3.0.4 → rowan_python-3.0.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.0.4"
+version = "3.0.5"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.12"

{rowan_python-3.0.4 → rowan_python-3.0.5}/rowan/__init__.py

@@ -1,17 +1,25 @@
 # ruff: noqa
 from . import constants
 from stjames import (
+    Atom,
     Constraint,
     ConstraintType,
+    ConformerGenSettingsUnion,
     Correction,
     Engine,
+    ETKDGSettings,
+    iMTDSettings,
     Method,
     Mode,
+    MultiStageOptSettings,
     OptimizationSettings,
+    PBCDFTSettings,
+    PeriodicCell,
     Settings,
     SolventSettings,
     Task,
 )
+from stjames.pbc_dft_settings import PBCDFTSmearing
 from stjames.optimization.freezing_string_method import (
     FSMInterpolation,
     FSMOptimizationCoordinates,

{rowan_python-3.0.4 → rowan_python-3.0.5}/rowan/molecule.py

@@ -87,6 +87,32 @@ class Molecule(BaseModel):
         """
         return cls(_stjames=stj)
 
+    @classmethod
+    def from_atoms(
+        cls,
+        atoms: list[stjames.Atom],
+        charge: int = 0,
+        multiplicity: int = 1,
+        cell: stjames.PeriodicCell | None = None,
+    ) -> Self:
+        """
+        Create molecule from a list of atoms.
+
+        :param atoms: List of Atom objects.
+        :param charge: Molecular charge (default 0).
+        :param multiplicity: Spin multiplicity (default 1).
+        :param cell: PeriodicCell for periodic boundary conditions.
+        :returns: Molecule instance.
+        """
+        return cls(
+            _stjames=stjames.Molecule(
+                atoms=atoms,
+                charge=charge,
+                multiplicity=multiplicity,
+                cell=cell,
+            )
+        )
+
     def to_xyz(self) -> str:
         """Convert to XYZ format string."""
         return self._stjames.to_xyz()
@@ -184,6 +210,11 @@ class Molecule(BaseModel):
         """Thermal correction to Gibbs free energy (Hartree)."""
         return self._stjames.thermal_free_energy_corr
 
+    @property
+    def cell(self) -> stjames.PeriodicCell | None:
+        """Unit cell for periodic boundary conditions."""
+        return self._stjames.cell
+
     @property
     def gradient(self) -> list[tuple[float, float, float]] | None:
         """Nuclear gradient (Hartree/Bohr)."""

{rowan_python-3.0.4 → rowan_python-3.0.5}/rowan/workflows/analogue_docking.py

@@ -162,6 +162,9 @@ def submit_analogue_docking_workflow(
     executable: str = "vina",
     scoring_function: str = "vinardo",
     exhaustiveness: float = 8,
+    num_conformers_per_analogue: int = 100,
+    require_posebusters: bool = False,
+    run_local_optimization: bool = False,
     name: str = "Analogue Docking Workflow",
     folder_uuid: str | None = None,
     folder: Folder | None = None,
@@ -178,6 +181,9 @@ def submit_analogue_docking_workflow(
     :param executable: Which docking implementation to use.
     :param scoring_function: Which docking scoring function to use.
     :param exhaustiveness: Which exhaustiveness to employ.
+    :param num_conformers_per_analogue: Maximum number of conformers to generate per analogue.
+    :param require_posebusters: Filter conformers based on PoseBusters validity before docking.
+    :param run_local_optimization: Whether to run a local opt in docking pocket or just score.
     :param name: Name of the workflow.
     :param folder_uuid: UUID of the folder to place the workflow in.
     :param folder: Folder object to store the workflow in.
@@ -207,6 +213,9 @@ def submit_analogue_docking_workflow(
         initial_molecule=initial_molecule,
         protein=protein,
         docking_settings=docking_settings,
+        num_conformers_per_analogue=num_conformers_per_analogue,
+        require_posebusters=require_posebusters,
+        run_local_optimization=run_local_optimization,
     )
 
     data = {

{rowan_python-3.0.4 → rowan_python-3.0.5}/rowan/workflows/basic_calculation.py

@@ -9,6 +9,7 @@ from stjames import (
     Engine,
     Method,
     OptimizationSettings,
+    PBCDFTSettings,
     Settings,
     SolventSettings,
 )
@@ -159,6 +160,7 @@ def submit_basic_calculation_workflow(
     corrections: list[str] | None = None,
     solvent_settings: SolventSettings | dict[str, Any] | None = None,
     opt_settings: OptimizationSettings | dict[str, Any] | None = None,
+    pbc_dft_settings: PBCDFTSettings | dict[str, Any] | None = None,
     preset: PresetName | None = None,
     name: str = "Basic Calculation Workflow",
     folder_uuid: str | None = None,
@@ -179,6 +181,10 @@ def submit_basic_calculation_workflow(
     :param corrections: Dispersion corrections, see `Correction`.
     :param solvent_settings: Solvent settings as a dict or `SolventSettings`.
     :param opt_settings: Optimization settings as a dict or `OptimizationSettings`.
+    :param pbc_dft_settings: Periodic boundary condition DFT settings as a dict or
+        `PBCDFTSettings`. Specifies the plane-wave cutoff (Hartree), Monkhorst–Pack
+        k-point grid, and optional smearing. When set, the engine is automatically
+        set to Quantum ESPRESSO unless ``engine`` is explicitly provided.
     :param preset: Named preset, mutually exclusive with method/engine/basis_set/corrections.
         - `general_nnp` — omol25_conserving_s on omol25
         - `organic_nnp` — aimnet2_wb97md3 on aimnet2
@@ -203,6 +209,9 @@ def submit_basic_calculation_workflow(
     if folder:
         folder_uuid = folder.uuid
 
+    if isinstance(pbc_dft_settings, dict):
+        pbc_dft_settings = PBCDFTSettings(**pbc_dft_settings)
+
     if preset is not None:
         if any(x is not None for x in [method, engine, corrections, basis_set]):
             raise ValueError(
@@ -214,6 +223,7 @@ def submit_basic_calculation_workflow(
             mode=mode,
             solvent_settings=solvent_settings,
             **({"opt_settings": opt_settings} if opt_settings else {}),
+            **({"pbc_dft_settings": pbc_dft_settings} if pbc_dft_settings else {}),
         )
     else:
         if method is None:
@@ -228,6 +238,10 @@ def submit_basic_calculation_workflow(
         if isinstance(opt_settings, dict):
             opt_settings = stjames.OptimizationSettings(**opt_settings)
 
+        # pbc_dft_settings implies Quantum ESPRESSO; override engine unless explicitly set
+        if pbc_dft_settings is not None and engine is None:
+            engine = Engine.QUANTUM_ESPRESSO
+
         settings_kwargs: dict[str, Any] = {
             "method": method,
             "basis_set": basis_set,
@@ -236,8 +250,12 @@ def submit_basic_calculation_workflow(
             "corrections": corrections or [],
             "solvent_settings": solvent_settings,
         }
+        if engine is not None:
+            settings_kwargs["engine"] = engine
         if opt_settings is not None:
             settings_kwargs["opt_settings"] = opt_settings
+        if pbc_dft_settings is not None:
+            settings_kwargs["pbc_dft_settings"] = pbc_dft_settings
         settings = stjames.Settings(**settings_kwargs)
 
     initial_molecule = molecule_to_dict(initial_molecule)

{rowan_python-3.0.4 → rowan_python-3.0.5}/rowan/workflows/pka.py

@@ -23,13 +23,15 @@ class pKaMicrostate:
     """
     Microstate from a pKa calculation.
 
-    Available fields depend on the pKa method used:
-    aimnet2_wagen2024 provides delta_g; chemprop_nevolianis2025 provides smiles and uncertainty.
+    Available fields depend on the pKa method used. 3D structure-based methods
+    (aimnet2_wagen2024, gxtb_wagen2026) populate delta_g. SMILES-based methods
+    (chemprop_nevolianis2025, starling) populate smiles; chemprop_nevolianis2025
+    also populates uncertainty.
 
     :param atom_index: Index of the protonation site atom.
     :param pka: Predicted pKa value.
-    :param smiles: SMILES of the microstate (chemprop_nevolianis2025 only).
-    :param delta_g: Free energy of (de)protonation in kcal/mol (aimnet2_wagen2024 only).
+    :param smiles: SMILES of the microstate (SMILES-based methods only).
+    :param delta_g: Free energy of (de)protonation in kcal/mol (3D structure-based methods only).
     :param uncertainty: Prediction uncertainty (chemprop_nevolianis2025 only).
     """
 
@@ -40,6 +42,12 @@ class pKaMicrostate:
     uncertainty: float | None = None
 
 
+# Methods grouped by input type and solvent support
+_PKA_3D_METHODS = {"aimnet2_wagen2024", "gxtb_wagen2026"}
+_PKA_SMILES_METHODS = {"chemprop_nevolianis2025", "starling"}
+_PKA_WATER_ONLY_METHODS = {"aimnet2_wagen2024", "gxtb_wagen2026", "starling"}
+
+
 @register_result("pka")
 class pKaResult(WorkflowResult):
     """Result from a pKa workflow."""
@@ -95,19 +103,19 @@ class pKaResult(WorkflowResult):
         """
         Optimized structure calculations (lazily fetched).
 
-        Only available for aimnet2_wagen2024 method (3D structure-based).
+        Only available for 3D structure-based methods (aimnet2_wagen2024, gxtb_wagen2026).
 
         .. note::
             Makes one API call per structure on first access.
             Results are cached. Call clear_cache() to refresh.
 
-        :raises ValueError: If method is chemprop_nevolianis2025 (no structures).
+        :raises ValueError: If method is SMILES-based (chemprop_nevolianis2025, starling).
         """
         method = self._workflow.microscopic_pka_method
-        if method == "chemprop_nevolianis2025":
+        if method in _PKA_SMILES_METHODS:
             raise ValueError(
-                "chemprop_nevolianis2025 is SMILES-based and does not produce structures. "
-                "Use aimnet2_wagen2024 for 3D structure calculations."
+                f"{method} is SMILES-based and does not produce structures. "
+                "Use aimnet2_wagen2024 or gxtb_wagen2026 for 3D structure calculations."
             )
         if "structures" not in self._cache:
             uuids = self._get_structure_uuids()
@@ -118,7 +126,9 @@ class pKaResult(WorkflowResult):
 def submit_pka_workflow(
     initial_molecule: MoleculeInput | str,
     pka_range: tuple[int, int] = (2, 12),
-    method: Literal["aimnet2_wagen2024", "chemprop_nevolianis2025"] = "aimnet2_wagen2024",
+    method: Literal[
+        "aimnet2_wagen2024", "gxtb_wagen2026", "chemprop_nevolianis2025", "starling"
+    ] = "aimnet2_wagen2024",
     solvent: SolventInput = "water",
     deprotonate_elements: list[int] | None = None,
     protonate_elements: list[int] | None = None,
@@ -136,7 +146,11 @@ def submit_pka_workflow(
     :param initial_molecule: Molecule to calculate pKa for.
         Accepts Molecule, stjames.Molecule, RDKit Mol, dict, or SMILES string.
     :param pka_range: Range of pKa values to calculate.
-    :param method: Algorithm used to compute pKa values.
+    :param method: Algorithm used to compute pKa values:
+        - ``aimnet2_wagen2024``: AIMNet2-based; requires 3D structure; water only.
+        - ``gxtb_wagen2026``: g-xTB-based; requires 3D structure; water only; full periodic table.
+        - ``chemprop_nevolianis2025``: Chemprop-based; requires SMILES; several solvents supported.
+        - ``starling``: SMILES-based; water only.
     :param solvent: Solvent in which pKa values will be computed.
     :param deprotonate_elements: Elements to deprotonate (atomic numbers).
     :param protonate_elements: Elements to protonate (atomic numbers).
@@ -148,7 +162,7 @@ def submit_pka_workflow(
     :param webhook_url: URL that Rowan will POST to when the workflow completes.
     :param is_draft: If True, submit the workflow as a draft without starting execution.
     :returns: Workflow object representing the submitted workflow.
-    :raises ValueError: If method and input type don't match.
+    :raises ValueError: If method and input type don't match, or solvent is unsupported.
     :raises requests.HTTPError: if the request to the API fails.
     """
     if folder and folder_uuid:
@@ -163,16 +177,17 @@ def submit_pka_workflow(
     else:
         mol_dict = molecule_to_dict(initial_molecule)
 
-    # Validate method/input compatibility
-    if method == "aimnet2_wagen2024" and not mol_dict:
+    if method in _PKA_3D_METHODS and not mol_dict:
         raise ValueError(
-            "aimnet2_wagen2024 requires a 3D structure. Provide a Molecule, not a SMILES string."
+            f"{method} requires a 3D structure. Provide a Molecule, not a SMILES string."
         )
-    if method == "chemprop_nevolianis2025" and not initial_smiles:
+    if method in _PKA_SMILES_METHODS and not initial_smiles:
         raise ValueError(
-            "chemprop_nevolianis2025 requires a SMILES string. "
+            f"{method} requires a SMILES string. "
             "Provide a SMILES string, not a 3D structure."
         )
+    if method in _PKA_WATER_ONLY_METHODS and solvent != "water":
+        raise ValueError(f"{method} only supports water as solvent.")
 
     protonate_elements = protonate_elements or [7]
     deprotonate_elements = deprotonate_elements or [7, 8, 16]

{rowan_python-3.0.4 → rowan_python-3.0.5}/rowan/workflows/strain.py

@@ -1,6 +1,7 @@
 """Strain workflow - calculate molecular strain energy."""
 
 import math
+from typing import Any
 
 import stjames
 
@@ -113,6 +114,7 @@ def submit_strain_workflow(
     harmonic_constraint_spring_constant: float = 5.0,
     constrain_hydrogens: bool = False,
     conf_gen_settings: stjames.ConformerGenSettingsUnion | None = None,
+    multistage_opt_settings: stjames.MultiStageOptSettings | None = None,
     name: str = "Strain Workflow",
     folder_uuid: str | None = None,
     folder: Folder | None = None,
@@ -128,7 +130,9 @@ def submit_strain_workflow(
         constraints (kcal/mol/A). Default 5.0.
     :param constrain_hydrogens: Whether to constrain hydrogen positions. Default False.
     :param conf_gen_settings: Conformer generation settings. Defaults to ETKDG with
-        max 50 conformers.
+        max 200 conformers.
+    :param multistage_opt_settings: Optimization settings for conformer ranking.
+        Defaults to AIMNet2/wB97M-D3 optimization with CPCMx singlepoint.
     :param name: Name of the workflow.
     :param folder_uuid: UUID of the folder to store the workflow in.
     :param folder: Folder object to store the workflow in.
@@ -144,12 +148,16 @@ def submit_strain_workflow(
         folder_uuid = folder.uuid
     initial_molecule = molecule_to_dict(initial_molecule)
 
-    workflow = stjames.StrainWorkflow(
-        initial_molecule=initial_molecule,
-        harmonic_constraint_spring_constant=harmonic_constraint_spring_constant,
-        constrain_hydrogens=constrain_hydrogens,
-        conf_gen_settings=conf_gen_settings or stjames.ETKDGSettings(max_confs=50),
-    )
+    workflow_kwargs: dict[str, Any] = {
+        "initial_molecule": initial_molecule,
+        "harmonic_constraint_spring_constant": harmonic_constraint_spring_constant,
+        "constrain_hydrogens": constrain_hydrogens,
+        "conf_gen_settings": conf_gen_settings or stjames.ETKDGSettings(max_confs=200),
+    }
+    if multistage_opt_settings is not None:
+        workflow_kwargs["multistage_opt_settings"] = multistage_opt_settings
+
+    workflow = stjames.StrainWorkflow(**workflow_kwargs)
 
     data = {
         "workflow_type": "strain",

{rowan_python-3.0.4 → rowan_python-3.0.5}/rowan/workflows/tautomer_search.py

@@ -1,6 +1,7 @@
 """Tautomer-search workflow - find tautomeric forms of molecules."""
 
 from dataclasses import dataclass
+from typing import Any
 
 import stjames
 
@@ -105,6 +106,8 @@ class TautomerResult(WorkflowResult):
 def submit_tautomer_search_workflow(
     initial_molecule: MoleculeInput,
     mode: Mode = Mode.CAREFUL,
+    conf_gen_settings: stjames.ConformerGenSettingsUnion | None = None,
+    multistage_opt_settings: stjames.MultiStageOptSettings | None = None,
     name: str = "Tautomer Search Workflow",
     folder_uuid: str | None = None,
     folder: Folder | None = None,
@@ -116,7 +119,11 @@ def submit_tautomer_search_workflow(
     Submits a tautomer-search workflow to the API.
 
     :param initial_molecule: Molecule to find tautomers for.
-    :param mode: Mode to run the calculation in (reckless, rapid, careful).
+    :param mode: *Deprecated.*
+    :param conf_gen_settings: Conformer generation settings. Defaults to ETKDG with
+        250 initial conformers, 20 max conformers, and 15 kcal/mol MMFF energy cutoff.
+    :param multistage_opt_settings: Optimization settings for tautomer ranking.
+        Defaults to AIMNet2/wB97M-D3 optimization with CPCMx singlepoint.
     :param name: Name of the workflow.
     :param folder_uuid: UUID of the folder to place the workflow in.
     :param folder: Folder object to store the workflow in.
@@ -132,14 +139,17 @@ def submit_tautomer_search_workflow(
         folder_uuid = folder.uuid
     initial_molecule = molecule_to_dict(initial_molecule)
 
-    workflow = stjames.TautomerWorkflow(
-        initial_molecule=initial_molecule,
-        mode=mode,
-    )
+    workflow_kwargs: dict[str, Any] = {"initial_molecule": initial_molecule, "mode": mode}
+    if conf_gen_settings is not None:
+        workflow_kwargs["conf_gen_settings"] = conf_gen_settings
+    if multistage_opt_settings is not None:
+        workflow_kwargs["multistage_opt_settings"] = multistage_opt_settings
+
+    workflow = stjames.TautomerWorkflow(**workflow_kwargs)
 
     data = {
         "workflow_type": "tautomers",
-        "workflow_data": workflow.model_dump(mode="json"),
+        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
         "initial_molecule": initial_molecule,
         "name": name,
         "folder_uuid": folder_uuid,

rowan_python-3.0.4/examples/pka.py

@@ -1,43 +0,0 @@
-"""
-Calculate the pKa of the conjugate acid of pyridine using the Rowan API.
-
-Experimental value ≈5.23
-
-See documentiation at: https://docs.rowansci.com/science/workflows/pka
-and preprint at: https://rowansci.com/publications/pka-prediction
-"""
-
-import rowan
-
-# Set your API key or use the ROWAN_API_KEY environment variable
-# rowan.api_key = "rowan-sk..."
-folder = rowan.get_folder("examples/pka")
-
-workflow = rowan.submit_pka_workflow(
-    initial_molecule=rowan.Molecule.from_smiles("c1ccccc1O"),
-    method="aimnet2_wagen2024",
-    mode="reckless",
-    name="Pyridine pKa",
-    folder=folder,
-)
-
-print(
-    f"View pKa with aimnet2_wagen2024 privately at: https://labs.rowansci.com/pka/{workflow.uuid}"
-)
-result = workflow.result()
-print(result)
-# e.g. <pKaResult acid=4.75>
-
-workflow2 = rowan.submit_pka_workflow(
-    initial_molecule="c1ccccc1O",
-    method="chemprop_nevolianis2025",
-    name="Pyridine pKa (ML)",
-    folder=folder,
-)
-
-print(
-    f"View pKa with chemprop_nevolianis2025 privately at: https://labs.rowansci.com/pka/{workflow2.uuid}"
-)
-result2 = workflow2.result()
-print(result2)
-# e.g. <pKaResult acid=4.75>