rowan-python 2.1.5__py3-none-any.whl → 2.1.7__py3-none-any.whl

rowan/workflow.py

@@ -5,6 +5,7 @@ from typing import Any, Literal, Self, TypeAlias
 import stjames
 from pydantic import BaseModel, Field
 from rdkit import Chem
+from stjames.optimization.freezing_string_method import FSMSettings
 
 from .protein import Protein
 from .utils import api_client
@@ -285,16 +286,21 @@ def retrieve_workflow(uuid: str) -> Workflow:
         return Workflow(**response.json())
 
 
-def retrieve_calculation_molecules(uuid: str) -> list[dict[str, Any]]:
+def retrieve_calculation_molecules(
+    uuid: str, return_frequencies: bool = False
+) -> list[dict[str, Any]]:
     """
     Retrieves a list of molecules from a calculation.
 
     :param uuid: The UUID of the calculation to retrieve molecules from.
+    :param return_frequencies: Whether to return the frequencies of the molecules.
     :return: A list of dictionaries representing the molecules in the calculation.
     :raises HTTPError: If the API request fails.
     """
     with api_client() as client:
-        response = client.get(f"/calculation/{uuid}/molecules")
+        response = client.get(
+            f"/calculation/{uuid}/molecules", params={"return_frequencies": return_frequencies}
+        )
         response.raise_for_status()
         return response.json()
 
@@ -352,9 +358,10 @@ def list_workflows(
 def submit_basic_calculation_workflow(
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
     method: stjames.Method | str = "uma_m_omol",
+    basis_set: stjames.BasisSet | str | None = None,
     tasks: list[str] | None = None,
     mode: str = "auto",
-    engine: str = "omol25",
+    engine: str | None = None,
     name: str = "Basic Calculation Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
@@ -364,7 +371,7 @@ def submit_basic_calculation_workflow(
 
     :param initial_molecule: The molecule to perform the calculation on.
     :param method: The method to use for the calculation.
-    See [list of available methods](https://github.com/rowansci/stjames-public/blob/master/stjames/method.py)
+    :param basis_set: The basis_set to use (if any).
     for options.
     :param tasks: A list of tasks to perform for the calculation.
     :param mode: The mode to run the calculation in. See [list of available modes](https://github.com/rowansci/stjames-public/blob/master/stjames/mode.py)
@@ -391,6 +398,7 @@ def submit_basic_calculation_workflow(
         initial_molecule=initial_molecule,
         settings=stjames.Settings(
             method=method,
+            basis_set=basis_set,
             tasks=tasks,
             mode=mode,
         ),
@@ -792,7 +800,7 @@ def submit_descriptors_workflow(
 def submit_scan_workflow(
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
     scan_settings: stjames.ScanSettings | dict[str, Any] | None = None,
-    calculation_engine: str = "omol25",
+    calculation_engine: str | None = None,
     calculation_method: stjames.Method | str = "uma_m_omol",
     wavefront_propagation: bool = True,
     name: str = "Scan Workflow",
@@ -835,7 +843,7 @@ def submit_scan_workflow(
         initial_molecule=initial_molecule,
         scan_settings=scan_settings,
         calc_settings=calc_settings,
-        calc_engine=calculation_engine,
+        calc_engine=calculation_engine or calculation_method.default_engine(),
         wavefront_propagation=wavefront_propagation,
     )
 
@@ -911,7 +919,6 @@ def submit_macropka_workflow(
 def submit_irc_workflow(
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | None = None,
     method: stjames.Method | str = "uma_m_omol",
-    engine: str = "omol25",
     preopt: bool = True,
     step_size: float = 0.05,
     max_irc_steps: int = 30,
@@ -926,7 +933,6 @@ def submit_irc_workflow(
     :param method: The computational method to use for the IRC calculation.
     See [list of available methods](https://github.com/rowansci/stjames-public/blob/master/stjames/method.py)
     for options.
-    :param engine: The computational engine to use for the calculation. See [list of available engines](https://github.com/rowansci/stjames-public/blob/master/stjames/engine.py)
     :param preopt: Whether to perform a pre-optimization of the molecule.
     :param step_size: The step size to use for the IRC calculation.
     :param max_irc_steps: The maximum number of IRC steps to perform.
@@ -953,12 +959,12 @@ def submit_irc_workflow(
             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,
@@ -980,6 +986,8 @@ 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 +1001,8 @@ 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 +1018,10 @@ 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 +1076,7 @@ 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 +1197,89 @@ 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())
+
+
+def submit_double_ended_ts_search_workflow(
+    reactant: dict[str, Any] | StJamesMolecule,
+    product: dict[str, Any] | StJamesMolecule,
+    calculation_settings: stjames.Settings | dict[str, Any] | None = None,
+    search_settings: FSMSettings | dict[str, Any] | None = None,
+    optimize_inputs: bool = False,
+    optimize_ts: bool = True,
+    name: str = "Double-Ended TS Search Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a double-ended transition state search workflow to the API.
+
+    :param reactant: reactant Molecule.
+    :param product: product Molecule.
+    :param calculation_settings: Settings to use for calculations.
+    :param search_settings: settings to use for the transition state search.
+    :param optimize_inputs: Whether to optimize the reactant and product before the search.
+    :param optimize_ts: Whether to optimize the found transition state.
+    :param name: name of the workflow.
+    :param folder_uuid: The UUID of the folder to place the workflow in.
+    :param max_credits: The maximum number of credits to use for the workflow.
+    :return: Workflow object representing the submitted workflow.
+    """
+    workflow = stjames.DoubleEndedTSSearchWorkflow(
+        reactant=reactant,
+        product=product,
+        calculation_settings=calculation_settings,
+        search_settings=search_settings,
+        optimize_inputs=optimize_inputs,
+        optimize_ts=optimize_ts,
+    )
+    data = {
+        "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(),
+        "max_credits": max_credits,
+    }
+
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())

{rowan_python-2.1.5.dist-info → rowan_python-2.1.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.5
+Version: 2.1.7
 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.dist-info → rowan_python-2.1.7.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=64II-cPOe_SFJK302Bm8hP62d_3_CgnTVYCbn3zKT7U,3334
-rowan/workflow.py,sha256=y5Jn-MuWYSNPimyrz4X5D2h7IJqeVViezrnLtuDmk0U,44988
+rowan/workflow.py,sha256=ec4ygHqsyldHn6-gpyPwzHfsGcQXRZOauIjdHtdzJuE,48826
 rowan/rowan_rdkit/__init__.py,sha256=EATX2VRzywzKxqkpCUMTf7RNQLkWsfi5VcCNDW6EIiw,503
 rowan/rowan_rdkit/chem_utils.py,sha256=i7-EmAcmvHYtc9NiZblLY_k2DoQKofAZo5KT2qtkUCI,34775
-rowan_python-2.1.5.dist-info/METADATA,sha256=iJPuEi74RV_XDnSZ2yWSQv5eY1mGzWEI5Oh0CmIgHwA,1599
-rowan_python-2.1.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-rowan_python-2.1.5.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-2.1.5.dist-info/RECORD,,
+rowan_python-2.1.7.dist-info/METADATA,sha256=XWltMwFRX9VyDOTy7rUE86IDXL8xBakq-SCcJpDBOPo,1599
+rowan_python-2.1.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+rowan_python-2.1.7.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-2.1.7.dist-info/RECORD,,