rowan-python 2.1.4__py3-none-any.whl → 2.1.6__py3-none-any.whl

rowan/constants.py

@@ -1 +1,3 @@
-API_URL = "https://api.rowansci.com"
+import os
+
+API_URL = os.getenv("ROWAN_API_URL", default="https://api.rowansci.com")

rowan/utils.py

@@ -47,6 +47,7 @@ def api_client() -> Generator[httpx.Client, None, None]:
     with httpx.Client(
         base_url=API_URL,
         headers={"X-API-Key": get_api_key()},
+        timeout=30,
     ) as client:
         yield client
 

rowan/workflow.py

@@ -860,8 +860,8 @@ def submit_macropka_workflow(
     max_pH: int = 14,
     min_charge: int = -2,
     max_charge: int = 2,
+    compute_solvation_energy: bool = False,
     compute_aqueous_solubility: bool = False,
-    compute_solvation_energy: bool = True,
     name: str = "Macropka Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
@@ -980,6 +980,8 @@ 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 +995,8 @@ 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 +1012,10 @@ 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,
@@ -1027,8 +1034,9 @@ def submit_docking_workflow(
     protein: str | Protein,
     pocket: list[list[float]],
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | None = None,
-    do_csearch: bool = True,
-    do_optimization: bool = True,
+    do_csearch: bool = False,
+    do_optimization: bool = False,
+    do_pose_refinement: bool = False,
     name: str = "Docking Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
@@ -1040,6 +1048,7 @@ def submit_docking_workflow(
     :param initial_molecule: The initial molecule to be docked
     :param do_csearch: Whether to perform a conformational search on the ligand.
     :param do_optimization: Whether to perform an optimization on the ligand.
+    :param do_pose_refinement: Whether or not to optimize output poses.
     :param name: The 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.
@@ -1061,6 +1070,7 @@ def submit_docking_workflow(
         pocket=pocket,
         do_csearch=do_csearch,
         do_optimization=do_optimization,
+        do_pose_refinement=do_pose_refinement,
     )
 
     data = {
@@ -1076,3 +1086,146 @@ def submit_docking_workflow(
         response = client.post("/workflow", json=data)
         response.raise_for_status()
         return Workflow(**response.json())
+
+
+def submit_ion_mobility_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    temperature: float = 300,
+    protonate: bool = False,
+    do_csearch: bool = True,
+    do_optimization: bool = True,
+    name: str = "Ion-Mobility Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits an ion-mobility workflow to the API.
+
+    :param initial_molecule: The molecule used in the scan.
+    :param temperature: The temperature at which to predict CCS values.
+    :param protonate: Whether or not to automatically detect protonation site.
+        If `True`, every basic site will be protonated and values returned for the most stable.
+    :param do_csearch: Whether to perform a conformational search on the molecule.
+    :param do_optimization: Whether to perform an optimization on the molecule.
+    :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.IonMobilityWorkflow(
+        initial_molecule=initial_molecule,
+        temperature=temperature,
+        protonate=protonate,
+        do_csearch=do_csearch,
+        do_optimization=do_optimization,
+    )
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "ion_mobility",
+        "workflow_data": workflow.model_dump(),
+        "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_nmr_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    solvent: str | None = "chloroform",
+    do_csearch: bool = True,
+    do_optimization: bool = True,
+    name: str = "NMR Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits an NMR-prediction workflow to the API.
+
+    :param initial_molecule: The molecule used in the scan.
+    :param solvent: The solvent in which to compute NMR spectra.
+    :param do_csearch: Whether to perform a conformational search on the input structure.
+    :param do_optimization: Whether to perform an optimization on the input structure.
+    :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_data = {"initial_molecule": initial_molecule, "solvent": solvent}
+
+    if not do_csearch:
+        workflow_data["conf_gen_settings"] = None
+
+    if not do_optimization:
+        workflow_data["multistage_opt_settings"] = None
+
+    workflow = stjames.NMRSpectroscopyWorkflow.model_validate(workflow_data)
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "nmr",
+        "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_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())

{rowan_python-2.1.4.dist-info → rowan_python-2.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.4
+Version: 2.1.6
 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>=0.0.83
+Requires-Dist: stjames>=0.0.109
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-2.1.4.dist-info → rowan_python-2.1.6.dist-info}/RECORD

@@ -1,15 +1,15 @@
 rowan/__init__.py,sha256=2rz6dW0l9DzawiFi6S0WSv8XlZq1CoTBKJrsJ1uesvk,171
-rowan/constants.py,sha256=ZZvv3L0b2y3dMGlWGeaRmx40J5tBrpxNxvJgjP1TNjg,37
+rowan/constants.py,sha256=emCH4m9OL2Hm5E-6mJGM_FgzrK_JrZT-FiKJ6pMNQ4Y,84
 rowan/folder.py,sha256=n9WkjHMweQLtVcWUvCttOrmezvUdbFxam_eDEMzLF_A,6791
 rowan/project.py,sha256=ALPPkMa_cg7w5OkXno1cs6acCofw8AOUYRSeWgr3L0o,3774
 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=uFgI-yTSHW6JY5KulpnGPdM3Xrl0UGYtne9OnDIkzz8,40729
+rowan/utils.py,sha256=64II-cPOe_SFJK302Bm8hP62d_3_CgnTVYCbn3zKT7U,3334
+rowan/workflow.py,sha256=EGcqPv2K-CCt8t_FSVAGTaI7QCM4BJdY--kN4PHvhOo,46749
 rowan/rowan_rdkit/__init__.py,sha256=EATX2VRzywzKxqkpCUMTf7RNQLkWsfi5VcCNDW6EIiw,503
 rowan/rowan_rdkit/chem_utils.py,sha256=i7-EmAcmvHYtc9NiZblLY_k2DoQKofAZo5KT2qtkUCI,34775
-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,,
+rowan_python-2.1.6.dist-info/METADATA,sha256=rNw5EUh2Dz3xfBKUtFHtIPykxSVegqydghdhhq-q3XI,1599
+rowan_python-2.1.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+rowan_python-2.1.6.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-2.1.6.dist-info/RECORD,,