rowan-python 2.0.0__py3-none-any.whl → 2.0.2__py3-none-any.whl

rowan/__init__.py

@@ -1,10 +1,8 @@
 # ruff: noqa
-
-from . import utils
-
 from . import constants
 
 from .folder import *
 from .workflow import *
 from .protein import *
 from .user import *
+from .utils import *

rowan/rowan_rdkit/chem_utils.py

@@ -97,24 +97,24 @@ apply_nest_asyncio()
 def _get_rdkit_mol_from_uuid(calculation_uuid: str) -> RdkitMol:
     stjames_mol_dict = rowan.retrieve_calculation_molecules(calculation_uuid)[-1]
 
-    return Chem.MolFromXYZBlock(stjames.Molecule(**stjames_mol_dict).to_xyz())  # type: ignore [attr-defined]
+    return Chem.MolFromXYZBlock(stjames.Molecule(**stjames_mol_dict).to_xyz())
 
 
 def _embed_rdkit_mol(rdkm: RdkitMol) -> RdkitMol:
     try:
-        AllChem.SanitizeMol(rdkm)
+        AllChem.SanitizeMol(rdkm)  # type: ignore [attr-defined]
     except Exception as e:
         raise ValueError("Molecule could not be generated -- invalid chemistry!") from e
 
-    rdkm = AllChem.AddHs(rdkm)
+    rdkm = AllChem.AddHs(rdkm)  # type: ignore [attr-defined]
     try:
-        assert AllChem.EmbedMolecule(rdkm, maxAttempts=200) >= 0
+        assert AllChem.EmbedMolecule(rdkm, maxAttempts=200) >= 0  # type: ignore [attr-defined]
     except AssertionError as e:
-        status1 = AllChem.EmbedMolecule(rdkm, maxAttempts=200, useRandomCoords=True)
+        status1 = AllChem.EmbedMolecule(rdkm, maxAttempts=200, useRandomCoords=True)  # type: ignore [attr-defined]
         if status1 < 0:
             raise ValueError("Cannot embed molecule!") from e
     try:
-        assert AllChem.MMFFOptimizeMolecule(rdkm, maxIters=200) >= 0  # type: ignore    [call-arg]
+        assert AllChem.MMFFOptimizeMolecule(rdkm, maxIters=200) >= 0  # type: ignore [attr-defined]
     except AssertionError:
         pass
 
@@ -477,9 +477,9 @@ async def _single_energy(
     get_api_key()
     method = stjames.Method(method)
 
-    if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+    if mol.GetNumConformers() == 0:
         mol = _embed_rdkit_mol(mol)
-        if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+        if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
 
     if method not in FAST_METHODS:
@@ -489,7 +489,7 @@ async def _single_energy(
 
     workflow_uuids = []
     for conformer in mol.GetConformers():
-        cid = conformer.GetId()  # type: ignore    [call-arg]
+        cid = conformer.GetId()
         stjames_mol = _rdkit_to_stjames(mol, cid)
         post = rowan.submit_workflow(
             name=name,
@@ -623,9 +623,9 @@ async def _single_optimize(
     get_api_key()
     method = stjames.Method(method)
 
-    if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+    if mol.GetNumConformers() == 0:
         mol = _embed_rdkit_mol(mol)
-        if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+        if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
 
     if method not in FAST_METHODS:
@@ -637,7 +637,7 @@ async def _single_optimize(
 
     workflow_uuids = []
     for conformer in mol.GetConformers():
-        cid = conformer.GetId()  # type: ignore    [call-arg]
+        cid = conformer.GetId()
         stjames_mol = _rdkit_to_stjames(mol, cid)
 
         post = rowan.submit_workflow(
@@ -677,7 +677,7 @@ async def _single_optimize(
     energies = [cacluation[-1]["energy"] for cacluation in calculations]
 
     for i, conformer in enumerate(optimized_mol.GetConformers()):
-        conformer.SetPositions(np.array(optimized_positions[i]))  # type: ignore  [attr-defined]
+        conformer.SetPositions(np.array(optimized_positions[i]))
 
     return {
         "molecule": mol,
@@ -796,9 +796,9 @@ async def _single_conformers(
     get_api_key()
     method = stjames.Method(method)
 
-    if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+    if mol.GetNumConformers() == 0:
         mol = _embed_rdkit_mol(mol)
-        if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+        if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
 
     if method not in FAST_METHODS:
@@ -858,12 +858,12 @@ async def _single_conformers(
     lowest_n_uuids = [item[1][0] for item in sorted_data[:num_conformers]]
     lowest_energies = [item[0] for item in sorted_data[:num_conformers]]
 
-    AllChem.EmbedMultipleConfs(mol, numConfs=num_conformers)
+    AllChem.EmbedMultipleConfs(mol, numConfs=num_conformers)  # type: ignore [attr-defined]
 
     for i, conformer in enumerate(mol.GetConformers()):
         atoms = rowan.retrieve_calculation_molecules(lowest_n_uuids[i])[-1]["atoms"]
         pos = [atom["position"] for atom in atoms]
-        conformer.SetPositions(np.array(pos))  # type: ignore  [attr-defined]
+        conformer.SetPositions(np.array(pos))
 
     return {
         "molecule": mol,
@@ -959,9 +959,9 @@ async def _single_charges(
     get_api_key()
     method = stjames.Method(method)
 
-    if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+    if mol.GetNumConformers() == 0:
         mol = _embed_rdkit_mol(mol)
-        if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+        if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
 
     if method not in FAST_METHODS:
@@ -971,7 +971,7 @@ async def _single_charges(
 
     workflow_uuids = []
     for conformer in mol.GetConformers():
-        cid = conformer.GetId()  # type: ignore    [call-arg]
+        cid = conformer.GetId()
 
         post = rowan.submit_workflow(
             name=name,

rowan/workflow.py

@@ -68,7 +68,7 @@ class Workflow(BaseModel):
         """
         Loads workflow data from the database and updates the current instance.
 
-        :param in_place: Whether to update the current instance in-place. 
+        :param in_place: Whether to update the current instance in-place.
         :return: The updated instance (self).
         :raises HTTPError: If the API request fails.
         """
@@ -217,7 +217,7 @@ class Workflow(BaseModel):
 
 
 def submit_workflow(
-    workflow_type: str,
+    workflow_type: stjames.WORKFLOW_NAME,
     workflow_data: dict[str, Any] | None = None,
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | None = None,
     initial_smiles: str | None = None,
@@ -241,6 +241,11 @@ def submit_workflow(
     :raises ValueError: If neither `initial_smiles` nor a valid `initial_molecule` is provided.
     :raises HTTPError: If the API request fails.
     """
+    if workflow_type not in stjames.WORKFLOW_MAPPING:
+        raise ValueError(
+            "Invalid workflow type. Must be one of:\n    " + "\n    ".join(stjames.WORKFLOW_MAPPING)
+        )
+
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
@@ -300,7 +305,7 @@ def list_workflows(
     public: bool | None = None,
     starred: bool | None = None,
     status: int | None = None,
-    workflow_type: str | None = None,
+    workflow_type: stjames.WORKFLOW_NAME | None = None,
     page: int = 0,
     size: int = 10,
 ) -> list[Workflow]:
@@ -411,7 +416,7 @@ def submit_conformer_search_workflow(
     conf_gen_mode: str = "rapid",
     final_method: stjames.Method | str = "aimnet2_wb97md3",
     solvent: str | None = None,
-    transistion_state: bool = False,
+    transition_state: bool = False,
     name: str = "Conformer Search Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
@@ -428,7 +433,7 @@ def submit_conformer_search_workflow(
     for options.
     :param solvent: The solvent to use for the final optimization. See [the list of available solvents](https://github.com/rowansci/stjames-public/blob/master/stjames/solvent.py)
         for valid values. Be aware that not all methods support solvents.
-    :param transistion_state: Whether to optimize the transition state.
+    :param transition_state: Whether to optimize the transition state.
     :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.
@@ -452,7 +457,7 @@ def submit_conformer_search_workflow(
         tasks=["optimize"],
         mode=stjames.Mode.AUTO,
         solvent_settings={"solvent": solvent, "model": solvent_model} if solvent else None,
-        opt_settings={"transition_state": transistion_state, "constraints": []},
+        opt_settings={"transition_state": transition_state, "constraints": []},
     )
 
     msos = stjames.MultiStageOptSettings(
@@ -466,7 +471,7 @@ def submit_conformer_search_workflow(
         "conf_gen_mode": conf_gen_mode,
         "mso_mode": "manual",
         "solvent": solvent,
-        "transistion_state": transistion_state,
+        "transition_state": transition_state,
     }
 
     data = {
@@ -639,7 +644,7 @@ def submit_fukui_workflow(
     optimization_method: str = "gfn2_xtb",
     fukui_method: str = "gfn1_xtb",
     solvent_settings: dict[str, str] | None = None,
-    name: str = "Redox Potential Workflow",
+    name: str = "Fukui Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
 ) -> Workflow:
@@ -647,9 +652,9 @@ def submit_fukui_workflow(
     Submits a fukui workflow to the API.
 
     :param initial_molecule: The molecule to calculate the fukui indices of.
-    :optimization_method: The method to use for the optimization.
-    :fukui_method: The method to use for the fukui calculation.
-    :solvent_settings: The solvent settings to use for the fukui calculation.
+    :param optimization_method: The method to use for the optimization.
+    :param fukui_method: The method to use for the fukui calculation.
+    :param solvent_settings: The solvent settings to use for the fukui calculation.
     :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.
@@ -665,9 +670,9 @@ def submit_fukui_workflow(
     fukui_settings = stjames.Settings(method=fukui_method, solvent_settings=solvent_settings)
 
     workflow_data = {
-        "opt_settings": optimization_settings,
+        "opt_settings": optimization_settings.model_dump(),
         "opt_engine": stjames.Method(optimization_method).default_engine(),
-        "fukui_settings": fukui_settings,
+        "fukui_settings": fukui_settings.model_dump(),
         "fukui_engine": stjames.Method(fukui_method).default_engine(),
     }
 
@@ -828,6 +833,56 @@ def submit_scan_workflow(
         return Workflow(**response.json())
 
 
+def submit_macropka_workflow(
+    initial_smiles: str,
+    min_pH: int = 0,
+    max_pH: int = 14,
+    min_charge: int = -2,
+    max_charge: int = 2,
+    compute_solvation_energy: bool = True,
+    name: str = "Macropka Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a macropka workflow to the API.
+
+    :param initial_smiles: The molecule used in the macropka workflow.
+    :param min_pH: The minimum pH to use in the 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_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.
+    :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.
+    """
+
+    workflow_data = {
+        "min_pH": min_pH,
+        "max_pH": max_pH,
+        "min_charge": min_charge,
+        "max_charge": max_charge,
+        "compute_solvation_energy": compute_solvation_energy,
+    }
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "macropka",
+        "workflow_data": workflow_data,
+        "initial_smiles": initial_smiles,
+        "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_irc_workflow(
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | None = None,
     method: stjames.Method | str = "uma_m_omol",

{rowan_python-2.0.0.dist-info → rowan_python-2.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.0.0
+Version: 2.0.2
 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-2.0.0.dist-info → rowan_python-2.0.2.dist-info}/RECORD

@@ -1,14 +1,14 @@
-rowan/__init__.py,sha256=KiUTRLxIjUZ__oJLeOzS28SfNPFLe5Y9PBIydjSkZFI,149
+rowan/__init__.py,sha256=KWt0ConmoDkmFZUk1lKO7eXFwRbaVU0oLLnYvOafLVc,148
 rowan/constants.py,sha256=ZZvv3L0b2y3dMGlWGeaRmx40J5tBrpxNxvJgjP1TNjg,37
 rowan/folder.py,sha256=n9WkjHMweQLtVcWUvCttOrmezvUdbFxam_eDEMzLF_A,6791
 rowan/protein.py,sha256=TOCsN50RaYh3Ja4GBxzH6R7qUk-Y9Xv7y1WU3buPFis,7778
 rowan/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rowan/user.py,sha256=Dl--NPUPATKCs2VmILsW8HnLiunG0Lxr0n6mKuHm21U,3891
 rowan/utils.py,sha256=SyKvrvlgZ2BKZKRKziZdVZvV_Y4Hld77Bris0lerA9o,3296
-rowan/workflow.py,sha256=Iq6ySvOxOJf30gIH9RtQMSRux9wgEVR0ctpMtjjgI8s,37488
+rowan/workflow.py,sha256=4BKDQJLVZsn65cM5SMfbub9M1GYOjF12GbdADhqaa1k,39496
 rowan/rowan_rdkit/__init__.py,sha256=EATX2VRzywzKxqkpCUMTf7RNQLkWsfi5VcCNDW6EIiw,503
-rowan/rowan_rdkit/chem_utils.py,sha256=1WAczzwNzIlghgP7eT2l2LhWW4yUpND5XC475q2lXaA,35044
-rowan_python-2.0.0.dist-info/METADATA,sha256=JdaZgAaitRmoHQ0Gl-jR7XyIGdXrw0-ktUNsKCw4ITA,1598
-rowan_python-2.0.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-rowan_python-2.0.0.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-rowan_python-2.0.0.dist-info/RECORD,,
+rowan/rowan_rdkit/chem_utils.py,sha256=i7-EmAcmvHYtc9NiZblLY_k2DoQKofAZo5KT2qtkUCI,34775
+rowan_python-2.0.2.dist-info/METADATA,sha256=dnQGAYLRXOsMxaKdBt5NjQBd6osWMXCDtNoTkwRjDIQ,1598
+rowan_python-2.0.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+rowan_python-2.0.2.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+rowan_python-2.0.2.dist-info/RECORD,,