rowan-python 2.1.13__py3-none-any.whl → 2.1.15__py3-none-any.whl

rowan/workflow.py

@@ -22,7 +22,7 @@ StJamesMolecule: TypeAlias = stjames.Molecule
 class Workflow(BaseModel):
     """A Rowan workflow.
 
-    Don’t instantiate this class directly. Instead use one of the submit workflow functions.
+    Don't instantiate this class directly. Instead use one of the submit workflow functions.
     Workflow data is not loaded by default to avoid unnecessary downloads that could impact
     performance. Call `load_data()` to fetch and attach the workflow data to this `Workflow` object.
 
@@ -575,7 +575,7 @@ def submit_basic_calculation_workflow(
 
 def submit_conformer_search_workflow(
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
-    conf_gen_mode: str = "rapid",
+    conf_gen_settings: stjames.ConformerGenSettings,
     final_method: stjames.Method | str = "aimnet2_wb97md3",
     solvent: str | None = None,
     transition_state: bool = False,
@@ -587,9 +587,7 @@ def submit_conformer_search_workflow(
     Submits a conformer search workflow to the API.
 
     :param initial_molecule: The molecule to perform the conformer search on.
-    :param conf_gen_mode: The mode to use for conformer generation. See
-    [list of available modes](https://github.com/rowansci/stjames-public/blob/master/stjames/mode.py)
-    for options.
+    :param conf_gen_settings: settings for conformer generation
     :param final_method: The method to use for the final optimization.
     See [list of available methods](https://github.com/rowansci/stjames-public/blob/master/stjames/method.py)
     for options.
@@ -631,8 +629,7 @@ def submit_conformer_search_workflow(
     workflow = stjames.ConformerSearchWorkflow(
         initial_molecule=initial_molecule,
         multistage_opt_settings=msos,
-        conf_gen_mode=conf_gen_mode,
-        mso_mode="manual",
+        conf_gen_settings=conf_gen_settings,
         solvent=solvent,
         transition_state=transition_state,
     )
@@ -1210,7 +1207,7 @@ def submit_protein_cofolding_workflow(
 def submit_docking_workflow(
     protein: str | Protein,
     pocket: list[list[float]],
-    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | None = None,
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
     executable: str = "vina",
     scoring_function: str = "vinardo",
     exhaustiveness: float = 8,
@@ -1255,7 +1252,7 @@ def submit_docking_workflow(
 
     workflow = stjames.DockingWorkflow(
         initial_molecule=initial_molecule,
-        target_uuid=protein,
+        protein=protein,
         pocket=pocket,
         do_csearch=do_csearch,
         do_optimization=do_optimization,
@@ -1475,8 +1472,20 @@ def submit_pose_analysis_md_workflow(
     protein: str | Protein,
     initial_smiles: str,
     num_trajectories: int = 1,
-    simulation_time_ns: int = 10,
+    equilibration_time_ns: float = 1,
+    simulation_time_ns: float = 10,
+    temperature: float = 300,
+    pressure_atm: float = 1.0,
+    langevin_timescale_ps: float = 1.0,
+    timestep_fs: float = 2,
+    constrain_hydrogens: bool = True,
+    nonbonded_cutoff: float = 8.0,
+    ionic_strength_M: float = 0.10,
+    water_buffer: float = 6.0,
     ligand_residue_name: str = "LIG",
+    protein_restraint_cutoff: float | None = None,
+    protein_restraint_constant: float = 100,
+    save_solvent: bool = False,
     name: str = "Pose-Analysis MD Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
@@ -1485,11 +1494,23 @@ def submit_pose_analysis_md_workflow(
     Submits a pose-analysis MD workflow to the API.
 
     :param protein: The *holo* protein on which MD will be run.
-        Can be input as a uuid or a Protein object.
+        Can be input as a UUID or a Protein object.
     :param initial_smiles: The SMILES for the ligand.
     :param num_trajectories: The number of trajectories to run.
-    :param simulation_time_ns: How long to run the simulation for, in nanoseconds.
+    :param equilibration_time_ns: how long to equilibrate trajectories for, in ns
+    :param simulation_time_ns: how long to run trajectories for, in ns
+    :param temperature: temperature, in K
+    :param pressure_atm: pressure, in atm
+    :param langevin_timescale_ps: timescale for the Langevin integrator, in ps⁻¹
+    :param timestep_fs: timestep, in femtoseconds
     :param ligand_residue_name: The name of the residue corresponding to the ligand.
+    :param constrain_hydrogens: whether or not to use SHAKE to freeze bonds to hydrogen
+    :param nonbonded_cutoff: nonbonded cutoff for particle-mesh Ewald, in Å
+    :param ionic_strength_M: ionic strength of the solution, in M (molar)
+    :param water_buffer: amount of water to add around the protein, in Å
+    :param protein_restraint_cutoff: cutoff past which alpha-carbons will be constrained, in Å
+    :param protein_restraint_constant: force constant for backbone restraints, in kcal/mol/Ų
+    :param save_solvent: whether to save solvent molecules
     :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.
@@ -1501,11 +1522,23 @@ def submit_pose_analysis_md_workflow(
         protein = protein.uuid
 
     workflow = stjames.PoseAnalysisMolecularDynamicsWorkflow(
-        protein_uuid=protein,
+        protein=protein,
         initial_smiles=initial_smiles,
         num_trajectories=num_trajectories,
+        equilibration_time_ns=equilibration_time_ns,
         simulation_time_ns=simulation_time_ns,
+        temperature=temperature,
+        pressure_atm=pressure_atm,
+        langevin_timescale_ps=langevin_timescale_ps,
+        timestep_fs=timestep_fs,
         ligand_residue_name=ligand_residue_name,
+        constrain_hydrogens=constrain_hydrogens,
+        nonbonded_cutoff=nonbonded_cutoff,
+        ionic_strength_M=ionic_strength_M,
+        water_buffer=water_buffer,
+        protein_restraint_cutoff=protein_restraint_cutoff,
+        protein_restraint_constant=protein_restraint_constant,
+        save_solvent=save_solvent,
     )
 
     data = {
@@ -1558,6 +1591,7 @@ def submit_batch_docking_workflow(
     workflow = stjames.BatchDockingWorkflow(
         initial_smiles_list=smiles_list,
         target=protein,
+        protein=protein,
         pocket=pocket,
         docking_settings=docking_settings,
     )
@@ -1710,3 +1744,143 @@ def submit_membrane_permeability_workflow(
         response = client.post("/workflow", json=data)
         response.raise_for_status()
         return Workflow(**response.json())
+
+
+def submit_analogue_docking_workflow(
+    analogues: list[str],
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    protein: str | Protein,
+    executable: str = "vina",
+    scoring_function: str = "vinardo",
+    exhaustiveness: float = 8,
+    name: str = "Analogue Docking Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits an analogue docking workflow to the API.
+
+    :param smiles_list: The SMILES strings to dock.
+    :param initial_molecule: The template to which to align molecules to.
+    :param protein: The protein to dock. Can be input as a uuid or a Protein object.
+    :param executable: Which docking implementation to use.
+    :param scoring_function: Which docking scoring function to use.
+    :param exhaustiveness: Which exhaustiveness to employ.
+    :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.
+    :return: A Workflow object representing the submitted batch docking workflow.
+    :raises requests.HTTPError: if the request to the API fails.
+    """
+
+    docking_settings = {
+        "executable": executable,
+        "exhaustiveness": exhaustiveness,
+        "scoring_function": scoring_function,
+    }
+
+    if isinstance(initial_molecule, StJamesMolecule):
+        initial_molecule = initial_molecule.model_dump(mode="json")
+    elif isinstance(initial_molecule, RdkitMol):
+        initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0).model_dump(
+            mode="json"
+        )
+
+    if isinstance(protein, Protein):
+        protein = protein.uuid
+
+    workflow = stjames.AnalogueDockingWorkflow(
+        analogues=analogues,
+        initial_molecule=initial_molecule,
+        protein=protein,
+        docking_settings=docking_settings,
+    )
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "initial_molecule": initial_molecule,
+        "workflow_type": "analogue_docking",
+        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
+        "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_protein_md_workflow(
+    protein: str | Protein,
+    num_trajectories: int = 1,
+    equilibration_time_ns: float = 1,
+    simulation_time_ns: float = 10,
+    temperature: float = 300,
+    pressure_atm: float = 1.0,
+    langevin_timescale_ps: float = 1.0,
+    timestep_fs: float = 2,
+    constrain_hydrogens: bool = True,
+    nonbonded_cutoff: float = 8.0,
+    ionic_strength_M: float = 0.10,
+    water_buffer: float = 6.0,
+    save_solvent: bool = False,
+    name: str = "Protein MD Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a pose-analysis MD workflow to the API.
+
+    :param protein: The *holo* protein on which MD will be run.
+        Can be input as a UUID or a Protein object.
+    :param num_trajectories: The number of trajectories to run.
+    :param equilibration_time_ns: how long to equilibrate trajectories for, in ns
+    :param simulation_time_ns: how long to run trajectories for, in ns
+    :param temperature: temperature, in K
+    :param pressure_atm: pressure, in atm
+    :param langevin_timescale_ps: timescale for the Langevin integrator, in ps⁻¹
+    :param timestep_fs: timestep, in femtoseconds
+    :param constrain_hydrogens: whether or not to use SHAKE to freeze bonds to hydrogen
+    :param nonbonded_cutoff: nonbonded cutoff for particle-mesh Ewald, in Å
+    :param ionic_strength_M: ionic strength of the solution, in M (molar)
+    :param water_buffer: amount of water to add around the protein, in Å
+    :param save_solvent: whether solvent should be saed
+    :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.
+    :return: A Workflow object representing the submitted workflow.
+    :raises requests.HTTPError: if the request to the API fails.
+    """
+
+    if isinstance(protein, Protein):
+        protein = protein.uuid
+
+    workflow = stjames.ProteinMolecularDynamicsWorkflow(
+        protein=protein,
+        num_trajectories=num_trajectories,
+        equilibration_time_ns=equilibration_time_ns,
+        simulation_time_ns=simulation_time_ns,
+        temperature=temperature,
+        pressure_atm=pressure_atm,
+        langevin_timescale_ps=langevin_timescale_ps,
+        timestep_fs=timestep_fs,
+        constrain_hydrogens=constrain_hydrogens,
+        nonbonded_cutoff=nonbonded_cutoff,
+        ionic_strength_M=ionic_strength_M,
+        water_buffer=water_buffer,
+        save_solvent=save_solvent,
+    )
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "protein_md",
+        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
+        "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-2.1.13.dist-info → rowan_python-2.1.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.13
+Version: 2.1.15
 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>=0.0.144
+Requires-Dist: stjames>=0.0.155
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-2.1.13.dist-info → rowan_python-2.1.15.dist-info}/RECORD

@@ -6,10 +6,10 @@ rowan/protein.py,sha256=mFSVCr-08bSikXBUtJtSWzjKcVAuBmTeRckn7JUHYSE,8810
 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=hsRh0J6bdNs78eByuL5G3_k1CrNQg2szR5sPPalWTMA,65376
+rowan/workflow.py,sha256=QQWHTZ_O3PF2WbegYLPIKiszOEYj1frPKbI8U-B1muc,72419
 rowan/rowan_rdkit/__init__.py,sha256=EATX2VRzywzKxqkpCUMTf7RNQLkWsfi5VcCNDW6EIiw,503
 rowan/rowan_rdkit/chem_utils.py,sha256=sKCzul2e0ldVYTBImhTwso7ddNgPKmvS-OmvCEjVJH0,34788
-rowan_python-2.1.13.dist-info/METADATA,sha256=3zsPCrGRWTd9snLuYFsleM0iDWkChWQaOEaiGExtLbY,1601
-rowan_python-2.1.13.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rowan_python-2.1.13.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-2.1.13.dist-info/RECORD,,
+rowan_python-2.1.15.dist-info/METADATA,sha256=1E2yvHK_we1jaf5zvI7q3V3vGkjlXDx1f7ma71P_Ef4,1601
+rowan_python-2.1.15.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rowan_python-2.1.15.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-2.1.15.dist-info/RECORD,,