rowan-python 2.1.14__py3-none-any.whl → 2.1.16__py3-none-any.whl

rowan/workflow.py

@@ -72,6 +72,21 @@ class Workflow(BaseModel):
     def __repr__(self) -> str:
         return f"<Workflow name='{self.name}' created_at='{self.created_at}' uuid='{self.uuid}'>"
 
+    def __str__(self) -> str:
+        created = self.created_at.strftime("%Y-%m-%d %H:%M:%S") if self.created_at else "N/A"
+        elapsed = f"{self.elapsed:.2f}s" if self.elapsed is not None else "not submitted"
+        status = self.status.name.lower() if self.status is not None else "not submitted"
+        lines = [
+            f"Workflow: {self.name}",
+            f"  UUID:     {self.uuid}",
+            f"  Type:     {self.workflow_type}",
+            f"  Status:   {status}",
+            f"  Created:  {created}",
+            f"  Elapsed:  {elapsed}",
+            f"  Credits charged:  {self.credits_charged}",
+        ]
+        return "\n".join(lines)
+
     def fetch_latest(self, in_place: bool = False) -> Self:
         """
         Loads workflow data from the database and updates the current instance.
@@ -371,13 +386,12 @@ def batch_submit_workflow(
     if names:
         if initial_molecules and len(names) != len(initial_molecules):
             logger.warning(
-                "The number of names is not the same as the number of initial "
-                "molecules. Generic names of the form 'Batch Workflow {i}' "
-                "will be used."
+                "The number of names is not the same as the number of initial molecules. "
+                "Generic names of the form 'Batch Workflow {i}' will be used."
             )
         if initial_smileses and len(names) != len(initial_smileses):
             logger.warning(
-                "The number of names is not the same as the number of initial SMILES."
+                "The number of names is not the same as the number of initial SMILES. "
                 "Generic names of the form 'Batch Workflow {i}' will be used."
             )
 
@@ -1166,18 +1180,20 @@ def submit_protein_cofolding_workflow(
 
     :param initial_protein_sequences: The sequences of the proteins to be cofolded.
     :param initial_smiles_list: A list of SMILES strings for the ligands to be cofolded with.
-    :param ligand_binding_affinity_index: The index of the ligand for which to compute the binding affinity.
+    :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 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.
     :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.
-    """  # noqa: E501
+    """
 
     workflow = stjames.ProteinCofoldingWorkflow(
         use_msa_server=use_msa_server,
@@ -1338,9 +1354,9 @@ def submit_nmr_workflow(
     max_credits: int | None = None,
 ) -> Workflow:
     """
-    Submits an NMR-prediction workflow to the API.
+    Submits a Nuclear Magnetic Resonance (NMR) prediction workflow to the API.
 
-    :param initial_molecule: The molecule used in the scan.
+    :param initial_molecule: The molecule to predict NMR spectra for.
     :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.
@@ -1491,7 +1507,7 @@ def submit_pose_analysis_md_workflow(
     max_credits: int | None = None,
 ) -> Workflow:
     """
-    Submits a pose-analysis MD workflow to the API.
+    Submits a Pose-Analysis Molecular Dynamics (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.
@@ -1618,7 +1634,7 @@ def submit_msa_workflow(
     max_credits: int | None = None,
 ) -> Workflow:
     """
-    Submits a multiple sequence alignment (MSA) workflow to the API.
+    Submits a Multiple Sequence Alignment (MSA) workflow to the API.
 
     :param initial_protein_sequences: List of protein sequences to align, as ProteinSequence objects
     sor strings.
@@ -1655,9 +1671,10 @@ def submit_admet_workflow(
     max_credits: int | None = None,
 ) -> Workflow:
     """
-    Submits an ADMET workflow to the API.
+    Submits an Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET)
+    workflow to the API.
 
-    :param initial_smiles: The molecule used in the workflow.
+    :param initial_smiles: The molecule to calculate ADMET properties for.
     :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.
@@ -1830,7 +1847,7 @@ def submit_protein_md_workflow(
     max_credits: int | None = None,
 ) -> Workflow:
     """
-    Submits a pose-analysis MD workflow to the API.
+    Submits a Protein Molecular Dynamics (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.
@@ -1884,3 +1901,330 @@ def submit_protein_md_workflow(
         response = client.post("/workflow", json=data)
         response.raise_for_status()
         return Workflow(**response.json())
+
+
+def submit_bde_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    mode: str = "rapid",
+    atoms: list[int] | None = None,
+    all_CH: bool = False,
+    all_CX: bool = False,
+    name: str = "BDE Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a bond dissociation energy (BDE) workflow to the API.
+
+    :param initial_molecule: The molecule to calculate BDEs for.
+    :param mode: The mode to run the calculation in.
+    :param atoms: List of atom indices (1-indexed) to dissociate.
+    :param all_CH: Whether to dissociate all C-H bonds.
+    :param all_CX: Whether to dissociate all C-X bonds (X = halogen).
+    :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(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"
+        )
+
+    workflow = stjames.BDEWorkflow(
+        initial_molecule=initial_molecule,
+        mode=mode,
+        atoms=atoms or [],
+        all_CH=all_CH,
+        all_CX=all_CX,
+    )
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "bde",
+        "workflow_data": workflow.model_dump(mode="json"),
+        "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_electronic_properties_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    method: stjames.Method | str = "b97_3c",
+    basis_set: str | None = None,
+    compute_density_cube: bool = True,
+    compute_electrostatic_potential_cube: bool = True,
+    compute_num_occupied_orbitals: int = 1,
+    compute_num_virtual_orbitals: int = 1,
+    name: str = "Electronic Properties Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits an electronic properties workflow to the API.
+
+    :param initial_molecule: The molecule to calculate electronic properties for.
+    :param method: The method to use for the calculation.
+    :param basis_set: The basis set to use (if any).
+    :param compute_density_cube: Whether to compute the density cube.
+    :param compute_electrostatic_potential_cube: Whether to compute the electrostatic
+        potential cube.
+    :param compute_num_occupied_orbitals: Number of occupied orbitals to save.
+    :param compute_num_virtual_orbitals: Number of virtual orbitals to save.
+    :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(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(method, str):
+        method = stjames.Method(method)
+
+    settings = stjames.Settings(method=method, basis_set=basis_set)
+
+    workflow = stjames.ElectronicPropertiesWorkflow(
+        initial_molecule=initial_molecule,
+        settings=settings,
+        compute_density_cube=compute_density_cube,
+        compute_electrostatic_potential_cube=compute_electrostatic_potential_cube,
+        compute_num_occupied_orbitals=compute_num_occupied_orbitals,
+        compute_num_virtual_orbitals=compute_num_virtual_orbitals,
+    )
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "electronic_properties",
+        "workflow_data": workflow.model_dump(mode="json"),
+        "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_hydrogen_bond_basicity_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    do_csearch: bool = True,
+    do_optimization: bool = True,
+    name: str = "Hydrogen Bond Basicity Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a hydrogen bond basicity workflow to the API.
+
+    :param initial_molecule: The molecule to calculate hydrogen bond basicity for.
+    :param do_csearch: Whether to perform a conformational search.
+    :param do_optimization: Whether to perform an optimization.
+    :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(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"
+        )
+
+    workflow = stjames.HydrogenBondBasicityWorkflow(
+        initial_molecule=initial_molecule,
+        do_csearch=do_csearch,
+        do_optimization=do_optimization,
+    )
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "hydrogen_bond_basicity",
+        "workflow_data": workflow.model_dump(mode="json"),
+        "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_multistage_optimization_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    mode: str = "rapid",
+    solvent: str | None = None,
+    xtb_preopt: bool = True,
+    transition_state: bool = False,
+    frequencies: bool = False,
+    name: str = "Multistage Optimization Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a multistage optimization workflow to the API.
+
+    :param initial_molecule: The molecule to optimize.
+    :param mode: The mode to run the calculation in.
+    :param solvent: The solvent to use for the final single-point calculation.
+    :param xtb_preopt: Whether to pre-optimize with xTB.
+    :param transition_state: Whether this is a transition state optimization.
+    :param frequencies: Whether to calculate frequencies.
+    :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(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"
+        )
+
+    workflow = stjames.MultiStageOptWorkflow(
+        initial_molecule=initial_molecule,
+        mode=mode,
+        solvent=solvent,
+        xtb_preopt=xtb_preopt,
+        transition_state=transition_state,
+        frequencies=frequencies,
+    )
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "multistage_opt",
+        "workflow_data": workflow.model_dump(mode="json"),
+        "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_spin_states_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    states: list[int],
+    mode: str = "rapid",
+    solvent: str | None = None,
+    xtb_preopt: bool = True,
+    frequencies: bool = False,
+    name: str = "Spin States Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a spin states workflow to the API.
+
+    :param initial_molecule: The molecule to calculate spin states for.
+    :param states: List of multiplicities to calculate
+        (e.g., [1, 3, 5] for singlet, triplet, quintet).
+    :param mode: The mode to run the calculation in.
+    :param solvent: The solvent to use for the calculation.
+    :param xtb_preopt: Whether to pre-optimize with xTB.
+    :param frequencies: Whether to calculate frequencies.
+    :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(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"
+        )
+
+    workflow = stjames.SpinStatesWorkflow(
+        initial_molecule=initial_molecule,
+        states=states,
+        mode=mode,
+        solvent=solvent,
+        xtb_preopt=xtb_preopt,
+        frequencies=frequencies,
+    )
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "spin_states",
+        "workflow_data": workflow.model_dump(mode="json"),
+        "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_protein_binder_design_workflow(
+    binder_design_input: dict[str, Any],
+    protocol: str = "protein-anything",
+    num_designs: int = 10,
+    budget: int = 2,
+    name: str = "Protein Binder Design Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a protein binder design workflow to the API.
+
+    :param binder_design_input: Input specification for the binder design (BoltzGenInput format).
+    :param protocol: The protocol to use.
+    :param num_designs: Number of designs to generate.
+    :param budget: Number of designs to return in the final diversity-optimized set.
+    :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.
+    """
+    workflow = stjames.ProteinBinderDesignWorkflow(
+        binder_design_input=binder_design_input,
+        binder_design_settings={
+            "protocol": protocol,
+            "num_designs": num_designs,
+            "budget": budget,
+        },
+    )
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "protein_binder_design",
+        "workflow_data": workflow.model_dump(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-2.1.14.dist-info → rowan_python-2.1.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.14
+Version: 2.1.16
 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-2.1.14.dist-info → rowan_python-2.1.16.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=QQWHTZ_O3PF2WbegYLPIKiszOEYj1frPKbI8U-B1muc,72419
+rowan/workflow.py,sha256=8HT80bQbzb7k4oPRNMdzH7vDrAX__BzzJ2pjzUA7ogk,85642
 rowan/rowan_rdkit/__init__.py,sha256=EATX2VRzywzKxqkpCUMTf7RNQLkWsfi5VcCNDW6EIiw,503
 rowan/rowan_rdkit/chem_utils.py,sha256=sKCzul2e0ldVYTBImhTwso7ddNgPKmvS-OmvCEjVJH0,34788
-rowan_python-2.1.14.dist-info/METADATA,sha256=GdXzsTQIY2SSuTUgVnerp8Cib41LCL2koTc1VuPvP5w,1601
-rowan_python-2.1.14.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rowan_python-2.1.14.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-2.1.14.dist-info/RECORD,,
+rowan_python-2.1.16.dist-info/METADATA,sha256=eGbLBIwJnW9Iy5J20hgX7cbrlb89mmXeWZskV8R3aWk,1601
+rowan_python-2.1.16.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rowan_python-2.1.16.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-2.1.16.dist-info/RECORD,,