rowan-python 3.0.6__py3-none-any.whl → 3.0.8__py3-none-any.whl

rowan/__init__.py

@@ -29,6 +29,7 @@ from stjames.optimization.freezing_string_method import (
 api_key: str | None = None
 project_uuid: str | None = None
 
+from .api_keys import *
 from .calculation import *
 from .folder import *
 from .molecule import *

rowan/api_keys.py

@@ -0,0 +1,144 @@
+import uuid
+from datetime import datetime
+from typing import Literal, Self
+
+from pydantic import BaseModel
+
+from .utils import api_client
+
+APIKeyScope = Literal["read", "read_write", "read_write_delete"]
+
+
+class APIKey(BaseModel):
+    """
+    Rowan API key.
+
+    :ivar uuid: UUID of the API key.
+    :ivar name: Human-readable name of the API key.
+    :ivar created_at: When the key was created.
+    :ivar expires_at: When the key expires.
+    :ivar is_expired: Whether the key has expired.
+    :ivar is_revoked: Whether the key has been revoked.
+    :ivar scope: Permission scope ("read", "read_write", or "read_write_delete").
+    :ivar can_manage_api_keys: Whether this key can create/list/revoke other API keys.
+    :ivar scoped_project_uuid: If set, the key can only access this project.
+    :ivar created_by_key_uuid: UUID of the API key used to create this one (if any).
+    :ivar revoked_at: When the key was revoked, if applicable.
+    :ivar last_used_at: When the key was last used, if known.
+    """
+
+    uuid: str
+    name: str
+    created_at: datetime
+    expires_at: datetime
+    is_expired: bool
+    is_revoked: bool
+    scope: str
+    can_manage_api_keys: bool
+    scoped_project_uuid: str | None = None
+    created_by_key_uuid: str | None = None
+    revoked_at: datetime | None = None
+    last_used_at: datetime | None = None
+
+    def __repr__(self) -> str:
+        return (
+            f"<APIKey name='{self.name}' scope='{self.scope}' "
+            f"scoped_project_uuid={self.scoped_project_uuid!r} uuid='{self.uuid}'>"
+        )
+
+    def revoke(self) -> Self:
+        """
+        Revoke this API key.
+
+        :returns: Updated APIKey object.
+        """
+        with api_client() as client:
+            response = client.post(f"/api_key/{self.uuid}/revoke")
+            response.raise_for_status()
+            return type(self)(**response.json())
+
+
+class CreatedAPIKey(BaseModel):
+    """
+    Result of creating a new API key.
+
+    The plaintext ``key`` is only available at creation time — store it now,
+    it cannot be retrieved later.
+
+    :ivar key: Plaintext API key. Save this; it is only returned once.
+    :ivar api_key: Metadata for the newly-created key.
+    """
+
+    key: str
+    api_key: APIKey
+
+
+def create_api_key(
+    name: str = "api-key",
+    scope: APIKeyScope = "read_write",
+    valid_days: int = 365,
+    scoped_project_uuid: str | None = None,
+) -> CreatedAPIKey:
+    """
+    Create a new API key.
+
+    The caller must currently authenticate with an unscoped key that has
+    ``can_manage_api_keys`` permission.
+
+    :param name: Human-readable name for the key.
+    :param scope: Permission scope. One of "read", "read_write", "read_write_delete".
+    :param valid_days: Number of days until the key expires.
+    :param scoped_project_uuid: If provided, restrict the key to a single project.
+    :returns: plaintext key together with its metadata; the plaintext key is
+        only returned once — store it immediately.
+    """
+    plaintext_key = f"rowan-sk{uuid.uuid4()}"
+    payload = {
+        "api_key": plaintext_key,
+        "name": name,
+        "scope": scope,
+        "valid_days": valid_days,
+        "scoped_project_uuid": scoped_project_uuid,
+    }
+    with api_client() as client:
+        response = client.post("/api_key", json=payload)
+        if response.status_code == 403:
+            raise PermissionError(
+                "API key creation rejected by the server (403). The key you are "
+                "authenticating with must be unscoped and have `can_manage_api_keys` "
+                "permission. Create a manager key from the Rowan web UI "
+                "(Account → API keys) and retry with that key."
+            )
+        response.raise_for_status()
+        return CreatedAPIKey(key=plaintext_key, api_key=APIKey(**response.json()))
+
+
+def list_api_keys(active: bool | None = True) -> list[APIKey]:
+    """
+    List API keys belonging to the current user.
+
+    :param active: If True (default), only return non-revoked, non-expired keys.
+        If False, only return revoked or expired keys. If None, return all keys.
+    :returns: List of APIKey objects.
+    """
+    params: dict[str, str] = {}
+    if active is not None:
+        params["active"] = "true" if active else "false"
+
+    with api_client() as client:
+        response = client.get("/api_key", params=params)
+        response.raise_for_status()
+        return [APIKey(**item) for item in response.json()]
+
+
+def revoke_api_key(uuid: str) -> APIKey:
+    """
+    Revoke an API key by UUID.
+
+    :param uuid: UUID of the key to revoke.
+    :returns: Updated APIKey object.
+    """
+    with api_client() as client:
+        response = client.post(f"/api_key/{uuid}/revoke")
+        response.raise_for_status()
+        return APIKey(**response.json())

rowan/workflows/__init__.py

@@ -84,6 +84,7 @@ from .multistage_optimization import (
 )
 from .nmr import NMRPeak, NMRResult, submit_nmr_workflow
 from .pka import pKaMicrostate, pKaResult, submit_pka_workflow
+from .pocket_detection import Pocket, PocketDetectionResult, submit_pocket_detection_workflow
 from .pose_analysis_md import PoseAnalysisMDResult, submit_pose_analysis_md_workflow
 from .protein_binder_design import (
     ProteinBinder,
@@ -91,7 +92,11 @@ from .protein_binder_design import (
     submit_protein_binder_design_workflow,
 )
 from .protein_cofolding import (
+    CofoldingModel,
     CofoldingResult,
+    ConstraintTarget,
+    ContactConstraint,
+    PocketConstraint,
     ProteinCofoldingResult,
     submit_protein_cofolding_workflow,
 )

rowan/workflows/electronic_properties.py

@@ -2,7 +2,10 @@
 
 from dataclasses import dataclass
 
+import httpx
 import stjames
+from pydantic import ValidationError
+from stjames import ENGINE_METHODS, Engine, Method
 
 from ..folder import Folder
 from ..types import MoleculeInput
@@ -30,6 +33,22 @@ class ElectronicPropertiesResult(WorkflowResult):
 
     _stjames_class = stjames.ElectronicPropertiesWorkflow
 
+    def __post_init__(self) -> None:
+        # Computed results (dipole, charges, cubes, orbitals, ...) live only in
+        # the gzipped S3 blob, not in the workflow's object_data row. Fetch and
+        # parse it once on construction so accessors below see populated data.
+        super().__post_init__()
+        if not self.complete:
+            return
+        try:
+            with api_client() as client:
+                response = client.get(f"/orbitals/{self.workflow_uuid}/compressed_json")
+                response.raise_for_status()
+                populated = stjames.ElectronicPropertiesWorkflow.model_validate(response.json())
+            object.__setattr__(self, "_workflow", populated)
+        except (httpx.HTTPError, ValidationError):
+            pass
+
     def __repr__(self) -> str:
         return f"<ElectronicPropertiesResult dipole={self.dipole} D>"
 
@@ -155,6 +174,7 @@ def submit_electronic_properties_workflow(
     :param webhook_url: URL that Rowan will POST to when the workflow completes.
     :param is_draft: If True, submit the workflow as a draft without starting execution.
     :returns: Workflow object representing the submitted workflow.
+    :raises ValueError: If the method is not supported by the psi4 engine.
     :raises requests.HTTPError: if the request to the API fails.
     """
     if folder and folder_uuid:
@@ -164,7 +184,15 @@ def submit_electronic_properties_workflow(
     initial_molecule = molecule_to_dict(initial_molecule)
 
     if isinstance(method, str):
-        method = stjames.Method(method)
+        method = Method(method)
+
+    supported_methods = ENGINE_METHODS[Engine.PSI4]
+    if method not in supported_methods:
+        supported_names = sorted(m.value for m in supported_methods)
+        raise ValueError(
+            f"Method '{method.value}' is not supported by the psi4 engine. "
+            f"Supported methods: {', '.join(supported_names)}"
+        )
 
     settings = stjames.Settings(method=method, basis_set=basis_set)
 

rowan/workflows/pka.py

@@ -188,7 +188,16 @@ def submit_pka_workflow(
     if method in _PKA_WATER_ONLY_METHODS and solvent != "water":
         raise ValueError(f"{method} only supports water as solvent.")
 
-    protonate_elements = protonate_elements or [7]
+    if method == "chemprop_nevolianis2025" and protonate_elements:
+        raise ValueError(
+            "chemprop_nevolianis2025 was only trained on deprotonation data; "
+            "protonation is disabled. Leave `protonate_elements` unset or pass []."
+        )
+
+    if method == "chemprop_nevolianis2025":
+        protonate_elements = []
+    else:
+        protonate_elements = protonate_elements or [7]
     deprotonate_elements = deprotonate_elements or [7, 8, 16]
 
     workflow = stjames.pKaWorkflow(

rowan/workflows/pocket_detection.py

@@ -0,0 +1,112 @@
+"""Pocket detection workflow - detect potential binding sites on a protein."""
+
+from dataclasses import dataclass
+
+import stjames
+
+from ..folder import Folder
+from ..protein import Protein
+from ..utils import api_client
+from .base import Workflow, WorkflowResult, register_result
+
+
+@dataclass(frozen=True, slots=True)
+class Pocket:
+    """
+    A detected binding pocket.
+
+    :param sphere_centers: centers of detected spheres, in Å
+    :param sphere_radii: radii of detected spheres, in Å
+    :param volume: pocket volume, in ų
+    :param score: druggability/quality score; larger is better
+    :param pocket_center: center of axis-aligned bounding box, in Å
+    :param pocket_sides: side lengths of axis-aligned bounding box, in Å
+    :param residue_numbers: residue numbers lining the pocket
+    """
+
+    sphere_centers: tuple[tuple[float, float, float], ...]
+    sphere_radii: tuple[float, ...]
+    volume: float
+    score: float
+    pocket_center: tuple[float, float, float]
+    pocket_sides: tuple[float, float, float]
+    residue_numbers: tuple[int, ...]
+
+
+@register_result("pocket_detection")
+class PocketDetectionResult(WorkflowResult):
+    """Result from a pocket-detection workflow."""
+
+    _stjames_class = stjames.PocketDetectionWorkflow
+
+    def __repr__(self) -> str:
+        return f"<PocketDetectionResult pockets={len(self.pockets)}>"
+
+    @property
+    def pockets(self) -> list[Pocket]:
+        """Detected pockets, in the order returned by the backend."""
+        raw = getattr(self._workflow, "pockets", []) or []
+        return [
+            Pocket(
+                sphere_centers=tuple(tuple(c) for c in p.sphere_centers),
+                sphere_radii=tuple(p.sphere_radii),
+                volume=p.volume,
+                score=p.score,
+                pocket_center=tuple(p.pocket_center),
+                pocket_sides=tuple(p.pocket_sides),
+                residue_numbers=tuple(p.residue_numbers),
+            )
+            for p in raw
+        ]
+
+
+def submit_pocket_detection_workflow(
+    protein: str | Protein,
+    merge_distance: float = 1.75,
+    name: str = "Pocket Detection Workflow",
+    folder_uuid: str | None = None,
+    folder: Folder | None = None,
+    max_credits: int | None = None,
+    webhook_url: str | None = None,
+    is_draft: bool = False,
+) -> Workflow:
+    """
+    Submits a pocket-detection workflow to the API.
+
+    :param protein: protein to analyze. Can be a UUID or a Protein object.
+    :param merge_distance: distance for merging pocket spheres, in Å
+    :param name: name of the workflow
+    :param folder_uuid: UUID of the folder to place the workflow in
+    :param folder: Folder object to store the workflow in
+    :param max_credits: maximum number of credits to use for the workflow
+    :param webhook_url: URL that Rowan will POST to when the workflow completes
+    :param is_draft: if True, submit the workflow as a draft without starting execution
+    :returns: Workflow object representing the submitted workflow
+    :raises requests.HTTPError: if the request to the API fails
+    """
+    if folder and folder_uuid:
+        raise ValueError("Provide either `folder` or `folder_uuid`, not both.")
+    if folder:
+        folder_uuid = folder.uuid
+    if isinstance(protein, Protein):
+        protein = protein.uuid
+
+    workflow = stjames.PocketDetectionWorkflow(
+        protein=protein,
+        merge_distance=merge_distance,
+    )
+
+    data = {
+        "workflow_type": "pocket_detection",
+        "workflow_data": workflow.model_dump(mode="json"),
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "max_credits": max_credits,
+        "webhook_url": webhook_url,
+        "is_draft": is_draft,
+    }
+
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())

rowan/workflows/protein_cofolding.py

@@ -9,8 +9,12 @@ from ..protein import Protein, retrieve_protein
 from ..utils import api_client
 from .base import Message, Workflow, WorkflowResult, parse_messages, register_result
 
-# Re-export cofolding model enum from stjames
 CofoldingModel = stjames.CofoldingModel
+# `ConstraintTarget` aliases stjames's `Token` - one position in an input
+# (a protein/nucleic-acid residue or a ligand atom) addressable by a constraint.
+ConstraintTarget = stjames.workflows.protein_cofolding.Token
+ContactConstraint = stjames.workflows.protein_cofolding.ContactConstraint
+PocketConstraint = stjames.workflows.protein_cofolding.PocketConstraint
 
 
 @dataclass(frozen=True, slots=True)
@@ -244,6 +248,9 @@ def submit_protein_cofolding_workflow(
     ligand_binding_affinity_index: int | None = None,
     use_msa_server: bool = True,
     use_potentials: bool = False,
+    contact_constraints: list[ContactConstraint] | None = None,
+    pocket_constraints: list[PocketConstraint] | None = None,
+    num_samples: int | None = None,
     compute_strain: bool = False,
     do_pose_refinement: bool = False,
     name: str = "Protein-Ligand Co-Folding",
@@ -260,6 +267,10 @@ def submit_protein_cofolding_workflow(
     Predicts the 3D structure of protein-protein, protein-ligand, protein-DNA,
     protein-RNA, or other biomolecular complexes.
 
+    See `examples/protein_cofolding_with_constraints.py` for a worked example
+    of using `ConstraintTarget`, `ContactConstraint`, and `PocketConstraint`
+    (Boltz-2 only).
+
     :param initial_protein_sequences: Protein sequences to be cofolded.
     :param initial_dna_sequences: DNA sequences to be cofolded.
     :param initial_rna_sequences: RNA sequences to be cofolded.
@@ -267,7 +278,10 @@ def submit_protein_cofolding_workflow(
     :param ligand_binding_affinity_index: 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 use_potentials: Whether to use potentials (inference-time steering) with Boltz.
+    :param contact_constraints: Boltz contact constraints between two tokens.
+    :param pocket_constraints: Boltz pocket constraints between a binder and contact tokens.
+    :param num_samples: Number of diffusion samples to generate. If None, uses the model default.
     :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.
@@ -302,6 +316,9 @@ def submit_protein_cofolding_workflow(
     workflow = stjames.ProteinCofoldingWorkflow(
         use_msa_server=use_msa_server,
         use_potentials=use_potentials,
+        contact_constraints=contact_constraints or [],
+        pocket_constraints=pocket_constraints or [],
+        num_samples=num_samples,
         model=model_str,
         ligand_binding_affinity_index=ligand_binding_affinity_index,
         initial_smiles_list=initial_smiles_list,

{rowan_python-3.0.6.dist-info → rowan_python-3.0.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.6
+Version: 3.0.8
 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>=0.0.174
+Requires-Dist: stjames<=0.0.182
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.0.6.dist-info → rowan_python-3.0.8.dist-info}/RECORD

@@ -1,4 +1,5 @@
-rowan/__init__.py,sha256=HvGc27Y6l1_E_mcvabDhmDOOtMrJ6ME7Cx8LfVKqyVs,835
+rowan/__init__.py,sha256=wiEroKH5I6VQ-tiseUcrNGJaS_0soFnYMX0EtpwyLIs,859
+rowan/api_keys.py,sha256=TvG5l5MmQ3Qt8Z3Y7jCA_lcrwEHuI7xHy-KLbIdQ8_A,4793
 rowan/calculation.py,sha256=lZZ52DxPsuJWCTzFZXjhauHK6dV0KCUwzoxtmoxSY48,3442
 rowan/config.py,sha256=3cVKHUNzkIPnN2bvx7l5sia7Zc5poXS8lKOJlowXyLA,21088
 rowan/constants.py,sha256=emCH4m9OL2Hm5E-6mJGM_FgzrK_JrZT-FiKJ6pMNQ4Y,84
@@ -12,7 +13,7 @@ rowan/user.py,sha256=Tnwz1-u_92ACt1xATQegtMj3FcosFsAG4m-4YuAkiyg,5955
 rowan/utils.py,sha256=c1s6Ze-OqLtfvrD23OV60otskejmj-CD88nNf8_nFcw,3636
 rowan/rowan_rdkit/__init__.py,sha256=EATX2VRzywzKxqkpCUMTf7RNQLkWsfi5VcCNDW6EIiw,503
 rowan/rowan_rdkit/chem_utils.py,sha256=ZWdLziT59Qr5JzjvV789CAyRq0m5JIawsOP4RxUbQQA,35529
-rowan/workflows/__init__.py,sha256=o2fN6V10mWt82QPr1UlbkyHzc2vtoIbkoiFZF2PgYow,4257
+rowan/workflows/__init__.py,sha256=CM3GKDTafp6vl79dWqSOvkVfwH1Ty8zuc8yzi65ABxM,4438
 rowan/workflows/admet.py,sha256=0_wIwXXLfHF-3kgGx_1EM1ljjaYHLeEijJ-GbMYxpL8,2904
 rowan/workflows/analogue_docking.py,sha256=LJpbbaug0tZ9Cg-m0b7EgGH5hJ5894fHOC16Wefx7mE,9206
 rowan/workflows/base.py,sha256=eLGyzTc9NpXBGC-FRjsaUwKP6RluWrz0ipDZ4jDY_jc,30103
@@ -24,7 +25,7 @@ rowan/workflows/constants.py,sha256=el8jWE9gnGTLNWn5_n_V0H362vIRneOqgy7BOQ8CScg,
 rowan/workflows/descriptors.py,sha256=rGrNca6kA4SzX5BAOjP6rE91MOLTvCWSYKF_LW2Z0y4,2963
 rowan/workflows/docking.py,sha256=wmE7QJu1uDHBDynTT1XesXXAZtpB6xLjZUKsHOQyCcU,7386
 rowan/workflows/double_ended_ts_search.py,sha256=abBblMkshhbzq5UTwIf-ovNFxY8Ltp2O-bGu_plkI58,7806
-rowan/workflows/electronic_properties.py,sha256=AVVtpIIO82GRETHbemCLI8tqM7QHmr7XrGbrQ_YB5w4,7108
+rowan/workflows/electronic_properties.py,sha256=ia4mlmgnioEuLDrcgDuxAyyI6VqRkdxBqshjb9uiEI8,8385
 rowan/workflows/fukui.py,sha256=wLimH3QmorSpvkovRPlI91VuxHG4J91F2EcLYqg3eP0,5112
 rowan/workflows/hydrogen_bond_donor_acceptor_strength.py,sha256=WWiEK_GlumIEgTTOaqw-Y5gPDkRkaePWcIjTdIocrPc,4916
 rowan/workflows/interaction_energy_decomposition.py,sha256=Kjwkb-pviFSFIIZNjMb9i8nAkdKrbjFftmG_lkYtE40,6120
@@ -35,10 +36,11 @@ rowan/workflows/membrane_permeability.py,sha256=oIDmB8qF_K_Kesv7o_FiljAk4dpptEeO
 rowan/workflows/msa.py,sha256=V3B1SyWPR8MT306hh9W-T9JTpi_E-XgAIeF9yRQZ7tI,5075
 rowan/workflows/multistage_optimization.py,sha256=HFVx8mnHxG97pDYyL6eOhNGmESqTxaKNgUdwrFpFUJ0,6456
 rowan/workflows/nmr.py,sha256=hergJdsiawKj7iV-jHxDOS03n_EnZcaCIt_ZTl34-JY,5183
-rowan/workflows/pka.py,sha256=Gh-rMrqZyHbpIpX2LaEiBzlqE4paIE58paSkHEQCoEU,8334
+rowan/workflows/pka.py,sha256=TCFSE5HI5JLPslKdbUvJe4IxrVaLExrI_3PnDfXtxTw,8691
+rowan/workflows/pocket_detection.py,sha256=aGHY0puxekp4c4nsNYHcvKCe1fsetygL04BcSvNFvE8,3864
 rowan/workflows/pose_analysis_md.py,sha256=UvotLhWv0_VAkKteZboOutDry7l-Zt1K6_SBx3EXqgM,9530
 rowan/workflows/protein_binder_design.py,sha256=J-9NSbRLdHb6JQRhY_vq43HlHCDCiQqrkOZUCAF-2dk,8604
-rowan/workflows/protein_cofolding.py,sha256=1R29XjAVjWHyelGG-mylP2GIamZbLCQKaaaFsCAnYgI,13012
+rowan/workflows/protein_cofolding.py,sha256=D2PVwL51H3traml1JDG-9jU3R0E29AdfR9Bk0tLX1Zw,14093
 rowan/workflows/protein_md.py,sha256=_n0IdmTQsunbP1geF-wUjXNMKNYV-ngmAPEMJlj0dkI,7021
 rowan/workflows/rbfe_graph.py,sha256=PLqzBRkxD7tPdBViYJZjgaCP8aA2UXKc9dD4odx5XUo,5788
 rowan/workflows/redox_potential.py,sha256=lg2Djev58oOmBmI4l3eIaGKafkNXMhwo17K2G7kQvjY,5319
@@ -49,7 +51,7 @@ rowan/workflows/solvent_dependent_conformers.py,sha256=ovvnhCE4xlkpdhccLHEq7oBJR
 rowan/workflows/spin_states.py,sha256=GZgBJPO6_ds9el4b7wbigIZ5213Z9DwXhokczJ5NDhs,7122
 rowan/workflows/strain.py,sha256=r0tlZoUlAslAiF7dPTpa9WlQFUAKyVjZ19zASjSS8Hs,6339
 rowan/workflows/tautomer_search.py,sha256=aqwXoj0ffWsb5gbvzfz_bpx5ifIfR_K07fbdWhU62Ko,5820
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