rowan-python 3.0.5__py3-none-any.whl → 3.0.7__py3-none-any.whl

rowan/molecule.py

@@ -52,28 +52,36 @@ class Molecule(BaseModel):
         return cls(_stjames=stjames.Molecule.from_smiles(smiles))
 
     @classmethod
-    def from_xyz(cls, xyz_string: str, charge: int = 0, multiplicity: int = 1) -> Self:
+    def from_xyz(
+        cls, xyz_string: str, charge: int | None = None, multiplicity: int | None = None
+    ) -> Self:
         """
-        Create molecule from XYZ string.
+        Create Molecule from XYZ string.
 
-        :param xyz_string: XYZ format string.
-        :param charge: Molecular charge (default 0).
-        :param multiplicity: Spin multiplicity (default 1).
-        :returns: Molecule instance.
+        :param xyz_string: XYZ format string
+        :param charge: charge
+        :param multiplicity: spin multiplicity
+        :returns: Molecule
         """
-        stj = stjames.Molecule.from_xyz(xyz_string)
-        stj = stjames.Molecule(atoms=stj.atoms, charge=charge, multiplicity=multiplicity)
-        return cls(_stjames=stj)
+        return cls(
+            _stjames=stjames.Molecule.from_xyz(
+                xyz_string,
+                charge=charge,
+                multiplicity=multiplicity,
+            )
+        )
 
     @classmethod
-    def from_xyz_file(cls, path: str | Path, charge: int = 0, multiplicity: int = 1) -> Self:
+    def from_xyz_file(
+        cls, path: str | Path, charge: int | None = None, multiplicity: int | None = None
+    ) -> Self:
         """
         Create molecule from XYZ file.
 
-        :param path: Path to XYZ file.
-        :param charge: Molecular charge (default 0).
-        :param multiplicity: Spin multiplicity (default 1).
-        :returns: Molecule instance.
+        :param path: path to XYZ file
+        :param charge: charge
+        :param multiplicity: spin multiplicity
+        :returns: Molecule
         """
         return cls.from_xyz(Path(path).read_text(), charge=charge, multiplicity=multiplicity)
 
@@ -82,8 +90,8 @@ class Molecule(BaseModel):
         """
         Create from stjames.Molecule.
 
-        :param stj: stjames.Molecule instance.
-        :returns: Molecule instance.
+        :param stj: stjames.Molecule
+        :returns: Molecule
         """
         return cls(_stjames=stj)
 

rowan/protein.py

@@ -305,7 +305,7 @@ def list_proteins(
 
 
 def upload_protein(
-    name: str, file_path: Path, project_uuid: str | Project | None = None
+    name: str, file_path: str | Path, project_uuid: str | Project | None = None
 ) -> Protein:
     """
     Uploads a protein from a PDB file to the API.
@@ -315,6 +315,7 @@ def upload_protein(
     :returns: Protein object representing the uploaded protein
     :raises requests.HTTPError: if the request to the API fails
     """
+    file_path = Path(file_path)
     if isinstance(project_uuid, Project):
         project_uuid = project_uuid.uuid
     with api_client() as client:

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,

rowan/workflows/electronic_properties.py

@@ -3,6 +3,7 @@
 from dataclasses import dataclass
 
 import stjames
+from stjames import ENGINE_METHODS, Engine, Method
 
 from ..folder import Folder
 from ..types import MoleculeInput
@@ -155,6 +156,7 @@ 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 +166,15 @@ 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

@@ -183,13 +183,21 @@ def submit_pka_workflow(
         )
     if method in _PKA_SMILES_METHODS and not initial_smiles:
         raise ValueError(
-            f"{method} requires a SMILES string. "
-            "Provide a SMILES string, not a 3D structure."
+            f"{method} requires a SMILES string. Provide a SMILES string, not a 3D structure."
         )
     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_python-3.0.5.dist-info → rowan_python-3.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.5
+Version: 3.0.7
 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-3.0.5.dist-info → rowan_python-3.0.7.dist-info}/RECORD

@@ -3,16 +3,16 @@ rowan/calculation.py,sha256=lZZ52DxPsuJWCTzFZXjhauHK6dV0KCUwzoxtmoxSY48,3442
 rowan/config.py,sha256=3cVKHUNzkIPnN2bvx7l5sia7Zc5poXS8lKOJlowXyLA,21088
 rowan/constants.py,sha256=emCH4m9OL2Hm5E-6mJGM_FgzrK_JrZT-FiKJ6pMNQ4Y,84
 rowan/folder.py,sha256=NkimVeHho9nwRXeS87U1tivEVL-1gL2Vqfz1fJ6XpNQ,9222
-rowan/molecule.py,sha256=MppZLHUAHzLCaIZtAbr2tpEULt5yRUR1B5npgFISCbE,10030
+rowan/molecule.py,sha256=KQJhbNF2vmR8okBduXVqG7qG3LXbABLKHanpNhA-0TY,10003
 rowan/project.py,sha256=Wy3VvhwIMIumAZD2s7hPk8jj4bAPHMDNvsqU23RRqFo,4598
-rowan/protein.py,sha256=Ma2tBFF52Rb-ME5vZy5M5juMlmphQVQRL0Q1EBvBeZg,14761
+rowan/protein.py,sha256=jyOM6g5eQH6KO8Eq07AiYBv2vZsGfbNOdtNOb2NWHFc,14799
 rowan/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rowan/types.py,sha256=rCAnUlCsemyBK9Bbus0pL-THoqNqJIQHaMoDferIfFU,471
 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=UTkqcsqtANh9TtaYXwOSYmTOvzR9ucQ_xhDupAFHROI,4351
 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 +24,7 @@ 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=2L0BUvhx0iT0k4gQf7hbceCpatznT2xui7rs6lpME7k,7564
 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
@@ -35,7 +35,8 @@ 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=YAnFq1zyJO3j9rfYCYyrl-C_o8uaFTpCqoldqiP7o1k,8349
+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
@@ -49,7 +50,7 @@ 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
-rowan_python-3.0.5.dist-info/METADATA,sha256=0wZHFNgNRDm1DwrdDVJJh1Xu05Xm8A31whsYlwCSVWM,1600
-rowan_python-3.0.5.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
-rowan_python-3.0.5.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-3.0.5.dist-info/RECORD,,
+rowan_python-3.0.7.dist-info/METADATA,sha256=-sirW_Q74BeqsjNRR4wAWYoV8ebpuNLzc6-8FrgOKRs,1600
+rowan_python-3.0.7.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
+rowan_python-3.0.7.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-3.0.7.dist-info/RECORD,,