rowan-python 3.1.14__tar.gz → 3.1.15__tar.gz

{rowan_python-3.1.14 → rowan_python-3.1.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: rowan-python
-Version: 3.1.14
+Version: 3.1.15
 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>=0.0.257
+Requires-Dist: stjames>=0.0.261
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.1.14 → rowan_python-3.1.15}/docs/workflows/analogue-docking.md

@@ -1,5 +1,8 @@
 # Analogue Docking
 
+Analogue docking generates at most 20 conformers per analogue by default. Override
+`num_conformers_per_analogue` when a broader search is needed.
+
 ::: rowan.workflows.analogue_docking
     handler: python
     options:

{rowan_python-3.1.14 → rowan_python-3.1.15}/docs/workflows/batch-docking.md

@@ -1,5 +1,9 @@
 # Batch Docking
 
+Use `num_poses_to_save` to retain the best pose for that many top-scoring compounds, and set
+`run_mmgbsa=True` to refine those saved poses. `result.refined_scores` maps every input SMILES
+to a `DockingScore` for a retained compound or `None` otherwise.
+
 ::: rowan.workflows.batch_docking
     handler: python
     options:

{rowan_python-3.1.14 → rowan_python-3.1.15}/docs/workflows/docking.md

@@ -3,6 +3,16 @@
 The docking workflow supports Vina docking and both noncovalent and covalent gnina docking.
 Passing `GninaSettings` selects gnina; it does not by itself enable covalent docking.
 
+## Induced-fit docking
+
+Pass `rowan.InducedFitSettings()` to `induced_fit_settings` when nearby receptor side chains may
+need to relax around the ligand. Induced fit requires Vina or QVina2 and adds substantial work
+beyond rigid docking.
+
+Results contain both rigid and induced-receptor poses ranked by `induced_fit_score`. Use
+`get_induced_receptor()` or `get_induced_receptors()` to retrieve the relaxed receptors associated
+with induced poses. See `examples/induced_fit_docking.py` for a complete example.
+
 ## Covalent docking
 
 Set both covalent atom indices on `GninaSettings` to form a bond between a known ligand atom and

{rowan_python-3.1.14 → rowan_python-3.1.15}/examples/binding_affinity.py

@@ -25,4 +25,4 @@ for name, score in zip(ligands.keys(), result.scores, strict=False):
     if score is None:
         print(f"{name}: scoring failed")
         continue
-    print(f"{name}: {score.binding_affinity:.2f} kcal/mol (strain: {score.strain})")
+    print(f"{name}: {score.binding_affinity:.2f} kcal/mol")

rowan_python-3.1.15/examples/induced_fit_docking.py

@@ -0,0 +1,61 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+# Dasatinib — redocked into its own ABL1 co-crystal structure (PDB: 2GQG)
+dasatinib = rowan.Molecule.from_smiles("Cc1nc(Nc2ncc(C(=O)Nc3c(C)cccc3Cl)s2)cc(N2CCN(CCO)CC2)n1")
+
+protein = rowan.create_protein_from_pdb_id("2GQG")
+protein = protein.select_chains(["A"])
+preparation_workflow = rowan.submit_protein_preparation_workflow(
+    protein=protein.uuid,
+    add_missing_method="pdbfixer",
+    name="Prepare ABL1",
+    folder=folder,
+)
+prepared_protein_uuid = preparation_workflow.result().prepared_protein_uuid
+
+# Pocket is [[center_x, center_y, center_z], [size_x, size_y, size_z]] in Å.
+center = [44.59, 79.75, 39.59]
+size = [24.15, 21.33, 19.88]
+
+# Induced-fit docking soft-docks candidate poses, relaxes the receptor around each with
+# restrained local minimization, and redocks into the relaxed receptor. It requires
+# VinaSettings with executable="vina" or "qvina2" (the default is "vina").
+induced_fit_settings = rowan.InducedFitSettings(
+    max_receptors=6,
+    flexible_sidechain_radius=5.0,
+)
+
+workflow = rowan.submit_docking_workflow(
+    prepared_protein_uuid,
+    pocket=[center, size],
+    initial_molecule=dasatinib,
+    induced_fit_settings=induced_fit_settings,
+    name="Dasatinib induced-fit docking",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/docking/{workflow.uuid}")
+
+result = workflow.result()
+print(result)
+
+# With induced-fit docking, poses are ranked by induced_fit_score rather than raw docking score.
+for i, score in enumerate(result.scores):
+    print(
+        f"  Pose {i}: induced_fit_score={score.induced_fit_score:.3f}  "
+        f"score={score.score:.3f}  receptor_strain={score.receptor_strain}"
+    )
+
+# Download the top-scoring complex and best-ranked relaxed receptor as PDBs
+complex_protein = result.get_complex(0)
+complex_protein.download_pdb_file(name="dasatinib_2GQG_induced_complex")
+print("Saved dasatinib_2GQG_induced_complex.pdb")
+
+induced_receptors = result.get_induced_receptors()
+if induced_receptors:
+    induced_receptors[0].download_pdb_file(name="dasatinib_2GQG_induced_receptor")
+    print("Saved dasatinib_2GQG_induced_receptor.pdb")

{rowan_python-3.1.14 → rowan_python-3.1.15}/examples/pose_analysis_md.py

@@ -45,5 +45,9 @@ print(
 )
 md_result = md_workflow.result()
 
-# print ligand RMSD by frame
-print(md_result.trajectories[0].ligand_rmsd)
+trajectory = md_result.trajectories[0]
+print(f"Ligand RMSD: {trajectory.ligand_rmsd}")
+print(f"Protein RMSD: {trajectory.protein_rmsd}")
+print(f"Protein RMSF: {trajectory.rmsf}")
+print(f"Potential energy: {trajectory.potential_energy} Hartree")
+print(f"MM/GBSA scores: {trajectory.mmgbsa_scores} kcal/mol")

rowan_python-3.1.15/examples/protein_cofolding_modified_inputs.py

@@ -0,0 +1,44 @@
+"""Cofolding with modified polymers and a covalent bond constraint."""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable.
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+protein = rowan.ProteinSequence(
+    sequence="ASA",
+    modifications=[rowan.ResidueModification(position=1, ccd="SEP")],
+)
+dna = rowan.DNASequence(
+    sequence="AC",
+    modifications=[rowan.NucleotideModification(position=1, ccd="5MC")],
+)
+rna = rowan.RNASequence(
+    sequence="AU",
+    modifications=[rowan.NucleotideModification(position=1, ccd="PSU")],
+)
+
+protein_atom = rowan.ConstraintTarget(
+    input_type="protein", input_index=0, token_index=1, atom_name="OG"
+)
+ligand_atom = rowan.ConstraintTarget(input_type="ligand", input_index=0, token_index=0)
+covalent_bond = rowan.BondConstraint(atom_1=protein_atom, atom_2=ligand_atom)
+
+workflow = rowan.submit_protein_cofolding_workflow(
+    initial_protein_sequences=[protein],
+    initial_dna_sequences=[dna],
+    initial_rna_sequences=[rna],
+    initial_smiles_list=["CBr"],
+    bond_constraints=[covalent_bond],
+    model=rowan.CofoldingModel.BOLTZ_2,
+    num_samples=1,
+    name="Modified polymers with covalent constraint",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/protein-cofolding/{workflow.uuid}")
+result = workflow.result()
+print(result)
+for i, prediction in enumerate(result.predictions):
+    print(f"  sample {i}: scores={prediction.scores}")

{rowan_python-3.1.14 → rowan_python-3.1.15}/examples/protein_md.py

@@ -21,3 +21,7 @@ md_workflow = rowan.submit_protein_md_workflow(
 )
 
 print(f"View MD workflow privately at: https://labs.rowansci.com/protein-md/{md_workflow.uuid}")
+trajectory = md_workflow.result().trajectories[0]
+print(f"Protein RMSD: {trajectory.protein_rmsd}")
+print(f"Protein RMSF: {trajectory.rmsf}")
+print(f"Potential energy: {trajectory.potential_energy} Hartree")

rowan_python-3.1.15/examples/temporary_workflow_sharing.py

@@ -0,0 +1,19 @@
+"""Example: temporarily share a workflow with anyone who has its link."""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable.
+# rowan.api_key = "rowan-sk..."
+
+workflow = rowan.retrieve_workflow("your-workflow-uuid")
+
+# Temporary shares can last for up to 120 minutes. This does not make the workflow
+# permanently public: `workflow.public` remains unchanged.
+workflow = workflow.temporarily_share(duration_minutes=60)
+
+print(f"Share URL: https://labs.rowansci.com/workflow/{workflow.uuid}")
+print(f"Public until: {workflow.public_until}")
+print(f"Temporary share active: {workflow.is_temporarily_public}")
+
+# End access before the expiration time if needed.
+# workflow = workflow.end_temporary_share()

{rowan_python-3.1.14 → rowan_python-3.1.15}/pixi.lock

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@@ -912,7 +912,7 @@ packages:
   name: rowan-python
   requires_dist:
   - httpx
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+  - stjames>=0.0.261
   - setuptools
   - rdkit
   - nest-asyncio
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   - mkdocs-section-index ; extra == 'docs'
   - mkdocs-literate-nav ; extra == 'docs'
   requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/65/e8/891341b63e2bb9e2aa3950583fa05182c572e80ec0d9542af24d57f0e923/stjames-0.0.263-py3-none-any.whl
+  name: stjames
+  version: 0.0.263
+  sha256: 3b5f1e79a8de0f73e1940f132a8546f6530a7925fe78b7a16d405ab14516e8cf
+  requires_dist:
+  - pydantic>=2.4
+  - numpy
+  - requests
+  - more-itertools
+  - rdkit ; extra == 'rdkit'
+  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/67/81/4add07e5172b7ac40d8ed5ff580409a7801a4fe26d529bdd915401dabfbe/typing_inspection-0.4.4-py3-none-any.whl
   name: typing-inspection
   version: 0.4.4
@@ -1627,17 +1638,6 @@ packages:
   - pysocks>=1.5.6,!=1.5.7 ; extra == 'socks'
   - chardet>=3.0.2,<8 ; extra == 'use-chardet-on-py3'
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/a2/38/803820d0533c768bc8da6519ca0cd76a82e36c413a3c1eeaf22aa524af6d/stjames-0.0.260-py3-none-any.whl
-  name: stjames
-  version: 0.0.260
-  sha256: 17a4b3ed20399b2e8a789a39615e40cb30ee8d2a58665b855989f5a4f32c5706
-  requires_dist:
-  - pydantic>=2.4
-  - numpy
-  - requests
-  - more-itertools
-  - rdkit ; extra == 'rdkit'
-  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/a3/9c/a1bda6439c19c4783d50df896142b67b9e7d432db36675d339a32778669d/coverage-7.16.0-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
   name: coverage
   version: 7.16.0

{rowan_python-3.1.14 → rowan_python-3.1.15}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.1.14"
+version = "3.1.15"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.12"
@@ -9,7 +9,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
-    "stjames>=0.0.257",
+    "stjames>=0.0.261",
     "setuptools",
     "rdkit",
     "nest-asyncio",

{rowan_python-3.1.14 → rowan_python-3.1.15}/rowan/__init__.py

@@ -15,6 +15,7 @@ from stjames import (
     ConformerClusteringSettings,
     ConformerGenSettingsUnion,
     Correction,
+    DNASequence,
     DockingSettings,
     Engine,
     ETKDGSettings,
@@ -22,6 +23,7 @@ from stjames import (
     GninaSettings,
     GreedyClusteringSettings,
     iMTDSettings,
+    InducedFitSettings,
     KMeansClusteringSettings,
     Method,
     Mode,
@@ -29,12 +31,15 @@ from stjames import (
     MultiStageOptSettings,
     NessoAffinitySettings,
     NMR_SUPPORTED_SOLVENTS,
+    NucleotideModification,
     OpenConfSettings,
     OptimizationSettings,
     PBCDFTSettings,
     PeriodicCell,
     ProteinSequence,
     ProteinForceField,
+    ResidueModification,
+    RNASequence,
     ScanSettings,
     Settings,
     Solvent,
@@ -71,7 +76,7 @@ from .api_keys import *
 from .calculation import *
 from .folder import *
 from .molecule import *
-from .types import ProteinUUID, RdkitMol, StJamesMolecule, StructureInput
+from .types import ProteinUUID, RdkitMol, SMILES, StJamesMolecule, StructureInput
 from .workflows import *
 from .project import *
 from .protein import *

{rowan_python-3.1.14 → rowan_python-3.1.15}/rowan/workflows/__init__.py

@@ -110,13 +110,19 @@ from .protein_binder_design import (
     submit_protein_binder_design_workflow,
 )
 from .protein_cofolding import (
+    BondConstraint,
     CofoldingModel,
     CofoldingResult,
     CofoldingTemplate,
     ConstraintTarget,
     ContactConstraint,
+    DNASequence,
+    NucleotideModification,
     PocketConstraint,
     ProteinCofoldingResult,
+    ProteinSequence,
+    ResidueModification,
+    RNASequence,
     submit_protein_cofolding_workflow,
 )
 from .protein_md import ProteinMDResult, submit_protein_md_workflow

{rowan_python-3.1.14 → rowan_python-3.1.15}/rowan/workflows/analogue_docking.py

@@ -191,8 +191,7 @@ def submit_analogue_docking_workflow(
     scoring_function: Literal["vina", "vinardo"] = "vinardo",
     exhaustiveness: int = 8,
     max_poses: int = 4,
-    num_conformers_per_analogue: int = 100,
-    require_posebusters: bool = False,
+    num_conformers_per_analogue: int = 20,
     run_local_optimization: bool = False,
     name: str = "Analogue Docking Workflow",
     folder_uuid: str | None = None,
@@ -214,7 +213,6 @@ def submit_analogue_docking_workflow(
     :param exhaustiveness: How many times Vina attempts to find a pose for each conformer.
     :param max_poses: Maximum number of poses generated per input conformer.
     :param num_conformers_per_analogue: Maximum number of conformers to generate per analogue.
-    :param require_posebusters: Filter conformers based on PoseBusters validity before docking.
     :param run_local_optimization: Whether to run a local opt in docking pocket or just score.
     :param name: Name of the workflow.
     :param folder_uuid: UUID of the folder to place the workflow in.
@@ -254,7 +252,6 @@ def submit_analogue_docking_workflow(
         protein=protein,
         docking_settings=docking_settings,
         num_conformers_per_analogue=num_conformers_per_analogue,
-        require_posebusters=require_posebusters,
         run_local_optimization=run_local_optimization,
     )
 

{rowan_python-3.1.14 → rowan_python-3.1.15}/rowan/workflows/base.py

@@ -75,9 +75,19 @@ class DispatchInfo:
 
 
 class WorkflowError(Exception):
-    """Raised when a workflow fails or is stopped."""
+    """Raised when a workflow cannot return a result.
 
-    pass
+    The complete backend log is available through :attr:`logfile` rather than being included in
+    the exception text. It provides diagnostic context only and is not a source of workflow result
+    values.
+
+    :param message: error summary
+    :param logfile: workflow log returned by the API, when available
+    """
+
+    def __init__(self, message: str, *, logfile: str = "") -> None:
+        self.logfile = logfile
+        super().__init__(message)
 
 
 @dataclass(slots=True, repr=False)
@@ -195,6 +205,8 @@ class Workflow(BaseModel):
     :param notes: Workflow notes.
     :param starred: Whether the workflow is starred.
     :param public: Whether the workflow is public.
+    :param public_until: Date and time until which the workflow is temporarily public.
+    :param is_temporarily_public: Whether temporary public access is currently active.
     :param workflow_type: Type of the workflow.
     :param data: Data of the workflow.
     :param email_when_complete: Whether to send an email when the workflow completes.
@@ -217,6 +229,8 @@ class Workflow(BaseModel):
     notes: str
     starred: bool
     public: bool
+    public_until: datetime | None = None
+    is_temporarily_public: bool = False
     workflow_type: str = Field(alias="object_type")
     data: dict[str, Any] | None = Field(default=None, alias="object_data")
     email_when_complete: bool
@@ -325,6 +339,58 @@ Workflow:  {self.name}
 
         return self
 
+    def temporarily_share(self, duration_minutes: int, in_place: bool = False) -> Self:
+        """Temporarily make the workflow publicly accessible.
+
+        Temporary sharing does not change :attr:`public`. The returned workflow instead records
+        the expiration in :attr:`public_until` and reports the active state through
+        :attr:`is_temporarily_public`.
+
+        :param duration_minutes: Number of minutes to share the workflow, up to 120.
+        :param in_place: Whether to update the current instance in-place.
+        :returns: Workflow with the temporary sharing state returned by the API.
+        :raises HTTPError: If the API request fails.
+        """
+        with api_client() as client:
+            response = client.post(
+                f"/workflow/{self.uuid}/temporarily_share",
+                params={"duration_minutes": duration_minutes},
+            )
+            response.raise_for_status()
+            data = response.json()
+
+        if not in_place:
+            return type(self).model_validate(data)
+
+        updated_workflow = self.model_validate(data)
+        for field_name in type(self).model_fields:
+            setattr(self, field_name, getattr(updated_workflow, field_name))
+
+        return self
+
+    def end_temporary_share(self, in_place: bool = False) -> Self:
+        """End temporary public access to the workflow.
+
+        Permanent public access through :attr:`public` is unaffected.
+
+        :param in_place: Whether to update the current instance in-place.
+        :returns: Workflow with the temporary sharing state returned by the API.
+        :raises HTTPError: If the API request fails.
+        """
+        with api_client() as client:
+            response = client.post(f"/workflow/{self.uuid}/end_temporary_share")
+            response.raise_for_status()
+            data = response.json()
+
+        if not in_place:
+            return type(self).model_validate(data)
+
+        updated_workflow = self.model_validate(data)
+        for field_name in type(self).model_fields:
+            setattr(self, field_name, getattr(updated_workflow, field_name))
+
+        return self
+
     def done(self) -> bool:
         """
         Check if the workflow has finished (success, failure, or stopped).
@@ -350,7 +416,8 @@ Workflow:  {self.name}
             If False, return immediately with whatever data is available.
         :param poll_interval: Seconds between status checks while waiting.
         :returns: WorkflowResult subclass with typed access to results.
-        :raises WorkflowError: If the workflow failed or was stopped.
+        :raises WorkflowError: If the workflow failed or was stopped. Inspect the exception's
+            `logfile` attribute for the backend log.
         """
         if self.status == stjames.Status.DRAFT:
             raise WorkflowError(
@@ -365,7 +432,13 @@ Workflow:  {self.name}
 
         if self.status in {stjames.Status.FAILED, stjames.Status.STOPPED}:
             status = self.status.name.lower()
-            raise WorkflowError(f"Workflow '{self.name}' {status} (uuid={self.uuid})")
+            message = f"Workflow '{self.name}' {status} (uuid={self.uuid})"
+            if self.logfile:
+                message += ". See WorkflowError.logfile for diagnostic details."
+            raise WorkflowError(
+                message,
+                logfile=self.logfile,
+            )
 
         if not self.data:
             status = self.status.name.lower() if self.status else "unknown"

{rowan_python-3.1.14 → rowan_python-3.1.15}/rowan/workflows/batch_docking.py

@@ -7,6 +7,7 @@ from ..protein import Protein
 from ..types import ProteinUUID
 from ..utils import api_client
 from .base import Workflow, WorkflowResult, register_result
+from .docking import DockingScore
 
 
 @register_result("batch_docking")
@@ -33,6 +34,29 @@ class BatchDockingResult(WorkflowResult):
         padded = list(scores) + [None] * (len(smiles_list) - len(scores))
         return dict(zip(smiles_list, padded, strict=True))
 
+    @property
+    def refined_scores(self) -> dict[str, DockingScore | None]:
+        """Saved docking results indexed by input SMILES."""
+        smiles_list = self._workflow.initial_smiles_list
+        scores = self._workflow.refined_scores or []
+        padded = list(scores) + [None] * (len(smiles_list) - len(scores))
+        return {
+            smiles: (
+                DockingScore(
+                    score=score.score,
+                    pose=score.pose,
+                    complex_pdb=score.complex_pdb,
+                    posebusters_valid=score.posebusters_valid,
+                    strain=score.strain,
+                    rmsd=score.rmsd,
+                    mmgbsa_score=score.mmgbsa_score,
+                )
+                if score is not None
+                else None
+            )
+            for smiles, score in zip(smiles_list, padded, strict=True)
+        }
+
 
 def submit_batch_docking_workflow(
     smiles_list: list[str],
@@ -41,6 +65,8 @@ def submit_batch_docking_workflow(
     executable: str = "vina",
     scoring_function: str = "vinardo",
     exhaustiveness: float = 8,
+    num_poses_to_save: int = 0,
+    run_mmgbsa: bool = False,
     name: str = "Batch Docking Workflow",
     folder_uuid: str | None = None,
     folder: Folder | None = None,
@@ -57,6 +83,9 @@ def submit_batch_docking_workflow(
     :param executable: Which docking implementation to use.
     :param scoring_function: Which docking scoring function to use.
     :param exhaustiveness: Docking exhaustiveness parameter.
+    :param num_poses_to_save: Number of top-scoring compounds whose best pose to save.
+    :param run_mmgbsa: Whether to refine the saved poses with MM/GBSA. Ignored when
+        `num_poses_to_save` is zero.
     :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.
@@ -84,6 +113,8 @@ def submit_batch_docking_workflow(
         protein=protein,
         pocket=pocket,
         docking_settings=docking_settings,
+        num_poses_to_save=num_poses_to_save,
+        run_mmgbsa=run_mmgbsa,
     )
 
     data = {

{rowan_python-3.1.14 → rowan_python-3.1.15}/rowan/workflows/binding_affinity.py

@@ -28,11 +28,9 @@ class BindingAffinityScore:
 
     :param binding_affinity: binding affinity in kcal/mol for SQM settings, or log10(M)
         for GNINA, AEV-PLIG, and NESSO settings.
-    :param strain: strain energy in kcal/mol, or None if not computed
     """
 
     binding_affinity: float
-    strain: float | None
 
 
 @register_result("binding_affinity")
@@ -50,10 +48,7 @@ class BindingAffinityResult(WorkflowResult):
         """Binding affinity scores in input order, with `None` for failed inputs."""
         return [
             (
-                BindingAffinityScore(
-                    binding_affinity=result.binding_affinity,
-                    strain=result.strain,
-                )
+                BindingAffinityScore(binding_affinity=result.binding_affinity)
                 if result is not None
                 else None
             )