rowan-python 3.2.0__py3-none-any.whl → 3.2.1__py3-none-any.whl

rowan/folder.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from datetime import datetime
 from typing import TYPE_CHECKING, Any, Self
 
 from pydantic import BaseModel
@@ -8,8 +9,6 @@ from .project import default_project, retrieve_project
 from .utils import api_client, get_project_uuid
 
 if TYPE_CHECKING:
-    from datetime import datetime
-
     from .workflows.base import Workflow
 
 
@@ -65,8 +64,6 @@ class Folder(BaseModel):
         for field_name in self.__class__.model_fields:
             setattr(self, field_name, getattr(updated_folder, field_name))
 
-        self.model_rebuild()
-
         return self
 
     def update(

rowan/protein.py

@@ -1,4 +1,3 @@
-import time
 import warnings
 from datetime import datetime
 from pathlib import Path
@@ -22,7 +21,6 @@ class Protein(BaseModel):
         created_at: creation date of the protein
         used_in_workflow: whether the protein is used in a workflow
         ancestor_uuid: UUID of the ancestor protein
-        sanitized: whether the protein is sanitized
         name: name of the protein
         data: data of the protein
         public: whether the protein is public
@@ -32,7 +30,6 @@ class Protein(BaseModel):
     created_at: datetime | None = None
     used_in_workflow: bool | None = None
     ancestor_uuid: str | None = None
-    sanitized: int | None = None
     name: str | None = None
     data: dict | None = None
     public: bool | None = None
@@ -188,7 +185,6 @@ class Protein(BaseModel):
         self.data = protein_data.get("data")
         self.public = protein_data.get("public")
         self.pocket = protein_data.get("pocket")
-        self.sanitized = protein_data.get("sanitized")
         self.used_in_workflow = protein_data.get("used_in_workflow")
         self._workflow_uuid = workflow_uuid
         return self
@@ -241,118 +237,6 @@ class Protein(BaseModel):
             response = client.delete(f"/protein/{self.uuid}")
             response.raise_for_status()
 
-    def sanitize(self, poll_interval: float = 10.0, timeout: float = 300.0) -> None:
-        """Sanitizes a protein and waits for the process to complete.
-
-        Protein sanitization runs asynchronously on the server. This method
-        submits the request then polls until sanitization succeeds, fails, or
-        times out.
-
-        Args:
-            poll_interval: seconds between status checks (default 10)
-            timeout: maximum seconds to wait before raising (default 300)
-
-        Raises:
-            RuntimeError: sanitization fails, is stopped, or times out
-            httpx.HTTPStatusError: any API request fails
-        """
-        with api_client() as client:
-            response = client.post(f"/protein/sanitize/{self.uuid}")
-            response.raise_for_status()
-
-        deadline = time.monotonic() + timeout
-        while time.monotonic() < deadline:
-            time.sleep(poll_interval)
-            self.refresh()
-            match self.sanitized:
-                case 2:  # success
-                    return
-                case 3:  # failed
-                    raise RuntimeError(
-                        f"Protein sanitization failed for {self.uuid}. "
-                        "Check the protein in the Rowan UI for details."
-                    )
-                case 4:  # stopped
-                    raise RuntimeError(f"Protein sanitization was stopped for {self.uuid}.")
-                case _:  # 1 (in progress) or None: keep polling
-                    pass
-
-        raise RuntimeError(f"Protein sanitization timed out after {timeout:.0f}s for {self.uuid}.")
-
-    def prepare(
-        self,
-        find_missing_residues: bool = True,
-        add_missing_atoms: bool = True,
-        remove_heterogens: bool = True,
-        keep_waters: bool = False,
-        remove_hydrogens: bool = False,
-        remove_invalid_hydrogens: bool = False,
-        add_hydrogens: bool = True,
-        add_hydrogen_ph: float = 7.0,
-        optimize_hydrogens: bool = True,
-        poll_interval: float = 10.0,
-        timeout: float = 300.0,
-    ) -> None:
-        """Quickly prepare a protein in place using PDBFixer and OpenMM.
-
-        Runs PDBFixer to fix nonstandard residues, add missing atoms/hydrogens,
-        and optionally optimizes hydrogen positions with OpenMM. This is the fast
-        preparation option and typically finishes in about a minute or less. Use
-        `submit_protein_preparation_workflow` for the full protein preparation workflow,
-        which can take around ten minutes but includes Boltz-2 missing-structure modeling,
-        terminal capping, selectable protonation methods, and retained non-polymers.
-
-        Args:
-            find_missing_residues: identify and model missing residues
-            add_missing_atoms: add missing heavy atoms to residues
-            remove_heterogens: remove ligands, salts, and other heterogens
-            keep_waters: preserve water molecules when removing heterogens
-            remove_hydrogens: remove all existing hydrogens before adding new ones
-            remove_invalid_hydrogens: remove hydrogens not matching the forcefield template
-            add_hydrogens: add missing hydrogen atoms
-            add_hydrogen_ph: pH used to determine protonation states when adding hydrogens
-            optimize_hydrogens: optimize hydrogen positions with OpenMM energy minimization
-            poll_interval: seconds between status checks (default 10)
-            timeout: maximum seconds to wait before raising (default 300)
-
-        Raises:
-            RuntimeError: preparation fails, is stopped, or times out
-            httpx.HTTPStatusError: any API request fails
-        """
-        params = {
-            "find_missing_residues": find_missing_residues,
-            "add_missing_atoms": add_missing_atoms,
-            "remove_heterogens": remove_heterogens,
-            "keep_waters": keep_waters,
-            "remove_hydrogens": remove_hydrogens,
-            "remove_invalid_hydrogens": remove_invalid_hydrogens,
-            "add_hydrogens": add_hydrogens,
-            "add_hydrogen_ph": add_hydrogen_ph,
-            "optimize_hydrogens": optimize_hydrogens,
-        }
-        with api_client() as client:
-            response = client.post(f"/protein/prepare/{self.uuid}", params=params)
-            response.raise_for_status()
-
-        deadline = time.monotonic() + timeout
-        while time.monotonic() < deadline:
-            time.sleep(poll_interval)
-            self.refresh()
-            match self.sanitized:
-                case 2:
-                    return
-                case 3:
-                    raise RuntimeError(
-                        f"Protein preparation failed for {self.uuid}. "
-                        "Check the protein in the Rowan UI for details."
-                    )
-                case 4:
-                    raise RuntimeError(f"Protein preparation was stopped for {self.uuid}.")
-                case _:
-                    pass
-
-        raise RuntimeError(f"Protein preparation timed out after {timeout:.0f}s for {self.uuid}.")
-
     def validate_protein_forcefield(self, exclude_residues: list[str | int] | None = None) -> None:
         """Validate that this protein can be parameterized with the MD forcefield.
 

rowan/workflows/binding_affinity.py

@@ -82,7 +82,8 @@ def submit_binding_affinity_workflow(
     input modes are supported:
 
     **Mode 1 – holo protein:** protein already contains the bound ligand. Pass
-    `ligand_residue_name` to identify which residue is the ligand vs. the receptor.
+    `ligand_residue_name` to identify which residue is the ligand vs. the receptor,
+    and exactly one entry in `ligand_smiles` describing that bound ligand.
     Do not pass `ligand_structures`.
 
     **Mode 2 – apo protein + external poses:** protein has no bound ligand. Pass
@@ -101,13 +102,15 @@ def submit_binding_affinity_workflow(
         protein: protein structure. Can be input as a UUID or a Protein object. Required
             unless `protein_sequences` is set (mode 3)
         ligand_residue_name: residue name identifying the ligand in a holo protein PDB
-            (mode 1 only)
+            (mode 1 only); requires exactly one matching `ligand_smiles` entry
         ligand_structures: external ligand poses to score, already in the protein's
             coordinate frame. Must have 3D coordinates (mode 2 only)
         protein_sequences: protein sequences to score against, in place of `protein`
             (mode 3, NESSO only)
-        ligand_smiles: ligand SMILES to score, in place of `ligand_residue_name`/
-            `ligand_structures` (mode 3, NESSO only)
+        ligand_smiles: exactly one SMILES describing the bound ligand with
+            `ligand_residue_name` (mode 1, all methods), or ligand SMILES to score without
+            structural ligand inputs (mode 3, NESSO only). Not accepted with
+            `ligand_structures`
         binding_affinity_settings: settings controlling how binding affinity is
             computed: `SinglePointEnergySettings` (SQM), `GninaAffinitySettings`,
             `AEVPLIGAffinitySettings`, or `NessoAffinitySettings`. Defaults to

rowan/workflows/protein_md.py

@@ -142,6 +142,7 @@ def submit_protein_md_workflow(
     nonbonded_cutoff: float = 8.0,
     ionic_strength_M: float = 0.0,
     water_buffer: float = 8.0,
+    frame_save_interval_ps: float = 10.0,
     save_solvent: bool = False,
     num_solvent_to_save: int | None = None,
     small_molecules: dict[str | int, str | None] | None = None,
@@ -178,6 +179,8 @@ def submit_protein_md_workflow(
         nonbonded_cutoff: nonbonded cutoff for particle-mesh Ewald, in A
         ionic_strength_M: ionic strength of the solution, in M (molar)
         water_buffer: amount of water to add around the protein, in A
+        frame_save_interval_ps: how often to save a frame to the trajectory, in ps; must be
+            an integer multiple of timestep_fs
         save_solvent: whether solvent should be saved
         num_solvent_to_save: keep this many solvent molecules nearest the binder, or all if None;
             only meaningful when save_solvent is True and a binder is present
@@ -246,6 +249,7 @@ def submit_protein_md_workflow(
         nonbonded_cutoff=nonbonded_cutoff,
         ionic_strength_M=ionic_strength_M,
         water_buffer=water_buffer,
+        frame_save_interval_ps=frame_save_interval_ps,
         save_solvent=save_solvent,
         num_solvent_to_save=num_solvent_to_save,
         small_molecules=small_molecules,

rowan/workflows/protein_preparation.py

@@ -75,7 +75,7 @@ def submit_protein_preparation_workflow(
     """Submit a protein-preparation workflow to the API.
 
     Full protein preparation can take around ten minutes, depending on the structure and
-    settings. For a faster PDBFixer/OpenMM-only path, use `Protein.prepare()`.
+    settings.
 
     Args:
         protein: protein to prepare, as a UUID or Protein object

rowan/workflows/relative_binding_free_energy_perturbation.py

@@ -140,6 +140,8 @@ class RelativeBindingFreeEnergyPerturbationResult(WorkflowResult):
         lambda_vals: list[float] | None = None,
         path: Path | str | None = None,
         name: str | None = None,
+        *,
+        leg: Literal["complex", "solvent"] = "complex",
     ) -> Path:
         """Download DCD trajectory files for a specific perturbation edge.
 
@@ -148,6 +150,7 @@ class RelativeBindingFreeEnergyPerturbationResult(WorkflowResult):
             lambda_vals: lambda values to download. Defaults to all windows
             path: directory to save the file to. Defaults to current directory
             name: custom name for the tar.gz file (without extension)
+            leg: thermodynamic leg whose trajectories should be downloaded
 
         Returns:
             path to the downloaded tar.gz file
@@ -163,27 +166,34 @@ class RelativeBindingFreeEnergyPerturbationResult(WorkflowResult):
         path = Path(path) if path is not None else Path.cwd()
         path.mkdir(parents=True, exist_ok=True)
 
-        params: dict = {"edge_index": edge_index}
-        if lambda_vals is not None:
-            params["lambda_vals"] = lambda_vals
+        params: dict = {"edge_index": edge_index, "leg": leg}
 
-        file_name = f"{name or f'edge_{edge_index}_trajectories'}.tar.gz"
+        default_name = (
+            f"edge_{edge_index}_trajectories"
+            if leg == "complex"
+            else f"edge_{edge_index}_{leg}_trajectories"
+        )
+        file_name = f"{name or default_name}.tar.gz"
         file_path = path / file_name
         return download_file(
             file_path,
             "POST",
             f"/trajectory/{self.workflow_uuid}/rbfe_trajectory_dcds",
             params=params,
+            json=lambda_vals,
         )
 
     def download_all_trajectories(
         self,
         path: Path | str | None = None,
+        *,
+        leg: Literal["complex", "solvent"] = "complex",
     ) -> list[Path]:
         """Download DCD trajectory files for all perturbation edges.
 
         Args:
             path: directory to save the files to. Defaults to current directory
+            leg: thermodynamic leg whose trajectories should be downloaded
 
         Returns:
             list of paths to the downloaded tar.gz files, one per edge
@@ -191,7 +201,9 @@ class RelativeBindingFreeEnergyPerturbationResult(WorkflowResult):
         Raises:
             httpx.HTTPStatusError: any API request fails
         """
-        return [self.download_edge_trajectories(i, path=path) for i in range(len(self.edges))]
+        return [
+            self.download_edge_trajectories(i, path=path, leg=leg) for i in range(len(self.edges))
+        ]
 
     @property
     def ligand_dg_results(self) -> dict[str, RelativeBindingFreeEnergyResult] | None:

{rowan_python-3.2.0.dist-info → rowan_python-3.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: rowan-python
-Version: 3.2.0
+Version: 3.2.1
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
@@ -12,22 +12,19 @@ Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.261
+Requires-Dist: stjames>=0.0.275
 Description-Content-Type: text/markdown
 
 # Rowan Python Library
 
 [![pypi](https://img.shields.io/pypi/v/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python)
 [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://docs.astral.sh/uv/)
-[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Downloads](https://img.shields.io/pypi/dm/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python/)
 [![License](https://img.shields.io/github/license/rowansci/rowan-python)](LICENSE)
 [![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/rowansci/rowan-python/test.yml?branch=master&logo=github-actions)](https://github.com/rowansci/rowan-python/actions)
-[![Typing: ty](https://img.shields.io/badge/typing-ty-EFC621.svg)](https://github.com/astral-sh/ty)
-<!-- Enable these badges with the corresponding tooling/services.
+[![ty](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ty/main/assets/badge/v0.json)](https://github.com/astral-sh/ty)
 [![Markdown style: rumdl](https://img.shields.io/badge/md%20style-rumdl-000000.svg)](https://rumdl.dev)
-[![Codecov](https://img.shields.io/codecov/c/github/rowansci/rowan-python)](https://codecov.io/gh/rowansci/rowan-python)
--->
 
 The Rowan Python library is the Python SDK for running Rowan computational chemistry workflows
 programmatically. Use it from scripts and applications to submit calculations, monitor workflow

{rowan_python-3.2.0.dist-info → rowan_python-3.2.1.dist-info}/RECORD

@@ -3,10 +3,10 @@ rowan/api_keys.py,sha256=ms8NAkLreFQcaEUPCf8lSf7T0x2OmrWCAT44N1cgocE,6955
 rowan/calculation.py,sha256=E1dAox4ScE3NHJXiKFZ3Lpmw2h7DKCVzcwRvGZ2H2cQ,3802
 rowan/config.py,sha256=ay6UxKLE9bbTxHFXxDfUXGRVJWJ1T-eS2_L4HF8mb_E,20927
 rowan/constants.py,sha256=emCH4m9OL2Hm5E-6mJGM_FgzrK_JrZT-FiKJ6pMNQ4Y,84
-rowan/folder.py,sha256=IhTPR2Wm4_roJJJdprRPd5C9GQQh6JkPDN8G_r6XSxU,13918
+rowan/folder.py,sha256=8Gb60oes78G7QTGm0EX-ofkmQEggv5cwseA7dRBIhok,13883
 rowan/molecule.py,sha256=1ueC_M2Yaubkt5eQlONCagShWPnoJfNNXgd0s7sslPM,15826
 rowan/project.py,sha256=N8DdNt7xCYHunIAqTvPmBGkH8thzwmguATo4Thfa13o,5479
-rowan/protein.py,sha256=6e_lvP-QEdEQ-WnAkPMsn3XdqDgItRG6fbepK6Xw-Kw,24544
+rowan/protein.py,sha256=AGHarvWfciSwWXfHnVjdUW47FML7vI4Kk4dYTeFfKAQ,19322
 rowan/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rowan/types.py,sha256=D0d6MW6MvLMs6UtNgGKlapFGOnPlzqFTk9EAgB9dwks,636
 rowan/user.py,sha256=wGwyp0uzifzJeC88yCC7pgxMhxuZ-LLWHfCcuPXcx44,6199
@@ -19,7 +19,7 @@ rowan/workflows/base.py,sha256=DR2k5VFMmv2sa9v4hYU_Fvzf8k2unp5nhPqvOd7NX64,39520
 rowan/workflows/basic_calculation.py,sha256=7o9jxEpDMiong2k3Ke1WCLwaSWZvKY5tqhbixnbQWbo,12945
 rowan/workflows/batch_docking.py,sha256=AtCp2-D_LOVxzSPmQ144zYIz5kft9NeRljELdRDU6vY,4941
 rowan/workflows/bde.py,sha256=4Yw27U2RPsuUDf9tw-7wPbw_4gaUcvDlQP8je7VJktU,7099
-rowan/workflows/binding_affinity.py,sha256=UbsaSLJwyaPxFgEAmDxqIYSxFm4ioKoXIJJPBeLDzJg,6285
+rowan/workflows/binding_affinity.py,sha256=O0fL_oQtMpYlmdaCvHTR7WSNfOENMPAN0OUBxO4640k,6553
 rowan/workflows/conformer_search.py,sha256=enx9HbFZVVYgHJP-HUFam63E0qCDq6jjGeXNuBXXlys,16311
 rowan/workflows/constants.py,sha256=iM9-6DyIe0N2ydyq-lRYP7VDufFmMrN5tDjnpUSlxF8,588
 rowan/workflows/covalent_inhibitor_scan.py,sha256=VcZhwW3HRuFuGZNedMPZBWbzuhGvz_B5pNJSIPyi9Kw,6721
@@ -43,18 +43,18 @@ rowan/workflows/pocket_detection.py,sha256=dFeCLB59v5-Izf54blrRzJhwUtBQX2SJyVKT_
 rowan/workflows/pose_analysis_md.py,sha256=ndfGS8oP8oQ3EXe83Wgbx1H8ZFURlm8IJZN34aDpqeE,10599
 rowan/workflows/protein_binder_design.py,sha256=ee3qYGzTzQsca9otnRz9Qjwj1X66LTCKqtTQ5EOzBHk,9181
 rowan/workflows/protein_cofolding.py,sha256=s4bLxlix4kAO_NzS75tc2wiEYqUxpFofxziUnxI2iUY,17422
-rowan/workflows/protein_md.py,sha256=4atIPGKxA1bISw6MlwrrRCwIj2Qhy7evgt5v6UPRBZc,12028
-rowan/workflows/protein_preparation.py,sha256=cpRkWHX5hOkR5LMGKJ-iS3ZJy2vMtuPGLNpqWN4q02g,5390
+rowan/workflows/protein_md.py,sha256=M4lbfEEvyxmhBWfz_Hf3whmNIYuHe3Q3HZzDcq-jYII,12264
+rowan/workflows/protein_preparation.py,sha256=8C04rhR4AiGiYJWZ8V06O4kpV443tGihcTk8rnNgscE,5325
 rowan/workflows/rbfe_graph.py,sha256=DBNxtmgw7BNSwOXFLpHDxJtfpheTpDPs8U3SYB2MXdE,8070
 rowan/workflows/redox_potential.py,sha256=0AV2nKTngEFw7VDDpDQvdeBo5u03Aklc2ak4bDWxUz0,5366
-rowan/workflows/relative_binding_free_energy_perturbation.py,sha256=52oUh8pZQGyFrpE5SRsRhYQU5MavnE92QwV5bR0N_Wg,15450
+rowan/workflows/relative_binding_free_energy_perturbation.py,sha256=dBQkM3wtbNVVkiXbB3RBBDUcme2OnWZkWFZdTUR8vlM,15872
 rowan/workflows/scan.py,sha256=MqV0NcjfInwxGlegOyWvAt8pwN0BdpsKvgCgTRkzdzU,7440
 rowan/workflows/solubility.py,sha256=Lws0lk4ifmtj84W_jyeOuaTpt8KM8-fceOggHrEYnmc,11211
 rowan/workflows/solvent_dependent_conformers.py,sha256=1dYf8UBVMRFELdwHzv3MI0pe12qoCAfohkaMiW3ak50,7460
 rowan/workflows/spin_states.py,sha256=C3hJEY4hccE1fCW4UjI4nIqGZLw9l2C2VKWCLiopSlY,9044
 rowan/workflows/strain.py,sha256=hq0dOlxnN72V4Sohr3qNFbOrjGmV01tc5zcF0HrL2-Y,6372
 rowan/workflows/tautomer_search.py,sha256=o5iFXHfcb6DvvWH7itA05hvWIrzxrc3a_9IDikYftiM,6351
-rowan_python-3.2.0.dist-info/METADATA,sha256=MbZFH7zmFqIBO5tVSvQCQwJ2JIdk3ZjXefIES14TvB0,4082
-rowan_python-3.2.0.dist-info/WHEEL,sha256=zOwg4jB6zX2kU910N-cMawjivD6tO8NEWvE12je1bVk,87
-rowan_python-3.2.0.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-3.2.0.dist-info/RECORD,,
+rowan_python-3.2.1.dist-info/METADATA,sha256=g0STX2NMLAvsvtvLRpJ8gaR6qBV-9SckC_SQzSaJzE0,3934
+rowan_python-3.2.1.dist-info/WHEEL,sha256=W3fkpkm7-wf9vBI5Z-7s0eWkeM-spu78I8Neb98DeEg,87
+rowan_python-3.2.1.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-3.2.1.dist-info/RECORD,,

{rowan_python-3.2.0.dist-info → rowan_python-3.2.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.32.0
+Generator: hatchling 1.32.4
 Root-Is-Purelib: true
 Tag: py3-none-any