rowan-python 3.1.8__tar.gz → 3.1.10__tar.gz

{rowan_python-3.1.8 → rowan_python-3.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.8
+Version: 3.1.10
 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>=0.0.228
+Requires-Dist: stjames<0.0.238,>=0.0.237
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.1.8 → rowan_python-3.1.10}/docs/index.md

@@ -209,6 +209,17 @@
       group_by_category: true
       filters: ["!^__"]
 
+## LogP
+::: rowan.workflows.logp
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
 ## MacropKa
 ::: rowan.workflows.macropka
     handler: python

{rowan_python-3.1.8 → rowan_python-3.1.10}/examples/covalent_inhibitor_scan.py

@@ -15,10 +15,13 @@ protein.prepare(remove_heterogens=False)
 protein_reactive_atom_index = 1571
 ligand_reactive_atom_index = 4492
 
+ligand_smiles = "CC(C)(C)C[C@@H](C#N)C(=O)N1CCC[C@H](C1)n2nc(c3ccc(Oc4ccccc4)cc3)c5c(N)ncnc25"
+
 workflow = rowan.submit_covalent_inhibitor_scan_workflow(
     protein=protein,
     protein_reactive_atom_index=protein_reactive_atom_index,
     ligand_reactive_atom_index=ligand_reactive_atom_index,
+    ligand_smiles=ligand_smiles,
     settings=rowan.CovalentInhibitorScanSettings(scan_num=4),
     name="BTK covalent inhibitor scan (Cys481, 4YHF)",
     folder=folder,

{rowan_python-3.1.8 → rowan_python-3.1.10}/examples/docking.py

@@ -35,5 +35,5 @@ for i, score in enumerate(result.scores):
 
 # Download the top-scoring protein–ligand complex as a PDB
 complex_protein = result.get_complex(0)
-complex_protein.download_pdb_file("dasatinib_2GQG_complex.pdb")
+complex_protein.download_pdb_file(name="dasatinib_2GQG_complex")
 print("Saved dasatinib_2GQG_complex.pdb")

rowan_python-3.1.10/examples/logp.py

@@ -0,0 +1,19 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+oseltamivir_SMILES = "C1CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H]([NH3+])C1CCC1"
+
+workflow = rowan.submit_logp_workflow(
+    initial_smiles=oseltamivir_SMILES,
+    method="chemprop_sangster2026",
+    name="Oseltamivir logP",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/logp/{workflow.uuid}")
+result = workflow.result()
+print(result)
+# e.g. <LogPResult logp=2.541>

{rowan_python-3.1.8 → rowan_python-3.1.10}/examples/protein_md.py

@@ -5,7 +5,7 @@ import rowan
 folder = rowan.get_folder("examples")
 
 protein = rowan.create_protein_from_pdb_id(
-    "crambin", "1CRN", project_uuid=rowan.default_project().uuid
+    "1CRN", name="crambin", project_uuid=rowan.default_project().uuid
 )
 
 protein.prepare()

{rowan_python-3.1.8 → rowan_python-3.1.10}/pixi.lock

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+      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.7.22-hbd8a1cb_0.conda
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-      - pypi: https://files.pythonhosted.org/packages/ef/2f/c5464532e965badff2f4c4c1a3a83f5697f0d7c407ed0cda44aaa99bb451/certifi-2026.6.17-py3-none-any.whl
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@@ -597,16 +597,16 @@ packages:
     - zstd >=1.5.7,<1.6.0a0
   size: 601375
   timestamp: 1764777111296
-- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.6.17-hbd8a1cb_0.conda
-  sha256: f8e3c730fa14ee3f170493779f06522c4acf89169f43db4f039727709b6419cf
-  md5: a9965dd99f683c5f444428f896635716
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.7.22-hbd8a1cb_0.conda
+  sha256: 0a0544cf95f64394fe4959286f5c71f5444ad58feb0602e53becb27448d24da6
+  md5: 0f51e2391ade309db462a55611263e9c
   depends:
   - __unix
   license: ISC
   purls: []
   run_exports: {}
-  size: 128866
-  timestamp: 1781708962055
+  size: 131780
+  timestamp: 1784754889428
 - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
   build_number: 8
   sha256: ad6d2e9ac39751cc0529dd1566a26751a0bf2542adb0c232533d32e176e21db5
@@ -820,7 +820,7 @@ packages:
   name: rowan-python
   requires_dist:
   - httpx
-  - stjames>=0.0.228
+  - stjames>=0.0.237,<0.0.238
   - setuptools
   - rdkit
   - nest-asyncio
@@ -851,6 +851,11 @@ packages:
   version: 3.32.0
   sha256: d396bea984af47333ef05e50eae7eff88c84256de6112aea0ec48a233c064fe3
   requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/0b/a7/71ac2cff56fec219ed242bb11b8efb69fcc4bec75db06fb7bfe35de520e6/certifi-2026.7.22-py3-none-any.whl
+  name: certifi
+  version: 2026.7.22
+  sha256: 62f22742b58a1a33014a2b6b706588a8d7e2a88ae7bd1a6ebe8c992928483775
+  requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/0b/d7/1959b9648791274998a9c3526f6d0ec8fd2233e4d4acce81bbae76b44b2a/python_dotenv-1.2.2-py3-none-any.whl
   name: python-dotenv
   version: 1.2.2
@@ -1072,6 +1077,11 @@ packages:
   version: 2.5.1
   sha256: 54ad769f17bc2d833b620851989f62054fb9ab93c969d9e1dc3c8e3d56beea21
   requires_python: '>=3.12'
+- pypi: https://files.pythonhosted.org/packages/42/ce/741cd197496a1abbf51352710fd15ed995d2a2be87189c1da26a450d6e83/ruff-0.16.0-py3-none-macosx_11_0_arm64.whl
+  name: ruff
+  version: 0.16.0
+  sha256: e01c21d10eb1b29f47b7454e1f4056db9a3f0260c646aa88457c610291db9f81
+  requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/49/d3/b8441a820a491ddfc024b0b0cf0393375b75ea13866d9c66727e54c2fc80/typing_extensions-4.16.0-py3-none-any.whl
   name: typing-extensions
   version: 4.16.0
@@ -1376,6 +1386,11 @@ packages:
   - pytest ; extra == 'dev'
   - tox ; extra == 'dev'
   - black ; extra == 'lint'
+- pypi: https://files.pythonhosted.org/packages/91/66/6bd3cf90500653d55dc0ffc8507aa8300bd49d0214b2e8cb4d3fef2943ba/ruff-0.16.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  name: ruff
+  version: 0.16.0
+  sha256: 4f11a8d11010301d0a398a2fdef67691feca7294da6aef55e2150e8fa2cd520b
+  requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/94/84/d9273cd09688070a6523c4aee4663a8538721b2b755c4962aafae0011e72/identify-2.6.19-py2.py3-none-any.whl
   name: identify
   version: 2.6.19
@@ -1681,11 +1696,6 @@ packages:
   - trove-classifiers>=2024.10.12 ; extra == 'tests'
   - defusedxml ; extra == 'xmp'
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/c9/10/74e53572aa758dfaa678c2a2646b5c5515d884b7ca56be4d2ce03ca4b560/ruff-0.15.22-py3-none-macosx_11_0_arm64.whl
-  name: ruff
-  version: 0.15.22
-  sha256: 11c1c715af53a09f714e011106bffc419751ec8232fcb5da42173284ea3fec6f
-  requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/ca/87/b4d6c38e0ccd5e85dc54cecdf933a152c60b28fe5d993a6d8a72fa6d5896/ast_serialize-0.6.0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
   name: ast-serialize
   version: 0.6.0
@@ -1782,6 +1792,17 @@ packages:
   - mkdocs-section-index ; extra == 'docs'
   - mkdocs-literate-nav ; extra == 'docs'
   requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/df/95/bdd01bbd523a63b113407c34c99af8495daa4651757cc28f3fabc393d131/stjames-0.0.237-py3-none-any.whl
+  name: stjames
+  version: 0.0.237
+  sha256: 790c32bdc829efe52b7ccc442083d0d95fc01587d4063a08ea73cd9f686f6d21
+  requires_dist:
+  - pydantic>=2.4
+  - numpy
+  - requests
+  - more-itertools
+  - rdkit ; extra == 'rdkit'
+  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/df/b2/87e62e8c3e2f4b32e5fe99e0b86d576da1312593b39f47d8ceef365e95ed/packaging-26.2-py3-none-any.whl
   name: packaging
   version: '26.2'
@@ -1808,17 +1829,6 @@ packages:
   version: 11.1.0
   sha256: 4b65538ae22f6fed0ce4874efd317463a7489796a0939fa66824dd542125a192
   requires_python: '>=3.10'
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-  name: stjames
-  version: 0.0.233
-  sha256: bd3bdf9c701b7649187c25c6d73e7bee46b5ac32cddad43c47979243a28d1023
-  requires_dist:
-  - pydantic>=2.4
-  - numpy
-  - requests
-  - more-itertools
-  - rdkit ; extra == 'rdkit'
-  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl
   name: python-dateutil
   version: 2.9.0.post0
@@ -1826,11 +1836,6 @@ packages:
   requires_dist:
   - six>=1.5
   requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*'
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-  name: certifi
-  version: 2026.6.17
-  sha256: 2227dcbaafe0d2f59279d1762ddddc37783ed4354594f194ffc31d20f41fc3db
-  requires_python: '>=3.7'
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   name: stack-data
   version: 0.6.3
@@ -1865,11 +1870,6 @@ packages:
   version: 3.4.9
   sha256: c25fe15c70c59eb7c5ce8c06a1f3fa1da0ecc5ea1e7a5922c40fd2fa9b0d5046
   requires_python: '>=3.7'
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-  name: ruff
-  version: 0.15.22
-  sha256: 365523eb91d9224e1bcb03b022fbf0facb8f9e23792a2c53d9d4b3924bdbdebb
-  requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/f7/ec/67fbef5d497f86283db54c22eec6f6140243aae73265799baaaa19cd17fb/ghp_import-2.1.0-py3-none-any.whl
   name: ghp-import
   version: 2.1.0

{rowan_python-3.1.8 → rowan_python-3.1.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.1.8"
+version = "3.1.10"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.12"
@@ -9,7 +9,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
-    "stjames>=0.0.228",
+    "stjames>=0.0.237,<0.0.238",
     "setuptools",
     "rdkit",
     "nest-asyncio",
@@ -83,6 +83,7 @@ ignore = [
     "PLR0911", # Too many returns
     "PLR0912", # Too many branches
     "PLR0913", # Too many arguments to function call
+    "PLR0917", # Too many positional arguments
     "PLR0914", # Too many locals
     "PLR0915", # Too many statements
     "PLR1702", # Too many nested-blocks

{rowan_python-3.1.8 → rowan_python-3.1.10}/rowan/__init__.py

@@ -3,6 +3,7 @@ from . import constants
 from stjames import (
     Atom,
     BandStructure,
+    Binder,
     BindingPoseContact,
     HydrationBridgeResidue,
     HydrationSite,
@@ -24,6 +25,7 @@ from stjames import (
     Mode,
     MSAFormat,
     MultiStageOptSettings,
+    NMR_SUPPORTED_SOLVENTS,
     OpenConfSettings,
     OptimizationSettings,
     PBCDFTSettings,

{rowan_python-3.1.8 → rowan_python-3.1.10}/rowan/protein.py

@@ -4,7 +4,8 @@ from datetime import datetime
 from pathlib import Path
 from typing import Any, Self
 
-from pydantic import BaseModel
+from pydantic import BaseModel, PrivateAttr
+from stjames.pdb import PDB, pdb_object_to_pdb_filestring
 
 from .project import Project
 from .utils import api_client
@@ -37,6 +38,8 @@ class Protein(BaseModel):
     public: bool | None = None
     pocket: list[list[float]] | None = None
 
+    _workflow_uuid: str | None = PrivateAttr(default=None)
+
     def __repr__(self) -> str:
         return f"<Protein name='{self.name}' created_at='{self.created_at}' uuid='{self.uuid}'>"
 
@@ -119,18 +122,24 @@ class Protein(BaseModel):
             response.raise_for_status()
             return Protein(**response.json())
 
-    def refresh(self, in_place: bool = True) -> Self:
+    def refresh(self, in_place: bool = True, workflow_uuid: str | None = None) -> Self:
         """
         Loads protein data
 
+        :param workflow_uuid: UUID of a workflow referencing this protein, for proteins reachable
+            only through a workflow you can read. Not needed for proteins from a workflow result.
         :returns: protein with loaded data
         """
+        workflow_uuid = workflow_uuid or self._workflow_uuid
+        params = {"workflow_uuid": workflow_uuid} if workflow_uuid else None
         with api_client() as client:
-            response = client.get(f"/protein/{self.uuid}")
+            response = client.get(f"/protein/{self.uuid}", params=params)
             response.raise_for_status()
             protein_data = response.json()
             if not in_place:
-                return self.__class__.model_validate(protein_data)
+                refreshed = self.__class__.model_validate(protein_data)
+                refreshed._workflow_uuid = workflow_uuid
+                return refreshed
 
         self.name = protein_data.get("name")
         self.data = protein_data.get("data")
@@ -138,6 +147,7 @@ class Protein(BaseModel):
         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
 
     def update(
@@ -291,7 +301,7 @@ class Protein(BaseModel):
 
         raise RuntimeError(f"Protein preparation timed out after {timeout:.0f}s for {self.uuid}.")
 
-    def validate_protein_forcefield(self, exclude_residue_names: list[str] | None = None) -> None:
+    def validate_protein_forcefield(self, exclude_residues: list[str | int] | None = None) -> None:
         """
         Validate that this protein can be parameterized with the MD forcefield.
 
@@ -299,16 +309,24 @@ class Protein(BaseModel):
         recognized by OpenMM and that there are no clashing atoms. Call this
         before submitting any MD workflow to catch preparation issues early.
 
-        Ligand residues (``LIG``) are always excluded — they are parameterized
-        separately by the MD workflow from the provided SMILES.
+        Ligand residues (`LIG`) are always excluded — they are parameterized
+        separately by the MD workflow from the provided SMILES. Pass the keys of a
+        binder's `small_molecules` to exclude those as well.
+
+        A name is matched case-insensitively and excludes only the first residue
+        with that name, so further copies are still validated. Integer entries are
+        0-based indices into the protein's sorted non-polymer records, and reference
+        a record without naming it.
 
         If validation fails, try re-preparing with ``remove_invalid_hydrogens=True``:
         ``protein.prepare(remove_invalid_hydrogens=True)``
 
-        :param exclude_residue_names: Additional residue names to skip during validation.
+        :param exclude_residues: additional residue names and/or 0-based non-polymer indices to skip
         :raises requests.HTTPError: if validation fails or the API request fails.
         """
-        excluded = list({"LIG"} | {name.upper() for name in (exclude_residue_names or [])})
+        entries: list[str | int] = ["LIG"]
+        entries += [r.upper() if isinstance(r, str) else r for r in exclude_residues or []]
+        excluded = list(dict.fromkeys(entries))
         with api_client() as client:
             response = client.post(
                 f"/protein/{self.uuid}/validate_forcefield",
@@ -316,42 +334,66 @@ class Protein(BaseModel):
             )
             response.raise_for_status()
 
-    def download_pdb_file(self, path: Path | str | None = None, name: str | None = None) -> None:
+    def download_pdb_file(
+        self,
+        path: Path | str | None = None,
+        name: str | None = None,
+        workflow_uuid: str | None = None,
+    ) -> None:
         """
-        Downloads the PDB file for a protein
+        Downloads the PDB file for a protein.
+
+        Builds the file locally from this protein's data, calling `refresh()` if needed, so it
+        works anywhere `refresh()` does — including proteins reachable only through a workflow.
 
         :param path: Directory to save the file to (defaults to current directory)
         :param name: Optional custom name for the file (defaults to protein name)
+        :param workflow_uuid: UUID of a workflow referencing this protein, for proteins reachable
+            only through a workflow you can read. Not needed for proteins from a workflow result.
         :raises requests.HTTPError: if the request to the API fails
         """
         path = Path(path) if path is not None else Path.cwd()
 
         path.mkdir(parents=True, exist_ok=True)
 
-        with api_client() as client:
-            response = client.get(f"/protein/{self.uuid}/get_pdb_file")
-            response.raise_for_status()
+        if self.data is None:
+            self.refresh(workflow_uuid=workflow_uuid)
+
+        pdb_object = PDB.model_validate(self.data)
+        pdb_string = pdb_object_to_pdb_filestring(
+            pdb=pdb_object,
+            header=True,
+            source=True,
+            keyword=True,
+            crystallography=True,
+            remark=False,
+        )
 
-        file_path = path / f"{name or self.name}.pdb"
-        with open(file_path, "wb") as f:
-            f.write(response.content)
+        file_path = path / f"{name or self.name or self.uuid}.pdb"
+        with open(file_path, "w") as f:
+            f.write(pdb_string)
 
 
-def retrieve_protein(uuid: str) -> Protein:
+def retrieve_protein(uuid: str, workflow_uuid: str | None = None) -> Protein:
     """
     Retrieves a protein from the API using its UUID.
 
     :param uuid: UUID of the protein to retrieve.
+    :param workflow_uuid: UUID of a workflow referencing this protein, for proteins reachable
+        only through a workflow you can read. Not needed for proteins from a workflow result.
     :returns: Protein object representing the retrieved protein.
     :raises requests.HTTPError: if the request to the API fails.
     """
+    params = {"workflow_uuid": workflow_uuid} if workflow_uuid else None
 
     with api_client() as client:
-        response = client.get(f"/protein/{uuid}")
+        response = client.get(f"/protein/{uuid}", params=params)
         response.raise_for_status()
         protein_data = response.json()
 
-    return Protein(**protein_data)
+    protein = Protein(**protein_data)
+    protein._workflow_uuid = workflow_uuid
+    return protein
 
 
 def list_proteins(

{rowan_python-3.1.8 → rowan_python-3.1.10}/rowan/workflows/__init__.py

@@ -83,6 +83,7 @@ from .interaction_energy_decomposition import (
 )
 from .ion_mobility import IonMobilityResult, submit_ion_mobility_workflow
 from .irc import IRCResult, submit_irc_workflow
+from .logp import LogPResult, submit_logp_workflow
 from .macropka import (
     MacropKaMicrostate,
     MacropKaResult,

{rowan_python-3.1.8 → rowan_python-3.1.10}/rowan/workflows/analogue_docking.py

@@ -160,7 +160,7 @@ class AnalogueDockingResult(WorkflowResult):
 
         cache_key = f"complex_{smiles}_{index}"
         if cache_key not in self._cache:
-            self._cache[cache_key] = retrieve_protein(uuid)
+            self._cache[cache_key] = retrieve_protein(uuid, workflow_uuid=self.workflow_uuid)
         return self._cache[cache_key]
 
     def get_complexes(self, smiles: str) -> list[Protein]:

{rowan_python-3.1.8 → rowan_python-3.1.10}/rowan/workflows/base.py

@@ -144,10 +144,10 @@ the server (a field is missing, extra, or the wrong type). Underlying validation
 RESULT_REGISTRY: dict[str, type[WorkflowResult]] = {}
 
 
-def register_result(workflow_type: str) -> Callable[[type[WorkflowResult]], type[WorkflowResult]]:
+def register_result[R: WorkflowResult](workflow_type: str) -> Callable[[type[R]], type[R]]:
     """Decorator to register a result class for a workflow type."""
 
-    def decorator(cls: type[WorkflowResult]) -> type[WorkflowResult]:
+    def decorator(cls: type[R]) -> type[R]:
         RESULT_REGISTRY[workflow_type] = cls
         return cls
 

{rowan_python-3.1.8 → rowan_python-3.1.10}/rowan/workflows/docking.py

@@ -133,7 +133,7 @@ class DockingResult(WorkflowResult):
 
         cache_key = f"complex_{index}"
         if cache_key not in self._cache:
-            self._cache[cache_key] = retrieve_protein(uuid)
+            self._cache[cache_key] = retrieve_protein(uuid, workflow_uuid=self.workflow_uuid)
         return self._cache[cache_key]
 
     def get_complexes(self) -> list[Protein]: