rowan-python 3.1.2__tar.gz → 3.1.4__tar.gz

{rowan_python-3.1.2 → rowan_python-3.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.2
+Version: 3.1.4
 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-3.1.2 → rowan_python-3.1.4}/docs/index.md

@@ -23,6 +23,16 @@
         - batch_submit_workflow
         - batch_poll_status
 
+::: rowan.calculation
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
 ## ADMET
 ::: rowan.workflows.admet
     handler: python
@@ -254,6 +264,17 @@
       group_by_category: true
       filters: ["!^__"]
 
+## Pocket Detection
+::: rowan.workflows.pocket_detection
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
 ## Pose Analysis MD
 ::: rowan.workflows.pose_analysis_md
     handler: python
@@ -397,6 +418,17 @@
       group_by_category: true
       filters: ["!^__"]
 
+## API Keys
+::: rowan.api_keys
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
 ## Folder Class and Functions
 ::: rowan.folder
     handler: python

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/batch_docking.py

@@ -13,7 +13,7 @@ ligands = [
 ]
 
 protein = rowan.create_protein_from_pdb_id(
-    "CDK2", "1HCK", project_uuid=rowan.default_project().uuid
+    "1HCK", name="CDK2", project_uuid=rowan.default_project().uuid
 )
 
 protein.prepare()

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/boltz_paired_msa.py

@@ -14,7 +14,7 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=["boltz"],
+    output_formats=[rowan.MSAFormat.BOLTZ],
     name="Boltz Paired MSA Example",
     folder=folder,
 )
@@ -23,7 +23,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("boltz", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.BOLTZ, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/boltz_single_msa.py

@@ -13,7 +13,7 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=["boltz"],
+    output_formats=[rowan.MSAFormat.BOLTZ],
     name="Boltz MSA Example",
     folder=folder,
 )
@@ -22,7 +22,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("boltz", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.BOLTZ, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/chai_paired_msa.py

@@ -25,7 +25,7 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=["chai"],
+    output_formats=[rowan.MSAFormat.CHAI],
     name="CHAI Paired MSA Example",
     folder=folder,
 )
@@ -34,7 +34,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("chai", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.CHAI, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/chai_single_msa.py

@@ -22,7 +22,7 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=["chai"],
+    output_formats=[rowan.MSAFormat.CHAI],
     name="CHAI MSA Example",
     folder=folder,
 )
@@ -31,7 +31,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("chai", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.CHAI, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/colabfold_paired_msa.py

@@ -14,7 +14,7 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=["colabfold"],
+    output_formats=[rowan.MSAFormat.COLABFOLD],
     name="Colabfold Paired MSA Example",
     folder=folder,
 )
@@ -23,7 +23,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("colabfold", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.COLABFOLD, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/colabfold_single_msa.py

@@ -13,7 +13,7 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=["colabfold"],
+    output_formats=[rowan.MSAFormat.COLABFOLD],
     name="Colabfold MSA Example",
     folder=folder,
 )
@@ -22,7 +22,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("colabfold", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.COLABFOLD, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

rowan_python-3.1.4/examples/docking.py

@@ -0,0 +1,39 @@
+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")
+if len(protein.chains) > 1:
+    protein = protein.select_chains([protein.chains[0]])
+protein.prepare()
+
+# Pocket is [[center_x, center_y, center_z], [size_x, size_y, size_z]] in Å.
+# For a co-crystal structure, extract these from the bound ligand's position.
+# Use rowan.submit_pocket_detection_workflow() when the binding site is unknown.
+center = [44.59, 79.75, 39.59]
+size = [24.15, 21.33, 19.88]
+workflow = rowan.submit_docking_workflow(
+    protein,
+    pocket=[center, size],
+    initial_molecule=dasatinib,
+    name="dasatinib docking (2GQG redock)",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/docking/{workflow.uuid}")
+
+result = workflow.result()
+print(result)
+
+for i, score in enumerate(result.scores):
+    print(f"  Pose {i}: score={score.score:.3f}  posebusters_valid={score.posebusters_valid}")
+
+# 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")
+print("Saved dasatinib_2GQG_complex.pdb")

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/docking_screen.py

@@ -19,7 +19,7 @@ workflows = []
 results = {}
 
 protein = rowan.create_protein_from_pdb_id(
-    "CDK2", "1HCK", project_uuid=rowan.default_project().uuid
+    "1HCK", name="CDK2", project_uuid=rowan.default_project().uuid
 )
 
 protein.prepare()
@@ -43,11 +43,14 @@ lowest_conformer_energy = 0
 for workflow, result in workflow_results:
     for conformer_uuid in result.conformers:
         energy = rowan.retrieve_calculation_molecules(conformer_uuid)[0]["energy"]
-        lowest_conformer_energy = min(lowest_conformer_energy, energy)
+        if energy is not None:
+            lowest_conformer_energy = min(lowest_conformer_energy, energy)
 
     sorted_scores = sorted(result.scores, key=lambda s: s.score)
     for score in sorted_scores:
         pose_energy = rowan.retrieve_calculation_molecules(score.pose)[0]["energy"]
+        if pose_energy is None:
+            continue
         strain = (pose_energy - lowest_conformer_energy) * HARTREE_TO_KCALMOL
         if score.posebusters_valid and strain < 4:
             results[workflow.name] = score

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/pocket_detection.py

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

rowan_python-3.1.4/examples/resubmit_with_perturbations.py

@@ -0,0 +1,39 @@
+"""
+Resubmit a completed workflow with a perturbed structure.
+
+Two strategies: random noise to break symmetry, or displacement along a
+vibrational mode to follow a reaction coordinate or escape a stuck geometry.
+"""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+# --- Option 1: random noise ---
+wf = rowan.retrieve_workflow("your-workflow-uuid")
+mol = wf.result().molecule
+
+perturbed_mol = mol.perturb()
+resubmit = rowan.submit_multistage_optimization_workflow(
+    initial_molecule=perturbed_mol,
+    name="cyclobutane opt - perturbed resubmit",
+    folder=folder,
+)
+print(f"https://labs.rowansci.com/multistage-opt/{resubmit.uuid}")
+
+# --- Option 2: displace along a vibrational mode ---
+# Requires a prior frequency calculation. Imaginary modes have negative frequency.
+ts_wf = rowan.retrieve_workflow("your-ts-freq-workflow-uuid")
+ts_mol = ts_wf.result().molecule
+
+imaginary_mode = next(m for m in ts_mol.vibrational_modes if m.frequency < 0)
+
+displaced_mol = ts_mol.displace_along_mode(mode=imaginary_mode, displacement=0.3)
+resubmit = rowan.submit_multistage_optimization_workflow(
+    initial_molecule=displaced_mol,
+    name="TS resubmit - displaced along imaginary mode",
+    folder=folder,
+)
+print(f"https://labs.rowansci.com/multistage-opt/{resubmit.uuid}")

{rowan_python-3.1.2 → rowan_python-3.1.4}/examples/scan.py

@@ -13,13 +13,13 @@ folder = rowan.get_folder("examples")
 workflow = rowan.submit_scan_workflow(
     initial_molecule=rowan.Molecule.from_smiles("O"),
     name="Water Angle scan",
-    scan_settings={
-        "type": "angle",
-        "atoms": [2, 1, 3],  # 1-indexed
-        "start": 100,
-        "stop": 110,
-        "num": 5,
-    },
+    scan_settings=rowan.ScanSettings(
+        type="angle",
+        atoms=[2, 1, 3],  # 1-indexed
+        start=100,
+        stop=110,
+        num=5,
+    ),
     calculation_method="GFN2-xTB",
     calculation_engine="xtb",
     folder=folder,

{rowan_python-3.1.2 → rowan_python-3.1.4}/pixi.lock

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       - pypi: https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/5b/54/662a4743aa81d9582ee9339d4ffa3c8fd40a4965e033d77b9da9774d3960/mkdocs_material_extensions-1.3.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/5d/39/b72e168daf9c00fb20c9fc996d00437ccecdef3102387775d29d7a62576d/numpy-2.5.0-cp314-cp314-macosx_11_0_arm64.whl
@@ -291,7 +290,6 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/bd/6e/95b0e537de1f4d4301f76f944642c6da50d1511cc7b3d64dc418a66c7509/wcwidth-0.8.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/bd/9c/4d95bb87eb2063d20db7b60faa3840c1b18025517ae857371c4dd55a6b3a/pyyaml-6.0.3-cp314-cp314-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/c1/ea/53f2148663b321f21b5a606bd5f191517cf40b7072c0497d3c92c4a13b1e/executing-2.2.1-py2.py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/c7/0d/67e5b4109ea4a837e80daa87c2c696711955e40449a97e8926672534def2/click-8.4.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/cb/b1/3846dd7f199d53cb17f49cba7e651e9ce294d8497c8c150530ed11865bb8/iniconfig-2.3.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/d1/fc/10ab7e80650a9c9e8f4f1105f8c8e73567f88ed0c06ada589ab81d38687c/mkdocstrings_python-2.0.5-py3-none-any.whl
@@ -310,7 +308,9 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/f1/d9/7fb5aa316bc299258e68c73ba3bddbc499654a07f151cba08f6153988714/pathspec-1.1.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/f4/7e/a72dd26f3b0f4f2bf1dd8923c85f7ceb43172af56d63c7383eb62b332364/pygments-2.20.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/f7/ec/67fbef5d497f86283db54c22eec6f6140243aae73265799baaaa19cd17fb/ghp_import-2.1.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/fb/e2/79c688af8b210d232694e31e59da9f6ec747bae31c3f5946e4e9b98860d5/click-8.4.2-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/fd/7b/122376b1fd3c62c1ed9dc80c931ace4844b3c55407b6fb2d199377c9736f/pydantic-2.13.4-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/fe/93/78d462e7d39968e58094dc57be7d09ffb14ce37da5b68ed70338a35a1f21/ruff-0.15.19-py3-none-macosx_11_0_arm64.whl
 packages:
 - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
   build_number: 20
@@ -1170,11 +1170,6 @@ packages:
   - pip ; extra == 'install-types'
   - orjson ; extra == 'faster-cache'
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/51/93/4769464c25cf7ab2acb3c7dda9cad3d867eb41c59565b3e2a9d17249c90c/ruff-0.15.18-py3-none-macosx_11_0_arm64.whl
-  name: ruff
-  version: 0.15.18
-  sha256: 08d4c86a68f2c3ec2c9d56380a71fb4a4f65373055cbb8caabd645e9102f38d4
-  requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl
   name: pluggy
   version: 1.6.0
@@ -1215,11 +1210,6 @@ packages:
   - more-itertools
   - rdkit ; extra == 'rdkit'
   requires_python: '>=3.11'
-- pypi: https://files.pythonhosted.org/packages/6d/ff/d353d6b7bbd73cc0ec37f4463d7540e45e894338abdd9964eee0de332708/ruff-0.15.18-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
-  name: ruff
-  version: 0.15.18
-  sha256: 5f0480ce690cbb6c4db6e5d08f19fce98e10ba131a8b60c1bcdac42771e3ae2d
-  requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/6e/94/be70f8ee9c45f2f62b39a1f0e9303bc20e138a8f3b8e50ffd89498e177e1/mkdocstrings-1.0.4-py3-none-any.whl
   name: mkdocstrings
   version: 1.0.4
@@ -1384,6 +1374,11 @@ packages:
   requires_dist:
   - typing-extensions>=4.14.1
   requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/89/3d/0b1f30f84bee9ae6ae8d349c2ba8b6f4b040966744efdd3acc804ae7c024/ruff-0.15.19-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  name: ruff
+  version: 0.15.19
+  sha256: 6a498f82e0f4d8904c4e0aea5139cdfac1f39d19a3c51d491292f63a36e83b2e
+  requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/8e/37/efad0257dc6e593a18957422533ff0f87ede7c9c6ea010a2177d738fb82f/pure_eval-0.2.3-py3-none-any.whl
   name: pure-eval
   version: 0.2.3
@@ -1770,13 +1765,6 @@ packages:
   - littleutils ; extra == 'tests'
   - rich ; python_full_version >= '3.11' and extra == 'tests'
   requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/c7/0d/67e5b4109ea4a837e80daa87c2c696711955e40449a97e8926672534def2/click-8.4.1-py3-none-any.whl
-  name: click
-  version: 8.4.1
-  sha256: 482be17c6991b8c19c5429a1e995d9b0efdbb63172824c41f99965dc0ade8ec2
-  requires_dist:
-  - colorama ; sys_platform == 'win32'
-  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/cb/b1/3846dd7f199d53cb17f49cba7e651e9ce294d8497c8c150530ed11865bb8/iniconfig-2.3.0-py3-none-any.whl
   name: iniconfig
   version: 2.3.0
@@ -1919,6 +1907,13 @@ packages:
   - markdown ; extra == 'dev'
   - flake8 ; extra == 'dev'
   - wheel ; extra == 'dev'
+- pypi: https://files.pythonhosted.org/packages/fb/e2/79c688af8b210d232694e31e59da9f6ec747bae31c3f5946e4e9b98860d5/click-8.4.2-py3-none-any.whl
+  name: click
+  version: 8.4.2
+  sha256: e6f9f66136c816745b9d65817da91d61d957fb16e02e4dcd0552553c5a197b76
+  requires_dist:
+  - colorama ; sys_platform == 'win32'
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/fd/7b/122376b1fd3c62c1ed9dc80c931ace4844b3c55407b6fb2d199377c9736f/pydantic-2.13.4-py3-none-any.whl
   name: pydantic
   version: 2.13.4
@@ -1931,3 +1926,8 @@ packages:
   - email-validator>=2.0.0 ; extra == 'email'
   - tzdata ; python_full_version >= '3.9' and sys_platform == 'win32' and extra == 'timezone'
   requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/fe/93/78d462e7d39968e58094dc57be7d09ffb14ce37da5b68ed70338a35a1f21/ruff-0.15.19-py3-none-macosx_11_0_arm64.whl
+  name: ruff
+  version: 0.15.19
+  sha256: 5a2c86ba6870dd415a9d9eb8be94d7924ebec6a26ffc7958ec7ca29d4bff967d
+  requires_python: '>=3.7'

{rowan_python-3.1.2 → rowan_python-3.1.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.1.2"
+version = "3.1.4"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.12"

{rowan_python-3.1.2 → rowan_python-3.1.4}/rowan/__init__.py

@@ -2,6 +2,8 @@
 from . import constants
 from stjames import (
     Atom,
+    BindingPoseContact,
+    ConformerGenSettings,
     Constraint,
     ConstraintType,
     ConformerClusteringSettings,
@@ -14,15 +16,19 @@ from stjames import (
     KMeansClusteringSettings,
     Method,
     Mode,
+    MSAFormat,
     MultiStageOptSettings,
     OpenConfSettings,
     OptimizationSettings,
     PBCDFTSettings,
     PeriodicCell,
+    ProteinSequence,
+    ScanSettings,
     Settings,
     Solvent,
     SolventSettings,
     Task,
+    VibrationalMode,
 )
 from stjames.workflows.relative_binding_free_energy_perturbation import RBFEGraph, RBFEGraphEdge
 from stjames.excited_state_settings import TDDFTSettings

{rowan_python-3.1.2 → rowan_python-3.1.4}/rowan/calculation.py

@@ -2,6 +2,7 @@
 
 from typing import Self
 
+import httpx
 import stjames
 from pydantic import BaseModel, ConfigDict, Field
 
@@ -62,10 +63,13 @@ class Calculation(BaseModel):
         :param in_place: If True, update this instance in-place. If False, return new instance.
         :returns: Updated Calculation object.
         """
-        with api_client() as client:
-            response = client.get(f"/calculation/{self.uuid}/stjames")
-            response.raise_for_status()
-            data = response.json()
+        try:
+            with api_client() as client:
+                response = client.get(f"/calculation/{self.uuid}/stjames")
+                response.raise_for_status()
+                data = response.json()
+        except httpx.TimeoutException as e:
+            raise TimeoutError(f"Timed out fetching calculation {self.uuid}.") from e
 
         molecules = _parse_molecules(data.get("molecules", []))
 
@@ -94,11 +98,15 @@ def retrieve_calculation(uuid: str) -> Calculation:
     :param uuid: UUID of the calculation to retrieve.
     :returns: Calculation object with the fetched data.
     :raises requests.HTTPError: If the API request fails.
+    :raises TimeoutError: If the response times out.
     """
-    with api_client() as client:
-        response = client.get(f"/calculation/{uuid}/stjames")
-        response.raise_for_status()
-        data = response.json()
+    try:
+        with api_client() as client:
+            response = client.get(f"/calculation/{uuid}/stjames")
+            response.raise_for_status()
+            data = response.json()
+    except httpx.TimeoutException as e:
+        raise TimeoutError(f"Timed out fetching calculation {uuid}.") from e
 
     molecules = _parse_molecules(data.get("molecules", []))