rowan-python 3.1.11__tar.gz → 3.1.13__tar.gz

{rowan_python-3.1.11 → rowan_python-3.1.13}/.claude-plugin/marketplace.json

@@ -10,8 +10,7 @@
       "name": "computational-chemistry-and-biology",
       "source": "./skills/computational-chemistry-and-biology",
       "description": "Run computational chemistry and structural biology calculations through Rowan MCP tools or rowan-python",
-      "skills": ["./"],
-      "strict": false
+      "strict": true
     }
   ]
 }

{rowan_python-3.1.11 → rowan_python-3.1.13}/.github/workflows/python-publish.yml

@@ -39,7 +39,7 @@ jobs:
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

{rowan_python-3.1.11 → rowan_python-3.1.13}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: rowan-python
-Version: 3.1.11
+Version: 3.1.13
 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-3.1.11 → rowan_python-3.1.13}/docs/api/api-keys.md

@@ -8,7 +8,7 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
 
 ::: rowan.utils
     handler: python
@@ -18,7 +18,7 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
       members:
         - api_credentials
         - get_api_key

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/api/calculation.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/api/folder.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/api/molecule.md

@@ -8,7 +8,7 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
 
 ::: rowan.utils
     handler: python
@@ -18,7 +18,7 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
       members:
         - smiles_to_stjames
 

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/api/project.md

@@ -8,7 +8,7 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
 
 ::: rowan.utils
     handler: python
@@ -18,6 +18,6 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
       members:
         - get_project_uuid

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/api/protein.md

@@ -8,7 +8,7 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
 
 ::: stjames.protein
     handler: python

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/api/user.md

@@ -8,7 +8,7 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
       members:
         - User
         - Organization

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/api/webhooks.md

@@ -8,7 +8,7 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
       members:
         - get_webhook_secret
         - create_webhook_secret

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/api/workflow.md

@@ -8,7 +8,7 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]
       members:
         - Workflow
         - WorkflowResult

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/index.md

@@ -33,9 +33,11 @@ it as an environment variable or set it directly on the module:
 
 ```python
 import os
+
 os.environ["ROWAN_API_KEY"]  # picked up automatically, or...
 
 import rowan
+
 rowan.api_key = "rowan-sk..."
 ```
 

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/admet.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/analogue-docking.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/basic-calculation.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/batch-docking.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/binding-affinity.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/bond-dissociation-energy.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/conformer-search.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/covalent-inhibitor-scan.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/descriptors.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/docking.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/double-ended-ts-search.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/electronic-properties.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/fukui.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/hydrogen-bond-donor-acceptor-strength.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/interaction-energy-decomposition.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/ion-mobility.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/irc.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/logp.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/macropka.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/membrane-permeability.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/msa.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/multistage-optimization.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/nmr.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/pka.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/pocket-detection.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/pose-analysis-md.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/protein-binder-design.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/protein-cofolding.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/protein-md.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

rowan_python-3.1.13/docs/workflows/protein-preparation.md

@@ -0,0 +1,11 @@
+# Protein preparation
+
+::: rowan.workflows.protein_preparation
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/rbfe-graph.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/redox-potential.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/relative-binding-free-energy-perturbation.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/scan.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/solubility.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/solvent-dependent-conformers.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/spin-states.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/strain.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/docs/workflows/tautomer-search.md

@@ -8,4 +8,4 @@
       show_root_toc_entry: false
       members_order: source
       group_by_category: true
-      filters: ["!^__"]
+      filters: ["!^_"]

{rowan_python-3.1.11 → rowan_python-3.1.13}/examples/analogue_docking.py

@@ -22,7 +22,7 @@ protein = rowan.upload_protein("1IEP receptor", data_dir / "1iep_receptorH.pdb")
 workflow = rowan.submit_analogue_docking_workflow(
     analogues=list(citalopram_analogues.values()),
     analogue_names=list(citalopram_analogues.keys()),
-    protein=protein,
+    protein=protein.uuid,
     initial_molecule=bound_pose,
     folder=folder,
 )

{rowan_python-3.1.11 → rowan_python-3.1.13}/examples/batch_docking.py

@@ -12,15 +12,17 @@ ligands = [
     "CCC(C)CN=C1NC=C2CCC(O)CC2=N1",
 ]
 
-protein = rowan.create_protein_from_pdb_id(
-    "1HCK", name="CDK2", project_uuid=rowan.default_project().uuid
+protein = rowan.create_protein_from_pdb_id("1HCK", name="CDK2")
+preparation_workflow = rowan.submit_protein_preparation_workflow(
+    protein=protein.uuid,
+    name="Prepare CDK2",
+    folder=folder,
 )
-
-protein.prepare()
+prepared_protein_uuid = preparation_workflow.result().prepared_protein_uuid
 
 workflow = rowan.submit_batch_docking_workflow(
     ligands,
-    protein.uuid,
+    prepared_protein_uuid,
     pocket=[[103.55, 100.59, 82.99], [27.76, 32.67, 48.79]],
     executable="qvina2",
     scoring_function="vina",

rowan_python-3.1.13/examples/batch_solubility.py

@@ -0,0 +1,21 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+smileses = ["CCO", "CC(=O)O", "c1ccccc1"]
+workflows = rowan.submit_solubility_workflow_group(
+    initial_smileses=smileses,
+    method="kingfisher",
+    solvents=["water"],
+    temperatures=[298.15],
+    names=["Ethanol", "Acetic acid", "Benzene"],
+    folder=folder,
+)
+
+for workflow in workflows:
+    print(f"View workflow privately at: https://labs.rowansci.com/solubility/{workflow.uuid}")
+
+results = [workflow.result() for workflow in workflows]
+print(results)

{rowan_python-3.1.11 → rowan_python-3.1.13}/examples/binding_affinity.py

@@ -12,7 +12,7 @@ all_ligands = rowan.load_named_ligands(data_dir / "tyk2_ligands.sdf")
 ligands = dict(list(all_ligands.items())[:3])
 
 workflow = rowan.submit_binding_affinity_workflow(
-    protein=protein,
+    protein=protein.uuid,
     ligand_structures=list(ligands.values()),
     name="Binding Affinity — TYK2 ligands",
     folder=folder,

{rowan_python-3.1.11 → rowan_python-3.1.13}/examples/covalent_docking.py

@@ -13,17 +13,33 @@ protein = rowan.create_protein_from_pdb_id("2Q3Z")
 # Chain A is TG2; chain X is a small covalently-bound peptide in the crystal, not
 # part of the protein. `protein.chains` order isn't guaranteed, so select by name.
 protein = protein.select_chains(["A"])
-protein.prepare()
+preparation_workflow = rowan.submit_protein_preparation_workflow(
+    protein=protein.uuid,
+    name="Prepare TG2",
+    folder=folder,
+)
+protein = preparation_workflow.result().get_prepared_protein()
 
 # Pocket is [[center_x, center_y, center_z], [size_x, size_y, size_z]] in Å.
 center = [-1.079, -3.081, 18.122]
 size = [22.22, 14.08, 21.74]
 
-# 0-based, all-atom (including hydrogens) indices of the reacting atoms.
-# Ligand: acrylamide's terminal =CH2 carbon. Protein: Cys277 SG, found by downloading
-# the prepared structure and locating that atom in file order.
+# 0-based, all-atom (including hydrogens) indices of the reacting atoms. The ligand's
+# acrylamide terminal =CH2 carbon is atom 0. Locate Cys277 SG from the prepared structure
+# so the protein index remains correct if preparation changes atom ordering.
 covalent_ligand_atom_index = 0
-covalent_protein_atom_index = 4293
+model = protein.data["models"][0]
+cys277 = model["polymer"]["A"]["residues"]["A.277"]
+cys277_sg_serial = next(
+    int(serial) for serial, atom in cys277["atoms"].items() if atom["name"] == "SG"
+)
+entities = [
+    residue for chain in model["polymer"].values() for residue in chain["residues"].values()
+]
+for section in ("non_polymer", "water", "branched"):
+    entities.extend(model.get(section, {}).values())
+atom_serials = sorted(int(serial) for entity in entities for serial in entity.get("atoms", {}))
+covalent_protein_atom_index = atom_serials.index(cys277_sg_serial)
 gnina_settings = rowan.GninaSettings(
     scoring_function="gnina_cnn",
     covalent_ligand_atom_index=covalent_ligand_atom_index,
@@ -31,7 +47,7 @@ gnina_settings = rowan.GninaSettings(
 )
 
 workflow = rowan.submit_docking_workflow(
-    protein,
+    protein.uuid,
     pocket=[center, size],
     initial_molecule=tg2_inhibitor,
     docking_settings=gnina_settings,

rowan_python-3.1.13/examples/covalent_inhibitor_scan.py

@@ -0,0 +1,59 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+# BTK, catalytic Cys481. 4YHF already has a covalently-bound small-molecule inhibitor
+# (residue 4C9) linked to Cys481 SG via the ligand's C1 atom.
+ligand_smiles = "CC(C)(C)C[C@@H](C#N)C(=O)N1CCC[C@H](C1)n2nc(c3ccc(Oc4ccccc4)cc3)c5c(N)ncnc25"
+
+protein = rowan.create_protein_from_pdb_id("4YHF")
+protein = protein.select_chains(["A"])
+preparation_workflow = rowan.submit_protein_preparation_workflow(
+    protein=protein.uuid,
+    retain_non_polymer={"4C9": ligand_smiles},
+    name="Prepare BTK inhibitor complex",
+    folder=folder,
+)
+protein = preparation_workflow.result().get_prepared_protein()
+
+# Locate Cys481 SG and the 4C9 ligand's C1 atom in the prepared structure, then convert
+# their atom serials to zero-based PDB record indices.
+model = protein.data["models"][0]
+cys481 = model["polymer"]["A"]["residues"]["A.481"]
+ligand_4c9 = next(residue for residue in model["non_polymer"].values() if residue["name"] == "4C9")
+protein_atom_serial = next(
+    int(serial) for serial, atom in cys481["atoms"].items() if atom["name"] == "SG"
+)
+ligand_atom_serial = next(
+    int(serial) for serial, atom in ligand_4c9["atoms"].items() if atom["name"] == "C1"
+)
+entities = [
+    residue for chain in model["polymer"].values() for residue in chain["residues"].values()
+]
+for section in ("non_polymer", "water", "branched"):
+    entities.extend(model.get(section, {}).values())
+atom_serials = sorted(int(serial) for entity in entities for serial in entity.get("atoms", {}))
+protein_reactive_atom_index = atom_serials.index(protein_atom_serial)
+ligand_reactive_atom_index = atom_serials.index(ligand_atom_serial)
+
+workflow = rowan.submit_covalent_inhibitor_scan_workflow(
+    protein=protein.uuid,
+    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,
+)
+
+print(
+    f"View workflow privately at: https://labs.rowansci.com/covalent-inhibitor-scan/{workflow.uuid}"
+)
+
+result = workflow.result()
+print(result)
+
+for distance, energy in result.get_energies():
+    print(f"  distance={distance:.3f} Å  energy={energy}")