rowan-python 3.1.14__tar.gz → 3.1.16__tar.gz

{rowan_python-3.1.14 → rowan_python-3.1.16}/.gitignore

@@ -1,5 +1,10 @@
 # Ignore environment file with ROWAN_API_KEY
 .env
+# Variant env files (.env.test, .env.single-tenant, ...); .envrc is tracked for direnv
+.env.*
+
+# macOS
+.DS_Store
 
 # Created by https://www.toptal.com/developers/gitignore/api/python
 # Edit at https://www.toptal.com/developers/gitignore?templates=python

{rowan_python-3.1.14 → rowan_python-3.1.16}/AGENTS.md

@@ -46,6 +46,12 @@ pixi run python examples/basic_calculation.py
 
 ## Code conventions
 
+### Documentation updates
+
+- Treat requests to check or update docs as keeping existing descriptions, examples, docstrings, and skill references accurate.
+- Make corrections where the relevant behavior is already documented. Don't add feature announcements, introductory callouts, or new sections just because a feature changed.
+- If a document doesn't discuss the affected behavior, usually leave it alone. Preserve its existing scope and emphasis unless the user asks for expanded documentation.
+
 ### Docstrings
 
 Format: reStructuredText-style. No types in docstrings, no leading articles.
@@ -100,7 +106,9 @@ Via ruff:
 
 ## Git authorization policy
 
-**Do not run `git commit`, `git push`, or any other git write commands without explicit permission from the user.**
+- Prepare changes on a local feature branch. Local commits are allowed as part of authorized development work.
+- The user handles pushing and opening PRs. Do not push branches, create PRs, or change remote branches unless the user explicitly requests that specific remote action.
+- A request to get changes ready for a PR means prepare the local branch, not publish it or open a PR.
 
 **Never add yourself as a commit author or co-author.** Do not include `Co-Authored-By:`, `Author:`, or any similar trailer that attributes the commit to an AI model or tool. Commits are attributed solely to the human developer.
 

{rowan_python-3.1.14 → rowan_python-3.1.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: rowan-python
-Version: 3.1.14
+Version: 3.1.16
 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
@@ -48,6 +48,23 @@ codex plugin marketplace add rowansci/rowan-python --ref master
 codex plugin add computational-chemistry-and-biology@rowan
 ```
 
+### Rowan MCP server (optional)
+
+The skill also works with the hosted Rowan MCP server, which provides Rowan tools directly to the
+agent. Add it once per client:
+
+```bash
+# Claude Code
+claude mcp add --transport http rowan https://mcp.rowansci.com/
+
+# Codex
+codex mcp add rowan --url https://mcp.rowansci.com/
+codex mcp login rowan
+```
+
+Both clients prompt for OAuth sign-in on first use. Without the server, the skill falls back to the
+Rowan Python SDK, which authenticates with `ROWAN_API_KEY` instead.
+
 Start a new Claude Code or Codex session after installation. For manual installation, download the
 [latest skill ZIP](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip)
 and extract it into your agent's skills directory.

{rowan_python-3.1.14 → rowan_python-3.1.16}/README.md

@@ -32,6 +32,23 @@ codex plugin marketplace add rowansci/rowan-python --ref master
 codex plugin add computational-chemistry-and-biology@rowan
 ```
 
+### Rowan MCP server (optional)
+
+The skill also works with the hosted Rowan MCP server, which provides Rowan tools directly to the
+agent. Add it once per client:
+
+```bash
+# Claude Code
+claude mcp add --transport http rowan https://mcp.rowansci.com/
+
+# Codex
+codex mcp add rowan --url https://mcp.rowansci.com/
+codex mcp login rowan
+```
+
+Both clients prompt for OAuth sign-in on first use. Without the server, the skill falls back to the
+Rowan Python SDK, which authenticates with `ROWAN_API_KEY` instead.
+
 Start a new Claude Code or Codex session after installation. For manual installation, download the
 [latest skill ZIP](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip)
 and extract it into your agent's skills directory.

{rowan_python-3.1.14 → rowan_python-3.1.16}/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-3.1.16/docs/workflows/basic-calculation.md

@@ -0,0 +1,35 @@
+# Basic Calculation
+
+## Configuration
+
+Use the exported enums instead of raw strings when setting the method and engine:
+
+```python
+import rowan
+
+molecule = rowan.Molecule.from_smiles("CCO")
+workflow = rowan.submit_basic_calculation_workflow(
+    initial_molecule=molecule,
+    tasks=["optimize"],
+    method=rowan.Method.GFN2_XTB,
+    engine=rowan.Engine.XTB,
+)
+```
+
+Pass an [`OptimizationSettings`](settings.md#stjames.opt_settings.OptimizationSettings) object or
+an equivalent dictionary to `opt_settings`. `optimize_cell` defaults to `False`; set it to `True`
+only when optimizing a periodic cell.
+
+```python
+opt_settings = rowan.OptimizationSettings(max_steps=200, optimize_cell=False)
+```
+
+::: rowan.workflows.basic_calculation
+    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-3.1.14 → rowan_python-3.1.16}/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-3.1.16}/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-3.1.16}/docs/workflows/settings.md

@@ -12,6 +12,21 @@
       members:
         - Settings
 
+## Basis sets
+
+Pass a basis set name as a string for ordinary calculations. Use `rowan.BasisSet` when configuring
+atom- or element-specific overrides.
+
+::: stjames.basis_set
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
 ::: stjames.opt_settings
     handler: python
     options:

{rowan_python-3.1.14 → rowan_python-3.1.16}/docs/workflows/types.md

@@ -3,54 +3,90 @@
 Value types shared across many workflows — the vocabulary you use for `preset`, `method`, and
 structural inputs regardless of which workflow you're submitting.
 
-## Method, Engine & Task
+Legacy enum members retained for parsing historical workflows are omitted below.
 
-::: stjames.method
+Enum members and their accepted string values are listed below. Import these types from `rowan`,
+not `stjames`.
+
+## Methods
+
+::: stjames.method.Method
     handler: python
     options:
       show_source: false
+      show_bases: false
       show_root_heading: false
       show_root_toc_entry: false
+      show_if_no_docstring: true
+      separate_signature: false
       members_order: source
       group_by_category: true
-      filters: ["!^_"]
+      filters:
+        - "!^_"
+        - "!^default_engine$"
+        - "!^(MACE_MP_0|MACE_MP_0B2_L|EGRET_1|EGRET_1E|EGRET_1T)$"
+        - "!^SMIRNOFF_2_(0_0|2_1)_AMBER_AM1BCC$"
 
-::: stjames.engine
+## Engines
+
+::: stjames.engine.Engine
     handler: python
     options:
       show_source: false
+      show_bases: false
       show_root_heading: false
       show_root_toc_entry: false
+      show_if_no_docstring: true
+      separate_signature: false
       members_order: source
       group_by_category: true
-      filters: ["!^_"]
+      filters:
+        - "!^_"
+        - "!^(EGRET|MACE|TERACHEM)$"
 
-::: stjames.task
+## Tasks
+
+::: stjames.task.Task
     handler: python
     options:
       show_source: false
+      show_bases: false
       show_root_heading: false
       show_root_toc_entry: false
+      show_if_no_docstring: true
+      separate_signature: false
       members_order: source
       group_by_category: true
-      filters: ["!^_"]
+      filters:
+        - "!^_"
+        - "!^STRESS$"
 
-::: stjames.correction
+## Corrections
+
+::: stjames.correction.Correction
     handler: python
     options:
       show_source: false
+      show_bases: false
       show_root_heading: false
       show_root_toc_entry: false
+      show_if_no_docstring: true
+      separate_signature: false
       members_order: source
       group_by_category: true
       filters: ["!^_"]
 
-::: stjames.mode
+## Modes
+
+::: stjames.mode.Mode
     handler: python
     options:
       show_source: false
+      show_bases: false
       show_root_heading: false
       show_root_toc_entry: false
+      show_if_no_docstring: true
+      separate_signature: false
       members_order: source
       group_by_category: true
       filters: ["!^_"]

{rowan_python-3.1.14 → rowan_python-3.1.16}/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-3.1.14 → rowan_python-3.1.16}/examples/docking.py

@@ -37,7 +37,7 @@ 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
+# Download the top-scoring protein–ligand complex as mmCIF
 complex_protein = result.get_complex(0)
-complex_protein.download_pdb_file(name="dasatinib_2GQG_complex")
-print("Saved dasatinib_2GQG_complex.pdb")
+complex_protein.download_structure(name="dasatinib_2GQG_complex")
+print("Saved dasatinib_2GQG_complex.cif")

{rowan_python-3.1.14 → rowan_python-3.1.16}/examples/electronic_properties.py

@@ -17,7 +17,9 @@ folder = rowan.get_folder("examples")
 
 workflow = rowan.submit_electronic_properties_workflow(
     initial_molecule=rowan.Molecule.from_smiles("C=O"),  # formaldehyde
-    method="b97_3c",  # default: lightweight DFT
+    method="r2scan",
+    basis_set="def2-svp",
+    engine="gpu4pyscf",
     compute_density_cube=True,
     compute_electrostatic_potential_cube=True,
     compute_num_occupied_orbitals=3,  # HOMO, HOMO-1, HOMO-2

rowan_python-3.1.16/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 mmCIF files
+complex_protein = result.get_complex(0)
+complex_protein.download_structure(name="dasatinib_2GQG_induced_complex")
+print("Saved dasatinib_2GQG_induced_complex.cif")
+
+induced_receptors = result.get_induced_receptors()
+if induced_receptors:
+    induced_receptors[0].download_structure(name="dasatinib_2GQG_induced_receptor")
+    print("Saved dasatinib_2GQG_induced_receptor.cif")

{rowan_python-3.1.14 → rowan_python-3.1.16}/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-3.1.16/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/examples/pdb_download.py → rowan_python-3.1.16/examples/protein_file_download.py

@@ -8,4 +8,8 @@ import rowan
 proteins = rowan.list_proteins()
 for protein in proteins:
     print(protein.name)
-    protein.download_pdb_file(name=protein.name, path=Path("pdb_files"))
+    protein.download_structure(
+        name=protein.name,
+        path=Path("protein_files"),
+        file_format="mmcif",  # Default; use "pdb" for PDB files
+    )

{rowan_python-3.1.14 → rowan_python-3.1.16}/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-3.1.16/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()