rowan-python 3.1.15__tar.gz → 3.1.16__tar.gz

{rowan_python-3.1.15 → 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-3.1.15 → 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-3.1.15 → rowan_python-3.1.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: rowan-python
-Version: 3.1.15
+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
@@ -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-3.1.15 → 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-3.1.16/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-3.1.15 → 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-3.1.15 → 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-3.1.15 → 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-3.1.15 → 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-3.1.15 → rowan_python-3.1.16}/examples/induced_fit_docking.py

@@ -50,12 +50,12 @@ for i, score in enumerate(result.scores):
         f"score={score.score:.3f}  receptor_strain={score.receptor_strain}"
     )
 
-# Download the top-scoring complex and best-ranked relaxed receptor as PDBs
+# Download the top-scoring complex and best-ranked relaxed receptor as mmCIF files
 complex_protein = result.get_complex(0)
-complex_protein.download_pdb_file(name="dasatinib_2GQG_induced_complex")
-print("Saved dasatinib_2GQG_induced_complex.pdb")
+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_pdb_file(name="dasatinib_2GQG_induced_receptor")
-    print("Saved dasatinib_2GQG_induced_receptor.pdb")
+    induced_receptors[0].download_structure(name="dasatinib_2GQG_induced_receptor")
+    print("Saved dasatinib_2GQG_induced_receptor.cif")

rowan_python-3.1.15/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
+    )