rowan-python 3.1.0__tar.gz → 3.1.2__tar.gz

rowan_python-3.1.2/.github/workflows/publish-skill.yml

@@ -0,0 +1,28 @@
+name: Publish Skill Zip
+
+on:
+  push:
+    branches: [master]
+    paths:
+      - 'skills/computational-chemistry-and-biology/**'
+      - '.github/workflows/publish-skill.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  publish:
+    if: github.repository == 'rowansci/rowan-python'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Zip skill
+        run: cd skills && zip -r ../computational-chemistry-and-biology-skill.zip computational-chemistry-and-biology
+      - name: Publish/refresh release
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: skill-latest
+          name: "Computational Chemistry & Biology Skill (latest)"
+          prerelease: true
+          files: computational-chemistry-and-biology-skill.zip

{rowan_python-3.1.0 → rowan_python-3.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.0
+Version: 3.1.2
 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>=0.0.204
+Requires-Dist: stjames>=0.0.208
 Description-Content-Type: text/markdown
 
 # Rowan Python Library
@@ -32,6 +32,8 @@ The documentation is available [here](https://docs.rowansci.com/python-api).
 
 Ships with a [skill](skills/computational-chemistry-and-biology/) that makes it easy for coding agents to use Rowan's tools to power chemistry and biology tasks. To use it, copy the directory into your agent's skills folder.
 
+Download the latest skill as a zip [here](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip), then unzip it into your agent's skills folder.
+
 ## Running examples
 
 To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.

{rowan_python-3.1.0 → rowan_python-3.1.2}/README.md

@@ -16,6 +16,8 @@ The documentation is available [here](https://docs.rowansci.com/python-api).
 
 Ships with a [skill](skills/computational-chemistry-and-biology/) that makes it easy for coding agents to use Rowan's tools to power chemistry and biology tasks. To use it, copy the directory into your agent's skills folder.
 
+Download the latest skill as a zip [here](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip), then unzip it into your agent's skills folder.
+
 ## Running examples
 
 To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.

rowan_python-3.1.2/examples/rbfe_resubmit.py

@@ -0,0 +1,51 @@
+"""Extend a converged RBFE graph with an additional ligand via reuse.
+
+A completed RBFE graph holds converged per-edge relative free energies (ddG) on
+each ligand-pair edge. Passing it back as `seed_graph` freezes those edges and
+their results, constructs only the edges incident to the new ligand (atom-mapping
+plus alchemical-path setup), and restricts the subsequent FEP to those edges -- the
+existing complex/solvent legs are not resimulated. A per-ligand relative binding
+free energy for the new ligand (relative to the reference ligand the graph is
+anchored on) is then recovered by re-solving the maximum-likelihood estimate over
+the augmented edge set.
+"""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+
+# UUID of a COMPLETED relative_binding_free_energy_perturbation workflow to extend.
+FINISHED_RBFE_UUID = "your-completed-rbfe-uuid"
+
+folder = rowan.get_folder("examples")
+
+finished = rowan.retrieve_workflow(FINISHED_RBFE_UUID).result()
+print(f"Finished study: {len(finished.ligands)} ligands, {len(finished.edges)} edges with ddG")
+
+# Combine the finished study's ligands with the newly designed one(s) to score.
+new_ligands = rowan.load_named_ligands("path/to/new_ligands.sdf")
+ligands = {**finished.ligands, **new_ligands}
+
+extended_graph = rowan.submit_relative_binding_free_energy_graph_workflow(
+    ligands=ligands,
+    seed_graph=finished.graph,
+    folder=folder,
+    name="RBFE Graph (extended)",
+).result()
+
+resubmit = rowan.submit_relative_binding_free_energy_perturbation_workflow(
+    graph_result=extended_graph,
+    protein=finished.protein,
+    folder=folder,
+    name="RBFE Perturbation (resubmit)",
+)
+print(
+    "Resubmitted! View at: "
+    f"https://labs.rowansci.com/relative-binding-free-energy-perturbation/{resubmit.uuid}"
+)
+
+result = resubmit.result()
+for name in new_ligands:
+    dg = result.ligand_dg_results[name]
+    print(f"{name}: dG = {dg.dg:.2f} +/- {dg.dg_err:.2f} kcal/mol")

{rowan_python-3.1.0 → rowan_python-3.1.2}/examples/retrieve_workflow.py

@@ -9,7 +9,7 @@ import rowan
 #   2. The last segment of the workflow URL in the Rowan UI:
 #      https://labs.rowansci.com/.../<uuid>
 #   3. Listed via rowan.list_workflows()
-workflow = rowan.retrieve_workflow("619fedc2-d8e9-4bbc-8780-170108d1f674")
+workflow = rowan.retrieve_workflow("your-workflow-uuid")
 
 result = workflow.result()
 print(result)