rowan-python 3.1.1__tar.gz → 3.1.3__tar.gz

{rowan_python-3.1.1 → rowan_python-3.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.1
+Version: 3.1.3
 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

rowan_python-3.1.3/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-3.1.1 → rowan_python-3.1.3}/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)