rowan-python 2.1.16__tar.gz → 3.0.1__tar.gz

{rowan_python-2.1.16 → rowan_python-3.0.1}/.gitignore

@@ -198,3 +198,11 @@ local/
 .pixi/
 
 cyp/
+
+# AI agent instructions (not part of the project source)
+AGENTS.md
+
+# MSA download output directories
+msa_directory/
+
+notes.md

{rowan_python-2.1.16 → rowan_python-3.0.1}/PKG-INFO

@@ -1,17 +1,17 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.16
+Version: 3.0.1
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
 Author-email: Corin Wagen <corin@rowansci.com>
 License-File: LICENSE
-Requires-Python: >=3.11
+Requires-Python: >=3.12
 Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.155
+Requires-Dist: stjames>=0.0.174
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

rowan_python-3.0.1/docs/index.md

@@ -0,0 +1,455 @@
+## Workflow Utilities
+::: rowan.workflows.base
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+      members:
+        - Workflow
+        - WorkflowResult
+        - WorkflowError
+        - Message
+        - Solvent
+        - Mode
+        - submit_workflow
+        - retrieve_workflow
+        - retrieve_workflows
+        - list_workflows
+        - batch_submit_workflow
+        - batch_poll_status
+
+## ADMET
+::: rowan.workflows.admet
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Analogue Docking
+::: rowan.workflows.analogue_docking
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Basic Calculation
+::: 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: ["!^__"]
+
+## Batch Docking
+::: rowan.workflows.batch_docking
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Bond Dissociation Energy
+::: rowan.workflows.bde
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Conformer Search
+::: rowan.workflows.conformer_search
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Descriptors
+::: rowan.workflows.descriptors
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Docking
+::: rowan.workflows.docking
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Double-Ended TS Search
+::: rowan.workflows.double_ended_ts_search
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Electronic Properties
+::: rowan.workflows.electronic_properties
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Fukui
+::: rowan.workflows.fukui
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Hydrogen Bond Donor/Acceptor Strength
+::: rowan.workflows.hydrogen_bond_donor_acceptor_strength
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Interaction Energy Decomposition
+::: rowan.workflows.interaction_energy_decomposition
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Ion Mobility
+::: rowan.workflows.ion_mobility
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## IRC
+::: rowan.workflows.irc
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## MacropKa
+::: rowan.workflows.macropka
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Membrane Permeability
+::: rowan.workflows.membrane_permeability
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## MSA
+::: rowan.workflows.msa
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Multistage Optimization
+::: rowan.workflows.multistage_optimization
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## NMR
+::: rowan.workflows.nmr
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## pKa
+::: rowan.workflows.pka
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Pose Analysis MD
+::: rowan.workflows.pose_analysis_md
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Protein Binder Design
+::: rowan.workflows.protein_binder_design
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Protein Cofolding
+::: rowan.workflows.protein_cofolding
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Protein MD
+::: rowan.workflows.protein_md
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## RBFE Graph
+::: rowan.workflows.rbfe_graph
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Relative Binding Free Energy Perturbation
+::: rowan.workflows.relative_binding_free_energy_perturbation
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Redox Potential
+::: rowan.workflows.redox_potential
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Scan
+::: rowan.workflows.scan
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Solubility
+::: rowan.workflows.solubility
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Solvent-Dependent Conformers
+::: rowan.workflows.solvent_dependent_conformers
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Spin States
+::: rowan.workflows.spin_states
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Strain
+::: rowan.workflows.strain
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Tautomer Search
+::: rowan.workflows.tautomer_search
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Folder Class and Functions
+::: rowan.folder
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## User Class and Functions
+::: rowan.user
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Protein Class and Functions
+::: rowan.protein
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Project Class and Functions
+::: rowan.project
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
+## Utilities
+::: rowan.utils
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      members:
+        - get_api_key
+        - get_project_uuid
+        - smiles_to_stjames

{rowan_python-2.1.16 → rowan_python-3.0.1}/examples/PROTAC_solubility.py

@@ -1,9 +1,12 @@
 # ruff: noqa: E501
 
+# WARNING: This example submits many workflows and will consume significant credits.
+
 import rowan
 
-# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# Set your API key or use the ROWAN_API_KEY environment variable
 # rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples/protac-solubility")
 
 PROTACs = {
     4564: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CCCCCCCCCN3C=C(CCCOC(=O)NCC4=CC=C(C(=O)NC5=CC=CC=C5N)C=C4)N=N3)C(C)(C)C)C=C2)SC=N1",
@@ -28,29 +31,25 @@ PROTACs = {
     2428: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)COCCOCCOCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
 }
 
-protac_solubility_folder = rowan.create_folder(name="PROTAC Solubility")
-
 workflows = []
 for id, smiles in PROTACs.items():
     workflows.append(
         rowan.submit_solubility_workflow(
             initial_smiles=smiles,
-            solubility_method="fastsolv",
+            method="fastsolv",
             solvents=["CS(=O)C"],
             temperatures=[293.15],
-            folder_uuid=protac_solubility_folder.uuid,
             name=f"solubility {id}",
+            folder=folder,
         )
     )
 
 
-for workflow in workflows:
-    workflow.wait_for_result()
-    workflow.fetch_latest(in_place=True)
+workflow_results = [w.result() for w in workflows]
 
 print(
     [
-        (workflow.name, workflow.data["solubilities"]["CS(=O)C"]["solubilities"])
-        for workflow in workflows
+        (w.name, r.data["solubilities"]["CS(=O)C"]["solubilities"])
+        for w, r in zip(workflows, workflow_results, strict=True)
     ]
 )

{rowan_python-2.1.16 → rowan_python-3.0.1}/examples/admet.py

@@ -1,15 +1,18 @@
 import rowan
 
-# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# Set your API key or use the ROWAN_API_KEY environment variable
 # rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
 
 oseltamivir_SMILES = "C1CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H]([NH3+])C1CCC1"
 
 workflow = rowan.submit_admet_workflow(
     initial_smiles=oseltamivir_SMILES,
     name="Oseltamivir ADMET",
+    folder=folder,
 )
 
 print(f"View workflow privately at: https://labs.rowansci.com/solubility/{workflow.uuid}")
-workflow.wait_for_result().fetch_latest(in_place=True)
-print(workflow)
+result = workflow.result()
+print(result)
+# e.g. <ADMETResult properties=42 preview={'mw': 180.16, 'tpsa': 75.3, ...}>

{rowan_python-2.1.16 → rowan_python-3.0.1}/examples/analogue_docking.py

@@ -1,27 +1,32 @@
 from pathlib import Path
 
-import stjames
-
 import rowan
 
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+
+folder = rowan.get_folder("examples")
+
 citalopram_analogues = [
     "CN(C)CCC[C@@]1(c2ccccc2)OCc2cc(C#N)ccc21",
     "CN(C)CCC[C@@]1(c2ccc(F)cc2)OCc2c(CC)c(C#N)ccc21",
     "CN(C)CCC[C@@]1(c2ccc(CCC)cc2)OCc2cc(C#N)ccc21",
 ]
 
-bound_pose = stjames.Molecule.from_file("examples/data/citalopram_1iep.xyz")
+data_dir = Path(__file__).parent / "data"
+bound_pose = rowan.Molecule.from_xyz_file(str(data_dir / "citalopram_1iep.xyz"))
 
-protein = rowan.upload_protein("1IEP receptor", Path("examples/data/1iep_receptorH.pdb"))
+protein = rowan.upload_protein("1IEP receptor", data_dir / "1iep_receptorH.pdb")
 
 workflow = rowan.submit_analogue_docking_workflow(
     analogues=citalopram_analogues,
     protein=protein,
     initial_molecule=bound_pose,
+    folder=folder,
 )
 
 print(f"View MD workflow privately at: https://labs.rowansci.com/analogue-docking/{workflow.uuid}")
-workflow.wait_for_result().fetch_latest(in_place=True)
+result = workflow.result()
 
-# print ligand RMSD by frame
-print(workflow.data)
+print(result)
+# e.g. <AnalogueDockingResult analogues=3 best=(-8.30, 'CN(C)CCC...')>

{rowan_python-2.1.16 → rowan_python-3.0.1}/examples/aqueous_solubility.py

@@ -1,18 +1,21 @@
 import rowan
 
-# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# Set your API key or use the ROWAN_API_KEY environment variable
 # rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
 
 oseltamivir_SMILES = "C1CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H]([NH3+])C1CCC1"
 
 workflow = rowan.submit_solubility_workflow(
     initial_smiles=oseltamivir_SMILES,
-    solubility_method="kingfisher",
+    method="kingfisher",
     solvents=["O"],
     temperatures=[298.15],
     name="Oseltamivir aqueous solubility",
+    folder=folder,
 )
 
 print(f"View workflow privately at: https://labs.rowansci.com/workflow/{workflow.uuid}")
-workflow.wait_for_result().fetch_latest(in_place=True)
-print(workflow)  # Solubility in log(mol/L), temperature in kelvin
+result = workflow.result()
+print(result)
+# e.g. <SolubilityResult solvents=['water']>

rowan_python-3.0.1/examples/basic_calculation.py

@@ -0,0 +1,24 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+workflow = rowan.submit_basic_calculation_workflow(
+    initial_molecule="CC(=C)C=C",
+    preset="semiempirical",
+    tasks=["optimize"],
+    name="Isoprene Optimization",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/calculation/{workflow.uuid}")
+
+# Stream optimization steps as they complete; final iteration is the complete result.
+for result in workflow.stream_result(poll_interval=3):
+    if result.calculation_uuid:
+        mols = rowan.retrieve_calculation_molecules(result.calculation_uuid)
+        print(f"  {len(mols)} opt steps, energy={mols[-1].get('energy') if mols else None}")
+
+print(result)
+# e.g. <BasicCalculationResult energy=-76.234567 H>

{rowan_python-2.1.16 → rowan_python-3.0.1}/examples/basic_calculation_from_json.py

@@ -1,11 +1,13 @@
 import json
+from pathlib import Path
 
 import rowan
 
-# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# Set your API key or use the ROWAN_API_KEY environment variable
 # rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
 
-with open("examples/data/workflow_example.json") as f:
+with open(Path(__file__).parent / "data/workflow_example.json") as f:
     workflow_data = json.load(f)
 
 workflow = rowan.submit_workflow(
@@ -13,8 +15,10 @@ workflow = rowan.submit_workflow(
     workflow_data=workflow_data,
     name="basic calculation from json",
     initial_molecule=workflow_data["initial_molecule"],
+    folder_uuid=folder,
 )
 
 print(f"View workflow privately at: https://labs.rowansci.com/calculation/{workflow.uuid}")
-workflow.wait_for_result().fetch_latest(in_place=True)
-print(workflow)
+result = workflow.result()
+print(result)
+# e.g. <BasicCalculationResult energy=-76.234567 H>