rowan-python 2.1.16__tar.gz → 3.0.0__tar.gz

{rowan_python-2.1.16 → rowan_python-3.0.0}/.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-3.0.0}/PKG-INFO

@@ -1,17 +1,17 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.16
+Version: 3.0.0
 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>=0.0.168
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-2.1.16 → rowan_python-3.0.0}/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-3.0.0}/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-3.0.0}/examples/analogue_docking.py

@@ -4,24 +4,31 @@ 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 = stjames.Molecule.from_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-3.0.0}/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-3.0.0/examples/basic_calculation.py

@@ -0,0 +1,28 @@
+from stjames import Method, Molecule
+
+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=Molecule.from_smiles("CC(=C)C=C"),
+    method=Method.OMOL25_CONSERVING_S,
+    tasks=["optimize"],
+    mode="auto",
+    engine="omol25",
+    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-3.0.0}/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>

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/basic_calculation_with_constraint.py

@@ -2,13 +2,15 @@ from stjames import Molecule
 
 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")
 
 workflow = rowan.submit_workflow(
     initial_molecule=Molecule.from_smiles("CCCC"),
     workflow_type="basic_calculation",
     name="Constrained Butane",
+    folder_uuid=folder,
     workflow_data={
         "settings": {
             "method": "gfn2_xtb",
@@ -28,5 +30,6 @@ workflow = rowan.submit_workflow(
 )
 
 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>

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/basic_calculation_with_solvent.py

@@ -2,8 +2,9 @@ from stjames import Method, Molecule
 
 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")
 
 
 def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, name: str) -> float:
@@ -11,21 +12,20 @@ def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, n
         initial_molecule=molecule,
         workflow_type="basic_calculation",
         name=f"{name} {method} optimization",
+        folder_uuid=folder,
         workflow_data={
             "settings": {"method": method, "tasks": ["optimize"]},
         },
     )
 
     print(f"View workflow privately at: https://labs.rowansci.com/calculation/{opt_workflow.uuid}")
-    opt_workflow.wait_for_result().fetch_latest(in_place=True)
-
-    calculation_uuid = opt_workflow.data["calculation_uuid"]
-    optimized_molecule = rowan.retrieve_calculation_molecules(calculation_uuid)[-1]
+    opt_result = opt_workflow.result()
 
     sp_workflow = rowan.submit_workflow(
-        initial_molecule=optimized_molecule,
+        initial_molecule=opt_result.molecule,
         workflow_type="basic_calculation",
         name=f"{name} {method} single point",
+        folder_uuid=folder,
         workflow_data={
             "settings": {
                 "method": method,
@@ -36,11 +36,9 @@ def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, n
     )
 
     print(f"View workflow privately at: https://labs.rowansci.com/calculation/{sp_workflow.uuid}")
-    sp_workflow.wait_for_result().fetch_latest(in_place=True)
+    sp_result = sp_workflow.result()
 
-    calculation_uuid = sp_workflow.data["calculation_uuid"]
-    final_molecule = rowan.retrieve_calculation_molecules(calculation_uuid)[0]
-    return final_molecule["energy"]
+    return sp_result.energy
 
 
 E1 = compute_energy_with_solvent_correction(

rowan_python-3.0.0/examples/batch_docking.py

@@ -0,0 +1,39 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+ligands = [
+    "CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1",
+    "CCC(C)CN=C1NCC2(CCCOC2)CN1",
+    "CC(C)CCNC1=NCC2CC(COC2=N)O1",
+    "CCC(CC)NC1=NCC2CC(CO)CC12",
+    "CCC(C)CN=C1NC=C2CCC(O)CC2=N1",
+]
+
+protein = rowan.create_protein_from_pdb_id(
+    "CDK2", "1HCK", project_uuid=rowan.default_project().uuid
+)
+
+protein.prepare()
+
+workflow = rowan.submit_batch_docking_workflow(
+    ligands,
+    protein.uuid,
+    pocket=[[103.55, 100.59, 82.99], [27.76, 32.67, 48.79]],
+    executable="qvina2",
+    scoring_function="vina",
+    folder=folder,
+)
+
+
+print(f"View workflow privately at: https://labs.rowansci.com/batch-docking/{workflow.uuid}")
+print(f"Workflow UUID: {workflow.uuid}")
+
+# Stream partial scores as each ligand completes; final iteration is the complete result.
+for result in workflow.stream_result(poll_interval=30):
+    completed = sum(s is not None for s in result.scores.values())
+    print(f"  {completed}/{len(ligands)} complete...")
+
+print(result.scores)  # dict of SMILES → best docking score

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/bde.py

@@ -24,16 +24,19 @@ from stjames import Molecule
 
 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")
 
 workflow = rowan.submit_bde_workflow(
     initial_molecule=Molecule.from_smiles("CCCC"),
     mode="rapid",
     all_CH=True,
     name="Butane BDE",
+    folder=folder,
 )
 
 print(f"View workflow privately at: https://labs.rowansci.com/bde/{workflow.uuid}")
-workflow.wait_for_result().fetch_latest(in_place=True)
-print(workflow.data)
+result = workflow.result()
+print(result)
+# e.g. <BDEResult energy=-152.234567 Ha bdes=8>

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/boltz_paired_msa.py

@@ -1,12 +1,11 @@
 import tarfile
 from pathlib import Path
 
-from stjames import MSAFormat
-
 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")
 
 msa_directory = Path("msa_directory")
 
@@ -15,13 +14,14 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=[MSAFormat.BOLTZ],
+    output_formats=["boltz"],
     name="Boltz Paired MSA Example",
+    folder=folder,
 )
 
-msa_workflow.wait_for_result().fetch_latest(in_place=True)
+msa_result = msa_workflow.result()
 
-msa_workflow.download_msa_files(MSAFormat.BOLTZ, path=msa_directory)
+msa_result.download_files("boltz", path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/boltz_single_msa.py

@@ -1,12 +1,11 @@
 import tarfile
 from pathlib import Path
 
-from stjames import MSAFormat
-
 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")
 
 msa_directory = Path("msa_directory")
 
@@ -14,13 +13,14 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=[MSAFormat.BOLTZ],
+    output_formats=["boltz"],
     name="Boltz MSA Example",
+    folder=folder,
 )
 
-msa_workflow.wait_for_result().fetch_latest(in_place=True)
+msa_result = msa_workflow.result()
 
-msa_workflow.download_msa_files(MSAFormat.BOLTZ, path=msa_directory)
+msa_result.download_files("boltz", path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/chai_paired_msa.py

@@ -2,12 +2,11 @@ import tarfile
 from pathlib import Path
 
 # from chai_lab.chai1 import run_inference
-from stjames import MSAFormat
-
 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")
 
 example_fasta = (
     ">protein|name=example-protein\n"
@@ -26,13 +25,14 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=[MSAFormat.CHAI],
+    output_formats=["chai"],
     name="CHAI Paired MSA Example",
+    folder=folder,
 )
 
-msa_workflow.wait_for_result().fetch_latest(in_place=True)
+msa_result = msa_workflow.result()
 
-msa_workflow.download_msa_files(MSAFormat.CHAI, path=msa_directory)
+msa_result.download_files("chai", path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/chai_single_msa.py

@@ -2,12 +2,11 @@ import tarfile
 from pathlib import Path
 
 # from chai_lab.chai1 import run_inference
-from stjames import MSAFormat
-
 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")
 
 example_fasta = (
     ">protein|name=example-protein\n"
@@ -23,13 +22,14 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=[MSAFormat.CHAI],
+    output_formats=["chai"],
     name="CHAI MSA Example",
+    folder=folder,
 )
 
-msa_workflow.wait_for_result().fetch_latest(in_place=True)
+msa_result = msa_workflow.result()
 
-msa_workflow.download_msa_files(MSAFormat.CHAI, path=msa_directory)
+msa_result.download_files("chai", path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

rowan_python-3.0.0/examples/cofolding_screen.py

@@ -0,0 +1,37 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples/cofolding-screen")
+
+HARTREE_TO_KCALMOL = 627.5096
+
+ligands = [
+    "CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1",
+    "CCC(C)CN=C1NCC2(CCCOC2)CN1",
+    "CC(C)CCNC1=NCC2CC(COC2=N)O1",
+    "CCC(CC)NC1=NCC2CC(CO)CC12",
+    "CCC(C)CN=C1NC=C2CCC(O)CC2=N1",
+]
+
+workflows = []
+results = {}
+
+for ligand in ligands:
+    workflow = rowan.submit_protein_cofolding_workflow(
+        initial_protein_sequences=[
+            "MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL"
+        ],
+        initial_smiles_list=[ligand],
+        ligand_binding_affinity_index=0,
+        name=f"Cofolding {ligand}",
+        folder=folder,
+    )
+    workflows.append(workflow)
+
+workflow_results = [(w, w.result()) for w in workflows]
+
+for workflow, result in workflow_results:
+    results[workflow.name] = result.affinity_score.probability_binary
+
+print(results)

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/colabfold_paired_msa.py

@@ -1,12 +1,11 @@
 import tarfile
 from pathlib import Path
 
-from stjames import MSAFormat
-
 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")
 
 msa_directory = Path("msa_directory")
 
@@ -15,13 +14,14 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=[MSAFormat.COLABFOLD],
+    output_formats=["colabfold"],
     name="Colabfold Paired MSA Example",
+    folder=folder,
 )
 
-msa_workflow.wait_for_result().fetch_latest(in_place=True)
+msa_result = msa_workflow.result()
 
-msa_workflow.download_msa_files(MSAFormat.COLABFOLD, path=msa_directory)
+msa_result.download_files("colabfold", path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/colabfold_single_msa.py

@@ -1,12 +1,11 @@
 import tarfile
 from pathlib import Path
 
-from stjames import MSAFormat
-
 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")
 
 msa_directory = Path("msa_directory")
 
@@ -14,13 +13,14 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=[MSAFormat.COLABFOLD],
+    output_formats=["colabfold"],
     name="Colabfold MSA Example",
+    folder=folder,
 )
 
-msa_workflow.wait_for_result().fetch_latest(in_place=True)
+msa_result = msa_workflow.result()
 
-msa_workflow.download_msa_files(MSAFormat.COLABFOLD, path=msa_directory)
+msa_result.download_files("colabfold", path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-2.1.16 → rowan_python-3.0.0}/examples/conformer_dependent_redox.py

@@ -3,21 +3,20 @@ from stjames import Molecule
 
 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..."
-
-conformer_dependent_redox_folder = rowan.create_folder(name="Conformer dependent redox workflows")
+folder = rowan.get_folder("examples/conformer-dependent-redox")
 
 workflow = rowan.submit_conformer_search_workflow(
     initial_molecule=Molecule.from_smiles("CC(C)Cc1ccc(C(=O)c2ccc(O)cc2)cc1"),
-    folder_uuid=conformer_dependent_redox_folder.uuid,
+    folder=folder,
 )
 print(f"View workflow privately at: https://labs.rowansci.com/workflow/{workflow.uuid}")
-workflow.wait_for_result().fetch_latest(in_place=True)
+csearch_result = workflow.result()
 
 redox_potential_workflows = []
 
-for conformer in workflow.data["conformer_uuids"][:10]:
+for conformer in csearch_result.conformer_uuids[:10]:
     uuid = conformer[0]
     molecule = rowan.retrieve_calculation_molecules(uuid)[0]
     stjames_molecule = stjames.Molecule.model_validate(molecule)
@@ -26,13 +25,10 @@ for conformer in workflow.data["conformer_uuids"][:10]:
             stjames_molecule,
             reduction=True,
             oxidization=True,
-            folder_uuid=conformer_dependent_redox_folder.uuid,
+            folder=folder,
         )
     )
 
-for workflow in redox_potential_workflows:
-    workflow.wait_for_workflow()
-    workflow.fetch_latest(in_place=True)
-
+redox_results = [w.result() for w in redox_potential_workflows]
 
-print([workflow.data["redox_potential"] for workflow in redox_potential_workflows])
+print([(r.oxidation_potential, r.reduction_potential) for r in redox_results])