rowan-python 2.1.12__tar.gz → 2.1.14__tar.gz

rowan_python-2.1.14/.envrc

@@ -0,0 +1,4 @@
+watch_file pixi.lock
+dotenv_if_exists .env
+
+eval "$(pixi shell-hook -e dev)"

{rowan_python-2.1.12 → rowan_python-2.1.14}/.github/workflows/build-and-deploy-docs.yml

@@ -3,6 +3,7 @@ name: Build & Deploy Rowan Python Docs
 on:
   release:
     types: [published]
+  workflow_dispatch:
 
 permissions:
   contents: read
@@ -16,8 +17,8 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          ref: main
-      
+          ref: master
+
       - name: Install Pixi
         uses: prefix-dev/setup-pixi@v0.9.1
         with:
@@ -39,4 +40,4 @@ jobs:
       - name: Deploy with rsync
         run: |
           rsync -avz --delete ./ \
-            ${{ secrets.DOCS_USERNAME }}@${{ secrets.DOCS_IP }}:{{ secrets.DOCS_TARGET_DIR }}
+            ${{ secrets.DOCS_USERNAME }}@${{ secrets.DOCS_IP }}:${{ secrets.DOCS_TARGET_DIR }}

{rowan_python-2.1.12 → rowan_python-2.1.14}/.github/workflows/test.yml

@@ -22,9 +22,9 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: prefix-dev/setup-pixi@v0.9.1
+      - uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          pixi-version: v0.56.0
+          pixi-version: v0.63.0
           cache: true
           environments: dev
 

{rowan_python-2.1.12 → rowan_python-2.1.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.12
+Version: 2.1.14
 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>=0.0.137
+Requires-Dist: stjames>=0.0.144
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/PROTAC_solubility.py

@@ -2,6 +2,9 @@
 
 import rowan
 
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
 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",
     2438: "CC(=O)N[C@H](C(=O)N1C[C@H](O)C[C@H]1C(=O)NCC1=CC=C(C2=C(C)N=CS2)C=C1OCCCCCCCCCCCC(=O)NC1=CC=C(C(=O)NC2=CC=CC=C2N)C=C1)C(C)(C)C",

rowan_python-2.1.14/examples/admet.py

@@ -0,0 +1,15 @@
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+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",
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/solubility/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow)

rowan_python-2.1.14/examples/analogue_docking.py

@@ -0,0 +1,27 @@
+from pathlib import Path
+
+import stjames
+
+import rowan
+
+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")
+
+protein = rowan.upload_protein("1IEP receptor", Path("examples/data/1iep_receptorH.pdb"))
+
+workflow = rowan.submit_analogue_docking_workflow(
+    analogues=citalopram_analogues,
+    protein=protein,
+    initial_molecule=bound_pose,
+)
+
+print(f"View MD workflow privately at: https://labs.rowansci.com/analogue-docking/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+
+# print ligand RMSD by frame
+print(workflow.data)

rowan_python-2.1.14/examples/aqueous_solubility.py

@@ -0,0 +1,18 @@
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+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",
+    solvents=["O"],
+    temperatures=[298.15],
+    name="Oseltamivir aqueous solubility",
+)
+
+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

rowan_python-2.1.14/examples/basic_calculation.py

@@ -0,0 +1,19 @@
+from stjames import Method, Molecule
+
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+workflow = rowan.submit_basic_calculation_workflow(
+    initial_molecule=Molecule.from_smiles("CC(=C)C=C"),
+    method=Method.OMOL25_CONSERVING_S,
+    tasks=["energy"],
+    mode="auto",
+    engine="omol25",
+    name="Isoprene Energy",
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/calculation/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow)

rowan_python-2.1.14/examples/basic_calculation_from_json.py

@@ -0,0 +1,20 @@
+import json
+
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+with open("examples/data/workflow_example.json") as f:
+    workflow_data = json.load(f)
+
+workflow = rowan.submit_workflow(
+    workflow_type="basic_calculation",
+    workflow_data=workflow_data,
+    name="basic calculation from json",
+    initial_molecule=workflow_data["initial_molecule"],
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/calculation/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow)

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/basic_calculation_with_constraint.py

@@ -2,9 +2,10 @@ from stjames import Molecule
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
 
-result = rowan.submit_workflow(
+workflow = rowan.submit_workflow(
     initial_molecule=Molecule.from_smiles("CCCC"),
     workflow_type="basic_calculation",
     name="Constrained Butane",
@@ -26,7 +27,6 @@ result = rowan.submit_workflow(
     },
 )
 
-result.wait_for_result()
-result.fetch_latest(in_place=True)
-
-print(result)
+print(f"View workflow privately at: https://labs.rowansci.com/calculation/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow)

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/basic_calculation_with_solvent.py

@@ -1,13 +1,13 @@
-# ruff: noqa
-from stjames import Molecule, Method
+from stjames import Method, Molecule
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
 
 
 def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, name: str) -> float:
-    opt = rowan.submit_workflow(
+    opt_workflow = rowan.submit_workflow(
         initial_molecule=molecule,
         workflow_type="basic_calculation",
         name=f"{name} {method} optimization",
@@ -16,13 +16,13 @@ def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, n
         },
     )
 
-    opt.wait_for_result()
-    opt.fetch_latest(in_place=True)
+    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.data["calculation_uuid"]
+    calculation_uuid = opt_workflow.data["calculation_uuid"]
     optimized_molecule = rowan.retrieve_calculation_molecules(calculation_uuid)[-1]
 
-    sp = rowan.submit_workflow(
+    sp_workflow = rowan.submit_workflow(
         initial_molecule=optimized_molecule,
         workflow_type="basic_calculation",
         name=f"{name} {method} single point",
@@ -35,10 +35,10 @@ def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, n
         },
     )
 
-    sp.wait_for_result()
-    sp.fetch_latest(in_place=True)
+    print(f"View workflow privately at: https://labs.rowansci.com/calculation/{sp_workflow.uuid}")
+    sp_workflow.wait_for_result().fetch_latest(in_place=True)
 
-    calculation_uuid = sp.data["calculation_uuid"]
+    calculation_uuid = sp_workflow.data["calculation_uuid"]
     final_molecule = rowan.retrieve_calculation_molecules(calculation_uuid)[0]
     return final_molecule["energy"]
 

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/batch_docking.py

@@ -2,6 +2,9 @@ import time
 
 import rowan
 
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
 ligands = [
     "CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1",
     "CCC(C)CN=C1NCC2(CCCOC2)CN1",
@@ -105,9 +108,6 @@ ligands = [
     "CC(C)C(CN)C1NCC2=C(SC=C2C)C1C",
 ]
 
-workflows = []
-results = {}
-
 protein = rowan.create_protein_from_pdb_id(
     "CDK2", "1HCK", project_uuid=rowan.default_project().uuid
 )
@@ -125,6 +125,6 @@ workflow = rowan.submit_batch_docking_workflow(
 )
 
 
+print(f"View workflow privately at: https://labs.rowansci.com/batch-docking/{workflow.uuid}")
 workflow.wait_for_result().fetch_latest(in_place=True)
-
 print(workflow.data["best_scores"])

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/bde.py

@@ -18,10 +18,10 @@ from stjames import Molecule
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
 
-# Run calculation remotely
-result = rowan.submit_workflow(
+workflow = rowan.submit_workflow(
     initial_molecule=Molecule.from_smiles("CCCC"),
     workflow_type="bde",
     name="Butane BDE",
@@ -31,7 +31,6 @@ result = rowan.submit_workflow(
     },
 )
 
-result.wait_for_result()
-result.fetch_latest(in_place=True)
-
-print(result)
+print(f"View workflow privately at: https://labs.rowansci.com/bde/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow)

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/boltz_paired_msa.py

@@ -5,7 +5,8 @@ from stjames import MSAFormat
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
 
 msa_directory = Path("msa_directory")
 

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/boltz_single_msa.py

@@ -5,7 +5,8 @@ from stjames import MSAFormat
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
 
 msa_directory = Path("msa_directory")
 

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/chai_paired_msa.py

@@ -6,7 +6,9 @@ from stjames import MSAFormat
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
 example_fasta = (
     ">protein|name=example-protein\n"
     "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR\n"

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/chai_single_msa.py

@@ -6,7 +6,9 @@ from stjames import MSAFormat
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
 example_fasta = (
     ">protein|name=example-protein\n"
     "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW\n"

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/cofolding_screen.py

@@ -1,5 +1,8 @@
 import rowan
 
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
 HARTREE_TO_KCALMOL = 627.5096
 
 ligands = [

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/colabfold_paired_msa.py

@@ -5,7 +5,8 @@ from stjames import MSAFormat
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
 
 msa_directory = Path("msa_directory")
 

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/colabfold_single_msa.py

@@ -5,7 +5,8 @@ from stjames import MSAFormat
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
 
 msa_directory = Path("msa_directory")
 

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/conformer_dependent_redox.py

@@ -3,20 +3,21 @@ from stjames import Molecule
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
 
-conformer_dependent_redox_folder = rowan.create_folder(name="Conformer dependent redox results")
+conformer_dependent_redox_folder = rowan.create_folder(name="Conformer dependent redox workflows")
 
-result = rowan.submit_conformer_search_workflow(
+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,
 )
-result.wait_for_result()
-result.fetch_latest(in_place=True)
+print(f"View workflow privately at: https://labs.rowansci.com/workflow/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
 
 redox_potential_workflows = []
 
-for conformer in result.data["conformer_uuids"][:10]:
+for conformer in workflow.data["conformer_uuids"][:10]:
     uuid = conformer[0]
     molecule = rowan.retrieve_calculation_molecules(uuid)[0]
     stjames_molecule = stjames.Molecule.model_validate(molecule)
@@ -30,7 +31,7 @@ for conformer in result.data["conformer_uuids"][:10]:
     )
 
 for workflow in redox_potential_workflows:
-    workflow.wait_for_result()
+    workflow.wait_for_workflow()
     workflow.fetch_latest(in_place=True)
 
 

{rowan_python-2.1.12 → rowan_python-2.1.14}/examples/conformers.py

@@ -21,11 +21,13 @@ from stjames import Molecule
 
 import rowan
 
-# rowan.api_key = ""
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
 
-# Run calculation remotely
-result = rowan.submit_conformer_search_workflow(
+workflow = rowan.submit_conformer_search_workflow(
     initial_molecule=Molecule.from_smiles("CCOCC"),
 )
 
-print(result.wait_for_result().fetch_latest(in_place=True))
+print(f"View workflow privately at: https://labs.rowansci.com/workflow/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow)