rowan-python 3.0.0__tar.gz → 3.0.3__tar.gz

{rowan_python-3.0.0 → rowan_python-3.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.0
+Version: 3.0.3
 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>=0.0.168
+Requires-Dist: stjames>=0.0.174
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

rowan_python-3.0.3/docs/index.md

@@ -0,0 +1,456 @@
+## 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
+        - DispatchInfo
+        - 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-3.0.0 → rowan_python-3.0.3}/examples/analogue_docking.py

@@ -1,7 +1,5 @@
 from pathlib import Path
 
-import stjames
-
 import rowan
 
 # Set your API key or use the ROWAN_API_KEY environment variable
@@ -16,7 +14,7 @@ citalopram_analogues = [
 ]
 
 data_dir = Path(__file__).parent / "data"
-bound_pose = stjames.Molecule.from_file(str(data_dir / "citalopram_1iep.xyz"))
+bound_pose = rowan.Molecule.from_xyz_file(str(data_dir / "citalopram_1iep.xyz"))
 
 protein = rowan.upload_protein("1IEP receptor", data_dir / "1iep_receptorH.pdb")
 

{rowan_python-3.0.0 → rowan_python-3.0.3}/examples/basic_calculation.py

@@ -1,5 +1,3 @@
-from stjames import Method, Molecule
-
 import rowan
 
 # Set your API key or use the ROWAN_API_KEY environment variable
@@ -7,11 +5,9 @@ import rowan
 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,
+    initial_molecule="CC(=C)C=C",
+    preset="semiempirical",
     tasks=["optimize"],
-    mode="auto",
-    engine="omol25",
     name="Isoprene Optimization",
     folder=folder,
 )

rowan_python-3.0.3/examples/basic_calculation_with_constraint.py

@@ -0,0 +1,28 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+molecule = rowan.Molecule.from_smiles("CCCC")
+
+# Constrain the C-C-C-C dihedral angle to 0 degrees during optimization.
+# Constraint types: "bond", "angle", "dihedral", "freeze_atoms"
+# Atoms are 1-indexed.
+workflow = rowan.submit_basic_calculation_workflow(
+    initial_molecule=molecule,
+    method="gfn2_xtb",
+    tasks=["optimize"],
+    name="Constrained Butane",
+    folder=folder,
+    opt_settings=rowan.OptimizationSettings(
+        constraints=[
+            rowan.Constraint(atoms=[4, 3, 2, 1], constraint_type="dihedral", value=0),
+        ]
+    ),
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/calculation/{workflow.uuid}")
+result = workflow.result()
+print(result)
+# e.g. <BasicCalculationResult energy=-13.657247 H>

{rowan_python-3.0.0 → rowan_python-3.0.3}/examples/basic_calculation_with_solvent.py

@@ -1,5 +1,3 @@
-from stjames import Method, Molecule
-
 import rowan
 
 # Set your API key or use the ROWAN_API_KEY environment variable
@@ -7,32 +5,27 @@ import rowan
 folder = rowan.get_folder("examples")
 
 
-def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, name: str) -> float:
-    opt_workflow = rowan.submit_workflow(
+def compute_energy_with_solvent_correction(
+    molecule: rowan.Molecule, method: rowan.Method, name: str
+) -> float:
+    opt_workflow = rowan.submit_basic_calculation_workflow(
         initial_molecule=molecule,
-        workflow_type="basic_calculation",
+        method=method,
+        tasks=["optimize"],
         name=f"{name} {method} optimization",
-        folder_uuid=folder,
-        workflow_data={
-            "settings": {"method": method, "tasks": ["optimize"]},
-        },
+        folder=folder,
     )
 
     print(f"View workflow privately at: https://labs.rowansci.com/calculation/{opt_workflow.uuid}")
     opt_result = opt_workflow.result()
 
-    sp_workflow = rowan.submit_workflow(
+    sp_workflow = rowan.submit_basic_calculation_workflow(
         initial_molecule=opt_result.molecule,
-        workflow_type="basic_calculation",
+        method=method,
+        tasks=["energy"],
+        solvent_settings={"solvent": "water", "model": "cpcmx"},
         name=f"{name} {method} single point",
-        folder_uuid=folder,
-        workflow_data={
-            "settings": {
-                "method": method,
-                "tasks": ["energy"],
-                "solvent_settings": {"solvent": "water", "model": "cpcmx"},
-            },
-        },
+        folder=folder,
     )
 
     print(f"View workflow privately at: https://labs.rowansci.com/calculation/{sp_workflow.uuid}")
@@ -42,6 +35,6 @@ def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, n
 
 
 E1 = compute_energy_with_solvent_correction(
-    Molecule.from_smiles("CC(=O)Oc1ccccc1C(=O)O"), Method.OMOL25_CONSERVING_S, "aspirin"
+    rowan.Molecule.from_smiles("CC(=O)Oc1ccccc1C(=O)O"), rowan.Method.OMOL25_CONSERVING_S, "aspirin"
 )
 print(E1)

{rowan_python-3.0.0 → rowan_python-3.0.3}/examples/bde.py

@@ -20,8 +20,6 @@ Available modes:
 See documentation at: https://docs.rowansci.com/science/workflows/bond-dissociation-energy
 """
 
-from stjames import Molecule
-
 import rowan
 
 # Set your API key or use the ROWAN_API_KEY environment variable
@@ -29,7 +27,7 @@ import rowan
 folder = rowan.get_folder("examples")
 
 workflow = rowan.submit_bde_workflow(
-    initial_molecule=Molecule.from_smiles("CCCC"),
+    initial_molecule=rowan.Molecule.from_smiles("CCCC"),
     mode="rapid",
     all_CH=True,
     name="Butane BDE",

{rowan_python-3.0.0 → rowan_python-3.0.3}/examples/conformer_dependent_redox.py

@@ -1,6 +1,3 @@
-import stjames
-from stjames import Molecule
-
 import rowan
 
 # Set your API key or use the ROWAN_API_KEY environment variable
@@ -8,7 +5,7 @@ import rowan
 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"),
+    initial_molecule=rowan.Molecule.from_smiles("CC(C)Cc1ccc(C(=O)c2ccc(O)cc2)cc1"),
     folder=folder,
 )
 print(f"View workflow privately at: https://labs.rowansci.com/workflow/{workflow.uuid}")
@@ -19,12 +16,12 @@ redox_potential_workflows = []
 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)
+    rowan_molecule = rowan.Molecule.model_validate(molecule)
     redox_potential_workflows.append(
         rowan.submit_redox_potential_workflow(
-            stjames_molecule,
+            rowan_molecule,
             reduction=True,
-            oxidization=True,
+            oxidation=True,
             folder=folder,
         )
     )

{rowan_python-3.0.0 → rowan_python-3.0.3}/examples/conformers.py

@@ -17,8 +17,6 @@ Rapid is recommended for most work.
 See documentation at: https://docs.rowansci.com/science/workflows/conformers
 """
 
-from stjames import Molecule
-
 import rowan
 
 # Set your API key or use the ROWAN_API_KEY environment variable
@@ -26,7 +24,7 @@ import rowan
 folder = rowan.get_folder("examples")
 
 workflow = rowan.submit_conformer_search_workflow(
-    initial_molecule=Molecule.from_smiles("CCOCC"),
+    initial_molecule=rowan.Molecule.from_smiles("CCOCC"),
     folder=folder,
 )
 

{rowan_python-3.0.0 → rowan_python-3.0.3}/examples/docking_screen.py

@@ -1,5 +1,3 @@
-import stjames
-
 import rowan
 
 # Set your API key or use the ROWAN_API_KEY environment variable
@@ -30,9 +28,10 @@ for ligand in ligands:
     workflow = rowan.submit_docking_workflow(
         protein.uuid,
         pocket=[[103.55, 100.59, 82.99], [27.76, 32.67, 48.79]],
-        initial_molecule=stjames.Molecule.from_smiles(ligand),
+        initial_molecule=rowan.Molecule.from_smiles(ligand),
         name=f"Docking {ligand}",
         folder=folder,
+        do_pose_refinement=False,
     )
     workflows.append(workflow)