rowan-python 3.0.7__tar.gz → 3.0.9__tar.gz

{rowan_python-3.0.7 → rowan_python-3.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.7
+Version: 3.0.9
 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>=0.0.174
+Requires-Dist: stjames>=0.0.183
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/PROTAC_solubility.py

@@ -44,6 +44,7 @@ for id, smiles in PROTACs.items():
         )
     )
 
+print(f"View folder privately at: https://labs.rowansci.com/folder/{folder.uuid}")
 
 workflow_results = [w.result() for w in workflows]
 

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/aqueous_solubility.py

@@ -15,7 +15,7 @@ workflow = rowan.submit_solubility_workflow(
     folder=folder,
 )
 
-print(f"View workflow privately at: https://labs.rowansci.com/workflow/{workflow.uuid}")
+print(f"View workflow privately at: https://labs.rowansci.com/solubility/{workflow.uuid}")
 result = workflow.result()
 print(result)
 # e.g. <SolubilityResult solvents=['water']>

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/boltz_paired_msa.py

@@ -19,6 +19,8 @@ msa_workflow = rowan.submit_msa_workflow(
     folder=folder,
 )
 
+print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.uuid}")
+
 msa_result = msa_workflow.result()
 
 msa_result.download_files("boltz", path=msa_directory)

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/boltz_single_msa.py

@@ -18,6 +18,8 @@ msa_workflow = rowan.submit_msa_workflow(
     folder=folder,
 )
 
+print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.uuid}")
+
 msa_result = msa_workflow.result()
 
 msa_result.download_files("boltz", path=msa_directory)

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/chai_paired_msa.py

@@ -30,6 +30,8 @@ msa_workflow = rowan.submit_msa_workflow(
     folder=folder,
 )
 
+print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.uuid}")
+
 msa_result = msa_workflow.result()
 
 msa_result.download_files("chai", path=msa_directory)

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/chai_single_msa.py

@@ -27,6 +27,8 @@ msa_workflow = rowan.submit_msa_workflow(
     folder=folder,
 )
 
+print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.uuid}")
+
 msa_result = msa_workflow.result()
 
 msa_result.download_files("chai", path=msa_directory)

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/cofolding_screen.py

@@ -29,6 +29,8 @@ for ligand in ligands:
     )
     workflows.append(workflow)
 
+print(f"View folder privately at: https://labs.rowansci.com/folder/{folder.uuid}")
+
 workflow_results = [(w, w.result()) for w in workflows]
 
 for workflow, result in workflow_results:

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/colabfold_paired_msa.py

@@ -19,6 +19,8 @@ msa_workflow = rowan.submit_msa_workflow(
     folder=folder,
 )
 
+print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.uuid}")
+
 msa_result = msa_workflow.result()
 
 msa_result.download_files("colabfold", path=msa_directory)

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/colabfold_single_msa.py

@@ -18,6 +18,8 @@ msa_workflow = rowan.submit_msa_workflow(
     folder=folder,
 )
 
+print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.uuid}")
+
 msa_result = msa_workflow.result()
 
 msa_result.download_files("colabfold", path=msa_directory)

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/conformer_dependent_redox.py

@@ -8,7 +8,7 @@ workflow = rowan.submit_conformer_search_workflow(
     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}")
+print(f"View folder privately at: https://labs.rowansci.com/folder/{folder.uuid}")
 csearch_result = workflow.result()
 
 redox_potential_workflows = []

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/conformers.py

@@ -28,7 +28,7 @@ workflow = rowan.submit_conformer_search_workflow(
     folder=folder,
 )
 
-print(f"View workflow privately at: https://labs.rowansci.com/workflow/{workflow.uuid}")
+print(f"View workflow privately at: https://labs.rowansci.com/conformer-search/{workflow.uuid}")
 
 result = workflow.result()
 print(result)

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/docking_screen.py

@@ -35,6 +35,7 @@ for ligand in ligands:
     )
     workflows.append(workflow)
 
+print(f"View folder privately at: https://labs.rowansci.com/folder/{folder.uuid}")
 
 workflow_results = [(w, w.result()) for w in workflows]
 

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/electronic_properties.py

@@ -16,17 +16,17 @@ import rowan
 folder = rowan.get_folder("examples")
 
 workflow = rowan.submit_electronic_properties_workflow(
-    initial_molecule=rowan.Molecule.from_smiles("c1ccccc1"),  # benzene
+    initial_molecule=rowan.Molecule.from_smiles("C=O"),  # formaldehyde
     method="b97_3c",  # default: lightweight DFT
     compute_density_cube=True,
     compute_electrostatic_potential_cube=True,
     compute_num_occupied_orbitals=3,  # HOMO, HOMO-1, HOMO-2
     compute_num_virtual_orbitals=3,  # LUMO, LUMO+1, LUMO+2
-    name="Benzene electronic properties",
+    name="Formaldehyde electronic properties",
     folder=folder,
 )
 
 print(f"View workflow privately at: https://labs.rowansci.com/orbitals/{workflow.uuid}")
 result = workflow.result()
 print(result)
-# e.g. <ElectronicPropertiesResult dipole=1.85 D>
+# e.g. <ElectronicPropertiesResult dipole=(0.0, 0.0, -2.33) D>

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/interaction_energy_decomposition.py

@@ -56,7 +56,7 @@ workflow = rowan.submit_interaction_energy_decomposition_workflow(
     name="Naphthalene-Guanine SAPT0",
 )
 
-print(f"View at: https://labs.rowansci.com/workflow/{workflow.uuid}")
+print(f"View at: https://labs.rowansci.com/interaction-energy-decomposition/{workflow.uuid}")
 
 result = workflow.result()
 print(result)

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/membrane_permeability.py

@@ -21,9 +21,10 @@ pypermm_workflow = rowan.submit_membrane_permeability_workflow(
     folder=folder,
 )
 
+print(f"View folder privately at: https://labs.rowansci.com/folder/{folder.uuid}")
 print("View these workflows privately:")
 print(f"\thttps://labs.rowansci.com/membrane-permeability/{gnn_mtl_workflow.uuid}")
-print(f"\thttps://labs.rowansci.com/mambrane-permeability/{pypermm_workflow.uuid}")
+print(f"\thttps://labs.rowansci.com/membrane-permeability/{pypermm_workflow.uuid}")
 gnn_mtl_result = gnn_mtl_workflow.result()
 pypermm_result = pypermm_workflow.result()
 

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/multistage_optimization.py

@@ -1,11 +1,8 @@
 """
 Perform a multistage geometry optimization using the Rowan API.
 
-Available modes:
-- "reckless": Fastest, least accurate
-- "rapid": Good balance of speed and accuracy (default)
-- "careful": More accurate, slower
-- "meticulous": Most accurate, slowest
+Each entry of `optimization_settings` runs in order; `singlepoint_settings`
+runs last on the final geometry.
 
 See documentation at: https://docs.rowansci.com/science/workflows/multistage-optimization
 """
@@ -16,9 +13,17 @@ import rowan
 # rowan.api_key = "rowan-sk..."
 folder = rowan.get_folder("examples")
 
+# r2scan_3c//gfn2_xtb//gfn_ff stack: GFN-FF pre-opt, GFN2-xTB opt, R²SCAN-3c singlepoint.
+optimization_settings = [
+    rowan.Settings(method=rowan.Method.GFN_FF, tasks=[rowan.Task.OPTIMIZE]),
+    rowan.Settings(method=rowan.Method.GFN2_XTB, tasks=[rowan.Task.OPTIMIZE]),
+]
+singlepoint_settings = rowan.Settings(method=rowan.Method.R2SCAN3C, tasks=[rowan.Task.ENERGY])
+
 workflow = rowan.submit_multistage_optimization_workflow(
     initial_molecule=rowan.Molecule.from_smiles("C1CCC1"),  # cyclobutane
-    mode="rapid",
+    optimization_settings=optimization_settings,
+    singlepoint_settings=singlepoint_settings,
     name="Multistage optimization cyclobutane",
     folder=folder,
 )

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/periodic_dft.py

@@ -15,7 +15,7 @@ import rowan
 
 # Set your API key or use the ROWAN_API_KEY environment variable
 # rowan.api_key = "rowan-sk..."
-folder = rowan.get_folder("examples/periodic_dft")
+folder = rowan.get_folder("examples")
 
 # Build bulk Al FCC primitive cell.
 # Lattice vectors in Angstrom; Al has 13 electrons so multiplicity=2.

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/phenol_pka.py

@@ -27,6 +27,7 @@ for name, smiles in phenols_to_compute.items():
         )
     )
 
+print(f"View folder privately at: https://labs.rowansci.com/folder/{folder.uuid}")
 
 workflow_results = [w.result() for w in workflows]
 

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/pka.py

@@ -27,6 +27,7 @@ workflow = rowan.submit_pka_workflow(
     name="Phenol pKa (aimnet2_wagen2024)",
     folder=folder,
 )
+print(f"View folder privately at: https://labs.rowansci.com/folder/{folder.uuid}")
 print(f"View at: https://labs.rowansci.com/pka/{workflow.uuid}")
 result = workflow.result()
 print(result)

rowan_python-3.0.9/examples/project_scoped_api_key.py

@@ -0,0 +1,31 @@
+"""Example: mint per-project API keys for several projects at once.
+
+A project-scoped key can only access the project it was created for —
+useful for handing limited access to collaborators, CI jobs, or analyses
+without exposing your full account.
+
+The plaintext key is only returned once at creation time — store it
+immediately. The caller must currently authenticate with an unscoped key
+that has ``can_manage_api_keys`` permission.
+"""
+
+import rowan
+
+# rowan.api_key = "rowan-sk..."
+
+campaigns = ["CDK2 campaign", "BTK campaign", "EGFR campaign"]
+
+results = []
+for campaign in campaigns:
+    project = rowan.create_project(name=campaign)
+    created = rowan.create_api_key(
+        name=f"{campaign.lower().replace(' ', '-')}-key",
+        scope="read_write",
+        valid_days=90,
+        scoped_project_uuid=project.uuid,
+    )
+    results.append((project.name, created.api_key.name, created.key))
+
+print("Plaintext keys (save these now — only returned once):")
+for project_name, key_name, key in results:
+    print(f"  {project_name} | {key_name} | {key}")

rowan_python-3.0.9/examples/protein_cofolding_with_constraints.py

@@ -0,0 +1,79 @@
+"""Cofolding with both pocket and contact constraints.
+
+Example: bovine trypsin + benzamidine, a textbook S1-pocket binder.
+Trypsin's S1 specificity pocket is anchored by Asp189 at its base, and
+benzamidine binds via a bidentate salt bridge between its amidinium group
+and the Asp189 carboxylate.
+
+We encode this prior knowledge with two constraints:
+
+1. PocketConstraint - the ligand must sit inside the S1 pocket, near the
+   catalytic triad (His57, Asp102, Ser195) and Asp189.
+2. ContactConstraint - the amidine carbon of benzamidine must come within
+   ~4 A of Asp189 (the salt bridge interaction).
+
+The four residues are located by their conserved chymotrypsin-family motifs
+in the sequence below: AAHCY (His), NNDIML (Asp triad), SDSSCK (S1 Asp
+before Cys191), GDSGGP (Ser).
+
+ConstraintTargets are constructed explicitly with (input_type, input_index,
+token_index) so the addressing scheme is unambiguous: input_index selects which
+protein / ligand in the input lists, and token_index is the residue index for
+proteins and the atom index for ligands. The same three fields appear in the
+cofolding submit form on labs.rowansci.com.
+"""
+
+import rowan
+
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+TRYPSIN = (
+    "IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNN"
+    "DIMLIKLKSAAYTSYDVPLGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGD"
+    "SGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN"
+)
+BENZAMIDINE = "NC(=N)c1ccccc1"
+
+# Targets for the four pocket-defining residues on the trypsin chain (protein 0).
+his57 = rowan.ConstraintTarget(input_type="protein", input_index=0, token_index=39)  # AAHCY
+asp102 = rowan.ConstraintTarget(input_type="protein", input_index=0, token_index=83)  # NNDIML
+asp189 = rowan.ConstraintTarget(input_type="protein", input_index=0, token_index=134)  # SDSSCK
+ser195 = rowan.ConstraintTarget(input_type="protein", input_index=0, token_index=166)  # GDSGGP
+
+# Target for the central amidine carbon of benzamidine (atom 1 in NC(=N)c1ccccc1).
+benzamidine_amidine_c = rowan.ConstraintTarget(input_type="ligand", input_index=0, token_index=1)
+
+pocket = rowan.PocketConstraint(
+    input_type="ligand",  # the binder being placed into the pocket
+    input_index=0,  # benzamidine is the first (and only) ligand
+    contacts=[his57, asp102, asp189, ser195],
+    max_distance=6.0,
+)
+
+salt_bridge = rowan.ContactConstraint(
+    token_1=benzamidine_amidine_c,
+    token_2=asp189,
+    max_distance=4.0,
+    force=True,
+)
+
+workflow = rowan.submit_protein_cofolding_workflow(
+    initial_protein_sequences=[TRYPSIN],
+    initial_smiles_list=[BENZAMIDINE],
+    ligand_binding_affinity_index=0,
+    pocket_constraints=[pocket],
+    contact_constraints=[salt_bridge],
+    use_potentials=True,  # required for force=True
+    num_samples=3,
+    name="Trypsin + Benzamidine (constrained)",
+    do_pose_refinement=True,
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/protein-cofolding/{workflow.uuid}")
+result = workflow.result()
+print(result)
+for i, pred in enumerate(result.predictions):
+    iptm = pred.scores.iptm if pred.scores else None
+    print(f"  sample {i}: iptm={iptm}")

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/solvent_dependent_conformers.py

@@ -13,7 +13,7 @@ workflow = rowan.submit_solvent_dependent_conformers_workflow(
     name="Alanine Dipeptide Solvent-Dependent Conformers",
 )
 
-print(f"View at: https://labs.rowansci.com/workflow/{workflow.uuid}")
+print(f"View at: https://labs.rowansci.com/solvent-dependent-conformers/{workflow.uuid}")
 
 result = workflow.result()
 print(result)

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/spin_states.py

@@ -2,13 +2,8 @@
 Calculate spin state energies using the Rowan API.
 
 This workflow predicts the lowest energy spin state by running multistage
-optimizations at different spin multiplicities.
-
-Available modes:
-- "reckless": Fastest, least accurate
-- "rapid": Good balance of speed and accuracy (default)
-- "careful": More accurate, slower
-- "meticulous": Most accurate, slowest
+optimizations at different spin multiplicities. The same
+`MultiStageOptSettings` is applied to each multiplicity.
 
 See documentation at: https://docs.rowansci.com/science/workflows/spin-states
 """
@@ -19,11 +14,19 @@ import rowan
 # rowan.api_key = "rowan-sk..."
 folder = rowan.get_folder("examples")
 
+# r2scan_3c//gfn2_xtb stack: GFN2-xTB opt, R²SCAN-3c singlepoint.
+mso_settings = rowan.MultiStageOptSettings(
+    optimization_settings=[
+        rowan.Settings(method=rowan.Method.GFN2_XTB, tasks=[rowan.Task.OPTIMIZE]),
+    ],
+    singlepoint_settings=rowan.Settings(method=rowan.Method.R2SCAN3C, tasks=[rowan.Task.ENERGY]),
+)
+
 # Methylene (CH2) - classic spin states example, triplet is ground state
 workflow = rowan.submit_spin_states_workflow(
     initial_molecule=rowan.Molecule.from_smiles("[CH2]"),
     states=[1, 3],  # singlet vs triplet
-    mode="rapid",
+    multistage_opt_settings=mso_settings,
     name="Methylene spin states",
     folder=folder,
 )

{rowan_python-3.0.7 → rowan_python-3.0.9}/examples/strain.py

@@ -8,7 +8,7 @@ folder = rowan.get_folder("examples")
 # here we'll investigate the strain of the autogenerated hexane conformer
 workflow = rowan.submit_strain_workflow(
     initial_molecule=rowan.Molecule.from_smiles("CCCCCC"),
-    name="test autogen hexane strain",
+    name="Hexane Strain",
     folder=folder,
 )