rowan-python 3.1.13__tar.gz → 3.1.15__tar.gz

{rowan_python-3.1.13 → rowan_python-3.1.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: rowan-python
-Version: 3.1.13
+Version: 3.1.15
 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<0.0.238,>=0.0.237
+Requires-Dist: stjames>=0.0.261
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.1.13 → rowan_python-3.1.15}/docs/workflows/analogue-docking.md

@@ -1,5 +1,8 @@
 # Analogue Docking
 
+Analogue docking generates at most 20 conformers per analogue by default. Override
+`num_conformers_per_analogue` when a broader search is needed.
+
 ::: rowan.workflows.analogue_docking
     handler: python
     options:

{rowan_python-3.1.13 → rowan_python-3.1.15}/docs/workflows/batch-docking.md

@@ -1,5 +1,9 @@
 # Batch Docking
 
+Use `num_poses_to_save` to retain the best pose for that many top-scoring compounds, and set
+`run_mmgbsa=True` to refine those saved poses. `result.refined_scores` maps every input SMILES
+to a `DockingScore` for a retained compound or `None` otherwise.
+
 ::: rowan.workflows.batch_docking
     handler: python
     options:

{rowan_python-3.1.13 → rowan_python-3.1.15}/docs/workflows/covalent-inhibitor-scan.md

@@ -1,5 +1,9 @@
 # Covalent Inhibitor Scan
 
+!!! warning "Beta"
+
+    This workflow is in beta. Its interface and behavior may change.
+
 ::: rowan.workflows.covalent_inhibitor_scan
     handler: python
     options:

rowan_python-3.1.15/docs/workflows/docking.md

@@ -0,0 +1,60 @@
+# Docking
+
+The docking workflow supports Vina docking and both noncovalent and covalent gnina docking.
+Passing `GninaSettings` selects gnina; it does not by itself enable covalent docking.
+
+## Induced-fit docking
+
+Pass `rowan.InducedFitSettings()` to `induced_fit_settings` when nearby receptor side chains may
+need to relax around the ligand. Induced fit requires Vina or QVina2 and adds substantial work
+beyond rigid docking.
+
+Results contain both rigid and induced-receptor poses ranked by `induced_fit_score`. Use
+`get_induced_receptor()` or `get_induced_receptors()` to retrieve the relaxed receptors associated
+with induced poses. See `examples/induced_fit_docking.py` for a complete example.
+
+## Covalent docking
+
+Set both covalent atom indices on `GninaSettings` to form a bond between a known ligand atom and
+protein atom. Covalent gnina docking requires `scoring_function="vina"`.
+
+Prepare the protein first, then resolve the reactive protein atom from the prepared structure.
+Protein preparation can change atom ordering and residue numbering.
+
+Supply the ligand in its expected post-reaction, covalently bound topology; gnina does not infer the
+reaction. For a Michael acceptor `C=CC(=O)NR`, use the hydrogen-capped product `CCC(=O)NR` and
+select the terminal β-carbon as the covalent ligand atom.
+
+```python
+prepared_protein = preparation_workflow.result().get_prepared_protein()
+reactive_protein_atom_index = prepared_protein.get_atom_index(
+    chain="A", residue=reactive_residue, atom="SG"
+)
+settings = rowan.GninaSettings(
+    scoring_function="vina",
+    covalent_ligand_atom_index=reactive_ligand_atom_index,
+    covalent_protein_atom_index=reactive_protein_atom_index,
+)
+workflow = rowan.submit_docking_workflow(
+    prepared_protein.uuid,
+    pocket=[center, size],
+    initial_molecule=ligand,
+    docking_settings=settings,
+)
+```
+
+Both indices are zero-based all-atom indices, including hydrogens. See
+`examples/covalent_docking.py` for a complete TG2 example.
+
+PoseBusters validation is skipped for covalent poses. Their `posebusters_valid` value is `None`,
+meaning not evaluated rather than failed; do not use it to reject covalent poses.
+
+::: 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: ["!^_"]

{rowan_python-3.1.13 → rowan_python-3.1.15}/docs/workflows/logp.md

@@ -1,5 +1,8 @@
 # LogP
 
+Available methods include the default Chemprop model, Crippen, and the higher-cost
+`method="cosmors"` conformer-ensemble calculation.
+
 ::: rowan.workflows.logp
     handler: python
     options:

{rowan_python-3.1.13 → rowan_python-3.1.15}/docs/workflows/macropka.md

@@ -1,5 +1,7 @@
 # MacropKa
 
+Choose `method="starling"` (default) or `method="starling_ii"` when submitting the workflow.
+
 ::: rowan.workflows.macropka
     handler: python
     options:

{rowan_python-3.1.13 → rowan_python-3.1.15}/docs/workflows/nmr.md

@@ -1,5 +1,8 @@
 # NMR
 
+Completed results expose both chemical shifts and typed J-coupling predictions through
+`result.predicted_couplings`.
+
 ::: rowan.workflows.nmr
     handler: python
     options:

{rowan_python-3.1.13 → rowan_python-3.1.15}/docs/workflows/pose-analysis-md.md

@@ -1,5 +1,8 @@
 # Pose Analysis MD
 
+Pose-analysis MD accepts selectable small-molecule, protein, and water force fields. Mean and
+medoid structures are available through the same result helpers as protein MD.
+
 ::: rowan.workflows.pose_analysis_md
     handler: python
     options:

rowan_python-3.1.15/docs/workflows/protein-md.md

@@ -0,0 +1,19 @@
+# Protein MD
+
+Protein MD accepts selectable small-molecule, protein, and water force fields. Results expose
+binder RMSD, MM/GBSA scores, mean-structure UUIDs, and medoid frame indices per trajectory. Use
+`get_mean_structure`, `download_mean_structure`, or `download_medoid_structure` to retrieve
+representative structures.
+
+For protein structures containing non-polymer ligands, pass their SMILES through
+`small_molecules` and select the residues to analyze through `rowan.Binder`.
+
+::: 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: ["!^_"]

{rowan_python-3.1.13 → rowan_python-3.1.15}/docs/workflows/solvent-dependent-conformers.md

@@ -1,5 +1,8 @@
 # Solvent-Dependent Conformers
 
+The default final correction is `"CPCMX"`. Pass `final_correction="COSMO_RS"` for the
+higher-cost COSMO-RS alternative.
+
 ::: rowan.workflows.solvent_dependent_conformers
     handler: python
     options:

{rowan_python-3.1.13 → rowan_python-3.1.15}/docs/workflows/tautomer-search.md

@@ -1,5 +1,8 @@
 # Tautomer Search
 
+Pass `final_correction="COSMO_RS"` to enable the optional higher-cost COSMO-RS correction.
+The default is no final correction.
+
 ::: rowan.workflows.tautomer_search
     handler: python
     options:

{rowan_python-3.1.13 → rowan_python-3.1.15}/examples/binding_affinity.py

@@ -11,6 +11,7 @@ protein = rowan.upload_protein("TYK2", data_dir / "tyk2_structure.pdb")
 all_ligands = rowan.load_named_ligands(data_dir / "tyk2_ligands.sdf")
 ligands = dict(list(all_ligands.items())[:3])
 
+# SQM-based scoring (default): binding_affinity in kcal/mol.
 workflow = rowan.submit_binding_affinity_workflow(
     protein=protein.uuid,
     ligand_structures=list(ligands.values()),
@@ -21,4 +22,7 @@ print(f"View at: https://labs.rowansci.com/binding-affinity/{workflow.uuid}")
 
 result = workflow.result()
 for name, score in zip(ligands.keys(), result.scores, strict=False):
-    print(f"{name}: {score.binding_affinity:.2f} kcal/mol (strain: {score.strain})")
+    if score is None:
+        print(f"{name}: scoring failed")
+        continue
+    print(f"{name}: {score.binding_affinity:.2f} kcal/mol")

rowan_python-3.1.15/examples/covalent_docking.py

@@ -0,0 +1,44 @@
+import rowan
+
+folder = rowan.get_folder("examples")
+
+tg2_inhibitor = rowan.Molecule.from_smiles(
+    "CCC(=O)NCCCC[C@H](NC(=O)Cc1ccc(Cl)c(Cl)c1)C(=O)N1CCN(C(=O)c2cccc3ccccc23)CC1"
+)
+
+protein = rowan.create_protein_from_pdb_id("2Q3Z")
+protein = protein.select_chains(["A"])
+preparation_workflow = rowan.submit_protein_preparation_workflow(
+    protein=protein.uuid,
+    name="Prepare TG2",
+    folder=folder,
+)
+protein = preparation_workflow.result().get_prepared_protein()
+
+center = [-1.079, -3.081, 18.122]
+size = [22.22, 14.08, 21.74]
+
+# Protein preparation renumbers Cys277 to residue 278.
+cys277_sg_index = protein.get_atom_index(chain="A", residue=278, atom="SG")
+gnina_settings = rowan.GninaSettings(
+    scoring_function="vina",
+    covalent_ligand_atom_index=0,
+    covalent_protein_atom_index=cys277_sg_index,
+)
+
+workflow = rowan.submit_docking_workflow(
+    protein.uuid,
+    pocket=[center, size],
+    initial_molecule=tg2_inhibitor,
+    docking_settings=gnina_settings,
+    name="TG2 covalent docking (Cys277, 2Q3Z)",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/docking/{workflow.uuid}")
+
+result = workflow.result()
+print(result)
+
+for i, score in enumerate(result.scores):
+    print(f"  Pose {i}: score={score.score:.3f}")

rowan_python-3.1.15/examples/covalent_inhibitor_scan.py

@@ -0,0 +1,45 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+# BTK, catalytic Cys481. 4YHF already has a covalently-bound small-molecule inhibitor
+# (residue 4C9) linked to Cys481 SG via the ligand's C1 atom.
+ligand_smiles = "CC(C)(C)C[C@@H](C#N)C(=O)N1CCC[C@H](C1)n2nc(c3ccc(Oc4ccccc4)cc3)c5c(N)ncnc25"
+
+protein = rowan.create_protein_from_pdb_id("4YHF")
+protein = protein.select_chains(["A"])
+preparation_workflow = rowan.submit_protein_preparation_workflow(
+    protein=protein.uuid,
+    retain_non_polymer={"4C9": ligand_smiles},
+    name="Prepare BTK inhibitor complex",
+    folder=folder,
+)
+protein = preparation_workflow.result().get_prepared_protein()
+
+# Protein preparation normalizes 4YHF's residue numbering: Cys481 becomes residue 101,
+# while the retained 4C9 ligand remains residue 701.
+protein_reactive_atom_index = protein.get_atom_index(chain="A", residue=101, atom="SG")
+ligand_reactive_atom_index = protein.get_atom_index(
+    chain="A", residue=701, atom="C1", entity_type="non_polymer"
+)
+
+workflow = rowan.submit_covalent_inhibitor_scan_workflow(
+    protein=protein.uuid,
+    protein_reactive_atom_index=protein_reactive_atom_index,
+    ligand_reactive_atom_index=ligand_reactive_atom_index,
+    reactant_smiles=ligand_smiles,
+    name="BTK covalent inhibitor scan (Cys481, 4YHF)",
+    folder=folder,
+)
+
+print(
+    f"View workflow privately at: https://labs.rowansci.com/covalent-inhibitor-scan/{workflow.uuid}"
+)
+
+result = workflow.result()
+print(result)
+
+for distance, free_energy in result.get_energies():
+    print(f"  distance={distance:.3f} Å  free_energy={free_energy} kcal/mol")

rowan_python-3.1.15/examples/induced_fit_docking.py

@@ -0,0 +1,61 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+# Dasatinib — redocked into its own ABL1 co-crystal structure (PDB: 2GQG)
+dasatinib = rowan.Molecule.from_smiles("Cc1nc(Nc2ncc(C(=O)Nc3c(C)cccc3Cl)s2)cc(N2CCN(CCO)CC2)n1")
+
+protein = rowan.create_protein_from_pdb_id("2GQG")
+protein = protein.select_chains(["A"])
+preparation_workflow = rowan.submit_protein_preparation_workflow(
+    protein=protein.uuid,
+    add_missing_method="pdbfixer",
+    name="Prepare ABL1",
+    folder=folder,
+)
+prepared_protein_uuid = preparation_workflow.result().prepared_protein_uuid
+
+# Pocket is [[center_x, center_y, center_z], [size_x, size_y, size_z]] in Å.
+center = [44.59, 79.75, 39.59]
+size = [24.15, 21.33, 19.88]
+
+# Induced-fit docking soft-docks candidate poses, relaxes the receptor around each with
+# restrained local minimization, and redocks into the relaxed receptor. It requires
+# VinaSettings with executable="vina" or "qvina2" (the default is "vina").
+induced_fit_settings = rowan.InducedFitSettings(
+    max_receptors=6,
+    flexible_sidechain_radius=5.0,
+)
+
+workflow = rowan.submit_docking_workflow(
+    prepared_protein_uuid,
+    pocket=[center, size],
+    initial_molecule=dasatinib,
+    induced_fit_settings=induced_fit_settings,
+    name="Dasatinib induced-fit docking",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/docking/{workflow.uuid}")
+
+result = workflow.result()
+print(result)
+
+# With induced-fit docking, poses are ranked by induced_fit_score rather than raw docking score.
+for i, score in enumerate(result.scores):
+    print(
+        f"  Pose {i}: induced_fit_score={score.induced_fit_score:.3f}  "
+        f"score={score.score:.3f}  receptor_strain={score.receptor_strain}"
+    )
+
+# Download the top-scoring complex and best-ranked relaxed receptor as PDBs
+complex_protein = result.get_complex(0)
+complex_protein.download_pdb_file(name="dasatinib_2GQG_induced_complex")
+print("Saved dasatinib_2GQG_induced_complex.pdb")
+
+induced_receptors = result.get_induced_receptors()
+if induced_receptors:
+    induced_receptors[0].download_pdb_file(name="dasatinib_2GQG_induced_receptor")
+    print("Saved dasatinib_2GQG_induced_receptor.pdb")

{rowan_python-3.1.13 → rowan_python-3.1.15}/examples/nmr.py

@@ -15,3 +15,7 @@ result = workflow.result()
 # print hydrogen peaks (atomic number 1 = hydrogen)
 for peak in result.predicted_peaks[1]:
     print(peak)
+
+# print predicted scalar J-couplings
+for coupling in result.predicted_couplings:
+    print(coupling)

{rowan_python-3.1.13 → rowan_python-3.1.15}/examples/pose_analysis_md.py

@@ -45,5 +45,9 @@ print(
 )
 md_result = md_workflow.result()
 
-# print ligand RMSD by frame
-print(md_result.trajectories[0].ligand_rmsd)
+trajectory = md_result.trajectories[0]
+print(f"Ligand RMSD: {trajectory.ligand_rmsd}")
+print(f"Protein RMSD: {trajectory.protein_rmsd}")
+print(f"Protein RMSF: {trajectory.rmsf}")
+print(f"Potential energy: {trajectory.potential_energy} Hartree")
+print(f"MM/GBSA scores: {trajectory.mmgbsa_scores} kcal/mol")

rowan_python-3.1.15/examples/protein_cofolding_modified_inputs.py

@@ -0,0 +1,44 @@
+"""Cofolding with modified polymers and a covalent bond constraint."""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable.
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+protein = rowan.ProteinSequence(
+    sequence="ASA",
+    modifications=[rowan.ResidueModification(position=1, ccd="SEP")],
+)
+dna = rowan.DNASequence(
+    sequence="AC",
+    modifications=[rowan.NucleotideModification(position=1, ccd="5MC")],
+)
+rna = rowan.RNASequence(
+    sequence="AU",
+    modifications=[rowan.NucleotideModification(position=1, ccd="PSU")],
+)
+
+protein_atom = rowan.ConstraintTarget(
+    input_type="protein", input_index=0, token_index=1, atom_name="OG"
+)
+ligand_atom = rowan.ConstraintTarget(input_type="ligand", input_index=0, token_index=0)
+covalent_bond = rowan.BondConstraint(atom_1=protein_atom, atom_2=ligand_atom)
+
+workflow = rowan.submit_protein_cofolding_workflow(
+    initial_protein_sequences=[protein],
+    initial_dna_sequences=[dna],
+    initial_rna_sequences=[rna],
+    initial_smiles_list=["CBr"],
+    bond_constraints=[covalent_bond],
+    model=rowan.CofoldingModel.BOLTZ_2,
+    num_samples=1,
+    name="Modified polymers with covalent constraint",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/protein-cofolding/{workflow.uuid}")
+result = workflow.result()
+print(result)
+for i, prediction in enumerate(result.predictions):
+    print(f"  sample {i}: scores={prediction.scores}")

{rowan_python-3.1.13 → rowan_python-3.1.15}/examples/protein_md.py

@@ -21,3 +21,7 @@ md_workflow = rowan.submit_protein_md_workflow(
 )
 
 print(f"View MD workflow privately at: https://labs.rowansci.com/protein-md/{md_workflow.uuid}")
+trajectory = md_workflow.result().trajectories[0]
+print(f"Protein RMSD: {trajectory.protein_rmsd}")
+print(f"Protein RMSF: {trajectory.rmsf}")
+print(f"Potential energy: {trajectory.potential_energy} Hartree")

rowan_python-3.1.15/examples/temporary_workflow_sharing.py

@@ -0,0 +1,19 @@
+"""Example: temporarily share a workflow with anyone who has its link."""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable.
+# rowan.api_key = "rowan-sk..."
+
+workflow = rowan.retrieve_workflow("your-workflow-uuid")
+
+# Temporary shares can last for up to 120 minutes. This does not make the workflow
+# permanently public: `workflow.public` remains unchanged.
+workflow = workflow.temporarily_share(duration_minutes=60)
+
+print(f"Share URL: https://labs.rowansci.com/workflow/{workflow.uuid}")
+print(f"Public until: {workflow.public_until}")
+print(f"Temporary share active: {workflow.is_temporarily_public}")
+
+# End access before the expiration time if needed.
+# workflow = workflow.end_temporary_share()