rowan-python 3.1.3__tar.gz → 3.1.5__tar.gz

{rowan_python-3.1.3 → rowan_python-3.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.3
+Version: 3.1.5
 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>=0.0.208
+Requires-Dist: stjames>=0.0.217
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.1.3 → rowan_python-3.1.5}/docs/index.md

@@ -23,6 +23,16 @@
         - batch_submit_workflow
         - batch_poll_status
 
+::: rowan.calculation
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
 ## ADMET
 ::: rowan.workflows.admet
     handler: python
@@ -45,6 +55,17 @@
       group_by_category: true
       filters: ["!^__"]
 
+## Binding Affinity
+::: rowan.workflows.binding_affinity
+    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
@@ -254,6 +275,17 @@
       group_by_category: true
       filters: ["!^__"]
 
+## Pocket Detection
+::: rowan.workflows.pocket_detection
+    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
@@ -397,6 +429,17 @@
       group_by_category: true
       filters: ["!^__"]
 
+## API Keys
+::: rowan.api_keys
+    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

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/batch_docking.py

@@ -13,7 +13,7 @@ ligands = [
 ]
 
 protein = rowan.create_protein_from_pdb_id(
-    "CDK2", "1HCK", project_uuid=rowan.default_project().uuid
+    "1HCK", name="CDK2", project_uuid=rowan.default_project().uuid
 )
 
 protein.prepare()

rowan_python-3.1.5/examples/binding_affinity.py

@@ -0,0 +1,24 @@
+from pathlib import Path
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+data_dir = Path(__file__).parent / "data"
+
+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])
+
+workflow = rowan.submit_binding_affinity_workflow(
+    protein=protein,
+    ligand_structures=list(ligands.values()),
+    name="Binding Affinity — TYK2 ligands",
+    folder=folder,
+)
+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})")

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/boltz_paired_msa.py

@@ -14,7 +14,7 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=["boltz"],
+    output_formats=[rowan.MSAFormat.BOLTZ],
     name="Boltz Paired MSA Example",
     folder=folder,
 )
@@ -23,7 +23,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("boltz", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.BOLTZ, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/boltz_single_msa.py

@@ -13,7 +13,7 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=["boltz"],
+    output_formats=[rowan.MSAFormat.BOLTZ],
     name="Boltz MSA Example",
     folder=folder,
 )
@@ -22,7 +22,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("boltz", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.BOLTZ, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/chai_paired_msa.py

@@ -25,7 +25,7 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=["chai"],
+    output_formats=[rowan.MSAFormat.CHAI],
     name="CHAI Paired MSA Example",
     folder=folder,
 )
@@ -34,7 +34,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("chai", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.CHAI, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/chai_single_msa.py

@@ -22,7 +22,7 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=["chai"],
+    output_formats=[rowan.MSAFormat.CHAI],
     name="CHAI MSA Example",
     folder=folder,
 )
@@ -31,7 +31,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("chai", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.CHAI, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/colabfold_paired_msa.py

@@ -14,7 +14,7 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=["colabfold"],
+    output_formats=[rowan.MSAFormat.COLABFOLD],
     name="Colabfold Paired MSA Example",
     folder=folder,
 )
@@ -23,7 +23,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("colabfold", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.COLABFOLD, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/colabfold_single_msa.py

@@ -13,7 +13,7 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=["colabfold"],
+    output_formats=[rowan.MSAFormat.COLABFOLD],
     name="Colabfold MSA Example",
     folder=folder,
 )
@@ -22,7 +22,7 @@ print(f"View workflow privately at: https://labs.rowansci.com/msa/{msa_workflow.
 
 msa_result = msa_workflow.result()
 
-msa_result.download_files("colabfold", path=msa_directory)
+msa_result.download_files(rowan.MSAFormat.COLABFOLD, path=msa_directory)
 
 tar_path = next(msa_directory.glob("*.tar.gz"))
 with tarfile.open(tar_path, "r") as tar_ref:

rowan_python-3.1.5/examples/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")
+
+# 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")
+if len(protein.chains) > 1:
+    protein = protein.select_chains([protein.chains[0]])
+protein.prepare()
+
+# Pocket is [[center_x, center_y, center_z], [size_x, size_y, size_z]] in Å.
+# For a co-crystal structure, extract these from the bound ligand's position.
+# Use rowan.submit_pocket_detection_workflow() when the binding site is unknown.
+center = [44.59, 79.75, 39.59]
+size = [24.15, 21.33, 19.88]
+workflow = rowan.submit_docking_workflow(
+    protein,
+    pocket=[center, size],
+    initial_molecule=dasatinib,
+    name="dasatinib docking (2GQG redock)",
+    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}  posebusters_valid={score.posebusters_valid}")
+
+# Download the top-scoring protein–ligand complex as a PDB
+complex_protein = result.get_complex(0)
+complex_protein.download_pdb_file("dasatinib_2GQG_complex.pdb")
+print("Saved dasatinib_2GQG_complex.pdb")

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/docking_screen.py

@@ -19,7 +19,7 @@ workflows = []
 results = {}
 
 protein = rowan.create_protein_from_pdb_id(
-    "CDK2", "1HCK", project_uuid=rowan.default_project().uuid
+    "1HCK", name="CDK2", project_uuid=rowan.default_project().uuid
 )
 
 protein.prepare()
@@ -43,11 +43,14 @@ lowest_conformer_energy = 0
 for workflow, result in workflow_results:
     for conformer_uuid in result.conformers:
         energy = rowan.retrieve_calculation_molecules(conformer_uuid)[0]["energy"]
-        lowest_conformer_energy = min(lowest_conformer_energy, energy)
+        if energy is not None:
+            lowest_conformer_energy = min(lowest_conformer_energy, energy)
 
     sorted_scores = sorted(result.scores, key=lambda s: s.score)
     for score in sorted_scores:
         pose_energy = rowan.retrieve_calculation_molecules(score.pose)[0]["energy"]
+        if pose_energy is None:
+            continue
         strain = (pose_energy - lowest_conformer_energy) * HARTREE_TO_KCALMOL
         if score.posebusters_valid and strain < 4:
             results[workflow.name] = score

rowan_python-3.1.5/examples/periodic_dft.py

@@ -0,0 +1,38 @@
+"""Band structure of bulk silicon using periodic DFT (Quantum ESPRESSO)."""
+
+import rowan
+
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+a = 5.431  # Å
+si = rowan.Molecule.from_atoms(
+    atoms=[
+        rowan.Atom(atomic_number=14, position=(0.0, 0.0, 0.0)),
+        rowan.Atom(atomic_number=14, position=(a / 4, a / 4, a / 4)),
+    ],
+    charge=0,
+    multiplicity=1,
+    cell=rowan.PeriodicCell(
+        lattice_vectors=((0.0, a / 2, a / 2), (a / 2, 0.0, a / 2), (a / 2, a / 2, 0.0))
+    ),
+)
+
+workflow = rowan.submit_basic_calculation_workflow(
+    initial_molecule=si,
+    tasks=["band_structure"],
+    method="PBE",
+    basis_set="SSSP_PBE_efficiency",
+    pbc_dft_settings=rowan.PBCDFTSettings(kpoints=(2, 2, 2)),
+    name="Si band structure",
+    folder=folder,
+)
+print(f"https://labs.rowansci.com/calculation/{workflow.uuid}")
+result = workflow.result()
+
+print(f"Symmetry:  space group {result.symmetry}")
+print(f"XRD peaks: {len(result.xrd_peaks)} reflections")
+print(f"Band gap:  {result.band_gap:.4f} Ha")  # ~0.020 Ha (PBE underestimates Si's 1.12 eV gap)
+print(f"VBM:       {result.band_structure.valence_band_maximum:.4f} Ha")
+print(f"CBM:       {result.band_structure.conduction_band_minimum:.4f} Ha")
+print(f"DOS:       {len(result.density_of_states)} points")

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/pocket_detection.py

@@ -5,7 +5,7 @@ import rowan
 folder = rowan.get_folder("examples")
 
 protein = rowan.create_protein_from_pdb_id(
-    "thymidine phosphorylase", "1OTP", project_uuid=rowan.default_project().uuid
+    "1OTP", name="thymidine phosphorylase", project_uuid=rowan.default_project().uuid
 )
 
 protein.prepare()

rowan_python-3.1.5/examples/resubmit_with_perturbations.py

@@ -0,0 +1,39 @@
+"""
+Resubmit a completed workflow with a perturbed structure.
+
+Two strategies: random noise to break symmetry, or displacement along a
+vibrational mode to follow a reaction coordinate or escape a stuck geometry.
+"""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+# --- Option 1: random noise ---
+wf = rowan.retrieve_workflow("your-workflow-uuid")
+mol = wf.result().molecule
+
+perturbed_mol = mol.perturb()
+resubmit = rowan.submit_multistage_optimization_workflow(
+    initial_molecule=perturbed_mol,
+    name="cyclobutane opt - perturbed resubmit",
+    folder=folder,
+)
+print(f"https://labs.rowansci.com/multistage-opt/{resubmit.uuid}")
+
+# --- Option 2: displace along a vibrational mode ---
+# Requires a prior frequency calculation. Imaginary modes have negative frequency.
+ts_wf = rowan.retrieve_workflow("your-ts-freq-workflow-uuid")
+ts_mol = ts_wf.result().molecule
+
+imaginary_mode = next(m for m in ts_mol.vibrational_modes if m.frequency < 0)
+
+displaced_mol = ts_mol.displace_along_mode(mode=imaginary_mode, displacement=0.3)
+resubmit = rowan.submit_multistage_optimization_workflow(
+    initial_molecule=displaced_mol,
+    name="TS resubmit - displaced along imaginary mode",
+    folder=folder,
+)
+print(f"https://labs.rowansci.com/multistage-opt/{resubmit.uuid}")

{rowan_python-3.1.3 → rowan_python-3.1.5}/examples/scan.py

@@ -13,13 +13,13 @@ folder = rowan.get_folder("examples")
 workflow = rowan.submit_scan_workflow(
     initial_molecule=rowan.Molecule.from_smiles("O"),
     name="Water Angle scan",
-    scan_settings={
-        "type": "angle",
-        "atoms": [2, 1, 3],  # 1-indexed
-        "start": 100,
-        "stop": 110,
-        "num": 5,
-    },
+    scan_settings=rowan.ScanSettings(
+        type="angle",
+        atoms=[2, 1, 3],  # 1-indexed
+        start=100,
+        stop=110,
+        num=5,
+    ),
     calculation_method="GFN2-xTB",
     calculation_engine="xtb",
     folder=folder,