rowan-python 3.1.4__tar.gz → 3.1.6__tar.gz

rowan_python-3.1.6/.agents/plugins/marketplace.json

@@ -0,0 +1,20 @@
+{
+  "name": "rowan",
+  "interface": {
+    "displayName": "Rowan"
+  },
+  "plugins": [
+    {
+      "name": "computational-chemistry-and-biology",
+      "source": {
+        "source": "local",
+        "path": "./"
+      },
+      "policy": {
+        "installation": "AVAILABLE",
+        "authentication": "ON_INSTALL"
+      },
+      "category": "Science"
+    }
+  ]
+}

rowan_python-3.1.6/.claude-plugin/marketplace.json

@@ -0,0 +1,17 @@
+{
+  "name": "rowan",
+  "owner": {
+    "name": "Rowan",
+    "email": "eli@rowansci.com"
+  },
+  "description": "Claude Code plugins for the Rowan computational chemistry platform",
+  "plugins": [
+    {
+      "name": "computational-chemistry-and-biology",
+      "source": "./skills/computational-chemistry-and-biology",
+      "description": "Run computational chemistry and structural biology calculations on the Rowan platform via the rowan Python package",
+      "skills": ["./"],
+      "strict": false
+    }
+  ]
+}

rowan_python-3.1.6/.codex-plugin/plugin.json

@@ -0,0 +1,37 @@
+{
+  "name": "computational-chemistry-and-biology",
+  "version": "0.0.1",
+  "description": "Run computational chemistry and structural biology calculations on the Rowan platform via the rowan-python package",
+  "skills": "./skills/",
+  "author": {
+    "name": "Rowan",
+    "email": "eli@rowansci.com",
+    "url": "https://rowansci.com"
+  },
+  "homepage": "https://rowansci.com",
+  "repository": "https://github.com/rowansci/rowan-python",
+  "license": "MIT",
+  "keywords": [
+    "computational chemistry",
+    "structural biology",
+    "molecular simulation",
+    "Rowan"
+  ],
+  "interface": {
+    "displayName": "Rowan Computational Chemistry",
+    "shortDescription": "Run computational chemistry and structural biology workflows with Rowan.",
+    "longDescription": "Use Rowan to choose and run molecular and protein workflows, including quantum chemistry, docking, molecular dynamics, protein structure prediction, and cheminformatics. The bundled skill provides workflow selection guidance, safe defaults, result retrieval patterns, and links to detailed workflow references.",
+    "developerName": "Rowan",
+    "category": "Science",
+    "capabilities": [
+      "Read",
+      "Compute"
+    ],
+    "websiteURL": "https://rowansci.com",
+    "defaultPrompt": [
+      "Run a Rowan calculation for this molecule.",
+      "Help me choose a Rowan workflow for my chemistry question.",
+      "Analyze this protein-ligand system with Rowan."
+    ]
+  }
+}

{rowan_python-3.1.4 → rowan_python-3.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.4
+Version: 3.1.6
 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>=0.0.228
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.1.4 → rowan_python-3.1.6}/docs/index.md

@@ -55,6 +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

rowan_python-3.1.6/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-3.1.6/examples/covalent_docking.py

@@ -0,0 +1,48 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+# TG2, catalytic Cys277, acrylamide inhibitor (k_inact record P21980-00).
+tg2_inhibitor = rowan.Molecule.from_smiles(
+    "C=CC(=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")
+# Chain A is TG2; chain X is a small covalently-bound peptide in the crystal, not
+# part of the protein. `protein.chains` order isn't guaranteed, so select by name.
+protein = protein.select_chains(["A"])
+protein.prepare()
+
+# Pocket is [[center_x, center_y, center_z], [size_x, size_y, size_z]] in Å.
+center = [-1.079, -3.081, 18.122]
+size = [22.22, 14.08, 21.74]
+
+# 0-based, all-atom (including hydrogens) indices of the reacting atoms.
+# Ligand: acrylamide's terminal =CH2 carbon. Protein: Cys277 SG, found by downloading
+# the prepared structure and locating that atom in file order.
+covalent_ligand_atom_index = 0
+covalent_protein_atom_index = 4293
+gnina_settings = rowan.GninaSettings(
+    scoring_function="gnina_cnn",
+    covalent_ligand_atom_index=covalent_ligand_atom_index,
+    covalent_protein_atom_index=covalent_protein_atom_index,
+)
+
+workflow = rowan.submit_docking_workflow(
+    protein,
+    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}  posebusters_valid={score.posebusters_valid}")

rowan_python-3.1.6/examples/covalent_inhibitor_scan.py

@@ -0,0 +1,35 @@
+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.
+protein = rowan.create_protein_from_pdb_id("4YHF")
+protein = protein.select_chains(["A"])
+protein.prepare(remove_heterogens=False)
+
+# 0-based indices of Cys481 SG and the ligand's C1 atom, found by downloading the
+# prepared PDB (protein.download_pdb_file()).
+protein_reactive_atom_index = 1571
+ligand_reactive_atom_index = 4492
+
+workflow = rowan.submit_covalent_inhibitor_scan_workflow(
+    protein=protein,
+    protein_reactive_atom_index=protein_reactive_atom_index,
+    ligand_reactive_atom_index=ligand_reactive_atom_index,
+    settings=rowan.CovalentInhibitorScanSettings(scan_num=4),
+    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, energy in result.get_energies():
+    print(f"  distance={distance:.3f} Å  energy={energy}")

{rowan_python-3.1.4 → rowan_python-3.1.6}/examples/double_ended_ts_search.py

@@ -22,22 +22,20 @@ H 0 0 2.3
 C 0 0 0
 N 0 0 1.2""",
 )
-fsm_settings = rowan.FSMSettings(
-    optimization_coordinates=rowan.FSMOptimizationCoordinates.CARTESIAN,
-    interpolation_method=rowan.FSMInterpolation.REDUNDANT_INTERNAL_COORDINATES,
-    min_num_nodes=7,
-    num_interpolation_points=5,
-    max_optimizer_iterations=3,
-    max_line_search_steps=2,
-    max_displacement=0.1,
-)
 
+# Freezing string method (FSM)
+search_settings = rowan.StringMethodSettings(
+    freeze=True,
+    interpolation_method=rowan.Interpolation.GEODESIC,
+)
+# Use `freeze=False` for the growing string method (GSM)
+# Use rowan.NEBSettings for nudged elastic band (NEB)
 
 workflow = rowan.submit_double_ended_ts_search_workflow(
     reactant=HCN,
     product=CNH,
     calculation_settings=rowan.Settings(method=rowan.Method.GFN2_XTB),
-    search_settings=fsm_settings,
+    search_settings=search_settings,
     optimize_inputs=True,
     optimize_ts=True,
     name="H-C≡N Isomerization",

rowan_python-3.1.6/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")