rowan-python 3.1.4__tar.gz → 3.1.5__tar.gz

{rowan_python-3.1.4 → rowan_python-3.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.4
+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-3.1.4 → rowan_python-3.1.5}/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-3.1.5/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-3.1.5/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")