rowan-python 2.1.14__tar.gz → 2.1.16__tar.gz

{rowan_python-2.1.14 → rowan_python-2.1.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.14
+Version: 2.1.16
 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>=0.0.144
+Requires-Dist: stjames>=0.0.155
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-2.1.14 → rowan_python-2.1.16}/examples/bde.py

@@ -11,6 +11,12 @@ Calculate the Bond-Dissociation Energy (BDE) of a molecule using the Rowan API.
 
 Rapid is recommended for most work.
 
+Available modes:
+- "reckless": Fastest, least accurate
+- "rapid": Good balance of speed and accuracy (default)
+- "careful": More accurate, slower
+- "meticulous": Most accurate, slowest
+
 See documentation at: https://docs.rowansci.com/science/workflows/bond-dissociation-energy
 """
 
@@ -21,16 +27,13 @@ import rowan
 # Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
 # rowan.api_key = "rowan-sk..."
 
-workflow = rowan.submit_workflow(
+workflow = rowan.submit_bde_workflow(
     initial_molecule=Molecule.from_smiles("CCCC"),
-    workflow_type="bde",
+    mode="rapid",
+    all_CH=True,
     name="Butane BDE",
-    workflow_data={
-        "mode": "reckless",
-        "all_CH": "true",
-    },
 )
 
 print(f"View workflow privately at: https://labs.rowansci.com/bde/{workflow.uuid}")
 workflow.wait_for_result().fetch_latest(in_place=True)
-print(workflow)
+print(workflow.data)

rowan_python-2.1.16/examples/electronic_properties.py

@@ -0,0 +1,31 @@
+"""
+Calculate electronic properties (orbitals, density, ESP) using the Rowan API.
+
+This workflow computes molecular orbitals, electron density, electrostatic potential,
+atom-centered charges, bond orders, and multipole moments.
+
+Note: This workflow does not optimize molecular geometries.
+
+See documentation at: https://docs.rowansci.com/science/workflows/orbitals
+"""
+
+from stjames import Molecule
+
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+workflow = rowan.submit_electronic_properties_workflow(
+    initial_molecule=Molecule.from_smiles("c1ccccc1"),  # benzene
+    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",
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/orbitals/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow.data)

rowan_python-2.1.16/examples/hydrogen_bond_basicity.py

@@ -0,0 +1,28 @@
+"""
+Calculate hydrogen bond acceptor/donor strength using the Rowan API.
+
+This workflow predicts pKBHX values of hydrogen-bond acceptors and pKa values
+of hydrogen-bond donors using neural network potentials and r2SCAN-3c.
+
+See documentation at: https://docs.rowansci.com/science/workflows/hydrogen-bond-basicity
+"""
+
+from stjames import Molecule
+
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+workflow = rowan.submit_hydrogen_bond_basicity_workflow(
+    initial_molecule=Molecule.from_smiles("CC(=O)N(C)C"),  # dimethylacetamide
+    do_csearch=True,  # run conformer search (default)
+    do_optimization=True,  # optimize structures (default)
+    name="DMA hydrogen bond basicity",
+)
+
+print(
+    f"View workflow privately at: https://labs.rowansci.com/hydrogen-bond-basicity/{workflow.uuid}"
+)
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow.data)

rowan_python-2.1.16/examples/multistage_optimization.py

@@ -0,0 +1,28 @@
+"""
+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
+
+See documentation at: https://docs.rowansci.com/science/workflows/multistage-optimization
+"""
+
+from stjames import Molecule
+
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+workflow = rowan.submit_multistage_optimization_workflow(
+    initial_molecule=Molecule.from_smiles("C1CCC1"),  # cyclobutane
+    mode="rapid",
+    name="Multistage optimization cyclobutane",
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/multistage-opt/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow.data)

rowan_python-2.1.16/examples/protein_binder_design.py

@@ -0,0 +1,57 @@
+# ruff: noqa: E501
+"""
+Design protein binders using BoltzGen via the Rowan API.
+
+This workflow generates, filters, and ranks protein designs that bind
+to given protein or small-molecule targets.
+
+Available protocols:
+- "protein-anything": Design proteins to bind proteins (default)
+- "peptide-anything": Design peptides to bind proteins
+- "protein-small_molecule": Design proteins to bind small molecules
+- "nanobody-anything": Design single-domain antibodies
+
+Sequence format for designable regions:
+- "140..180": Design a protein of 140-180 residues
+- "9A9C": Design 9 residues, fix an alanine, design 9 more, fix a cysteine
+- "MKTAYIAKQ": Fixed amino-acid sequence (no designable region)
+
+See documentation at: https://docs.rowansci.com/science/workflows/protein-binder-design
+"""
+
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+# Design a protein to bind brilacidin (antimicrobial small molecule)
+# Based on: https://github.com/HannesStark/boltzgen/blob/main/example/protein_binding_small_molecule/brilacidin.yaml
+binder_design_input = {
+    "protein_entities": [
+        {
+            "id": "A",
+            "sequence": "140..180",  # design a 140-180 residue protein binder
+        },
+    ],
+    "ligand_entities": [
+        {
+            "id": "B",
+            # brilacidin - antimicrobial small molecule
+            "smiles": "C1CNC[C@@H]1OC2=C(C=C(C=C2NC(=O)C3=CC(=NC=N3)C(=O)NC4=CC(=CC(=C4O[C@@H]5CCNC5)NC(=O)CCCCN=C(N)N)C(F)(F)F)C(F)(F)F)NC(=O)CCCCN=C(N)N",
+        },
+    ],
+}
+
+workflow = rowan.submit_protein_binder_design_workflow(
+    binder_design_input=binder_design_input,
+    protocol="protein-small_molecule",
+    num_designs=10,  # number of designs to generate
+    budget=2,  # number of designs to return after diversity filtering
+    name="Brilacidin binder design",
+)
+
+print(
+    f"View workflow privately at: https://labs.rowansci.com/protein-binder-design/{workflow.uuid}"
+)
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow.data)

rowan_python-2.1.16/examples/spin_states.py

@@ -0,0 +1,33 @@
+"""
+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
+
+See documentation at: https://docs.rowansci.com/science/workflows/spin-states
+"""
+
+from stjames import Molecule
+
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+# Methylene (CH2) - classic spin states example, triplet is ground state
+workflow = rowan.submit_spin_states_workflow(
+    initial_molecule=Molecule.from_smiles("[CH2]"),
+    states=[1, 3],  # singlet vs triplet
+    mode="rapid",
+    name="Methylene spin states",
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/spin-states/{workflow.uuid}")
+workflow.wait_for_result().fetch_latest(in_place=True)
+print(workflow.data)