rowan-python 3.0.12__tar.gz → 3.1.0__tar.gz

{rowan_python-3.0.12 → rowan_python-3.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.12
+Version: 3.1.0
 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>=0.0.183
+Requires-Dist: stjames>=0.0.204
 Description-Content-Type: text/markdown
 
 # Rowan Python Library
@@ -28,6 +28,10 @@ The Rowan Python library provides convenient access to the Rowan API from applic
 
 The documentation is available [here](https://docs.rowansci.com/python-api).
 
+## Agent skill
+
+Ships with a [skill](skills/computational-chemistry-and-biology/) that makes it easy for coding agents to use Rowan's tools to power chemistry and biology tasks. To use it, copy the directory into your agent's skills folder.
+
 ## Running examples
 
 To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.

{rowan_python-3.0.12 → rowan_python-3.1.0}/README.md

@@ -12,6 +12,10 @@ The Rowan Python library provides convenient access to the Rowan API from applic
 
 The documentation is available [here](https://docs.rowansci.com/python-api).
 
+## Agent skill
+
+Ships with a [skill](skills/computational-chemistry-and-biology/) that makes it easy for coding agents to use Rowan's tools to power chemistry and biology tasks. To use it, copy the directory into your agent's skills folder.
+
 ## Running examples
 
 To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.

{rowan_python-3.0.12 → rowan_python-3.1.0}/docs/index.md

@@ -408,6 +408,17 @@
       group_by_category: true
       filters: ["!^__"]
 
+## Molecule Class and Functions
+::: rowan.molecule
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
 ## User Class and Functions
 ::: rowan.user
     handler: python

{rowan_python-3.0.12 → rowan_python-3.1.0}/examples/basic_calculation.py

@@ -5,8 +5,8 @@ import rowan
 folder = rowan.get_folder("examples")
 
 workflow = rowan.submit_basic_calculation_workflow(
-    initial_molecule="CC(=C)C=C",
-    preset="semiempirical",
+    initial_molecule=rowan.Molecule.from_smiles("CC(=C)C=C"),
+    preset="rapid_semiempirical",
     tasks=["optimize"],
     name="Isoprene Optimization",
     folder=folder,

rowan_python-3.1.0/examples/bde.py

@@ -0,0 +1,62 @@
+"""
+Calculate Bond-Dissociation Energies (BDE) with the Rowan API.
+
+`mode` is a BDE method string (the level of theory):
+- "omol25_conserving_s": neural network potential (default)
+- "g_xtb//gfn2_xtb": semiempirical
+- "r2scan3c//gfn2_xtb": DFT single point
+
+Choose which bonds to break:
+- all_CH=True / all_CX=True: every C-H / every C-X (carbon-halogen) bond
+- fragment_indices=[[...]]: 1-indexed atoms of a fragment to split off (each fragment must
+  connect to the rest by a single bond) -- e.g. [[9]] splits off one hydrogen,
+  [[3, 9]] splits off a whole group like -OH
+
+Use the bond finders to get indices: rowan.find_ch_bonds(mol), rowan.find_cx_bonds(mol),
+or rowan.find_bonds(mol, element_a, element_b, distance_max).
+
+See documentation at: https://docs.rowansci.com/science/workflows/bond-dissociation-energy
+"""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+mol = rowan.Molecule.from_smiles("CCCC")  # butane
+
+# Break every C-H bond and report each one's BDE.
+workflow = rowan.submit_bde_workflow(
+    initial_molecule=mol,
+    mode="omol25_conserving_s",
+    all_CH=True,
+    name="Butane C-H BDEs",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/bde/{workflow.uuid}")
+result = workflow.result()
+print(result)
+print(result.bdes)
+# e.g. <BDEResult energy=-... Ha bdes=...>
+
+
+# To target a specific bond instead of a whole class, pass its fragment atoms (1-indexed).
+# This reaches bonds the all_CH / all_CX flags don't cover -- here, the ethanol O-H bond.
+ethanol = rowan.Molecule.from_smiles("CCO")
+oh_bonds = rowan.find_bonds(ethanol, element_a=8, element_b=1, distance_max=1.1)
+oh_hydrogen = oh_bonds[0][1]  # the hydroxyl H
+
+oh_workflow = rowan.submit_bde_workflow(
+    initial_molecule=ethanol,
+    mode="omol25_conserving_s",
+    fragment_indices=[[oh_hydrogen]],  # split off that H -> the ethanol O-H BDE
+    name="Ethanol O-H BDE",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/bde/{oh_workflow.uuid}")
+oh_result = oh_workflow.result()
+print(oh_result)
+print(oh_result.bdes)

rowan_python-3.1.0/examples/conformers.py

@@ -0,0 +1,25 @@
+"""
+Calculate the conformers of a molecule using the Rowan API.
+
+Conformer generation defaults to OpenConf; pass `conf_gen_settings=` to choose a
+different generator (ETKDG, iMTD-GC, MCMM).
+
+See documentation at: https://docs.rowansci.com/science/workflows/conformers
+"""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+workflow = rowan.submit_conformer_search_workflow(
+    initial_molecule=rowan.Molecule.from_smiles("CCOCC"),
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/conformer-search/{workflow.uuid}")
+
+result = workflow.result()
+print(result)
+# e.g. <ConformerSearchResult conformers=12>

rowan_python-3.1.0/examples/conformers_screen.py

@@ -0,0 +1,46 @@
+"""
+Rank a conformer ensemble you already have, using the Rowan API (screen-only mode).
+
+Conformer search normally *generates* conformers and then optimizes, deduplicates,
+and ranks them. If you already have 3D geometries -- from another tool (RDKit,
+CREST, OpenBabel), a crystal or MD ensemble, an SDF on disk, or a previous
+workflow -- you can skip generation by passing them as `initial_conformers`. Rowan
+then runs only the screening half: optimize each at a consistent level of theory,
+deduplicate, and rank by energy.
+
+The conformers must be a genuine ensemble of one molecule with identical atom
+ordering (they are compared atom-by-atom during deduplication). Reading them from a
+single multi-conformer SDF, as below, guarantees that. Leave `conf_gen_settings` as
+None.
+
+See documentation at: https://docs.rowansci.com/science/workflows/conformers
+"""
+
+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")
+
+# Read a multi-conformer SDF: eight conformers of ibuprofen, one molecule, consistent
+# atom ordering across every record.
+sdf_path = Path(__file__).parent / "data" / "ibuprofen_conformers.sdf"
+conformers = rowan.Molecule.molecules_from_sdf(sdf_path)
+print(f"read {len(conformers)} conformers from {sdf_path.name}")
+
+workflow = rowan.submit_conformer_search_workflow(
+    initial_conformers=conformers,
+    conf_gen_settings=None,  # screen-only: skip generation, just optimize/dedup/rank
+    name="Conformer Screen",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/conformer-search/{workflow.uuid}")
+
+result = workflow.result()
+print(result)
+# e.g. <ConformerSearchResult conformers=3>  (8 supplied -> deduplicated and ranked)
+
+print("relative energies (kcal/mol):", [round(e, 2) for e in result.get_energies(relative=True)])