rowan-python 2.1.5__tar.gz → 2.1.7__tar.gz

{rowan_python-2.1.5 → rowan_python-2.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.5
+Version: 2.1.7
 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>=0.0.104
+Requires-Dist: stjames>=0.0.109
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-2.1.5 → rowan_python-2.1.7}/examples/basic_calculation_with_constraint.py

@@ -9,7 +9,6 @@ result = rowan.submit_workflow(
     workflow_type="basic_calculation",
     name="Constrained Butane",
     workflow_data={
-        "engine": "xtb",
         "settings": {
             "method": "gfn2_xtb",
             "tasks": ["optimize"],

{rowan_python-2.1.5 → rowan_python-2.1.7}/examples/basic_calculation_with_solvent.py

@@ -13,7 +13,6 @@ def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, n
         name=f"{name} {method} optimization",
         workflow_data={
             "settings": {"method": method, "tasks": ["optimize"]},
-            "engine": "omol25",
         },
     )
 
@@ -33,7 +32,6 @@ def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, n
                 "tasks": ["energy"],
                 "solvent_settings": {"solvent": "water", "model": "cpcmx"},
             },
-            "engine": "omol25",
         },
     )
 

rowan_python-2.1.7/examples/double_ended_ts_search.py

@@ -0,0 +1,58 @@
+"""
+Run a double-ended transition state search using Rowan.
+
+See documentation at: https://docs.rowansci.com/science/workflows/double-ended-ts-search
+"""
+
+from stjames import Method, Molecule, Settings
+from stjames.optimization.freezing_string_method import (
+    FSMInterpolation,
+    FSMOptimizationCoordinates,
+    FSMSettings,
+)
+
+import rowan
+
+# rowan.api_key = ""
+HCN = Molecule.from_xyz(
+    """\
+H 0 0 -1.1
+C 0 0 0
+N 0 0 1.2""",
+)
+CNH = Molecule.from_xyz(
+    """\
+H 0 0 2.3
+C 0 0 0
+N 0 0 1.2""",
+)
+fsm_settings = FSMSettings(
+    optimization_coordinates=FSMOptimizationCoordinates.CARTESIAN,
+    interpolation_method=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,
+)
+
+
+# Run calculation remotely
+result = rowan.submit_double_ended_ts_search_workflow(
+    reactant=HCN,
+    product=CNH,
+    calculation_settings=Settings(method=Method.GFN2_XTB),
+    search_settings=fsm_settings,
+    optimize_inputs=True,
+    optimize_ts=True,
+    name="H-C≡N Isomerization",
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/workflow/{result.uuid}")
+result.wait_for_result().fetch_latest(in_place=True)
+
+assert result and result.data
+print(result.data["forward_string_distances"])
+print(result.data["backward_string_distances"])
+
+print(result)

{rowan_python-2.1.5 → rowan_python-2.1.7}/examples/protein_cofolding.py

@@ -12,6 +12,8 @@ result = rowan.submit_protein_cofolding_workflow(
     ],
     ligand_binding_affinity_index=0,
     name="Torcetrapib Cofolding",
+    do_pose_refinement=True,
+    compute_strain=True,
 )
 
 print(result.wait_for_result().fetch_latest(in_place=True))

rowan_python-2.1.7/examples/strain.py

@@ -0,0 +1,16 @@
+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..."
+
+# ordinarily, we'd try a 3D conformer and see what the strain is.
+# here we'll investigate the strain of the autogenerated hexane conformer
+result = rowan.submit_strain_workflow(
+    initial_molecule=Molecule.from_smiles("CCCCCC"),
+    name="test autogen hexane strain",
+)
+
+
+print(result.wait_for_result().fetch_latest(in_place=True))