PyPI - rowan-python - Versions diffs - 2.1.6__tar.gz → 2.1.7__tar.gz - Mend

rowan-python 2.1.6tar.gz → 2.1.7tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (53) hide show

{rowan_python-2.1.6 → rowan_python-2.1.7}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.6
+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

{rowan_python-2.1.6 → rowan_python-2.1.7}/examples/basic_calculation_with_constraint.py RENAMED Viewed

@@ -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-2.1.6 → rowan_python-2.1.7}/examples/basic_calculation_with_solvent.py RENAMED Viewed

@@ -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 ADDED Viewed

@@ -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-2.1.6 → rowan_python-2.1.7}/pixi.lock RENAMED Viewed

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+  - ipython[matplotlib] ; extra == 'test-extra'
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{rowan_python-2.1.6 → rowan_python-2.1.7}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.1.6"
+version = "2.1.7"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.9"
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 convention = "numpy"
 [tool.mypy]
-exclude = ["scripts", "benchmark", "build", "subrepos/stjames/tests", "subrepos/aimnet2calc", "feature", "examples"]
+exclude = ["examples"]
 plugins = ["pydantic.mypy"]
 warn_unused_ignores = true

{rowan_python-2.1.6 → rowan_python-2.1.7}/rowan/workflow.py RENAMED Viewed

@@ -5,6 +5,7 @@ from typing import Any, Literal, Self, TypeAlias
 import stjames
 from pydantic import BaseModel, Field
 from rdkit import Chem
+from stjames.optimization.freezing_string_method import FSMSettings
 from .protein import Protein
 from .utils import api_client
@@ -285,16 +286,21 @@ def retrieve_workflow(uuid: str) -> Workflow:
         return Workflow(**response.json())
-def retrieve_calculation_molecules(uuid: str) -> list[dict[str, Any]]:
+def retrieve_calculation_molecules(
+    uuid: str, return_frequencies: bool = False
+) -> list[dict[str, Any]]:
     """
     Retrieves a list of molecules from a calculation.
     :param uuid: The UUID of the calculation to retrieve molecules from.
+    :param return_frequencies: Whether to return the frequencies of the molecules.
     :return: A list of dictionaries representing the molecules in the calculation.
     :raises HTTPError: If the API request fails.
     """
     with api_client() as client:
-        response = client.get(f"/calculation/{uuid}/molecules")
+        response = client.get(
+            f"/calculation/{uuid}/molecules", params={"return_frequencies": return_frequencies}
+        )
         response.raise_for_status()
         return response.json()
@@ -352,9 +358,10 @@ def list_workflows(
 def submit_basic_calculation_workflow(
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
     method: stjames.Method | str = "uma_m_omol",
+    basis_set: stjames.BasisSet | str | None = None,
     tasks: list[str] | None = None,
     mode: str = "auto",
-    engine: str = "omol25",
+    engine: str | None = None,
     name: str = "Basic Calculation Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
@@ -364,7 +371,7 @@ def submit_basic_calculation_workflow(
     :param initial_molecule: The molecule to perform the calculation on.
     :param method: The method to use for the calculation.
-    See [list of available methods](https://github.com/rowansci/stjames-public/blob/master/stjames/method.py)
+    :param basis_set: The basis_set to use (if any).
     for options.
     :param tasks: A list of tasks to perform for the calculation.
     :param mode: The mode to run the calculation in. See [list of available modes](https://github.com/rowansci/stjames-public/blob/master/stjames/mode.py)
@@ -391,6 +398,7 @@ def submit_basic_calculation_workflow(
         initial_molecule=initial_molecule,
         settings=stjames.Settings(
             method=method,
+            basis_set=basis_set,
             tasks=tasks,
             mode=mode,
         ),
@@ -792,7 +800,7 @@ def submit_descriptors_workflow(
 def submit_scan_workflow(
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
     scan_settings: stjames.ScanSettings | dict[str, Any] | None = None,
-    calculation_engine: str = "omol25",
+    calculation_engine: str | None = None,
     calculation_method: stjames.Method | str = "uma_m_omol",
     wavefront_propagation: bool = True,
     name: str = "Scan Workflow",
@@ -835,7 +843,7 @@ def submit_scan_workflow(
         initial_molecule=initial_molecule,
         scan_settings=scan_settings,
         calc_settings=calc_settings,
-        calc_engine=calculation_engine,
+        calc_engine=calculation_engine or calculation_method.default_engine(),
         wavefront_propagation=wavefront_propagation,
     )
@@ -911,7 +919,6 @@ def submit_macropka_workflow(
 def submit_irc_workflow(
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | None = None,
     method: stjames.Method | str = "uma_m_omol",
-    engine: str = "omol25",
     preopt: bool = True,
     step_size: float = 0.05,
     max_irc_steps: int = 30,
@@ -926,7 +933,6 @@ def submit_irc_workflow(
     :param method: The computational method to use for the IRC calculation.
     See [list of available methods](https://github.com/rowansci/stjames-public/blob/master/stjames/method.py)
     for options.
-    :param engine: The computational engine to use for the calculation. See [list of available engines](https://github.com/rowansci/stjames-public/blob/master/stjames/engine.py)
     :param preopt: Whether to perform a pre-optimization of the molecule.
     :param step_size: The step size to use for the IRC calculation.
     :param max_irc_steps: The maximum number of IRC steps to perform.
@@ -953,12 +959,12 @@ def submit_irc_workflow(
             corrections=[],
             mode="auto",
         ),
-        engine=engine,
         preopt=preopt,
         step_size=step_size,
         max_irc_steps=max_irc_steps,
         mode="manual",
     )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
@@ -1229,3 +1235,51 @@ def submit_strain_workflow(
         response = client.post("/workflow", json=data)
         response.raise_for_status()
         return Workflow(**response.json())
+def submit_double_ended_ts_search_workflow(
+    reactant: dict[str, Any] | StJamesMolecule,
+    product: dict[str, Any] | StJamesMolecule,
+    calculation_settings: stjames.Settings | dict[str, Any] | None = None,
+    search_settings: FSMSettings | dict[str, Any] | None = None,
+    optimize_inputs: bool = False,
+    optimize_ts: bool = True,
+    name: str = "Double-Ended TS Search Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a double-ended transition state search workflow to the API.
+    :param reactant: reactant Molecule.
+    :param product: product Molecule.
+    :param calculation_settings: Settings to use for calculations.
+    :param search_settings: settings to use for the transition state search.
+    :param optimize_inputs: Whether to optimize the reactant and product before the search.
+    :param optimize_ts: Whether to optimize the found transition state.
+    :param name: name of the workflow.
+    :param folder_uuid: The UUID of the folder to place the workflow in.
+    :param max_credits: The maximum number of credits to use for the workflow.
+    :return: Workflow object representing the submitted workflow.
+    """
+    workflow = stjames.DoubleEndedTSSearchWorkflow(
+        reactant=reactant,
+        product=product,
+        calculation_settings=calculation_settings,
+        search_settings=search_settings,
+        optimize_inputs=optimize_inputs,
+        optimize_ts=optimize_ts,
+    )
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "double_ended_ts_search",
+        "workflow_data": workflow.model_dump(),
+        "initial_molecule": reactant if isinstance(reactant, dict) else reactant.model_dump(),
+        "max_credits": max_credits,
+    }
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())