PyPI - rowan-python - Versions diffs - 2.1.4__tar.gz → 2.1.5__tar.gz - Mend

rowan-python 2.1.4tar.gz → 2.1.5tar.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 (52) hide show

{rowan_python-2.1.4 → rowan_python-2.1.5}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.4
+Version: 2.1.5
 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>=0.0.83
+Requires-Dist: stjames>=0.0.104
 Description-Content-Type: text/markdown
 # Rowan Python Library

rowan_python-2.1.5/examples/ion_mobility.py ADDED Viewed

@@ -0,0 +1,17 @@
+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..."
+result = rowan.submit_ion_mobility_workflow(
+    Molecule.from_smiles("c1ccccn1"),
+    name="pyridinium CCS",
+    protonate=True,
+)
+result.wait_for_result().fetch_latest(in_place=True)
+print(result.data["average_ccs"])  # Å**2

rowan_python-2.1.5/examples/nmr.py ADDED Viewed

@@ -0,0 +1,17 @@
+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..."
+result = rowan.submit_nmr_workflow(
+    Molecule.from_smiles("O[C@H]1[C@H](C(C)C)CC[C@@H](C)C1"),
+    name="menthol NMR",
+)
+result.wait_for_result().fetch_latest(in_place=True)
+# print hydrogen peaks
+for peak in result.data["predicted_peaks"]["1"]:
+    print(peak)

{rowan_python-2.1.4 → rowan_python-2.1.5}/pixi.lock RENAMED Viewed

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{rowan_python-2.1.4 → rowan_python-2.1.5}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.1.4"
+version = "2.1.5"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -9,7 +9,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
-    "stjames>=0.0.83",
+    "stjames>=0.0.104",
     "setuptools",
     "rdkit",
     "nest-asyncio",

rowan_python-2.1.5/rowan/constants.py ADDED Viewed

@@ -0,0 +1,3 @@
+import os
+API_URL = os.getenv("ROWAN_API_URL", default="https://api.rowansci.com")

{rowan_python-2.1.4 → rowan_python-2.1.5}/rowan/utils.py RENAMED Viewed

@@ -47,6 +47,7 @@ def api_client() -> Generator[httpx.Client, None, None]:
     with httpx.Client(
         base_url=API_URL,
         headers={"X-API-Key": get_api_key()},
+        timeout=30,
     ) as client:
         yield client

{rowan_python-2.1.4 → rowan_python-2.1.5}/rowan/workflow.py RENAMED Viewed

@@ -860,8 +860,8 @@ def submit_macropka_workflow(
     max_pH: int = 14,
     min_charge: int = -2,
     max_charge: int = 2,
+    compute_solvation_energy: bool = False,
     compute_aqueous_solubility: bool = False,
-    compute_solvation_energy: bool = True,
     name: str = "Macropka Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
@@ -1027,8 +1027,9 @@ def submit_docking_workflow(
     protein: str | Protein,
     pocket: list[list[float]],
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | None = None,
-    do_csearch: bool = True,
-    do_optimization: bool = True,
+    do_csearch: bool = False,
+    do_optimization: bool = False,
+    do_pose_refinement: bool = False,
     name: str = "Docking Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
@@ -1040,6 +1041,7 @@ def submit_docking_workflow(
     :param initial_molecule: The initial molecule to be docked
     :param do_csearch: Whether to perform a conformational search on the ligand.
     :param do_optimization: Whether to perform an optimization on the ligand.
+    :param do_pose_refinement: Whether or not to optimize output poses.
     :param name: The 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.
@@ -1061,6 +1063,7 @@ def submit_docking_workflow(
         pocket=pocket,
         do_csearch=do_csearch,
         do_optimization=do_optimization,
+        do_pose_refinement=do_pose_refinement
     )
     data = {
@@ -1076,3 +1079,108 @@ def submit_docking_workflow(
         response = client.post("/workflow", json=data)
         response.raise_for_status()
         return Workflow(**response.json())
+def submit_ion_mobility_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    temperature: float = 300,
+    protonate: bool = False,
+    do_csearch: bool = True,
+    do_optimization: bool = True,
+    name: str = "Ion-Mobility Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits an ion-mobility workflow to the API.
+    :param initial_molecule: The molecule used in the scan.
+    :param temperature: The temperature at which to predict CCS values.
+    :param protonate: Whether or not to automatically detect protonation site.
+        If `True`, every basic site will be protonated and values returned for the most stable.
+    :param do_csearch: Whether to perform a conformational search on the molecule.
+    :param do_optimization: Whether to perform an optimization on the molecule.
+    :param name: The name of the workflow.
+    :param folder_uuid: The UUID of the folder to store the workflow in.
+    :param max_credits: The maximum number of credits to use for the workflow.
+    :return: A Workflow object representing the submitted workflow.
+    :raises requests.HTTPError: if the request to the API fails.
+    """
+    if isinstance(initial_molecule, StJamesMolecule):
+        initial_molecule = initial_molecule.model_dump()
+    elif isinstance(initial_molecule, RdkitMol):
+        initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
+    workflow = stjames.IonMobilityWorkflow(
+        initial_molecule=initial_molecule,
+        temperature=temperature,
+        protonate=protonate,
+        do_csearch=do_csearch,
+        do_optimization=do_optimization,
+    )
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "ion_mobility",
+        "workflow_data": workflow.model_dump(),
+        "initial_molecule": initial_molecule,
+        "max_credits": max_credits,
+    }
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())
+def submit_nmr_workflow(
+    initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol,
+    solvent: str | None = "chloroform",
+    do_csearch: bool = True,
+    do_optimization: bool = True,
+    name: str = "NMR Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits an NMR-prediction workflow to the API.
+    :param initial_molecule: The molecule used in the scan.
+    :param solvent: The solvent in which to compute NMR spectra.
+    :param do_csearch: Whether to perform a conformational search on the input structure.
+    :param do_optimization: Whether to perform an optimization on the input structure.
+    :param name: The name of the workflow.
+    :param folder_uuid: The UUID of the folder to store the workflow in.
+    :param max_credits: The maximum number of credits to use for the workflow.
+    :return: A Workflow object representing the submitted workflow.
+    :raises requests.HTTPError: if the request to the API fails.
+    """
+    if isinstance(initial_molecule, StJamesMolecule):
+        initial_molecule = initial_molecule.model_dump()
+    elif isinstance(initial_molecule, RdkitMol):
+        initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
+    workflow_data = {"initial_molecule": initial_molecule, "solvent": solvent}
+    if not do_csearch:
+        workflow_data["conf_gen_settings"] = None
+    if not do_optimization:
+        workflow_data["multistage_opt_settings"] = None
+    workflow = stjames.NMRSpectroscopyWorkflow.model_validate(workflow_data)
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "nmr",
+        "workflow_data": workflow.model_dump(serialize_as_any=True),
+        "initial_molecule": initial_molecule,
+        "max_credits": max_credits,
+    }
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())

rowan_python-2.1.4/rowan/constants.py DELETED Viewed

	@@ -1 +0,0 @@
1	- API_URL = "https://api.rowansci.com"

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rowan-python 2.1.4__tar.gz → 2.1.5__tar.gz

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