rowan-python 2.0.0__tar.gz → 2.0.1__tar.gz

{rowan_python-2.0.0 → rowan_python-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.0.0
+Version: 2.0.1
 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-2.0.1/examples/basic_calculation_from_json.py

@@ -0,0 +1,20 @@
+import json
+
+import rowan
+
+# rowan.api_key = ""
+
+with open("examples/data/workflow_example.json", "r") as f:
+    workflow_data = json.load(f)
+
+result = rowan.submit_workflow(
+    workflow_type="basic_calculation",
+    workflow_data=workflow_data,
+    name="basic calculation from json",
+    initial_molecule=workflow_data["initial_molecule"],
+)
+
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+
+print(result)

rowan_python-2.0.1/examples/basic_calculation_with_constraint.py

@@ -0,0 +1,33 @@
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+result = rowan.submit_workflow(
+    initial_molecule=Molecule.from_smiles("CCCC"),
+    workflow_type="basic_calculation",
+    name="Constrained Butane",
+    workflow_data={
+        "engine": "xtb",
+        "settings": {
+            "method": "gfn2_xtb",
+            "tasks": ["optimize"],
+            "mode": "auto",
+            "opt_settings": {
+                "constraints": [
+                    {
+                        "atoms": [4, 3, 2, 1],
+                        "constraint_type": "dihedral",
+                        "value": 0,
+                    },
+                ]
+            },
+        },
+    },
+)
+
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+
+print(result)

rowan_python-2.0.1/examples/basic_calculation_with_solvent.py

@@ -0,0 +1,55 @@
+# ruff: noqa
+
+import os
+import sys
+
+from stjames import Molecule, Method
+
+import rowan
+
+# rowan.api_key = ""
+
+
+def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, name: str) -> float:
+    opt = rowan.submit_workflow(
+        initial_molecule=molecule,
+        workflow_type="basic_calculation",
+        name=f"{name} {method} optimization",
+        workflow_data={
+            "settings": {"method": method, "tasks": ["optimize"]},
+            "engine": "omol25",
+        },
+    )
+
+    opt.wait_for_result()
+    opt.fetch_latest(in_place=True)
+
+    calculation_uuid = opt.data["calculation_uuid"]
+    optimized_molecule = rowan.retrieve_calculation_molecules(calculation_uuid)[-1]
+
+    sp = rowan.submit_workflow(
+        initial_molecule=optimized_molecule,
+        workflow_type="basic_calculation",
+        name=f"{name} {method} single point",
+        workflow_data={
+            "settings": {
+                "method": method,
+                "tasks": ["energy"],
+                "solvent_settings": {"solvent": "water", "model": "cpcmx"},
+            },
+            "engine": "omol25",
+        },
+    )
+
+    sp.wait_for_result()
+    sp.fetch_latest(in_place=True)
+
+    calculation_uuid = sp.data["calculation_uuid"]
+    final_molecule = rowan.retrieve_calculation_molecules(calculation_uuid)[0]
+    return final_molecule["energy"]
+
+
+E1 = compute_energy_with_solvent_correction(
+    Molecule.from_smiles("CC(=O)Oc1ccccc1C(=O)O"), Method.OMOL25_CONSERVING_S, "aspirin"
+)
+print(E1)

{rowan_python-2.0.0 → rowan_python-2.0.1}/examples/bde.py

@@ -31,4 +31,7 @@ result = rowan.submit_workflow(
     },
 )
 
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+
 print(result)

rowan_python-2.0.1/examples/data/workflow_example.json

@@ -0,0 +1,190 @@
+{
+    "mode": "auto",
+    "engine": "xtb",
+    "messages": [],
+    "settings": {
+      "mode": "rapid",
+      "tasks": [
+        "optimize"
+      ],
+      "method": "gfn2_xtb",
+      "basis_set": null,
+      "corrections": [],
+      "opt_settings": {
+        "max_steps": 250,
+        "constraints": [
+          {
+            "atoms": [
+              4,
+              3,
+              2,
+              1
+            ],
+            "value": 0,
+            "constraint_type": "dihedral"
+          }
+        ],
+        "optimize_cell": false,
+        "energy_threshold": 0.00005,
+        "transition_state": false,
+        "recalc_hess_every": 0,
+        "max_gradient_threshold": 0.005,
+        "rms_gradient_threshold": 0.0035
+      },
+      "scf_settings": {
+        "soscf": false,
+        "max_iters": 250
+      },
+      "level_of_theory": "gfn2_xtb",
+      "compute_settings": {
+        "compute_type_used": null,
+        "requested_compute_type": "cpu"
+      },
+      "solvent_settings": null,
+      "thermochem_settings": {
+        "temperature": 298,
+        "concentration": 0.0408740470708,
+        "scaling_factor": 1,
+        "cutoff_frequency": 100
+      }
+    },
+    "calculation_uuid": "54027970-5efb-42df-8125-c8984d8ca7eb",
+    "initial_molecule": {
+      "cell": null,
+      "atoms": [
+        {
+          "position": [
+            -1.57731622,
+            0.46259034,
+            0.02288227
+          ],
+          "atomic_number": 6
+        },
+        {
+          "position": [
+            -0.55246934,
+            -0.31349805,
+            -0.78986664
+          ],
+          "atomic_number": 6
+        },
+        {
+          "position": [
+            0.65178196,
+            -0.77563238,
+            0.03104792
+          ],
+          "atomic_number": 6
+        },
+        {
+          "position": [
+            1.5013315,
+            0.37070813,
+            0.55769072
+          ],
+          "atomic_number": 6
+        },
+        {
+          "position": [
+            -1.17009891,
+            1.41344062,
+            0.37886292
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            -1.91277475,
+            -0.11690438,
+            0.88874548
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            -2.45332233,
+            0.68757176,
+            -0.59399069
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            -0.21575239,
+            0.30052639,
+            -1.63326648
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            -1.04230601,
+            -1.19688302,
+            -1.21658189
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            0.31558706,
+            -1.39539838,
+            0.87044712
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            1.28031633,
+            -1.41330121,
+            -0.60197473
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            2.39258685,
+            -0.02154188,
+            1.05803044
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            0.95227634,
+            0.97534316,
+            1.28543953
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            1.83015992,
+            1.0229789,
+            -0.25746596
+          ],
+          "atomic_number": 1
+        }
+      ],
+      "charge": 0,
+      "dipole": null,
+      "energy": null,
+      "smiles": "CCCC",
+      "stress": null,
+      "elapsed": null,
+      "gradient": null,
+      "velocities": null,
+      "multiplicity": 1,
+      "homo_lumo_gap": null,
+      "scf_completed": null,
+      "scf_iterations": null,
+      "mulliken_charges": null,
+      "calculation_index": null,
+      "vibrational_modes": null,
+      "zero_point_energy": null,
+      "thermal_energy_corr": null,
+      "thermal_enthalpy_corr": null,
+      "mulliken_spin_densities": null,
+      "thermal_free_energy_corr": null
+    }
+  }
+  

rowan_python-2.0.1/examples/macropka.py

@@ -0,0 +1,13 @@
+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_macropka_workflow(
+    # oseltamivir
+    initial_smiles="C1CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H]([NH3+])C1CCC1",
+    name="Oseltamivir macropka",
+)
+
+
+print(result)

{rowan_python-2.0.0 → rowan_python-2.0.1}/pixi.lock

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@@ -522,10 +524,10 @@ packages:
   - markdown ; extra == 'dev'
   - flake8 ; extra == 'dev'
   - wheel ; extra == 'dev'
-- pypi: https://files.pythonhosted.org/packages/58/c6/5c20af38c2a57c15d87f7f38bee77d63c1d2a3689f74fefaf35915dd12b2/griffe-1.7.3-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/bf/c4/a839fcc28bebfa72925d9121c4d39398f77f95bcba0cf26c972a0cfb1de7/griffe-1.8.0-py3-none-any.whl
   name: griffe
-  version: 1.7.3
-  sha256: c6b3ee30c2f0f17f30bcdef5068d6ab7a2a4f1b8bf1a3e74b56fffd21e1c5f75
+  version: 1.8.0
+  sha256: 110faa744b2c5c84dd432f4fa9aa3b14805dd9519777dd55e8db214320593b02
   requires_dist:
   - colorama>=0.4
   requires_python: '>=3.9'
@@ -583,6 +585,16 @@ packages:
   purls: []
   size: 12129203
   timestamp: 1720853576813
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/icu-75.1-hfee45f7_0.conda
+  sha256: 9ba12c93406f3df5ab0a43db8a4b4ef67a5871dfd401010fbe29b218b2cbe620
+  md5: 5eb22c1d7b3fc4abb50d92d621583137
+  depends:
+  - __osx >=11.0
+  license: MIT
+  license_family: MIT
+  purls: []
+  size: 11857802
+  timestamp: 1720853997952
 - pypi: https://files.pythonhosted.org/packages/7a/cd/18f8da995b658420625f7ef13f037be53ae04ec5ad33f9b718240dcfd48c/identify-2.6.12-py2.py3-none-any.whl
   name: identify
   version: 2.6.12
@@ -841,28 +853,29 @@ packages:
   purls: []
   size: 71829
   timestamp: 1748393749336
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.3-hee844dc_0.conda
-  sha256: 10891c917031d27c546d397f22e09c449c6c10782f2c0a069f361a502d286f3c
-  md5: 4fe4c3b7ce84cda6508b6d78f0ce72e3
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.3-hee844dc_1.conda
+  sha256: 8c4faf560815a6d6b5edadc019f76d22a45171eaa707a1f1d1898ceda74b2e3f
+  md5: 18d2ac95b507ada9ca159a6bd73255f7
   depends:
   - __glibc >=2.17,<3.0.a0
   - icu >=75.1,<76.0a0
   - libgcc >=14
   - libzlib >=1.3.1,<2.0a0
-  license: Unlicense
+  license: blessing
   purls: []
-  size: 935794
-  timestamp: 1752825101149
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.50.3-hf8de324_0.conda
-  sha256: d5bfc49bf5f68318830dfc359739386e32413a873072fc78994ced6af3fd08df
-  md5: 4366ba8a8b7a283aaaca877597be65df
+  size: 936339
+  timestamp: 1753262589168
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.50.3-h4237e3c_1.conda
+  sha256: 248ba9622ee91c3ae1266f7b69143adf5031e1f2d94b6d02423e192e47531697
+  md5: 6d034f4604ac104a1256204af7d1a534
   depends:
   - __osx >=11.0
+  - icu >=75.1,<76.0a0
   - libzlib >=1.3.1,<2.0a0
-  license: Unlicense
+  license: blessing
   purls: []
-  size: 899228
-  timestamp: 1752825238869
+  size: 902818
+  timestamp: 1753262833682
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_3.conda
   sha256: 7650837344b7850b62fdba02155da0b159cf472b9ab59eb7b472f7bd01dff241
   md5: 6d11a5edae89fe413c0569f16d308f5a
@@ -1041,10 +1054,10 @@ packages:
   version: 1.3.1
   sha256: adff8b62700b25cb77b53358dad940f3ef973dd6db797907c49e3c2ef3ab4e31
   requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/98/14/22533a578bf8b187e05d67e2c1721ce10e3f526610eebaf7a149d557ea7a/mkdocstrings-0.29.1-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/de/b4/3c5eac68f31e124a55d255d318c7445840fa1be55e013f507556d6481913/mkdocstrings-0.30.0-py3-none-any.whl
   name: mkdocstrings
-  version: 0.29.1
-  sha256: 37a9736134934eea89cbd055a513d40a020d87dfcae9e3052c2a6b8cd4af09b6
+  version: 0.30.0
+  sha256: ae9e4a0d8c1789697ac776f2e034e2ddd71054ae1cf2c2bb1433ccfd07c226f2
   requires_dist:
   - jinja2>=2.11.1
   - markdown>=3.6
@@ -1535,8 +1548,8 @@ packages:
   requires_python: '>=3.8'
 - pypi: ./
   name: rowan-python
-  version: 2.0.0
-  sha256: e457de628362332f67ec3a1c50a1c9bb219a33e5d321010b810735aefd26c268
+  version: 2.0.1
+  sha256: 538deecdcbfe274e9b6bd98bc1db5ff036d409d503774710ad34fb5aeda726e0
   requires_dist:
   - httpx
   - stjames>=0.0.83

{rowan_python-2.0.0 → rowan_python-2.0.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.0.0"
+version = "2.0.1"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.9"

{rowan_python-2.0.0 → rowan_python-2.0.1}/rowan/__init__.py

@@ -1,10 +1,8 @@
 # ruff: noqa
-
-from . import utils
-
 from . import constants
 
 from .folder import *
 from .workflow import *
 from .protein import *
 from .user import *
+from .utils import *

{rowan_python-2.0.0 → rowan_python-2.0.1}/rowan/workflow.py

@@ -68,7 +68,7 @@ class Workflow(BaseModel):
         """
         Loads workflow data from the database and updates the current instance.
 
-        :param in_place: Whether to update the current instance in-place. 
+        :param in_place: Whether to update the current instance in-place.
         :return: The updated instance (self).
         :raises HTTPError: If the API request fails.
         """
@@ -217,7 +217,7 @@ class Workflow(BaseModel):
 
 
 def submit_workflow(
-    workflow_type: str,
+    workflow_type: stjames.WORKFLOW_NAME,
     workflow_data: dict[str, Any] | None = None,
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | None = None,
     initial_smiles: str | None = None,
@@ -241,6 +241,11 @@ def submit_workflow(
     :raises ValueError: If neither `initial_smiles` nor a valid `initial_molecule` is provided.
     :raises HTTPError: If the API request fails.
     """
+    if workflow_type not in stjames.WORKFLOW_MAPPING:
+        raise ValueError(
+            "Invalid workflow type. Must be one of:\n    " + "\n    ".join(stjames.WORKFLOW_MAPPING)
+        )
+
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
@@ -300,7 +305,7 @@ def list_workflows(
     public: bool | None = None,
     starred: bool | None = None,
     status: int | None = None,
-    workflow_type: str | None = None,
+    workflow_type: stjames.WORKFLOW_NAME | None = None,
     page: int = 0,
     size: int = 10,
 ) -> list[Workflow]:
@@ -828,6 +833,56 @@ def submit_scan_workflow(
         return Workflow(**response.json())
 
 
+def submit_macropka_workflow(
+    initial_smiles: str,
+    min_pH: int = 0,
+    max_pH: int = 14,
+    min_charge: int = -2,
+    max_charge: int = 2,
+    compute_solvation_energy: bool = True,
+    name: str = "Macropka Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a macropka workflow to the API.
+
+    :param initial_smiles: The molecule used in the macropka workflow.
+    :param min_pH: The minimum pH to use in the macropka workflow.
+    :param max_pH: The maximum pH to use in the macropka workflow.
+    :param min_charge: The minimum charge to use in the macropka workflow.
+    :param max_charge: The maximum charge to use in the macropka workflow.
+    :param compute_solvation_energy: Whether to compute the solvation energy.
+    :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.
+    """
+
+    workflow_data = {
+        "min_pH": min_pH,
+        "max_pH": max_pH,
+        "min_charge": min_charge,
+        "max_charge": max_charge,
+        "compute_solvation_energy": compute_solvation_energy,
+    }
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "macropka",
+        "workflow_data": workflow_data,
+        "initial_smiles": initial_smiles,
+        "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_irc_workflow(
     initial_molecule: dict[str, Any] | StJamesMolecule | RdkitMol | None = None,
     method: stjames.Method | str = "uma_m_omol",