PyPI - rowan-python - Versions diffs - 2.1.1__tar.gz → 2.1.3__tar.gz - Mend

rowan-python 2.1.1tar.gz → 2.1.3tar.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 (48) hide show

{rowan_python-2.1.1 → rowan_python-2.1.3}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.1
+Version: 2.1.3
 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-2.1.3/examples/basic_calculation.py ADDED Viewed

@@ -0,0 +1,21 @@
+# ruff: noqa
+from stjames import Molecule, Method
+import rowan
+# rowan.api_key = ""
+result = rowan.submit_basic_calculation_workflow(
+    initial_molecule=Molecule.from_smiles("CC(=C)C=C"),
+    method=Method.OMOL25_CONSERVING_S,
+    tasks=["energy"],
+    mode="auto",
+    engine="omol25",
+    name="Isoprene Energy",
+)
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+print(result)

{rowan_python-2.1.1 → rowan_python-2.1.3}/examples/basic_calculation_with_solvent.py RENAMED Viewed

@@ -1,8 +1,4 @@
 # ruff: noqa
-import os
-import sys
 from stjames import Molecule, Method
 import rowan

rowan_python-2.1.3/examples/fukui_index.py ADDED Viewed

@@ -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..."
+result = rowan.submit_fukui_workflow(
+    initial_molecule=Molecule.from_smiles("C1=CC=C(C=C1)C(=O)O"),
+    optimization_method="gfn2_xtb",
+    fukui_method="gfn1_xtb",
+    name="Benzoic Acid Fukui",
+)
+print(result.wait_for_result().fetch_latest(in_place=True))

rowan_python-2.1.3/examples/redox_potential.py ADDED Viewed

@@ -0,0 +1,21 @@
+"""
+Calculate the redox potential of a molecule using the Rowan API.
+See documentiation at: https://docs.rowansci.com/science/workflows/redox-potential
+"""
+from stjames import Molecule
+import rowan
+# rowan.api_key = ""
+result = rowan.submit_redox_potential_workflow(
+    initial_molecule=Molecule.from_smiles("C1=CC=C(C=C1)C(=O)O"),
+    mode="reckless",
+    name="Benzoic Acid Redox Potential",
+    oxidization=True,
+    reduction=True,
+)
+print(result.wait_for_result().fetch_latest(in_place=True))

rowan_python-2.1.3/examples/tautomer.py ADDED Viewed

@@ -0,0 +1,15 @@
+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_tautomer_search_workflow(
+    initial_molecule=Molecule.from_smiles("O=C1C=CC=CN1"),
+    mode="reckless",
+    name="2-Pyridone Tautomers",
+)
+print(result.wait_for_result().fetch_latest(in_place=True))

{rowan_python-2.1.1 → rowan_python-2.1.3}/pixi.lock RENAMED Viewed

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   - certifi>=2017.4.17
   - pysocks>=1.5.6,!=1.5.7 ; extra == 'socks'
   - chardet>=3.0.2,<6 ; extra == 'use-chardet-on-py3'
-  requires_python: '>=3.8'
+  requires_python: '>=3.9'
 - pypi: ./
   name: rowan-python
-  version: 2.1.1
-  sha256: 73d6bc87006a2cb62e35e15b2e7cf63fe9f57221430af510ea4d83e105001d15
+  version: 2.1.3
+  sha256: 42fdb4e667a0c2c279bbf99762920eda972eb32ca9f885b57dcf438815833ecc
   requires_dist:
   - httpx
   - stjames>=0.0.83
@@ -1504,15 +1491,15 @@ packages:
   - nest-asyncio
   requires_python: '>=3.9'
   editable: true
-- pypi: https://files.pythonhosted.org/packages/99/9d/e91f84dfe3866fa648c10512904991ecc326fd0b66578b324ee6ecb8f725/ruff-0.12.8-py3-none-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/2c/0d/15b72c5fe6b1e402a543aa9d8960e0a7e19dfb079f5b0b424db48b7febab/ruff-0.12.11-py3-none-macosx_11_0_arm64.whl
   name: ruff
-  version: 0.12.8
-  sha256: 2fae54e752a3150f7ee0e09bce2e133caf10ce9d971510a9b925392dc98d2fec
+  version: 0.12.11
+  sha256: d69fb9d4937aa19adb2e9f058bc4fbfe986c2040acb1a4a9747734834eaa0bfd
   requires_python: '>=3.7'
-- pypi: https://files.pythonhosted.org/packages/e8/67/0c3c9179a3ad19791ef1b8f7138aa27d4578c78700551c60d9260b2c660d/ruff-0.12.8-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/80/22/3c6cef96627f89b344c933781ed38329bfb87737aa438f15da95907cbfd5/ruff-0.12.11-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
   name: ruff
-  version: 0.12.8
-  sha256: 560e0cd641e45591a3e42cb50ef61ce07162b9c233786663fdce2d8557d99818
+  version: 0.12.11
+  sha256: 4fc58f9266d62c6eccc75261a665f26b4ef64840887fc6cbc552ce5b29f96cc8
   requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl
   name: setuptools
@@ -1594,10 +1581,10 @@ packages:
   - pygments ; extra == 'tests'
   - littleutils ; extra == 'tests'
   - cython ; extra == 'tests'
-- pypi: https://files.pythonhosted.org/packages/5b/90/184bc0c808dc643dfd35bd6cca3c7cf0e23cc8a8982fa93fdd9d5d5e7710/stjames-0.0.99-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/ed/96/f3b274b32a711fad65f317731411a6fefc65c6d738926dc9d1e607bddb81/stjames-0.0.102-py3-none-any.whl
   name: stjames
-  version: 0.0.99
-  sha256: 28019a6dd4e4dab576aae7b5eb0b6477539ce79a8e22b02f11af2b1b91c32c4a
+  version: 0.0.102
+  sha256: 234b3e9680d1eaaf613cb8cc9f2084f8fe4920d0ac566e1e503c9e8d4ff73a4e
   requires_dist:
   - pydantic>=2.4
   - numpy
@@ -1643,10 +1630,10 @@ packages:
   - pytest-mypy-testing ; extra == 'test'
   - pytest>=7.0,<8.2 ; extra == 'test'
   requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/b5/00/d631e67a838026495268c2f6884f3711a15a9a2a96cd244fdaea53b823fb/typing_extensions-4.14.1-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl
   name: typing-extensions
-  version: 4.14.1
-  sha256: d1e1e3b58374dc93031d6eda2420a48ea44a36c2b4766a4fdeb3710755731d76
+  version: 4.15.0
+  sha256: f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548
   requires_python: '>=3.9'
 - pypi: https://files.pythonhosted.org/packages/17/69/cd203477f944c353c31bade965f880aa1061fd6bf05ded0726ca845b6ff7/typing_inspection-0.4.1-py3-none-any.whl
   name: typing-inspection

{rowan_python-2.1.1 → rowan_python-2.1.3}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.1.1"
+version = "2.1.3"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.9"

{rowan_python-2.1.1 → rowan_python-2.1.3}/rowan/protein.py RENAMED Viewed

@@ -162,7 +162,7 @@ def list_proteins(
     return [Protein(**item) for item in results]
-def upload_protein(name: str, file_path: Path) -> Protein:
+def upload_protein(name: str, file_path: Path, project_uuid: str | None = None) -> Protein:
     """
     Uploads a protein from a PDB file to the API.
@@ -181,7 +181,11 @@ def upload_protein(name: str, file_path: Path) -> Protein:
         protein_data = conversion_response.json()
         # Step 2: Use the converted data to create the final protein object.
-        creation_payload = {"name": name, "protein_data": protein_data, "ancestor_uuid": None}
+        creation_payload = {
+            "name": name,
+            "protein_data": protein_data,
+            "project_uuid": project_uuid,
+        }
         final_response = client.post("/protein", json=creation_payload)
         final_response.raise_for_status()
@@ -189,7 +193,7 @@ def upload_protein(name: str, file_path: Path) -> Protein:
         return Protein(**final_response.json())
-def create_protein_from_pdb_id(name: str, code: str, project_uuid: str) -> Protein:
+def create_protein_from_pdb_id(name: str, code: str, project_uuid: str | None = None) -> Protein:
     """
     Creates a protein from a PDB ID.

{rowan_python-2.1.1 → rowan_python-2.1.3}/rowan/workflow.py RENAMED Viewed

@@ -387,20 +387,21 @@ def submit_basic_calculation_workflow(
     if isinstance(method, str):
         method = stjames.Method(method)
-    workflow_data = {
-        "settings": {
-            "method": method.name,
-            "tasks": tasks,
-            "mode": mode,
-        },
-        "engine": engine,
-    }
+    workflow = stjames.BasicCalculationWorkflow(
+        initial_molecule=initial_molecule,
+        settings=stjames.Settings(
+            method=method,
+            tasks=tasks,
+            mode=mode,
+        ),
+        engine=engine,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "basic_calculation",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -466,19 +467,20 @@ def submit_conformer_search_workflow(
         optimization_settings=[opt_settings],
     )
-    workflow_data = {
-        "multistage_opt_settings": msos.model_dump(),
-        "conf_gen_mode": conf_gen_mode,
-        "mso_mode": "manual",
-        "solvent": solvent,
-        "transition_state": transition_state,
-    }
+    workflow = stjames.ConformerSearchWorkflow(
+        initial_molecule=initial_molecule,
+        multistage_opt_settings=msos,
+        conf_gen_mode=conf_gen_mode,
+        mso_mode="manual",
+        solvent=solvent,
+        transition_state=transition_state,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "conformer_search",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -516,13 +518,17 @@ def submit_solubility_workflow(
     if not temperatures:
         temperatures = [273.15, 298.15, 323.15, 348.15, 373.15]
-    workflow_data = {"solvents": solvents, "temperatures": temperatures}
+    workflow = stjames.SolubilityWorkflow(
+        initial_smiles=initial_smiles,
+        solvents=solvents,
+        temperatures=temperatures,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "solubility",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_smiles": initial_smiles,
         "max_credits": max_credits,
     }
@@ -567,18 +573,19 @@ def submit_pka_workflow(
     protonate_elements = protonate_elements or [7]
     deprotonate_elements = deprotonate_elements or [7, 8, 16]
-    workflow_data = {
-        "pka_range": pka_range,
-        "deprotonate_elements": deprotonate_elements,
-        "protonate_elements": protonate_elements,
-        "mode": mode,
-    }
+    workflow = stjames.pKaWorkflow(
+        initial_molecule=initial_molecule,
+        pka_range=pka_range,
+        deprotonate_elements=deprotonate_elements,
+        protonate_elements=protonate_elements,
+        mode=mode,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "pka",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -618,17 +625,18 @@ def submit_redox_potential_workflow(
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
-    workflow_data = {
-        "oxidation": oxidization,
-        "reduction": reduction,
-        "mode": mode,
-    }
+    workflow = stjames.RedoxPotentialWorkflow(
+        initial_molecule=initial_molecule,
+        oxidation=oxidization,
+        reduction=reduction,
+        mode=mode,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "redox_potential",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -669,6 +677,12 @@ def submit_fukui_workflow(
     optimization_settings = stjames.Settings(method=optimization_method)
     fukui_settings = stjames.Settings(method=fukui_method, solvent_settings=solvent_settings)
+    stjames.FukuiIndexWorkflow(
+        initial_molecule=initial_molecule,
+        optimization_settings=optimization_settings,
+        fukui_settings=fukui_settings,
+    )
     workflow_data = {
         "opt_settings": optimization_settings.model_dump(),
         "opt_engine": stjames.Method(optimization_method).default_engine(),
@@ -716,15 +730,16 @@ def submit_tautomer_search_workflow(
     elif isinstance(initial_molecule, RdkitMol):
         initial_molecule = StJamesMolecule.from_rdkit(initial_molecule, cid=0)
-    workflow_data = {
-        "mode": mode,
-    }
+    workflow = stjames.TautomerWorkflow(
+        initial_molecule=initial_molecule,
+        mode=mode,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "tautomers",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -805,24 +820,27 @@ def submit_scan_workflow(
     if isinstance(calculation_method, str):
         calculation_method = stjames.Method(calculation_method)
-    workflow_data = {
-        "wavefront_propagation": wavefront_propagation,
-        "scan_settings": scan_settings,
-        "calc_engine": calculation_engine,
-        "calc_settings": {
-            "method": calculation_method.name,
-            "corrections": [],
-            "tasks": ["optimize"],
-            "mode": "auto",
-            "opt_settings": {"constraints": []},
-        },
-    }
+    calc_settings = stjames.Settings(
+        method=calculation_method,
+        tasks=["optimize"],
+        corrections=[],
+        mode="auto",
+        opt_settings={"constraints": []},
+    )
+    workflow = stjames.ScanWorkflow(
+        initial_molecule=initial_molecule,
+        scan_settings=scan_settings,
+        calc_settings=calc_settings,
+        calc_engine=calculation_engine,
+        wavefront_propagation=wavefront_propagation,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "scan",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -860,19 +878,20 @@ def submit_macropka_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,
-    }
+    workflow = stjames.MacropKaWorkflow(
+        initial_smiles=initial_smiles,
+        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,
+        "workflow_data": workflow.model_dump(),
         "initial_smiles": initial_smiles,
         "max_credits": max_credits,
     }
@@ -920,25 +939,25 @@ def submit_irc_workflow(
     if isinstance(method, str):
         method = stjames.Method(method)
-    workflow_data = {
-        "settings": {
-            "method": method.name,
-            "tasks": [],
-            "corrections": [],
-            "mode": "auto",
-        },
-        "engine": engine,
-        "preopt": preopt,
-        "step_size": step_size,
-        "max_irc_steps": max_irc_steps,
-        "mode": "manual",
-    }
+    workflow = stjames.IRCWorkflow(
+        initial_molecule=initial_molecule,
+        settings=stjames.Settings(
+            method=method,
+            tasks=[],
+            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,
         "workflow_type": "irc",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }
@@ -975,19 +994,20 @@ def submit_protein_cofolding_workflow(
     :return: A Workflow object representing the submitted workflow.
     :raises requests.HTTPError: if the request to the API fails.
     """  # noqa: E501
-    workflow_data = {
-        "use_msa_server": use_msa_server,
-        "use_potentials": use_potentials,
-        "model": model,
-        "ligand_binding_affinity_index": ligand_binding_affinity_index,
-        "initial_smiles_list": initial_smiles_list,
-        "initial_protein_sequences": initial_protein_sequences,
-    }
+    workflow = stjames.ProteinCofoldingWorkflow(
+        use_msa_server=use_msa_server,
+        use_potentials=use_potentials,
+        model=model,
+        ligand_binding_affinity_index=ligand_binding_affinity_index,
+        initial_smiles_list=initial_smiles_list,
+        initial_protein_sequences=initial_protein_sequences,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "protein_cofolding",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "max_credits": max_credits,
     }
@@ -1029,18 +1049,19 @@ def submit_docking_workflow(
     if isinstance(protein, Protein):
         protein = protein.uuid
-    workflow_data = {
-        "target_uuid": protein,
-        "pocket": pocket,
-        "do_csearch": do_csearch,
-        "do_optimization": do_optimization,
-    }
+    workflow = stjames.DockingWorkflow(
+        initial_molecule=initial_molecule,
+        target_uuid=protein,
+        pocket=pocket,
+        do_csearch=do_csearch,
+        do_optimization=do_optimization,
+    )
     data = {
         "name": name,
         "folder_uuid": folder_uuid,
         "workflow_type": "docking",
-        "workflow_data": workflow_data,
+        "workflow_data": workflow.model_dump(),
         "initial_molecule": initial_molecule,
         "max_credits": max_credits,
     }