PyPI - rowan-python - Versions diffs - 2.1.2__tar.gz → 2.1.3__tar.gz - Mend

rowan-python 2.1.2tar.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-2.1.2 → rowan_python-2.1.3}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.2
+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-2.1.2 → 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-2.1.2 → rowan_python-2.1.3}/pixi.lock RENAMED Viewed

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@@ -439,17 +439,17 @@ packages:
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+- pypi: https://files.pythonhosted.org/packages/73/dd/508420fb47d09d904d962f123221bc249f64b5e56aa93d5f5f7603be475f/coverage-7.10.6-cp313-cp313-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
   name: coverage
-  version: 7.10.5
-  sha256: 2b96bfdf7c0ea9faebce088a3ecb2382819da4fbc05c7b80040dbc428df6af44
+  version: 7.10.6
+  sha256: 0f3f56e4cb573755e96a16501a98bf211f100463d70275759e73f3cbc00d4f27
   requires_dist:
   - tomli ; python_full_version <= '3.11' and extra == 'toml'
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+- pypi: https://files.pythonhosted.org/packages/eb/86/2e161b93a4f11d0ea93f9bebb6a53f113d5d6e416d7561ca41bb0a29996b/coverage-7.10.6-cp313-cp313-macosx_11_0_arm64.whl
   name: coverage
-  version: 7.10.5
-  sha256: 8002dc6a049aac0e81ecec97abfb08c01ef0c1fbf962d0c98da3950ace89b869
+  version: 7.10.6
+  sha256: 95d91d7317cde40a1c249d6b7382750b7e6d86fad9d8eaf4fa3f8f44cf171e80
   requires_dist:
   - tomli ; python_full_version <= '3.11' and extra == 'toml'
   requires_python: '>=3.9'
@@ -462,10 +462,10 @@ packages:
   name: distlib
   version: 0.4.0
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+- pypi: https://files.pythonhosted.org/packages/c1/ea/53f2148663b321f21b5a606bd5f191517cf40b7072c0497d3c92c4a13b1e/executing-2.2.1-py2.py3-none-any.whl
   name: executing
-  version: 2.2.0
-  sha256: 11387150cad388d62750327a53d3339fad4888b39a6fe233c3afbb54ecffd3aa
+  version: 2.2.1
+  sha256: 760643d3452b4d777d295bb167ccc74c64a81df23fb5e08eff250c425a4b2017
   requires_dist:
   - asttokens>=2.1.0 ; extra == 'tests'
   - ipython ; extra == 'tests'
@@ -571,10 +571,10 @@ packages:
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   requires_python: '>=3.8'
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+- pypi: https://files.pythonhosted.org/packages/08/2a/5628a99d04acb2d2f2e749cdf4ea571d2575e898df0528a090948018b726/ipython-9.5.0-py3-none-any.whl
   name: ipython
-  version: 9.4.0
-  sha256: 25850f025a446d9b359e8d296ba175a36aedd32e83ca9b5060430fe16801f066
+  version: 9.5.0
+  sha256: 88369ffa1d5817d609120daa523a6da06d02518e582347c29f8451732a9c5e72
   requires_dist:
   - colorama ; sys_platform == 'win32'
   - decorator
@@ -600,7 +600,7 @@ packages:
   - sphinx>=1.3 ; extra == 'doc'
   - typing-extensions ; extra == 'doc'
   - pytest ; extra == 'test'
-  - pytest-asyncio<0.22 ; extra == 'test'
+  - pytest-asyncio ; extra == 'test'
   - testpath ; extra == 'test'
   - packaging ; extra == 'test'
   - ipython[test] ; extra == 'test-extra'
@@ -1003,20 +1003,20 @@ packages:
   - mkdocstrings-python-legacy>=0.2.1 ; extra == 'python-legacy'
   - mkdocstrings-python>=1.16.2 ; extra == 'python'
   requires_python: '>=3.9'
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+- pypi: https://files.pythonhosted.org/packages/d5/8f/ce008599d9adebf33ed144e7736914385e8537f5fc686fdb7cceb8c22431/mkdocstrings_python-1.18.2-py3-none-any.whl
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-  version: 1.18.0
-  sha256: f5056d8afe9a9683ad0c59001df1ecd9668b51c19b9a6b4dc0ff02cc9b76265a
+  version: 1.18.2
+  sha256: 944fe6deb8f08f33fa936d538233c4036e9f53e840994f6146e8e94eb71b600d
   requires_dist:
   - mkdocstrings>=0.30
   - mkdocs-autorefs>=1.4
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   - typing-extensions>=4.0 ; python_full_version < '3.11'
   requires_python: '>=3.9'
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+- pypi: https://files.pythonhosted.org/packages/a4/8e/469e5a4a2f5855992e425f3cb33804cc07bf18d48f2db061aec61ce50270/more_itertools-10.8.0-py3-none-any.whl
   name: more-itertools
-  version: 10.7.0
-  sha256: d43980384673cb07d2f7d2d918c616b30c659c089ee23953f601d6609c67510e
+  version: 10.8.0
+  sha256: 52d4362373dcf7c52546bc4af9a86ee7c4579df9a8dc268be0a2f949d376cc9b
   requires_python: '>=3.9'
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   name: mypy
@@ -1248,10 +1248,10 @@ packages:
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   - virtualenv>=20.10.0
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-- pypi: https://files.pythonhosted.org/packages/ce/4f/5249960887b1fbe561d9ff265496d170b55a735b76724f10ef19f9e40716/prompt_toolkit-3.0.51-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/84/03/0d3ce49e2505ae70cf43bc5bb3033955d2fc9f932163e84dc0779cc47f48/prompt_toolkit-3.0.52-py3-none-any.whl
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-  version: 3.0.51
-  sha256: 52742911fde84e2d423e2f9a4cf1de7d7ac4e51958f648d9540e0fb8db077b07
+  version: 3.0.52
+  sha256: 9aac639a3bbd33284347de5ad8d68ecc044b91a762dc39b7c21095fcd6a19955
   requires_dist:
   - wcwidth
   requires_python: '>=3.8'
@@ -1481,8 +1481,8 @@ packages:
   requires_python: '>=3.9'
 - pypi: ./
   name: rowan-python
-  version: 2.1.2
-  sha256: de8a1541322c4b6721fe37f8aa52b2a8679f35670d2728089d7eee93eca9b396
+  version: 2.1.3
+  sha256: 42fdb4e667a0c2c279bbf99762920eda972eb32ca9f885b57dcf438815833ecc
   requires_dist:
   - httpx
   - stjames>=0.0.83
@@ -1491,15 +1491,15 @@ packages:
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   requires_python: '>=3.9'
   editable: true
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   name: ruff
-  version: 0.12.10
-  sha256: 1f68433c4fbc63efbfa3ba5db31727db229fa4e61000f452c540474b03de52a9
+  version: 0.12.11
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   name: ruff
-  version: 0.12.10
-  sha256: d59e58586829f8e4a9920788f6efba97a13d1fa320b047814e8afede381c6839
+  version: 0.12.11
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{rowan_python-2.1.2 → rowan_python-2.1.3}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.1.2"
+version = "2.1.3"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.9"

{rowan_python-2.1.2 → 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,
     }