rowan-python 1.1.1__tar.gz → 1.1.4__tar.gz

{rowan_python-1.1.1 → rowan_python-1.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 1.1.1
+Version: 1.1.4
 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-1.1.1 → rowan_python-1.1.4}/pixi.lock

@@ -44,7 +44,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.0.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.10-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.5-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.5.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.23.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2024.10.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
@@ -145,7 +145,7 @@ environments:
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       - pypi: https://files.pythonhosted.org/packages/f3/26/3e1bbe954fde7ee22a6e7d31582c642aad9e84ffe4b5fb61e63b87cd326f/pydantic-2.10.4-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/8d/f0/49129b27c43396581a635d8710dae54a791b17dfc50c70164866bbf865e3/pydantic_core-2.27.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
-      - pypi: https://files.pythonhosted.org/packages/9e/c2/f80c5f3d91a7e1da7ddc0545493726a22060aa1f26f5f300dc096132f1a5/stjames-0.0.46-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/cd/4c/d2bec5035d0c101ec8a703c778e9c15a3cf7b6bb905b7c719a7911ecd6aa/stjames-0.0.47-py3-none-any.whl
       - pypi: .
       osx-arm64:
       - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.8.0-pyhd8ed1ab_0.conda
@@ -183,7 +183,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.0.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/icu-75.1-hfee45f7_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.10-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.5-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.5.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.23.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2024.10.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/kiwisolver-1.4.7-py312h6142ec9_0.conda
@@ -272,7 +272,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/f3/26/3e1bbe954fde7ee22a6e7d31582c642aad9e84ffe4b5fb61e63b87cd326f/pydantic-2.10.4-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/d3/f3/c97e80721735868313c58b89d2de85fa80fe8dfeeed84dc51598b92a135e/pydantic_core-2.27.2-cp312-cp312-macosx_11_0_arm64.whl
-      - pypi: https://files.pythonhosted.org/packages/9e/c2/f80c5f3d91a7e1da7ddc0545493726a22060aa1f26f5f300dc096132f1a5/stjames-0.0.46-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/cd/4c/d2bec5035d0c101ec8a703c778e9c15a3cf7b6bb905b7c719a7911ecd6aa/stjames-0.0.47-py3-none-any.whl
       - pypi: .
 packages:
 - kind: conda
@@ -1219,25 +1219,23 @@ packages:
   timestamp: 1733211921194
 - kind: conda
   name: importlib_resources
-  version: 6.4.5
-  build: pyhd8ed1ab_1
-  build_number: 1
+  version: 6.5.2
+  build: pyhd8ed1ab_0
   subdir: noarch
   noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.5-pyhd8ed1ab_1.conda
-  sha256: 461199e429a3db01f0a673f8beaac5e0be75b88895952fb9183f2ab01c5c3c24
-  md5: 15798fa69312d433af690c8c42b3fb36
+  url: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.5.2-pyhd8ed1ab_0.conda
+  sha256: acc1d991837c0afb67c75b77fdc72b4bf022aac71fedd8b9ea45918ac9b08a80
+  md5: c85c76dc67d75619a92f51dfbce06992
   depends:
   - python >=3.9
   - zipp >=3.1.0
   constrains:
-  - importlib-resources >=6.4.5,<6.4.6.0a0
+  - importlib-resources >=6.5.2,<6.5.3.0a0
   license: Apache-2.0
-  license_family: APACHE
   purls:
   - pkg:pypi/importlib-resources?source=hash-mapping
-  size: 32701
-  timestamp: 1733231441973
+  size: 33781
+  timestamp: 1736252433366
 - kind: conda
   name: jsonschema
   version: 4.23.0
@@ -1797,6 +1795,7 @@ packages:
   - libgcc >=13
   - ncurses >=6.5,<7.0a0
   license: BSD-2-Clause
+  license_family: BSD
   purls: []
   size: 134657
   timestamp: 1736191912705
@@ -1813,6 +1812,7 @@ packages:
   - __osx >=11.0
   - ncurses >=6.5,<7.0a0
   license: BSD-2-Clause
+  license_family: BSD
   purls: []
   size: 107634
   timestamp: 1736192034117
@@ -2364,6 +2364,7 @@ packages:
   - libgcc >=13
   - libstdcxx >=13
   license: BSD-3-Clause
+  license_family: BSD
   purls: []
   size: 8581512
   timestamp: 1736096097093
@@ -2382,6 +2383,7 @@ packages:
   - libboost >=1.86.0,<1.87.0a0
   - libcxx >=18
   license: BSD-3-Clause
+  license_family: BSD
   purls: []
   size: 6394406
   timestamp: 1736096289303
@@ -3563,6 +3565,7 @@ packages:
   - reportlab
   - sqlalchemy
   license: BSD-3-Clause
+  license_family: BSD
   purls:
   - pkg:pypi/rdkit?source=hash-mapping
   size: 19836609
@@ -3595,6 +3598,7 @@ packages:
   - reportlab
   - sqlalchemy
   license: BSD-3-Clause
+  license_family: BSD
   purls:
   - pkg:pypi/rdkit?source=hash-mapping
   size: 18523747
@@ -3757,9 +3761,9 @@ packages:
   timestamp: 1687519707123
 - kind: pypi
   name: rowan-python
-  version: 1.1.1
+  version: 1.1.2
   path: .
-  sha256: 3dde2ca599cde358e919526f776a1c5854e235152f6465b60ed1bb0b13dcbc70
+  sha256: 93e92c09a03fcce0fdad13ed38af8fc022695d9e093c292a0618470c024e0cb5
   requires_python: '>=3.8'
   editable: true
 - kind: conda
@@ -3956,9 +3960,9 @@ packages:
   timestamp: 1729066546472
 - kind: pypi
   name: stjames
-  version: 0.0.46
-  url: https://files.pythonhosted.org/packages/9e/c2/f80c5f3d91a7e1da7ddc0545493726a22060aa1f26f5f300dc096132f1a5/stjames-0.0.46-py3-none-any.whl
-  sha256: 0307c3fc6912a74cefd208db7e278fb7010180fd20ebd9e8453bf1e381d27515
+  version: 0.0.47
+  url: https://files.pythonhosted.org/packages/cd/4c/d2bec5035d0c101ec8a703c778e9c15a3cf7b6bb905b7c719a7911ecd6aa/stjames-0.0.47-py3-none-any.whl
+  sha256: dc15a6fbe7a676d7f5678012be62e94a0cf7c63f05d297181f0aba582744ae15
   requires_dist:
   - pydantic>=2.4
   - numpy

{rowan_python-1.1.1 → rowan_python-1.1.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "1.1.1"
+version = "1.1.4"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.8"

rowan_python-1.1.4/rowan/rowan_rdkit/__init__.py

@@ -0,0 +1,5 @@
+from .chem_utils import (run_pka, run_tautomers, run_conformers, run_energy, 
+run_optimize, batch_pka, batch_tautomers, batch_energy, batch_optimize, batch_conformers, run_charges, batch_charges)
+
+__all__ = ["run_pka", "run_tautomers", "run_energy", "run_conformers", "run_optimize", 
+           "batch_pka", "batch_tautomers", "batch_energy", "batch_optimize",  "batch_conformers", "run_charges", "batch_charges"]

{rowan_python-1.1.1 → rowan_python-1.1.4}/rowan/rowan_rdkit/chem_utils.py

@@ -5,7 +5,6 @@ import rowan
 import copy
 import asyncio
 import logging
-import math
 from rowan.utils import get_api_key
 import stjames
 import time
@@ -36,7 +35,7 @@ def _get_rdkit_mol_from_uuid(calculation_uuid: str) -> RdkitMol:
     rdkm = Chem.MolFromXYZBlock(stjames_mol.to_xyz())
     return rdkm
 
-def embed_rdkit_mol(rdkm: RdkitMol):
+def _embed_rdkit_mol(rdkm: RdkitMol):
     try:
         AllChem.SanitizeMol(rdkm)
     except Exception as e:
@@ -58,9 +57,9 @@ def embed_rdkit_mol(rdkm: RdkitMol):
     
     return rdkm
 
-def rdkit_to_cctk(rdkm: RdkitMol, cid: int = 0) -> cctk.Molecule:
+def _rdkit_to_cctk(rdkm: RdkitMol, cid: int = 0) -> cctk.Molecule:
     if len(rdkm.GetConformers()) == 0:
-        rdkm = embed_rdkit_mol(rdkm)
+        rdkm = _embed_rdkit_mol(rdkm)
     try:
         nums = [atom.GetAtomicNum() for atom in rdkm.GetAtoms()]
         geom = rdkm.GetConformers()[cid].GetPositions()
@@ -68,7 +67,7 @@ def rdkit_to_cctk(rdkm: RdkitMol, cid: int = 0) -> cctk.Molecule:
     except IndexError as e:
         raise ConversionError("RDKit molecule does not have a conformer with the given ID") from e
     
-def cctk_to_stjames(cmol: cctk.Molecule) -> stjames.Molecule:
+def _cctk_to_stjames(cmol: cctk.Molecule) -> stjames.Molecule:
     atomic_numbers = cmol.atomic_numbers.view(np.ndarray)
     geometry = cmol.geometry.view(np.ndarray)
     atoms = []
@@ -77,11 +76,11 @@ def cctk_to_stjames(cmol: cctk.Molecule) -> stjames.Molecule:
 
     return stjames.Molecule(atoms=atoms, charge=cmol.charge, multiplicity=cmol.multiplicity)
 
-def rdkit_to_stjames(rdkm: RdkitMol, cid: int = 0) -> stjames.Molecule:
-    cmol = rdkit_to_cctk(rdkm, cid)
-    return cctk_to_stjames(cmol)
+def _rdkit_to_stjames(rdkm: RdkitMol, cid: int = 0) -> stjames.Molecule:
+    cmol = _rdkit_to_cctk(rdkm, cid)
+    return _cctk_to_stjames(cmol)
 
-def pka(mol: RdkitMol,
+def run_pka(mol: RdkitMol,
         mode: pKaMode = "rapid",
         timeout: int = 600,
         name: str = "pKa API Workflow",
@@ -126,7 +125,7 @@ async def _single_pka(mol: RdkitMol,
     post = rowan.Workflow.submit(
         name=name,
         workflow_type="pka",
-        initial_molecule=rdkit_to_stjames(mol),
+        initial_molecule=_rdkit_to_stjames(mol),
         workflow_data={
             "pka_range": pka_range,
             "deprotonate_elements": deprotonate_elements,
@@ -168,7 +167,7 @@ async def _single_pka(mol: RdkitMol,
     return {"acidic_pkas": acidic_pkas, "basic_pkas": basic_pkas}
 
 
-def tautomers(mol: RdkitMol,
+def run_tautomers(mol: RdkitMol,
               mode: TautomerMode = "reckless",
               timeout: int = 600,
               name: str = "Tautomers API Workflow",
@@ -211,7 +210,7 @@ async def _single_tautomers(mol: RdkitMol,
     post = rowan.Workflow.submit(
         name=name,
         workflow_type="tautomers",
-        initial_molecule=rdkit_to_stjames(mol),
+        initial_molecule=_rdkit_to_stjames(mol),
         workflow_data={
             "mode": mode,
         },
@@ -238,7 +237,7 @@ async def _single_tautomers(mol: RdkitMol,
     #return relative weights too 
     return tautomers
 
-def energy(
+def run_energy(
     mol: RdkitMol,
     method: str = "aimnet2_wb97md3",
     engine: str = "aimnet2",
@@ -302,7 +301,7 @@ async def _single_energy(
     method = stjames.Method(method)
 
     if mol.GetNumConformers() == 0:
-        mol = embed_rdkit_mol(mol)
+        mol = _embed_rdkit_mol(mol)
         if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
 
@@ -314,7 +313,7 @@ async def _single_energy(
     workflow_uuids = []
     for conformer in mol.GetConformers():
         cid = conformer.GetId()
-        stjames_mol = rdkit_to_stjames(mol, cid)
+        stjames_mol = _rdkit_to_stjames(mol, cid)
         get_api_key()
         post = rowan.Workflow.submit(
             name=name,
@@ -351,7 +350,7 @@ async def _single_energy(
     return [{"conformer_index": index, "energy": energy} for index, energy in enumerate(energies)]
         
         
-def optimize(
+def run_optimize(
     mol: RdkitMol,
     method: str = "aimnet2_wb97md3",
     engine: str = "aimnet2",
@@ -424,7 +423,7 @@ async def _single_optimize(
     method = stjames.Method(method)
     
     if mol.GetNumConformers() == 0:
-        mol = embed_rdkit_mol(mol)
+        mol = _embed_rdkit_mol(mol)
         if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
 
@@ -438,7 +437,7 @@ async def _single_optimize(
     workflow_uuids = []
     for conformer in mol.GetConformers():
         cid = conformer.GetId()
-        stjames_mol = rdkit_to_stjames(mol, cid)
+        stjames_mol = _rdkit_to_stjames(mol, cid)
         get_api_key()
         post = rowan.Workflow.submit(
             name=name,
@@ -486,7 +485,7 @@ async def _single_optimize(
 
     return return_dict
 
-def conformers(mol: RdkitMol, num_conformers=10,
+def run_conformers(mol: RdkitMol, num_conformers=10,
                method: str = "aimnet2_wb97md3",
                mode: str = "rapid",
                return_energies: bool = False,
@@ -540,7 +539,7 @@ async def _single_conformers(mol: RdkitMol, num_conformers=10,
     method = stjames.Method(method)
     
     if mol.GetNumConformers() == 0:
-        mol = embed_rdkit_mol(mol)
+        mol = _embed_rdkit_mol(mol)
         if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
 
@@ -552,7 +551,7 @@ async def _single_conformers(mol: RdkitMol, num_conformers=10,
     post = rowan.Workflow.submit(
         name=name,
         workflow_type="conformer_search",
-        initial_molecule=rdkit_to_stjames(mol),
+        initial_molecule=_rdkit_to_stjames(mol),
         workflow_data={
         "conf_gen_mode": "rapid",
         "mode": mode,
@@ -608,3 +607,119 @@ async def _single_conformers(mol: RdkitMol, num_conformers=10,
         return_dict["energies"] = lowest_energies
 
     return return_dict
+
+def run_charges(
+    mol: RdkitMol,
+    method: str = "aimnet2_wb97md3",
+    engine: str = "aimnet2",
+    mode: str = "auto",
+    timeout: int = 600,
+    name: str = "Charges API Workflow",
+    folder_uuid: Optional[stjames.UUID] = None
+):
+    """
+    Computes atom-centered charges for the given molecule.
+
+    :param mol: the input molecule
+    :param method: the method with which to compute the molecule's energy
+    :raises: MethodTooSlowError if the method is invalid
+    :returns: a dictionary with the charges and the conformer index
+    """
+    return asyncio.run(_single_charges(mol, method, engine, mode, timeout, name, folder_uuid))
+
+def batch_charges(
+    mols: List[RdkitMol],
+    method: str = "aimnet2_wb97md3",
+    engine: str = "aimnet2",
+    mode: str = "auto",
+    timeout: int = 600,
+    name: str = "Charges API Workflow",
+    folder_uuid: Optional[stjames.UUID] = None
+):
+    """
+    Computes the energy for the given molecule.
+
+    :param mol: the input molecule
+    :param method: the method with which to compute the molecule's energy
+    :raises: MethodTooSlowError if the method is invalid
+    :returns: a list of dictionaries with the charges and the conformer index
+    """
+    loop = asyncio.new_event_loop()
+    asyncio.set_event_loop(loop)
+    tasks = [_single_charges(mol, method, engine, mode, timeout, name, folder_uuid) for mol in mols]
+    results = loop.run_until_complete(asyncio.gather(*tasks))
+    return results
+
+async def _single_charges(
+    mol: RdkitMol,
+    method: str = "aimnet2_wb97md3",
+    engine: str = "aimnet2",
+    mode: str = "auto",
+    timeout: int = 600,
+    name: str = "Energy API Workflow",
+    folder_uuid: Optional[stjames.UUID] = None
+):
+    """
+    Computes the energy for the given molecule.
+
+    :param mol: the input molecule
+    :param method: the method with which to compute the molecule's energy
+    :param engine: the engine
+    :param mode:
+    :param timeout: the timeout in seconds
+    :raises: MethodTooSlowError if the method is invalid
+    :returns: a dictionary with the charges and the conformer index
+    """
+    get_api_key()
+
+    method = stjames.Method(method)
+
+    if mol.GetNumConformers() == 0:
+        mol = _embed_rdkit_mol(mol)
+        if mol.GetNumConformers() == 0:
+            raise NoConformersError("This molecule has no conformers")
+
+    if method not in FAST_METHODS:
+        raise MethodTooSlowError(
+            "This method is too slow; try running this through our web interface."
+        )
+
+    workflow_uuids = []
+    for conformer in mol.GetConformers():
+        cid = conformer.GetId()
+        stjames_mol = _rdkit_to_stjames(mol, cid)
+        get_api_key()
+        post = rowan.Workflow.submit(
+            name=name,
+            workflow_type="basic_calculation",
+            initial_molecule=stjames_mol,
+            workflow_data={
+            "settings": {
+                        "method": method.value,
+                        "corrections": [],
+                        "tasks": [
+                            "charge"
+                        ],
+                        "mode": mode,
+                        "opt_settings": {
+                            "constraints": []
+                        }
+                    },
+            "engine": engine
+                },
+            folder_uuid=folder_uuid
+        )
+        
+        workflow_uuids.append(post["uuid"])
+        
+    start = time.time()
+    while not all(rowan.Workflow.is_finished(uuid) for uuid in workflow_uuids):
+        await asyncio.sleep(5)
+        if time.time() - start > timeout:
+            raise TimeoutError("Workflow timed out")
+        
+    workflow_results = [rowan.Workflow.retrieve(uuid) for uuid in workflow_uuids]
+    charges_list = [rowan.Calculation.retrieve(workflow["object_data"]["calculation_uuid"])["molecules"][-1]["mulliken_charges"] for workflow in workflow_results]
+
+    return [{"conformer_index": index, "charges": charges} for index, charges in enumerate(charges_list)]
+ 

rowan_python-1.1.1/rowan/rowan_rdkit/__init__.py

@@ -1,3 +0,0 @@
-from .chem_utils import pka, tautomers, conformers, energy, optimize, batch_pka, batch_tautomers, batch_energy, batch_optimize, batch_conformers
-
-__all__ = ["pka", "tautomers", "energy", "conformers", "optimize", "batch_pka", "batch_tautomers", "batch_energy", "batch_optimize",  "batch_conformers"]