Can't resolve "trans-2-EICOSENE"

[fedebenelli]

print("trans-2-EICOSENE")
ug.get_groups(ug.joback, NAME)

IndexError                                Traceback (most recent call last)
Cell In[201], [line 5](vscode-notebook-cell:?execution_count=201&line=5)
      [1](vscode-notebook-cell:?execution_count=201&line=1) # df = pd.DataFrame({"id":names, **params})
      [2](vscode-notebook-cell:?execution_count=201&line=2) # df.to_csv("pures/only_dens/params.csv", index=False)
      [4](vscode-notebook-cell:?execution_count=201&line=4) print(NAME)
----> [5](vscode-notebook-cell:?execution_count=201&line=5) ug.get_groups(ug.joback, NAME)

File ~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:52, in get_groups(model, identifier, identifier_type)
     [32](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:32) """Obtain the FragmentationModel's subgroups of an RDkit Mol object.
     [33](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:33) 
     [34](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:34) Parameters
   (...)
     [49](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:49)     FragmentationModel's subgroups
     [50](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:50) """
     [51](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:51) # RDKit Mol object
---> [52](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:52) mol_object = instantiate_mol_object(identifier, identifier_type)
     [54](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:54) # =========================================================================
     [55](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:55) # Direct detection of groups presence and occurences
     [56](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:56) # =========================================================================
     [57](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:57) groups, groups_ocurrences = detect_groups(
     [58](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:58)     mol_object=mol_object, model=model
     [59](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_model_groups.py:59) )

File ~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_rdkit_object.py:37, in instantiate_mol_object(identifier, identifier_type)
...
---> [37](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_rdkit_object.py:37)     pcp_object = pcp.get_compounds(identifier, identifier_type)[0]
     [38](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_rdkit_object.py:38)     smiles = pcp_object.canonical_smiles
     [39](https://file+.vscode-resource.vscode-cdn.net/home/ruther/docs/research/thermo/algos/yaeos-fitting/~/docs/programming/python/virtualenvs/thermo/lib/python3.12/site-packages/ugropy/core/get_rdkit_object.py:39)     chem_object = Chem.MolFromSmiles(smiles)

[SalvadorBrandolin]

The identifier "trans-2-EICOSENE" doesn't figure in PubChem. The IndexError is from pubchempy I have to give a better error message. Using 2-Eicosene works.

[SalvadorBrandolin]

Now on the dev branch, the error message is improved.

from ugropy import joback

joback.get_groups("trans-2-EICOSENE")

File ~/code/ugropy/ugropy/core/get_rdkit_object.py:42, in instantiate_mol_object(identifier, identifier_type)
     40         chem_object = Chem.MolFromSmiles(smiles)
     41     except IndexError:
---> 42         raise ValueError(
     43             f"Could not find a molecule with the name '{identifier}' on "
     44             "PubChem"
     45         )
     47 elif identifier_type.lower() == "mol":
     48     chem_object = identifier

ValueError: Could not find a molecule with the name 'trans-2-EICOSENE' on PubChem