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The structure is converted into PIKAChU's molecular representation.
Observed behavior:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\general.py", line 45, in read_smiles
structure = smiles.smiles_to_structure()
File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\smiles\smiles.py", line 496, in smiles_to_structure
structure.refine_structure()
File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\chem\structure.py", line 916, in refine_structure
self.aromatic_cycles = self.find_aromatic_cycles()
File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\chem\structure.py", line 781, in find_aromatic_cycles
self.promote_lone_pairs_in_aromatic_cycles(aromatic_cycles)
File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\chem\structure.py", line 731, in promote_lone_pairs_in_aromatic_cycles
atom.promote_lone_pair_to_p_orbital()
File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\chem\atom.py", line 512, in promote_lone_pair_to_p_orbital
p_orbital = p_orbitals[-1]
IndexError: list index out of range
We used the latest version on pipy which we installed via pip install pikachu-chem.
I will build a work-around for our application for now, but I would appreciate your help a lot!
Thank you in advance!
Otto
The text was updated successfully, but these errors were encountered:
Thank you very much for pointing this out! Unfortunately, PIKAChU has not been extensively tested with sulfur-containing aromatic rings; I will take a deep dive into the code sometime before the new year and see what is going on!
Hey there!
When reading SMILES strings using PIKAChU, @Mar-Gol ran into the following problem:
Minimal example for reproduction:
Expected behavior:
Observed behavior:
pip install pikachu-chem
.I will build a work-around for our application for now, but I would appreciate your help a lot!
Thank you in advance!
Otto
The text was updated successfully, but these errors were encountered: