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Steps to Reproduce
Use Indigo library (Bingo cartridge). Describe environment Indigo built from master branch, commit: 1fd76de Python 3.11.3 in Ubuntu Linux
Add script or SQL to reproduce the issue
from indigo import Indigo indigo = Indigo() for mol in indigo.iterateCDXFile("US06168934-20010102-C00008.CDX"): print("heavy atoms:", mol.countHeavyAtoms()) print("smiles:", mol.smiles())
--------------------------------------------------------------------------- IndigoException Traceback (most recent call last) Cell In[18], line 6 3 indigo = Indigo() 5 for mol in indigo.iterateCDXFile("US06168934-20010102-C00008.CDX"): ----> 6 print("heavy atoms:", mol.countHeavyAtoms()) 7 print("smiles:", mol.smiles()) File [~/.pyenv/versions/3.11.3/envs/uspto-patents/lib/python3.11/site-packages/indigo/indigo/indigo_object.py:3009](https://file+.vscode-resource.vscode-cdn.net/home/eloy/patent_chem/example_files/~/.pyenv/versions/3.11.3/envs/uspto-patents/lib/python3.11/site-packages/indigo/indigo/indigo_object.py:3009), in IndigoObject.countHeavyAtoms(self) 3002 def countHeavyAtoms(self): 3003 """Molecule method returns the number of heavy atoms 3004 3005 Returns: 3006 int: heavy atom count 3007 """ -> 3009 return IndigoLib.checkResult( 3010 self._lib().indigoCountHeavyAtoms(self.id) 3011 ) File [~/.pyenv/versions/3.11.3/envs/uspto-patents/lib/python3.11/site-packages/indigo/indigo/indigo_lib.py:1001](https://file+.vscode-resource.vscode-cdn.net/home/eloy/patent_chem/example_files/~/.pyenv/versions/3.11.3/envs/uspto-patents/lib/python3.11/site-packages/indigo/indigo/indigo_lib.py:1001), in IndigoLib.checkResult(result, exception_class) 999 if result < 0: 1000 assert IndigoLib.lib -> 1001 raise exception_class(IndigoLib.lib.indigoGetLastError()) 1002 return result IndigoException: stoi
Expected behavior Molecule being parsed
Actual behavior it seems some items in CDX file fail to parse. The issue happens in several of the USPTO CDX files. I could upload more examples.
Attachments US06168934-20010102-C00008.zip
Indigo/Bingo version Indigo built from master branch, commit: 1fd76de
The text was updated successfully, but these errors were encountered:
#1159 IndigoException: stoi when reading USPTO CDX file (#1170)
2d696a2
even1024
Successfully merging a pull request may close this issue.
Steps to Reproduce
Use Indigo library (Bingo cartridge). Describe environment
Indigo built from master branch, commit: 1fd76de
Python 3.11.3 in Ubuntu Linux
Add script or SQL to reproduce the issue
Expected behavior
Molecule being parsed
Actual behavior
it seems some items in CDX file fail to parse. The issue happens in several of the USPTO CDX files. I could upload more examples.
Attachments
US06168934-20010102-C00008.zip
Indigo/Bingo version
Indigo built from master branch, commit: 1fd76de
The text was updated successfully, but these errors were encountered: