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Error when running the process_crossdock.py

See original GitHub issue

Great work! I’m having a little trouble when I run the data processing program.

****
Invariant Violation
inconsistent state
Violation occurred on line 311 in file /home/conda/feedstock_root/build_artifacts/rdkit_1649923731950/work/Code/GraphMol/Canon.cpp
Failed Expression: ((firstFromAtom2->getBeginAtomIdx() == atom2->getIdx()) ^ (secondFromAtom2->getBeginAtomIdx() == atom2->getIdx()))
****


16957/16957 successful:  17%|█████████▎                                             | 16957/99929 [00:26<02:07, 649.32it/s]
Traceback (most recent call last):
  File "process_crossdock.py", line 378, in <module>
    train_smiles = compute_smiles(lig_coords, lig_one_hot, lig_mask)
  File "process_crossdock.py", line 126, in compute_smiles
    mol = Chem.MolToSmiles(mol)
RuntimeError: Invariant Violation
	inconsistent state
	Violation occurred on line 311 in file Code/GraphMol/Canon.cpp
	Failed Expression: ((firstFromAtom2->getBeginAtomIdx() == atom2->getIdx()) ^ (secondFromAtom2->getBeginAtomIdx() == atom2->getIdx()))
	RDKIT: 2022.03.1
	BOOST: 1_74

Issue Analytics

State:
Created a year ago
Comments:7

Top GitHub Comments

2reactions

HBioquantcommented, Oct 29, 2022

I also meet the trouble. ** Open Babel Warning in PerceiveBondOrders Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is /tmp/tmp6d1d0i03)

[04:06:37]

Invariant Violation inconsistent state Violation occurred on line 306 in file /home/conda/feedstock_root/build_artifacts/rdkit_1603468918536/work/Code/GraphMol/Canon.cpp Failed Expression: ((firstFromAtom2->getBeginAtomIdx() == atom2->getIdx()) ^ (secondFromAtom2->getBeginAtomIdx() == atom2->getIdx()))

16957/16957 successful: 17%|█████▎ | 16957/99929 [00:50<04:08, 333.78it/s] Traceback (most recent call last): File “process_crossdock.py”, line 378, in <module> train_smiles = compute_smiles(lig_coords, lig_one_hot, lig_mask) File “process_crossdock.py”, line 126, in compute_smiles mol = Chem.MolToSmiles(mol) RuntimeError: Invariant Violation inconsistent state Violation occurred on line 306 in file Code/GraphMol/Canon.cpp Failed Expression: ((firstFromAtom2->getBeginAtomIdx() == atom2->getIdx()) ^ (secondFromAtom2->getBeginAtomIdx() == atom2->getIdx())) RDKIT: 2020.09.1 BOOST: 1_74

0reactions

yuanqiducommented, Dec 22, 2022

Thanks again for your patience, I have updated the code with the error-catching part.