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ValueError('mapping overlap') triggered - unclear how #53
Description
I am trying to add atom-mapping to around 90,000 reactions, using the following code:
from rdkit import Chem
am_rxns = []
for i, smiles_rxn in enumerate(rxns):
start = time.time()
r_mol = Chem.MolFromSmiles(smiles_rxn.split('>>')[0])
for a in range(r_mol.GetNumAtoms()):
r_mol.GetAtomWithIdx(a).ClearProp('molAtomMapNumber')
p_mol = Chem.MolFromSmiles(smiles_rxn.split('>>')[1])
for a in range(p_mol.GetNumAtoms()):
p_mol.GetAtomWithIdx(a).ClearProp('molAtomMapNumber')
smiles_rxn = Chem.MolToSmiles(r_mol, canonical=True) + ">>" + Chem.MolToSmiles(p_mol, canonical=True)
chython_smiles = smiles(smiles_rxn)
chython_smiles.reset_mapping() # assign atom mappings with the chython library
regular_smiles = format(chython_smiles, 'm')
am_rxns.append(regular_smiles)
At random points during the processing of these reactions, I get the exception shown below:
File "/scratch/project_2006950/multi-step-retrosynthesis/code/multidiff/mol_utils.py", line 85, in atom_map_reaction
chython_smiles.reset_mapping() # assign atom mappings with the chython library
File "/projappl/project_2006950/retrodiffuser/lib/python3.9/site-packages/chython/algorithms/mapping/attention.py", line 109, in reset_mapping
if self.fix_mapping(): # fix common mistakes in mechanisms
File "/projappl/project_2006950/retrodiffuser/lib/python3.9/site-packages/chython/algorithms/mapping/fixmapper.py", line 67, in fix_mapping
m.remap(mapping)
File "/projappl/project_2006950/retrodiffuser/lib/python3.9/site-packages/chython/containers/molecule.py", line 331, in remap
h = super().remap(mapping, copy=copy)
File "/projappl/project_2006950/retrodiffuser/lib/python3.9/site-packages/chython/containers/graph.py", line 168, in remap
raise ValueError('mapping overlap')
What's curious is that no specific input triggers this exception, so I am unsure how to reproduce it. I got it on 4 different machines though, each time for a different reaction. When I run the code on that specific reaction again I don't get any errors... Sorry if this is not very helpful, I will write an update once I have more information. Just thought I'll share in case somebody else came across the same issue.
I am using chython version 1.78 on both Linux and Mac OS.
Activity
stsouko commentedon Jan 13, 2025
Hi, Could provide 1-2 examples, please?