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rxn.RunReactants mismatch directional bonds in a heterocycle ring #7944

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m-hyin opened this issue Oct 21, 2024 · 0 comments
Open

rxn.RunReactants mismatch directional bonds in a heterocycle ring #7944

m-hyin opened this issue Oct 21, 2024 · 0 comments
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@m-hyin
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m-hyin commented Oct 21, 2024

Describe the bug
rxn.RunReactants mismatch directional bonds in a heterocycle ring when two aromatic atoms are connected by directional bonds.

To Reproduce
from rdkit import Chem
from rdkit.Chem import rdChemReactions

rxn = rdChemReactions.ReactionFromSmarts("[O:1]=[c:2]1/[c:3](=[C:4]/[c:5]2:[c:10]:[c:9]:[c:8]:[c:7]:[c:6]:2):[s:11]:[c:12]2:[n:13]:1-[N:14]-[C:15]-[N:20]-[N:21]=2>>[S:11]=[C:12]1-[N:13]-[N:14]-[C:15]-[N:20]-[N:21]-1.[O]=[C:4]-[c:5]1:[c:10]:[c:9]:[c:8]:[c:7]:[c:6]:1.[C]-[C]-[O]-[C:2](=[O:1])-[C:3]-[Cl]")

reacts = [Chem.MolFromSmiles('[O:1]=[c:2]1/[c:3](=[CH:4]/[c:5]2[cH:6][cH:7][cH:8][cH:9][cH:10]2)[s:11][c:12]2[n:13]1[NH:14][C:15]1([CH2:16][CH2:17][CH2:18][CH2:19]1)[NH:20][N:21]=2')]

products = rxn.RunReactants(reacts)
len(products)
0

rxn.GetReactants()[0].GetBondWithIdx(1).GetBondType()
rdkit.Chem.rdchem.BondType.SINGLE
reacts[0].GetBondWithIdx(1).GetBondType()
rdkit.Chem.rdchem.BondType.AROMATIC

Expected behavior
The rxn is supposed to work for reactants and yield products. Bond 2-3 is the same directional bond by aromatic atoms ([c:2]1/[c:3]) for both rxn and reacts.

Configuration (please complete the following information):

  • RDKit version: 2024.03.4
  • OS: Windows
  • Python version (if relevant): 3.12.4
  • Are you using conda? No
  • If you are using conda, which channel did you install the rdkit from?
  • If you are not using conda: how did you install the RDKit? pip install
@m-hyin m-hyin added the bug label Oct 21, 2024
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