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MolStandardize: uncharger failing in molecules with zwitterionic sulfone #5317

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greglandrum opened this issue May 22, 2022 · 0 comments · Fixed by #5319
Closed

MolStandardize: uncharger failing in molecules with zwitterionic sulfone #5317

greglandrum opened this issue May 22, 2022 · 0 comments · Fixed by #5319
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bug
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2022_03_3

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@greglandrum
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Describe the bug

In [46]: m = Chem.MolFromSmiles("C[S+2]([O-])([O-])C([O-])C(=O)O")

In [47]: uc = rdMolStandardize.Uncharger()

In [48]: Chem.MolToSmiles(uc.uncharge(m))
Out[48]: 'C[S+2]([O-])([O-])C([O-])C(=O)O'

That should be C[S+2]([O-])([O-])C(O)C(=O)O

Configuration (please complete the following information):

  • RDKit version: 2022.03 and master
  • OS: all
@greglandrum greglandrum added this to the 2022_03_3 milestone May 22, 2022
greglandrum added a commit to greglandrum/rdkit that referenced this issue May 22, 2022
@greglandrum
Fixes rdkit#5317
137cc5e
@greglandrum greglandrum mentioned this issue May 22, 2022
Merged
greglandrum added a commit that referenced this issue May 30, 2022
@greglandrum @ptosco
Fix a couple of problems with MolStandardize (#5319)
fb49a33 
* Fixes #5317

* Fixes #5318

* Fixes #5320

* Update Code/GraphMol/MolStandardize/Charge.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
greglandrum added a commit that referenced this issue Jun 2, 2022
@greglandrum @ptosco
Fix a couple of problems with MolStandardize (#5319)
bb96e59 
* Fixes #5317

* Fixes #5318

* Fixes #5320

* Update Code/GraphMol/MolStandardize/Charge.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
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Fix a couple of problems with MolStandardize greglandrum/rdkit
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