Rdkit: Error breaking StereoBonds in reactions

[mc-robinson]

Version '2019.09.3'

I am just noting this strange behavior where the intramolecular reaction does not seem to be allowed when disconnecting a bond to an atom that is part of a separate double bond.

Example to reproduce

mol = Chem.MolFromSmiles('Cc1ccc(C(=O)/C=C/c2cnc3ccccc3n2)cc1')
rxn = AllChem.ReactionFromSmarts('[c:1][C:2](=[O])[C:3]>>([*:1][C:2]#[N].[*:3][Mg][Cl])')
p = rxn.RunReactants((Chem.AddHs(mol),))

gives

RuntimeError: Pre-condition Violation
    bgnIdx not connected to begin atom of bond
    Violation occurred on line 283 in file Code/GraphMol/Bond.cpp
    Failed Expression: getOwningMol().getBondBetweenAtoms(getBeginAtomIdx(), bgnIdx) != nullptr
    RDKIT: 2019.09.3
    BOOST: 1_67

Though removing the outer parentheses to give rxn = AllChem.ReactionFromSmarts('[c:1][C:2](=[O])[C:3]>>[*:1][C:2]#[N].[*:3][Mg][Cl]') makes the reaction work perfectly fine. I am somewhat confused by this and appreciate any help with the issue. Thanks!

[autodataming]

[mc-robinson]

Interesting, thanks. So the main difference seems to be the version?

[autodataming]

Interesting, thanks. So the main difference seems to be the version?

You could try to run the code in the different version.

[bp-kelley]

This does look like a bug, but it isn't with the components, it appears to be with chirality:

This fails:

mol = Chem.MolFromSmiles('C(=O)/C=C/C')
rxn = AllChem.ReactionFromSmarts('[C:2](=[O])[C:3]>>[C:2]#[N][*:3]')
rxn.RunReactants([mol])

This passes:

mol = Chem.MolFromSmiles('C(=O)C=CC')
rxn = AllChem.ReactionFromSmarts('[C:2](=[O])[C:3]>>[C:2]#[N][*:3]')
rxn.RunReactants([mol])

[bp-kelley]

@greglandrum Chirality issues should get auto assigned to you :)