#5 SMARTS matcher does not recognize aromatic atoms

closed-fixed
None
9
2003-08-26
2003-08-26
No

SMARTS matcher does not recognize all aromatic atoms in:

Oc1c(O)c2cccc3ccc4cccc1c4c23 4,5-dihydroxypyrene
Oc1c(O)c2ccccc2c3ccccc13 9,10-dihydroxyphenanthrene

Discussion

    • status: open --> closed-fixed
     
  • Logged In: YES
    user_id=169818

    This error was caused by a bug in the aromaticity typer.
    The typer uses default bridging root atoms for
    double-checking the pre-assigned aromaticity flags. If the
    root atom is trapped by two other aromatic ring atoms, this
    can cause false negative detection of these bridging ring atoms.

    The bug fix tries to avoid bridging ring atoms for
    double-checking aromaticity, if this is not possible a
    warning will be shown for this molecule. This warning can
    only occur when the treated rings are inner rings, so this
    should not be a serious problem, because if the outer rings
    are aromatic, the inner ring must be aromatic, too. Anyway,
    the warning will be printed !