[Cdk-devel] connectivity problem

[Ralf S. <ra...@ar...>]

Hello,
draw a propane molecule: H3C-CH2-CH3 and replace the middle C
with a Cl or an H atom. The resulting molecule with Cl seems
to be an allowed and connected molecule (also in MSketch), while
the same with H triggers an exception on cleanup in JCP,
probably because it's not recognized as connected by the
ConnectivityChecker.

My question: before I file a bug on this, I would like to know
how H3C-H-CH3 should be treated: is it an allowed molecule,
and connected? Because if it's not allowed as a connected entity
(H bridges, DNA etc?) then the H placement should have separated
the two halves already, contrary to H3C-Cl-CH3.

Is there a consensus on this? Is H a special case?