[Cdk-devel] [ jchempaint-Feature Requests-838051 ] fused rings give 'wrong structure'

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Feature Requests item #838051, was opened at 2003-11-07 19:26
Message generated for change (Settings changed) made by egonw
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Category: None
Group: None
Status: Open
Priority: 5
Submitted By: Peter Murray-Rust (petermr)
Assigned to: Nobody/Anonymous (nobody)
>Summary: fused rings give 'wrong structure'

Initial Comment:
when hexagons are combined to create polycyclic 
hydrocarbons, only one bond is fused. thus if  a 
hexagon is added to the 1,8 positions of naphthalene, 
there is a picture of three fused hexagons looking like 
C1CC2CCCC3CCCC(C1)C23 but the SMILES is C1CCC23
(CCCC3(CCCC2(C1))). Using layout reveals that bonds 
are overlapped rather than being fused. I think all other 
packages assume that when template rings overlap 
exactly the bonds are fused. Perhaps JCP should give a 
visual indication of exactly overlapping bonds






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Comment By: Egon Willighagen (egonw)
Date: 2003-11-20 11:32

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Yes, but that's not really a bug... that's just a missing 
feature of auto laying out the result... If you do a 
subsequent clean up (the broom button), it should 
resolve... but I agree that it is confusing. 

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Comment By: Nobody/Anonymous (nobody)
Date: 2003-11-14 17:09

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egon, peter is talking about that specific position between
the two rings in, say, decaline (lets call them 6-ring-a and
six-ring-b, both are fused with one shared bond). Say you
fuse an additional six-ring-c to one of the two bonds in
six-ring-b that have one atom  shared by both six-ring-b and
six-ring-a. Then, the newly fused six-ring-c will share one
bond with six-ring-b, *but* due to the all-120-degree-nature
of this system, an additional atom of six-ring-c will
overlap with one atom in six-ring-a without being fused but
you cannot see it. (a painting would make it much easier :-))

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Comment By: Egon Willighagen (egonw)
Date: 2003-11-14 16:30

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Ummm... doesn't JCP do that then? When I fuse rings, the 
bond/atom at which point it is attached is highlighted 
(grey)... if only one atom is highlighten, then it only 
gets added to one atom. But maybe the highlight mechanism 
is confusing in this case? Because I could not reproduce 
the problem, I've take the latter situation as what is 
happening, and made this bug a feature request. 

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