Menu
▾
▴
#166 Renderer2D can't draw stereochemistry inside rings
Some ring system for natural and syntetic products has
many stereo bonds inside ring systems. But Renderer2D
doesn't draw these bonds and that's wrong from a
chemist's point of view, because many rings has alpha
and beta bonds inside the rings. For examples:
cis-trans ring systems.
Logged In: YES
user_id=125666
This is an important but complex area, so it's important to
know what is reasonable. Does "stereo" relate to atom stereo
(wedge/hatch) or bond stereo - this isn't very clear (alpha
and beta suggest atom stereo, which cis/trans could be
either E/Z or atom stereo).
If the renderer already has author coordinates then
presumably it uses those. Is the problem that these are not
decorated with wedge and hatch? Or is the problem that the
wedge and hatch aren't drawn if they are cyclic?
My suggestion is that this isn't a bug as much as a topic for
discussion. (I have spent a year on a IUPAC committee
discussing this area and expect to spend 3 more, so it's
valuable to get input.)
Peter
Logged In: YES
user_id=57779
Hi Peter !
I work with sesquiterpene Lactones (STL) and I am developing
an expert system to do structural elucidation of STLs and
when I mean stereo, stereo is related to bonds. See the
attached file and you will note that stereochemistry of
lactone ring aren't corrected drawn with CDK.
"If the renderer already has author coordinates then
presumably it uses those. Is the problem that these are not
decorated with wedge and hatch? Or is the problem that the
wedge and hatch aren't drawn if they are cyclic?"
wedge and harch aren't drawn if they are cyclic, so that, if
a ring has wedge or harch bonds these decorations aren't drawn.
Ricardo.
MOL File of the STL
Logged In: YES
user_id=25678
I can confirm that cyclic bonds are now drawn with wedges.
The behaviour should be changed.
Logged In: YES
user_id=25678
Applied patch sent by Ricardo.