[Cdk-devel] [ cdk-Bugs-884935 ] Renderer2D can't draw stereochemistry inside rings

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Bugs item #884935, was opened at 2004-01-26 19:16
Message generated for change (Comment added) made by egonw
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Category: org.openscience.cdk.renderer
Group: None
>Status: Closed
Resolution: Accepted
Priority: 5
Submitted By: Ricardo Stefani (rstefani)
>Assigned to: Egon Willighagen (egonw)
Summary: Renderer2D can't draw stereochemistry inside rings 

Initial Comment:
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.   

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>Comment By: Egon Willighagen (egonw)
Date: 2004-01-27 12:18

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Applied patch sent by Ricardo. 

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Comment By: Egon Willighagen (egonw)
Date: 2004-01-27 08:48

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I can confirm that cyclic bonds are now drawn with wedges. 
The behaviour should be changed. 

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Comment By: Ricardo Stefani (rstefani)
Date: 2004-01-26 21:05

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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.

 

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Comment By: Peter Murray-Rust (petermr)
Date: 2004-01-26 20:16

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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


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