#166 Renderer2D can't draw stereochemistry inside rings

closed
5
2012-10-08
2004-01-26
No

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.

Discussion

  • Peter Murray-Rust

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    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

     
  • Ricardo Stefani

    Ricardo Stefani - 2004-01-26

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    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.

     
  • Ricardo Stefani

    Ricardo Stefani - 2004-01-26

    MOL File of the STL

     
  • Egon Willighagen

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    user_id=25678

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

     
  • Egon Willighagen

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    user_id=25678

    Applied patch sent by Ricardo.

     

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