#133 Seven Membered ring preferably in different orientation

open
jchempaint (25)
5
2012-10-08
2009-09-14
pmatos
No

Hi,

When trying to draw a seven membered ring and I call clean structure. It comes out on its side. One of the bonds should be flat on the bottom with a pointy one on top.

See image attached.
P

Discussion

  • pmatos
    pmatos
    2009-09-14

     
    Attachments
  • Stefan Kuhn
    Stefan Kuhn
    2009-09-15

    This is really a problem of the SDG. I assign this to Christoph, he might have an idea if it can be done easily or how hard it is. I have no idea about the SDG.

     
  • This is a general and much more profound problem with my SDG code - the final global rotation of the outcome to a generally accepted form is not performed. I don't think this is a problem - I just never found the time to do it. If you take a steroid with some side chains and clean it up, you will see what I mean :-)
    To overcome the problem, I suggest a quick fix for the worst problem first and then work on a clean solution.
    The quick-fix would be a 2D Kabsch-Alignment (CDK code) of the outcome of the SDG to give at leat the approximately correct solution.
    For a clean solution, we would need to assemble the accepted rules for putting the axes of structures and then implement those.