#158 Better E/Z bond support needed

None
closed
nobody
None
5
2016-08-10
2010-06-10
No

While there is some support for E/Z and E_OR_Z bonds, this isn't fully supported, as far as I can tell:

  1. SMILES reading and writing (I think there is at least some support for writing the configuration across double bonds in the canonical smiles bit), but I think more is needed here.

  2. 2-D structure depiction should respect this information and render molecules accordingly.

Discussion

  • Egon Willighagen

    I fully support this feature request.

     
  • John May

    John May - 2012-10-23

    Hello 2010... we now has an object model for double bonds - check out Egon's last commit

    The next step is to add this into SMILES and include the tetrahedral chirality code.

    As another side point I've recently written a library perceive E/Z from 2D/3D coordinates. Once testing is complete it should be possible to plug this in under the CDK to allow double bond perception and better (can do pseudosymetric labels) tetrahedral perception.

    Unfortunately the second request is a little more tricky

    2-D structure depiction should respect this information and render molecules accordingly.

    I don't know much about structure layout but I'd imagine this would involve some kind of locking of coordinates around tetrahedral atoms and double bonds. Suggestions are most welcome.

    J

     
    Last edit: John May 2012-10-23
  • Egon Willighagen

    • status: open --> closed
    • Group: -->
     
  • Egon Willighagen

    Fully supported in SMILES in-/output.

     

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