#93 SMILES parser doesn't deduce radical centres

None
closed
nobody
None
5
2016-08-10
2006-10-25
No

Radicals can be deduced in SMILES strings from
hydrogen-deficient atoms. E.g.

CC[CH2] == ethyl radical
CCO[O] == ethyl peroxy radical

I've tested these on OpenBabel and Marvin and both read
the SMILES correctly. CDK adds hydrogens instead.

[footnote]
Openbabel has a good Wiki page on radical SMILES
extensions at
http://openbabel.sourceforge.net/wiki/Radicals_and_SMILES_extensions.

Discussion

  • Egon Willighagen

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    user_id=25678

    Radicals are not supported in SMILES, an sich. Try it on
    depict [1]: you get an error. Funnily enough I read that OB
    wiki page some days earlier, and I read it in that it really
    was an extension. CDK does not support this extension. Yet
    at least. Default SMILES does not support it, so making this
    a feature request.

    BTW, thanx for the detailed report!

     
  • Egon Willighagen

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    user_id=25678

    I think I forgot something :)

    1.http://www.daylight.com/daycgi/depict

     
  • John May

    John May - 2016-08-10

    Tricky... these would be possible but CC[CH] for example, is that a singlet or triplet?

     
    • John May

      John May - 2016-08-10

      Using CXSMILES:
      CC[CH2] |^2:1|
      CC[CH] |^2:2|
      CC[CH] |^2:3|

       
  • John May

    John May - 2016-08-10
    • status: open --> closed
    • Group: -->
     

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