#92 Smiles Parser/Generator Problems

closed
nobody
None
1
2012-10-08
2003-09-05
No

I'm having trouble using the smiles parser and
generator classes in org.openscience.cdk.smiles
directory, especially in creating smiles that
incorporate stereochemistry (bond up and bond down).
In addition, sometime when I generate smiles, there is
an "SP1" string in the smiles, however, the parser does
not understand the string.

Can someone please suggest a way of overcoming the
above problems and generating / parsing smiles better.

Thanks.

Discussion

  • Egon Willighagen

    Logged In: YES
    user_id=25678

    This is a algorithm inconsistency and should be considered a
    bug.

     
  • Egon Willighagen

    Logged In: YES
    user_id=25678

    I think the bug is fixed, i.e. it will not fail on
    stereochemistry, but it still cannot interpret it
    either... If you think that the bug is still existing (in
    CVS or next release), then please reopen the bug. It would
    be nice then to have the SMILES string on which it fails.