#1257 Generate Isom. SMILES from alliin ignores chiral sulfur

cdk-1.4.x
closed
John May
5
2013-12-18
2012-10-03
Ralf Stephan
No

While chiral carbons are properly dealt with, the chiral sulfur in e.g. allin or omeprazol is ignored. Input: see attached MOL. Output:
chiral SMILES: [H]OC(=O)C@(C([H])([H])S(=O)C([H])([H])C([H])=C([H])[H])N([H])[H]

Compare with http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9576089&loc=ec_rcs
which has C=CCS@CC@@HN

http://en.wikipedia.org/wiki/Sulfoxide

Discussion

  • Ralf Stephan
    Ralf Stephan
    2012-10-03

    alliin.mol

     
    Attachments
  • John May
    John May
    2012-10-03

    When it comes to SMILES... Mein Name ist Hase, Ich weiß von nichts

    However I think this might be a simple fix in the parser. Will take a look tomorrow morning.

     
  • John May
    John May
    2012-10-04

    Hi Ralf,

    Just to clarify is this bug is reading mol files and generating Isomeric SMILES?
    If it's from a mol the chirality is only currently being loaded in master.

     
  • I think we currently do not support this... the sulphur has only three neighbors, but has tetrahedral chirality because the lone pair is the fourth group, and very much fixed, unlike with NH3-like compounds...

    However, the ITetrahedralStereochemistry assumes four IAtom's ...

     
  • John May
    John May
    2012-10-04

    Definitely a tricky case. It's not to difficult to support this exact instance but there are other cases where the lone pairs play a role.

    However, the ITetrahedralStereochemistry assumes four IAtom's ...
    did we decide on the implicit hydrogen cases?

    The SMILES generator actually looks to be doing all it's own calculations on the chirality which should probably be refactored out so we can unit test just the chirality perception... thats a lot of work though.

     
  • Ralf Stephan
    Ralf Stephan
    2012-10-04

    I just checked, it's also ignored when simply drawing a sulfoxide. I know this is rare per se. However, there are more elements as part of chiral groups besides C, N, S. Just search for "chiral phosphorus".

     
  • John May
    John May
    2013-12-18

    • status: open --> closed
     
  • John May
    John May
    2013-12-18

    Resolved in > 1.5