#1201 Se.2 Atomtype - missing, or erroneous?

cdk-1.4.x
closed
None
9
2013-01-05
2012-02-02
No

The CDKAtomTypeMatcher perceives a type "Se.2", while there is no such type in the ontology

https://github.com/cdk/cdk/blob/master/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java#L250

since the case statement looks fine in the atom type matcher (in the sense that a single selenium atom does occur), presumably it got lost from the great atomtype patch flood of 2011.

Discussion

  • OK, I searched ChemSpider for neutral Se's with just one neighbor but that does not find any...

    So, shall we remove Se.2 then?

     
  • Hi, I get the same error on this compound:
    http://www.hmdb.ca/metabolites/HMDB04119
    with SMILES NC(CC[SeH])C(O)=O in cdk 1.5.0 from rcdklibs-1.5.0
    Yours, Steffen

     
  • John May
    John May
    2012-10-28

    • milestone: --> cdk-1.0.x/
    • priority: 7 --> 9
     
  • John May
    John May
    2012-10-28

    Increased priority - this needs a definitive decision. Personally I have found this error many times.

    additional patch: https://sourceforge.net/p/cdk/patches/558/

     
  • John May
    John May
    2012-10-28

    • milestone: cdk-1.0.x/ --> cdk-1.4.x/
     
  • So, just to make clear, this is the single selenium atom type, with no neighbors at all.

    Do we want to have this atom type?

     
  • John May
    John May
    2012-10-29

     
    • Ha... well, "of course" I meant an uncharged selenium atom without any neighbors :)

      Selenide is actually a different atom type, which we also do not have, according to my Groovy Cheminformatics book.. (the table in the appendix is really handy...)

       
  • Rajarshi Guha
    Rajarshi Guha
    2013-01-04

    Has this been applied to the master (ie 1.5) branch?

     
    • labels: cdk-atomtype -->
    • status: open --> closed
     
  • Yes, this patch has been applied.