#1333 SMILES not canonical for salts

cdk-1.4.x
closed
nobody
None
1
2014-03-14
2014-03-11
Stefan Kuhn
No

Canonicalization of smiles does not work with salts. The order of the ions seem to be arbitrary (respectively depending on order in molecule object). I attach to mol files, they are identical (and have the same inchi), but the cdk smiles generated via mdlreader/smilesgenerator are [N+].B-(Cl)(Cl)Cl/B-(Cl)(Cl)Cl.[N+]. It looks like the order of atoms matters.

2 Attachments

Discussion

  • John May

    John May - 2014-03-11

    Fixed in 1.5.-

    Cl[B-](Cl)(Cl)Cl.[NH4+] 30080715
    Cl[B-](Cl)(Cl)Cl.[NH4+] 20071971
    
     
  • John May

    John May - 2014-03-13
    • status: open --> wont-fix
     
  • John May

    John May - 2014-03-14
    • status: wont-fix --> closed