Fragmenter can generate incorrect valencies on aromatic N

User 7c177bab3b

07-03-2011 17:36:32

Hi


When marking attachment points with smiles output, fragmenter does not remove the hydrogen from an aromatic nitrogen, e.g. for N-substituted pyrrole.


Using the following command:


fragment -c Fragmenter.xml tt1.smi -f smiles -p S


where tt1.smi contains "c1cccn1CC", produces:


*[nH]1cccc1
CC*


Thanks


Stephen

ChemAxon fb166edcbd

08-03-2011 13:56:25

Yes, this is a problem with special aromatic atoms and it will be fixed in the 5.5 release coming out soon. Thanks for the report.