Fragmenter can generate incorrect valencies on aromatic N

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

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.