We are developing a standardization procedure, pushing molecules through their Kekulé forms prior to submission to tautomer enumeration/analysis - which has the merit to clearly show what double bonds and H are migrating. However, we quickly run into trouble with... imidazole, which would NOT be kekulized whatever you do - unless you add an explicit H on a nitrogen
echo "c1ncnc1"| standardizer -f smiles:u-a -c "dearomatize" returns "c1ncnc1" ??
echo "c1n([H])cnc1"| standardizer -f smiles:u-a -c "dearomatize" returns "N1C=CN=C1" - which is what we want!
However, it's a pity that one needs to explicitly add this H, which is not needed (it's not like there were some net negative charge in c1ncnc1, so the box should know that a H is missing!!). I temporarily fixed the issue by forcing a standardizer "hydrogenation" of a N atom prior ro the "dearomatize" command, and the eventual "dehydrogenize"...