valence problem in aromatic rings - a workaround

Problem:


aromatic N atoms may or may not have an attached implicit H


in an aromatic ring of size 5, since only one N atom in the ring


has an attached implicit H. However, sometimes I have


erronous structures drawn in Marvin, for example a


pyrrole with no attached implicit H:





n1cccc1











The correct form is:





[nH]1cccc1











How to transform the erronous pyrrole structure


n1cccc1 to the correct form [nH]1cccc1?

This happens because Marvin does not perform


a ring-search to check whether there is another N atom in the


same aromatic ring. This check is skipped for efficiency.


You can use Standardizer with the attached configuration to


perform the desired transformation:

Code:

standardize -c standardizer.xml "n1cccc1" c1cc[nH]c1

or

Code:

standardize -c "[n:1]1cccc1>>[H:2][n:1]1nccc1" "n1cccc1" c1cc[nH]c1

Another example:

Code:

standardize -c standardizer.xml "C(c1ccccc1)c2ccnc2" C(c1ccccc1)c2cc[nH]c2

or

Code:

standardize -c "[n:1]1cccc1>>[H:2][n:1]1nccc1" "C(c1ccccc1)c2ccnc2" C(c1ccccc1)c2cc[nH]c2

The standardizer configuration XML:


http://www.chemaxon.hu/forum/files/standardizer.xml