Problem displaying protonated amine groups/ammonium ions

I am attempting to visualize compounds in MarvinView 5.7 based of their SMILES. The compounds were downloaded from BioCyc. BioCyc leaves out hydrogens in their amine group/ammonium ion SMILES (e.g.  for ammonium chloride is  [Cl-][N+]). MarvinView then reads those compounds as nitrogen radicals (ammonium chloride would be displayed as [Cl-  NH2+]) which, of course, isn't right. I had previously been using MarvinView 3.5.1, and that version correctly displayed these type of compounds (no radicals). Is there anyway I can get MarvinView 5.7 to automatically add the extra hydrogen, so they won't be displayed as radicals? Thank you.

Hi,

I moved this topic to the structure representation forum, because it is related to SMILES import. You will get an answer soon.

Best regards,

Akos

Hi!

According to the SMILES documentation if you write an atom inside square brackets you should define the number of  implicit Hydrogen atoms. In the mentioned early version this was a bug, which is fixed.

Regarding the question how can you reach the same functionality? You should remove all radical information from the atoms and run valenceCheck on the molecule.

Here is a simple API example:

Molecule m = MolImporter.importMol("[Cl-][N+]");
for (MolAtom a : m.getAtomArray()) {
    a.setRadical(0);
}
m.valenceCheck();

I hope this helps

Andras