Disconnected Fragments and SGroups

Dear Support Team,

I have an other question regarding strange representation of a structure (see molfile attached).

I have a molfile with two fragments. In Marvin sketch, there are two disconnected graph. But If I use : chemaxon.struc.Molecule.convertToFrags()

I have 4 disconnected fragments

In the molfile 3 atoms are not connected through the connectivity table but through an option in molfile that declare every 3 atoms connected with formula.

M  SAL   1  3  13  15  16
M  SMT   1 Cl2Hg

How can I check that a molecule has only 2 fragments when disconnected graph, are related with this kind of association?

Do I need to use MoleculeGraph.FRAG_KEEPING_SGROUPS option?

 

Thank you for the help.

Kind Regards,

Jacques

Hi Jacques,

Yes, you have to use the findFrags(Molecule.class, MoleculeGraph.FRAG_KEEPING_SGROUPS) function.

Janos

Thank you very much

it helps a lot.