the problem seems to be at the level of the method "addFragmentBonds"
of GenerateFragments class.
the bond order from the mainMolecule is not trasferred to the targetMolecule.
all the bonds of the fragment are single, but with AROMATIC flag when the 
original bond was aromatic...


Dear all

I would like to export each the Murcko fragments from my molecule 
as different molfiles... I'm using this code:

GenerateFragments gf=new GenerateFragments();
gf.generateMurckoFragments(molecule, true, true, 0);
List fragments=gf.getMurckoFrameworks();
Molecule m;
for (int i=0; i<fragments.size();i++){
m = (Molecule) fragments.get(i);
MDLWriter writer = new MDLWriter(new FileWriter(new File("test"+i+".mol")));

The problem: the molecule from molfile loose any information about bond orders:

even if the smiles of the last fragment is c1cccc(c1)C5CCCC(c2nc3cc4ccccc4(nc3([nH]2)))C5,
in the MDL Mol file all the bonds are single ("1").

Is there anything missing in my script?

Thanks in advance,

Matteo Floris.

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