atom.getHybridizationState()

Hello Chemaxon,

Please help me understand why the following code is not behaving:

imp.setFileName(pSDF);

mol = imp.read();

mol.aromatize(true);

mol.clean (3,"S{fine}",null);

for (int i=0; i<mol.getAtomCount(); i++)
    {
        chemaxon.struc.MolAtom atom = mol.getAtom(i);
        atom.getHybridizationState(); // always returns 0, does above aromatize call not work?

    }

Please can you tell me what the return values could be and how they relate

to the hybridization states sp/sp2/sp3 please?

Many thanks,

Daniel.

 

 

Hi,

0 value means HS_UNKNOWN, see: http://www.chemaxon.com/marvin/help/developer/beans/api/constant-values.html#chemaxon.struc.MolAtom.HS_UNKNOWN. You got this value because the sp-hybridization state hadn't been calculated yet.

Before retrieving the hybridization values, the MoleculeGraph.calcHybridization() function has to be called.

see API doc http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/struc/MolAtom.html#getHybridizationState().

You may place a mol.calcHybridization() call after aromatization and before the retrieval.

Bye,

Robert