private void setActiveCenters ( IAtomContainer reactant ) throws CDKException { Iterator < IAtom > atoms = reactant . atoms ( ) . iterator ( ) ; while ( atoms . hasNext ( ) ) { IAtom atom = atoms . next ( ) ; if ( reactant . getConnectedLonePairsCount ( atom ) > 0 && reactant . getConnectedSingleElectronsCount ( atom ) == 0 ) atom . setFlag ( CDKConstants . REACTIVE_CENTER , true ) ; } }
set the active center for this molecule . The active center will be heteroatoms which contain at least one group of lone pair electrons .