public static IAtomContainer createAllCarbonAllSingleNonAromaticBondAtomContainer ( IAtomContainer atomContainer ) throws CloneNotSupportedException { IAtomContainer query = ( IAtomContainer ) atomContainer . clone ( ) ; for ( int i = 0 ; i < query . getBondCount ( ) ; i ++ ) { query . getBond ( i ) . setOrder ( IBond . Order . SINGLE ) ; query . getBond ( i ) . setFlag ( CDKConstants . ISAROMATIC , false ) ; query . getBond ( i ) . setFlag ( CDKConstants . SINGLE_OR_DOUBLE , false ) ; query . getBond ( i ) . getBegin ( ) . setSymbol ( "C" ) ; query . getBond ( i ) . getBegin ( ) . setHybridization ( null ) ; query . getBond ( i ) . getEnd ( ) . setSymbol ( "C" ) ; query . getBond ( i ) . getEnd ( ) . setHybridization ( null ) ; query . getBond ( i ) . getBegin ( ) . setFlag ( CDKConstants . ISAROMATIC , false ) ; query . getBond ( i ) . getEnd ( ) . setFlag ( CDKConstants . ISAROMATIC , false ) ; } return query ; }
Generates a cloned atomcontainer with all atoms being carbon all bonds being single non - aromatic