public static double [ ] [ ] getMatrix ( IAtomContainer container ) { IBond bond = null ; int indexAtom1 ; int indexAtom2 ; double [ ] [ ] conMat = new double [ container . getAtomCount ( ) ] [ container . getAtomCount ( ) ] ; for ( int f = 0 ; f < container . getBondCount ( ) ; f ++ ) { bond = container . getBond ( f ) ; indexAtom1 = container . indexOf ( bond . getBegin ( ) ) ; indexAtom2 = container . indexOf ( bond . getEnd ( ) ) ; conMat [ indexAtom1 ] [ indexAtom2 ] = BondManipulator . destroyBondOrder ( bond . getOrder ( ) ) ; conMat [ indexAtom2 ] [ indexAtom1 ] = BondManipulator . destroyBondOrder ( bond . getOrder ( ) ) ; } return conMat ; }
Returns the connection matrix representation of this AtomContainer .