private double calculateAngleBetweenTwoLines ( Vector3d a , Vector3d b , Vector3d c , Vector3d d ) { Vector3d firstLine = new Vector3d ( ) ; firstLine . sub ( a , b ) ; Vector3d secondLine = new Vector3d ( ) ; secondLine . sub ( c , d ) ; Vector3d firstVec = new Vector3d ( firstLine ) ; Vector3d secondVec = new Vector3d ( secondLine ) ; return firstVec . angle ( secondVec ) ; }
this method calculates the angle between two bonds given coordinates of their atoms