code: 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);
      }
docs: this method calculates the angle between two bonds given coordinates of their atoms