Calculator for a connection matrix representation of this AtomContainer. An
adjacency matrix is a matrix of square NxN matrix, where N is the number of
atoms in the AtomContainer. If the i-th and the j-th atom in the
atomcontainer share a bond, the element i,j in the matrix is set to the
bond order value. Otherwise it is zero. See (Trinijastic, N., Chemical Graph Theory, 1992, CRC Press).