We describe a method and its implementation for calculating electronic structure and electron transport without approximating the structure using periodic supercells. This effectively removes spurious periodic images and interference effects. Our method is based on already established methods readily available in the nonequilibrium Green's function formalism and allows for nonequilibrium transport. We present examples of a nitrogen defect in graphene, finite voltage bias transport in a point contact to graphene, and a graphene-nanoribbon junction. This method is less costly, in terms of CPU hours, than the supercell approximation.