We present a general-purpose approach for calculating quantum transport properties of contact-molecule-contact systems, based on nonequilibrium surface Green's function matching. The method is quite general and may be applied to systems described at different levels of accuracy, e.g., tight binding and ab initio. The computer program TARABORD that implements the general formalism is applied to various nanoscale systems. Our results for infinite carbon chain and porphyrin tapes are shown to be in good agreement with previous studies. We further apply the method to a polythiophene-based nanodevice and explain the main features of transport characteristics in terms of the molecular energy levels and coupling to gold nanocontacts. (c) 2005 Elsevier B.V All rights reserved.