The ability to constructs switches, diodes and electronic mixers using polymers represents the future of nano-electronics. Unfortunately new effects must be considered when dealing with such structures. Elastic or ballistic electronic transport is no longer sufficient to model correctly the system. In this work we aim at extending the common approach to conductance by introducing inelastic transport in a fully multi-channel system where also Pauli exclusion principle is fully included. The model is then applied to Pt-H2 -Pt breaking junctions and Ni-Au-Ni structure in order to understand the potentials and the limits of this new methodology.