We derive energy and momentum flux expressions, for systems composed of a general class of semi-flexible molecules, in the Ciccotti-Ferrario-Ryckaert linear constraint formalism. According to this formalism, the whole set of Cartesian coordinates is divided into basic (independent) and secondary (dependent) subsets. It is found that energy and momentum flux vectors have a simple and general expression using both basic and secondary coordinates. In the case of non-equilibrium molecular dynamics, we give general and simple heat and shear flow algorithms, deriving the dissipative fluxes in the space of all Cartesian coordinates. In comparison with previous derivations for some models of flexible molecules, the present approach has more general applicability. Moreover, it leads to more efficient equilibrium and non-equilibrium molecular dynamics calculations of transport coefficients, and requires minimal programming effort.