In this work, a general Monte Carlo framework is proposed for applying numerical knot invariants in simulations of systems containing knotted one-dimensional ring-shaped objects like polymers and vortex lines in fluids, superfluids or other quantum liquids. A general prescription for smoothing the sharp corners appearing in discrete knots consisting of segments joined together is provided. Smoothing is very important for the correct evaluation of numerical knot invariants. A discrete version of framing is adopted in order to eliminate singularities that are possibly arising when computing the invariants. The presented algorithms for smoothing, eliminating potentially dangerous singularities and speeding up the calculations are quite general and can be applied to any discrete knot defined off- or on-lattice. This is one of the first attempts to use numerical knot invariants in order to avoid potential topology breakings during the sampling process taking place in computer simulations, in which millions of knot conformations are randomly generated. As an application, the energy domain of knotted polymer rings subjected to short-range interactions is studied using the so-called Vassiliev knot invariant of degree 2.