Accurately extracting local molecular structures is essential for understanding the mechanisms of phase and structural transitions. A promising method to characterize the local molecular structure is defining the value of the local order parameter (LOP) for each particle. This work develops the Molecular Assembly structure Learning package for Identifying Order parameters (MALIO), a machine learning package that can propose an optimal (set of) LOP(s) quickly and automatically for a huge number of LOP species and various methods of selecting neighboring particles for the calculation. We applied this package to distinguish between the nematic and smectic phases of uniaxial liquid crystal molecules, and selected candidate LOPs that could be used to precisely observe the nematic-smectic phase transition. The LOP candidates were used to observe the nucleation and subsequent percolation transition, and the effect of the choice of LOP species and neighboring particles on the statistics of local molecular structures (clusters) was examined. The procedure revealed the time evolution of the number of clusters and the dependence of the percolation curve on the number of neighboring particles for each LOP species. The LOP species with the lowest dependence on the number of neighboring particles was the best-performing LOP species in the MALIO screening strategy. These results not only show that machine learning can powerfully screen a huge number of LOP species and suggest only a few promising candidates, but also indicate that MALIO can select the best LOP species.