To improve RMSD clustering we apply a pre-clustering filter to remove especially noisy trajectory frames, such as those found in the high temperature regions of the folding simulations. Inclusion of a pre-clustering filter of trajectory structures has made clustering more reliable in several instances of clustering of bio molecular structures. In the preclustering filter, the user specifies a filter percentage, and analyze_foldamers optimizes a neighbor cutoff radius and neighbor density cutoff using Scipy minimize with the Nelder-14