The code file is composed with : -Distance.py This script takes as input the aladip_implicit.txt file and return output, the distance matrix with conformation key at the beginning of the line: 54, 0.2545, 0.3121, 0.0123, .... , 0.14534 ... 4758, 0.1445, 0.454, 0.1511, ... , 0.2154

This script takes two arguments :

• m the number of conformation which we will focus on.
• k the number of conformation we keep to compute RMSD distance. Example: Computing RMSD with 10 000 conformations in dimension 5 000 would be : python Distance.py 10000 5000

-dataprocessing.py This script takes as input the output from Distance.py and return rsmd.txt, the distance matrix without conformation key. 0.2545, 0.3121, 0.0123, .... , 0.14534 ... 0.1445, 0.454, 0.1511, ... , 0.2154

-Vizualizing.py This script takes as input the output from Distance.py, clusters.txt from ToMATo, and dihedral.txt file, the 2D projection. This script plots the 2D projection with clusters.

-Indicate path of aladip_implicit.txt file in Distance.py -Run Distance.py with m and k arguments. -Indicate path of output file from Distance.py in dataprocessing.py -Run dataprocessing.py -Run main_w_density.cpp from ToMATo on rmsd.txt, the output file from dataprocessing.py -Indicate path of output file, clusters.txt file and dihedral.txt in vizualizing.py. -Run vizualizing.py