### Local Persistent Homology

1. The data "coord_TMAO_N_F1.txt" in folder "PER_COORD_TMAO" is from the MD simulation. 

2. The matlab file "create_local_network.m" is used for the generatation of the local atom coordinates (i.e., coordinates of atoms around the central point). 
The local coordiate data ("Local_TMAO_N* .txt") is stored in "PH_INPUT_R15" folder (Note that 15 \AA is the cutoff distance). 

3. The script "ripser_script.sh" is used for the generatation of persistent barcodes, which are saved in "PH_OUT_R15" folder.

### Boltzmann Entropy
1. The matlab code "Bolzmann_entropy.m" is used for the calculation of Boltzmann Persistent Entropy (BPE). The inputs are the barcodes from folder "PH_OUT_R15".
 
