README

This README would normally document whatever steps are necessary to get your application up and running.

What is this repository for?

• dataset used in the article "A deep graph network-enhanced sampling approach to efficiently explore the space of reduced representations of proteins"
• the setup scripts for the Wang Landau exploration of the space of CG mappings

folders

• dataset
• dgn_exploration

dataset

A folder that contains five files:

• 2_graphs_dataset.dat: it contains the structure of the two input graphs for 6d93 and 4ake
• 4ake_smaps_def_scaled.txt : values of smap for 4ake
• 6d93_smaps_def_scaled.txt : values of smap for 6d93
• 4ake_mappings_def.txt: mappings for 4ake
• 6d93_mappings_def.txt: mappings for 6d93

dgn_exploration

This folder contains the trained neural network and the python script to perform Wang Landau exploration in the space of available mappings.

1. setup a conda environment

1. create the GRAWL (deep GRAph network Wang Landau) conda environment:

   conda create -n GRAWL python=3.7 (conda create -n GRAWL_gpu python=3.7)

2. activate the desired environment. This may vary as it depends on how your shell has been configured with conda (see here)

   conda activate GRAWL (conda activate GRAWL_gpu)

3. set up the environment

   ./install_cpu.sh (./install_gpu.sh)

2. running the Wang Landau exploration of the space

The python script GRAWL.py requires a parameter file in input. Two files "parameters.dat" are already present in the folder.

python3 GRAWL.py parameters_4ake.dat

python3 GRAWL.py parameters_6d93.dat