This repository contains the script to reproduce the results of the blog post Coronavirus “SARS-CoV-2” conformational change-points detected with optical random features as well as the results of Optical Random Features versus SARS-CoV-2 Glycoprotein Trajectory: Round#2.
We advise creating a virtualenv before running these commands. You can create one with python3 -m venv <venv_name>. Activate it with source <path_to_venv>/bin/activate before proceeding. We used python 3.7for all the simulations.
- Clone the repository and then do
pip install -r requirements.txt. - Download the dataset from this page. You should put the dataset in the same folder as the repository. Otherwise, make sure to update the variable
path traj.
For replicating the results of Coronavirus “SARS-CoV-2” conformational change-points detected with optical random features: start by running
python newma_coronavirus.py
This outputs a numpy zipped archive. To analyse the results and create your own plot, use the notebook notebooks/corona_exploration.ipynb.
For replicating the results of Optical Random Features versus SARS-CoV-2 Glycoprotein Trajectory: Round#2: start by running
python newma_coronavirus_DESRES.py
This outputs a numpy zipped archive. To analyse the results and create your own plot, use the notebook notebooks/corona_exploration_DESRES.ipynb.
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All our results were obtains on a Intel(R) Xeon(R) Gold 6128 CPU @3.40GHz with 12 cores.