ENMs Workshop

This workshop includes the Week 1 lesson on ENMs and py-rcsb-api.

Website

This repository includes a GitHub Pages site in the repository root built from markdown files with Jekyll.

After pushing to GitHub, enable Settings -> Pages and publish from:

• Branch: your default branch
• Folder: / (root)

The site homepage will be served at: https://locitran.github.io/ENMs_workshop/

This website presents the workshop materials in a browser-friendly format, including the introduction to elastic network models, the py-rcsb-api lesson, additional theory notes, and the overall workshop outline.

GitHub Pages will render the markdown pages in the repository root automatically through Jekyll.

Website Tree

• Home: https://locitran.github.io/ENMs_workshop/
• Workshop Outline: https://locitran.github.io/ENMs_workshop/outline/
• Week 1 Introduction: https://locitran.github.io/ENMs_workshop/intro-enms/
• Week 1 py-rcsb-api: https://locitran.github.io/ENMs_workshop/py-rcsb-api/
• Two-particle motion: https://locitran.github.io/ENMs_workshop/two-particle-motion/

Files

• docs/Week1-py-rcsb-api.md: workshop notes for py-rcsb-api
• docs/Week1-ENMs-Introduction.md: ENM introduction notes
• notebooks/: source Jupyter notebooks
• notebooks-html/: exported HTML versions of the notebooks
• _layouts/, _config.yml, index.md, docs/: Jekyll site for GitHub Pages
• requirements.txt: Python packages for this workshop
• check_setup.py: simple setup test

Getting Started

1. Log in to A100

ssh -l <your_login_name> 140.114.97.192

Use your assigned login name and password.

2. Download the workshop from GitHub

Go to the directory where you want to place the repository, then run:

git clone https://github.com/locitran/ENMs_workshop.git
cd ENMs_workshop

3. Run Jupiter notebook in A100

Refer to this hackMD https://hackmd.io/Y9HZatmrSnqtHcC7X6tc-Q

4. Export notebooks to HTML

To generate HTML versions of all notebooks and store them in notebooks-html, run:

jupyter nbconvert --to html --output-dir=notebooks-html notebooks/*.ipynb

Notes:

• This keeps the source notebooks in notebooks/.
• The exported HTML files are written to notebooks-html/.
• Example: notebooks/uniprot.ipynb becomes notebooks-html/uniprot.html.
• If a notebook has saved cell outputs, figures, or tables, they will be included in the HTML export.

Setup With Conda

Please use conda for this workshop.

If you do not have Miniconda yet, follow the Miniconda section in this HackMD first: https://hackmd.io/JTdM-ho2Siqx3F01vDdkow?view#Miniconda

Then create and activate an environment:

conda create --name <your_env_name> python=<python_version>
conda activate <your_env_name>

Example:

conda create --name enm_workshop python=3.11
conda activate enm_workshop

After that, install the package requirements:

pip install -r requirements.txt

Install yanglab As A Package

The yanglab code under ENMs_workshop/yanglab can now be installed as a local Python package because this project includes a pyproject.toml.

From the ENMs_workshop directory:

cd ENMs_workshop
pip install -e . --no-build-isolation

If you also want the notebook and plotting dependencies used in the workshop:

pip install -e ".[workshop]" --no-build-isolation

You can then import the package with:

import yanglab
print(yanglab.__version__)

Test

This test should import rcsbapi and run a small example. It needs internet access.

python check_setup.py