ioNERDSS 2.2

Package for preparing NERDSS inputs and analysing outputs.

Try NERDSS / ioNERDSS online

Try NERDSS / ioNERDSS on the webserver at nerdssdemo.org without local installation.

ionerdss is a Python library for building NERDSS-ready models from structures, running simulation workflows, and analyzing simulation outputs.

Installation

Recommended: Install in an isolated environment We strongly recommend installing ioNERDSS in an isolated environment using a package manager like conda or mamba to avoid conflicts with existing Python libraries.

Using Conda

# Create a new environment with Python 3.10 or later
conda create -n ionerdss python=3.10
conda activate ionerdss

1. From PyPI

Requires Python 3.10 or later.

pip install ioNERDSS

To include optional features:

pip install "ioNERDSS[jupyter]"
pip install "ioNERDSS[ovito_rendering]"
pip install "ioNERDSS[proaffinity]"

The ODE pipeline does not require a separate extra; it is included in the main package install.

2. For development

git clone https://github.com/JohnsonBiophysicsLab/ionerdss.git
cd ionerdss
pip install -e ".[test,jupyter]"
pytest

For the full contributor environment:

pip install -e ".[all]"

To run simulations for structures generated from ioNERDSS you will also need to install NERDSS.

NERDSS installation instructions - NERDSS Github

Usage

import ionerdss as ion

system = ion.build_system_from_pdb(
    source="6bno",
    workspace_path="6bno_dir",
    ode_enabled=True,
)

analyzer = ion.Analyzer("path/to/simulation/root")
analyzer.plot.free_energy()

Tutorials

Current examples live under tutorials/ and are the supported starting point for notebook-based workflows:

• tutorials/quick_start_6bno.ipynb
• tutorials/ionerdss_tutorial_5l93.ipynb
• tutorials/ionerdss_tutorial_6bno.ipynb
• tutorials/ionerdss_tutorial_8y7s.ipynb
• tutorials/additional_examples/4yd9.ipynb

Open them locally with Jupyter:

git clone https://github.com/JohnsonBiophysicsLab/ionerdss.git
cd ionerdss
pip install -e ".[jupyter]"
jupyter lab tutorials/

Hosted documentation and tutorial index:

• Docs: johnsonbiophysicslab.github.io/ionerdss
• Tutorials page: Tutorials

Run a quick trial with our server

Go to the NERDSS server.

Documentation

The documentation site is published with GitHub Pages from the website/ folder.

To preview it locally:

pip install -e ".[docs]"
mkdocs serve -f website/mkdocs.yml

Then open http://127.0.0.1:8000/.

Running tests

pytest

Docker development environment

docker build --no-cache -t ionerdss_dev .
docker run -it --rm -v $(pwd):/app -p 8888:8888 ionerdss_dev

This creates a containerized environment with Jupyter Lab accessible at http://localhost:8888.

License

This project is licensed under the GPL-3.0 License.