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]"
Install proaffinity into an environment of its own: it pins numpy 1.x, which conflicts with the numpy 2 required by the OVITO renderer.
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]"
[all] covers everything except proaffinity, which needs its own environment (see above).
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.ipynbtutorials/ionerdss_tutorial_5l93.ipynbtutorials/ionerdss_tutorial_6bno.ipynbtutorials/ionerdss_tutorial_8y7s.ipynbtutorials/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.
Release files for ioNERDSS 2.2.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| ionerdss-2.2.3.tar.gz | 26.7 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| ionerdss-2.2.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 53.5 MB
Release files / ionerdss-2.2.3.tar.gz
| Download URL | ionerdss-2.2.3.tar.gz |
|---|---|
| Size | 26.7 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / ionerdss-2.2.3-py3-none-any.whl
| Download URL | ionerdss-2.2.3-py3-none-any.whl |
|---|---|
| Size | 26.8 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
