Getting Started

Install from PyPI

pip install ioNERDSS

Optional extras (for proaffinity-GNN predicition of protein-protein interaction free energy and jupyter notebook):

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

Development install

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

First model build

import ionerdss as ion

system = ion.build_system_from_pdb(
    source="5l93",
    workspace_path="5l93_dir",
    generate_visualizations=True,
    generate_nerdss_files=True,
)

The generated workspace can include:

  • structures/ for fetched or normalized structures
  • visualizations/ for coarse-grained outputs
  • nerdss_files/ for .mol files and parms.inp
  • ode_results/ when the ODE pipeline is enabled
  • logs/ for pipeline execution details

Local docs preview

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

Open http://127.0.0.1:8000/.