ioNERDSS

ioNERDSS provides a Python-first interface for assembling NERDSS models from structures, managing simulation inputs, and analyzing simulation outputs.

What is documented here

  • The supported top-level API exposed by import ionerdss as ion
  • The current structure-to-model pipeline under ionerdss.model.pdb
  • Simulation utilities in ionerdss.nerdss_simulation
  • Analysis tools in ionerdss.analysis
  • The ODE pipeline for reaction-network kinetics

Core workflow

  1. Build a System from a PDB identifier or a local structure file.
  2. Export NERDSS files and optional visualizations into a workspace.
  3. Run or modify a NERDSS simulation from that workspace.
  4. Analyze outputs with the Analyzer API.

Quick start

import ionerdss as ion

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

simulation = ion.Simulation("6bno_dir/nerdss_files")
simulation.print_inp_file()

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

Where to go next

  • Start with Getting Started for install and local preview steps.
  • Use Tutorials for the maintained notebooks in tutorials/.
  • Browse API Reference for module-level details pulled from the package docstrings.