API Reference¶

The current public API is concentrated around a small set of entry points:

ionerdss.build_system_from_pdb for the high-level structure-to-system workflow
ionerdss.prepare_structure_validation_for_system for exporting the one-copy validation setup
ionerdss.compare_structure_to_design for rigid-alignment RMSD checks against the design target
ionerdss.System for the serialized molecular system container
ionerdss.Simulation for editing and running NERDSS input workspaces
ionerdss.Analyzer for post-processing simulation outputs
ionerdss.ODEPipelineConfig and ionerdss.run_ode_pipeline for kinetic precomputation
ionerdss.visualize_trajectory_ovito for OVITO-based trajectory rendering
ionerdss.convert_simularium for Simularium export

Additional top-level dataclasses exposed for structure validation include:

Use the pages in this section for the currently supported import surface rather than the removed Read the Docs layout.