Top-Level API

These are the main objects and helpers exposed from import ionerdss as ion.

Public entry points

  • build_system_from_pdb: convenience wrapper for the structure-to-system pipeline.
  • System: top-level molecular system container with registries and JSON serialization.
  • Simulation: helper for editing and running a NERDSS workspace.
  • Analyzer: entry point for post-processing simulation outputs.
  • ODEPipelineConfig: configuration object for ODE solves.
  • run_ode_pipeline: execute the ODE workflow.
  • platonic_solid_generator: build a platonic-solid-based model.
  • build_system_from_plat: convenience helper for platonic solid workflows.
  • prepare_structure_validation_for_system: export the irreversible one-copy validation setup.
  • compare_structure_to_design: align observed coordinates against the design target and report RMSD.
  • StructureValidationConfig: configuration dataclass for the validation workflow.
  • StructureValidationArtifacts: generated files and metadata from validation export.
  • StructureAlignmentResult: output object returned by rigid alignment.
  • visualize_trajectory_ovito: render XYZ trajectories to GIFs with OVITO.
  • convert_simularium: export simulation outputs to Simularium.

build_system_from_pdb

import ionerdss as ion

system = ion.build_system_from_pdb(
    source="4v6x",
    workspace_path="4v6x_dir",
    ode_enabled=True,
    count_transition=True,
)

Parameters

  • source: PDB identifier such as "4v6x" or a local PDB/mmCIF path.
  • workspace_path: output directory for generated files. Defaults to <source>_dir.
  • fetch_format: optional remote structure format.
  • molecule_counts: optional explicit counts for NERDSS export.
  • structure_validation: if True, export a one-copy-per-type validation setup during the build.
  • structure_validation_options: optional settings forwarded to the validation export workflow.
  • **hyperparams_kwargs: any field accepted by PDBModelHyperparameters.

Returns

A populated System object ready for export, simulation setup, or analysis.

Structure validation helpers

prepare_structure_validation_for_system

Prepare the special validation deck that exports one representative copy per molecule type, forces off-rates to zero, adds titration behavior, and writes the designed target coordinates for later comparison.

Typical return values are packaged in StructureValidationArtifacts, including:

  • chosen molecule counts
  • designed coarse-grained coordinates
  • target JSON file path
  • generated NERDSS input files

compare_structure_to_design

Rigidly align observed coarse-grained coordinates onto the design target and compute RMSD.

This function accepts either:

  • dictionaries keyed by molecule type
  • ordered coordinate arrays

It returns a StructureAlignmentResult containing labels, RMSD, the rotation and translation, and the aligned coordinates.

Rendering and export helpers

visualize_trajectory_ovito

Render an XYZ trajectory using OVITO and optionally save it as a GIF. This requires the ovito_rendering optional extra.

convert_simularium

Convert supported simulation outputs into Simularium files for interactive 3D viewing.