System Model

System is the top-level serialized container for a generated molecular model.

What it contains

  • workspace_path
  • pdb_id
  • units
  • molecule_types
  • molecule_instances
  • interface_types
  • interface_instances

Serialization

System supports:

  • to_dict()
  • to_json()
  • from_dict()
  • from_json()

These methods preserve the model structure and rebuild internal cross-references after loading.

Inspection

  • validate_system(): returns {"errors": [...], "warnings": [...]} from basic consistency checks, such as interface types that name an unknown molecule type.
  • get_summary(): returns the registry counts and the molecule and interface type names.

Example

from ionerdss.model.components.system import System

system = System(workspace_path="workspace", pdb_id="1ABC")
system.to_json("model.json")
restored = System.from_json("model.json")