Architecture

PILOTS is structured as:

• IO layer: readers produce canonical :c++:type:Frame objects

• Selection layer: AtomGroup + TopoGroup -> combined atom selections

• Topology layer: optional; parsed once and injected via :c++:type:SystemContext

• Algorithm layer (K): reusable graph/index/geometry + stats + mapping + polymer classifier

• SDK layer (L): handles/views + output+state helpers for measures

• Measures: physics definitions that plug into the Runner pipeline

The key goal is: adding a measure should not require changing Runner or main.