Module chunk 

Atoms in chunks: columnar within a chunk, chunked across the structure.

A chunk is at once the unit of storage, of cache residency, of parallel work and of summary statistics. Sized so its hot columns stay in second-level cache while a kernel runs, it bounds the working set by the chunk rather than by the structure — a distance calculation over a ribosome touches the same amount of memory at a time as one over a lysozyme.

Structs

AtomChunk

A contiguous run of atoms, stored column by column.

AtomChunkStats

Everything a chunk knows about itself without reading a row.

AtomRecord

One atom’s worth of everything a chunk stores.

ChunkBuilder

Accumulates atoms and closes chunks at residue boundaries.

ElementMask

The set of elements present, one bit per atomic number.

Extremes

A running minimum and maximum over values that may not all be recorded.

Enums

ParentMapping

How an atom’s residue is recovered.

Constants

TARGET_CHUNK_ATOMS

Atoms per chunk before a new one is started.