Batches

Molecules have two representations.

Type	Mutability	Layout	For
MolBuilder	mutable	array of structs, one molecule	building: parsing, constructing reaction products
MolBatch	immutable	struct of arrays + CSR, across molecules	algorithms, parallelism, zero-copy export

They convert both ways through MolBatchBuilder::push and MolView::to_builder, and the round trip is identity — checked by test.

Python has Mol only

The Python Mol wraps MolBuilder. MolBatch is not wrapped yet; it is reachable from Rust today. See Python API.

Why columnar

The usual molecule graph is an adjacency list plus heap-allocated atom objects, so vertex properties live behind pointers — walking the atom properties of a 40-atom molecule is 40 random accesses.

MolBatch puts every atom's value for one property into a single contiguous array, with adjacency in CSR form. Three things follow directly from that layout:

1. Sequential access — walking a property is one contiguous scan, not a pointer chase
2. Zero copy — a column can be exposed as a numpy or Arrow buffer as is
3. Cheap parallelism — split on molecule offsets, no shared state

These are consequences of the layout and hold without measuring anything. How much end-to-end speed the layout buys is a separate question that needs benchmarks, and is not claimed here.

Index convention

Inside a batch, indices are global — continuous across molecules. That is the natural form for CSR. User-facing local indices (0-based within a molecule) come from MolView, which holds a reference to the batch plus a molecule number and copies nothing.