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Adding structured datasets for detailed performance characterization #104

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Distinct classes of molecules present different challenges for computing assembly indices. Here we add two new data sets, one composed entirely of fused rings, and one composed entirely of tree-like molecules. Both datasets contain only hydrocarbons (e.g. there are no heteroatoms), and they contain only single or double bonds.

The fused ring molecules are selected from an existing dataset: https://pubs.rsc.org/en/content/articlehtml/2024/cp/d4cp01027b

The tree-like molecules are derived from the properties of fused ring molecules. For each fused-ring molecule we construct a tree-like molecule with the same number of bonds and the same share of single vs double bonds.

This PR contains the scripts required to generate the data and the files themselves.

There are additional molecule classes that could be of interest once we have benchmarks on these data.

@colemathis colemathis requested a review from jdaymude July 25, 2025 23:50
@jdaymude jdaymude added the data Additions or modifications to reference datasets label Aug 4, 2025
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