Paper and v1 differences

Need the exact paper features?

Use the dev-v0 branch. Its environment, APIs, data, and checkpoints differ from v1.

The PrexSyn paper describes the original research system. The current v1 code keeps the projection architecture and C++ data engine but does not expose every paper feature.

Area	Paper	Current v1
Chemical-space projection	ECFP4-conditioned generation and ranking	Supported; benchmark script included
Descriptor conditioning	ECFP4, FCFP4, BRICS fragments, and physicochemical descriptors	ECFP4 and FCFP4 registered
Composite property queries	AND, OR, and NOT composition	Deprecated
Property-conditioned generation	Included	Deprecated
Molecular optimization	Query-space optimization and paper benchmarks	Standard GuacaMol tasks supported with the ECFP4 genetic sampler; composite-query tasks remain deprecated
Data engine	Multithreaded C++ generation and detokenization	Supported by PrexSyn Engine 1.1

The maintained v1 reproduction paths cover chemical-space projection and the standard molecular-optimization benchmark.