open-topoqa-featurizer

This is the sibling clean-room to open-topodockq-featurizer-environment, and the contrast between them is the point. TopoQA’s upstream code is unlicensed, so it was never read: this featurizer is reproduced from the paper alone (Han 2025, bbaf083). It emits the 172-dimensional node features — 32 conventional plus 140 element-specific persistent homology — and 11-dimensional edge features.

Because it was built from the specification rather than the code, it fixes the released code’s (x, y, y) coordinate defect by construction rather than by patch. It also means there is no bit-exact oracle here, unlike the TopoDockQ featurizer. Divergence from the upstream checkpoint is the correct outcome, not a bug, so validation is against the paper spec and structural invariants instead: 19 tests including a real mkdssp end-to-end run.

Every runtime dependency is on public channels — numpy, gudhi, biopython, and Bioconda’s dssp-environment for mkdssp — so the fixture stages just one path recipe. Verified green with a solved linux-64 lock; publishing the recipe reaches L3 or L4.