QuPepFold

QupepFold is a small, research-oriented toolkit that turns short amino-acid sequences into quantum bitstring encodings, optimizes them with a CVaR-VQE routine, and exports 3D PDB files (with CONECT records) for high-probability folds. It’s built to be easy to run, easy to inspect, and easy to tweak.

Installation and easy way to use in CLI

pip3 install qupepfold pip3 install pylatexenc

qupepfold --seq APRLFHG --tries 30 --alpha 0.025 --write-csv --out ./results

What to expect in output in terminal

Qubit mapping (config/interaction/ancilla counts) Best CVaR energy Most probable bitstring (with probability) Lowest-energy bitstring (with energy)

Results in the output folder

1. output_summary.txt — quick result summary
2. optimal_circuit.png — ansatz diagram (no measurements)
3. cvar_scatter.png — CVaR value per multi-start iteration
4. bitstring_histogram.png — bar chart for states ≥ threshol
5. bitstring_summary.csv — [bitstring, cfg_bits, probability, energy, exported_PDB3D]
6. bitstring_summary_cvar.csv — same distribution (kept for continuity)
7. most_negative_energy_breakdown.png + .csv — component energies (backbone/MJ/distance/locality) for the lowest energy state
8. pdb3d/*.pdb — one PDB per exported bitstring, with CONECT bonds
9. pdb3d_bitstrings_ge_2pct.zip — bundle of those PDBs

Uninstall

pip3 uninstall qupepfold