How akshayuttarkarc/qupepfold works
QuPepFold is a command-line peptide-folding simulator: a user supplies an amino-acid sequence and run options, and the CLI maps the sequence to qubits, runs CVaR-VQE, evaluates the resulting bitstring distribution, and can export reports, plots, and 3D PDB structures. The core module also covers the distinct mapping, energy, circuit, simulation, and structure-generation stages. The CLI and selected core routines are sampled; some internal optimizer wiring is described by the package documentation rather than shown in the excerpts.
Main entry points: cli.py CLI orchestration · qupepfold.py State probabilities
Components 16
CLI workflow
- CLI orchestration
QuPepFold/qupepfold/cli.py
Quantum folding
- Qubit mapping
QuPepFold/qupepfold/qupepfold.py - MJ interactions
QuPepFold/qupepfold/qupepfold.py - Ansatz circuit
QuPepFold/qupepfold/qupepfold.py - CVaR optimizer
QuPepFold/qupepfold/qupepfold.py - CVaR objective
QuPepFold/qupepfold/qupepfold.py - Energy evaluation
QuPepFold/qupepfold/qupepfold.py - State probabilities
QuPepFold/qupepfold/qupepfold.py
Structure export
- 3D backbone builder
QuPepFold/qupepfold/qupepfold.py - PDB exporter
QuPepFold/qupepfold/qupepfold.py
Result outputs
- Summary and CSV
QuPepFold/qupepfold/cli.py - Plots and circuit
QuPepFold/qupepfold/cli.py - Energy breakdown
QuPepFold/qupepfold/qupepfold.py
Other components
- CLI user
- Aer simulator
- Output directory
Connections 23
- CLI user → CLI orchestration: provides options
- CLI orchestration → Qubit mapping: maps sequence
- CLI orchestration → MJ interactions: builds matrix
- CLI orchestration → CVaR optimizer: optimizes
- CVaR optimizer → Ansatz circuit: evaluates circuit
- CVaR optimizer → CVaR objective: minimizes
- CVaR objective → State probabilities: requests probabilities
- CVaR objective → Energy evaluation: scores states
- Energy evaluation → MJ interactions: reads energies
- State probabilities → Ansatz circuit: simulates
- State probabilities → Aer simulator: runs statevector
- CLI orchestration → Ansatz circuit: builds optimum circuit
- CLI orchestration → State probabilities: computes distribution
- CLI orchestration → Energy evaluation: evaluates states
- CLI orchestration → Summary and CSV: writes summaries
- CLI orchestration → Plots and circuit: renders results
- CLI orchestration → Energy breakdown: requests breakdown
- CLI orchestration → PDB exporter: exports folds
- PDB exporter → 3D backbone builder: builds coordinates
- Summary and CSV → Output directory: writes files
- Plots and circuit → Output directory: writes images
- Energy breakdown → Output directory: writes analysis
- PDB exporter → Output directory: writes PDBs