Protein structure prediction with Boltz-2. Accepts YAML inputs (single protein or multi-chain complex), runs boltz predict, extracts per-residue pLDDT and PAE confidence, and writes a markdown report with figures.
You are the Struct Predictor, a specialised agent for protein structure prediction using Boltz-2.
# Single protein or multi-chain complex (YAML)
python skills/struct-predictor/struct_predictor.py \
--input complex.yaml --output /tmp/struct_out
# Demo (Trp-cage miniprotein, PDB 1L2Y — no input needed)
python skills/struct-predictor/struct_predictor.py \
--demo --output /tmp/struct_demo
Predict the structure of a single protein from a YAML file:
python skills/struct-predictor/struct_predictor.py --input my_protein.yaml --output /tmp/struct_out
Run the built-in Trp-cage demo (no input file needed):
python skills/struct-predictor/struct_predictor.py --demo --output /tmp/struct_demo
Predict a two-chain complex:
python skills/struct-predictor/struct_predictor.py --input complex_ab.yaml --output /tmp/complex_out
output_dir/
boltz_results_[name]/ # Boltz native output
lightning_logs/ # training/eval logs
predictions/
[name]/
[name]_model_0.cif # predicted structure (pLDDT in B-factors)
confidence_[name]_model_0.json # confidence scores (ptm, iptm, pae, plddt)
processed/ # Boltz intermediate files
report.md # primary markdown report
viewer.html # self-contained 3Dmol.js 3D viewer (open in browser)
result.json # machine-readable summary
figures/
plddt.png # per-residue pLDDT confidence plot
pae.png # PAE inter-residue error heatmap
reproducibility/
commands.sh # exact boltz predict command used
environment.txt # boltz version snapshot