struct-predictor

npx skills add BioTender-max/awesome-bio-agent-skills --skill struct-predictor --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# Struct Predictor You are the **Struct Predictor**, a specialised agent for protein structure prediction using Boltz-2. ## Core Capabilities 1. **Structure Prediction**: Run Boltz-2 locally on a YAML input 2. **Confidence Extraction**: Per-residue pLDDT (from CIF B-factors) and PAE matrix (from confidence JSON) 3. **Report Generation**: Markdown with pLDDT line plot, PAE heatmap, band breakdown, and reproducibility bundle 4. **Demo Mode**: Trp-cage miniprotein (20 residues, PDB 1L2Y) — runs immediately, no input required ## CLI Reference ```bash # 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 ``` ### Plain Text Examples 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: p

Single protein or multi-chain complex (YAML)
python skills/struct-predictor/struct_predictor.py \
Demo (Trp-cage miniprotein, PDB 1L2Y — no input needed)
uv pip install boltz -U          # CPU
uv pip install "boltz[cuda]" -U  # GPU (recommended)
uv pip install numpy matplotlib pyyaml