Scientific question

Which residue pairs are close in three dimensions—i.e. candidate contacts—for a folded chain?

What we would conclude with this

Contact maps summarize tertiary organization without a full structural model; long-range contacts often separate folded from extended states in real analyses.

Synthetic data

72 residues; 3D coordinates from a helical path with noise; pairwise Cα distances stored as an edge list. Seed: 42. See demos/scientific-structural-contacts/data/generate.py.

Approach

Rebuild the symmetric distance matrix; mark contacts where distance ≤ 8 Å and **

i − j

≥ 2** (exclude immediate sequence neighbors).

Key outputs

Reproduce

cd demos/scientific-structural-contacts
python3 data/generate.py
python3 src/run.py

Dependencies: demos/requirements.txt.