structscope

Work in progress — structscope is under active development. CLI flags, feature field names, and output formats may change between releases. Pin a version tag (e.g. v0.4.1) for reproducible workflows.

structscope is a Rust-native structural bioinformatics toolkit for canonical protein structure parsing, graph-native representations, reproducible feature extraction, and analytical outputs.

This repository currently contains a bootstrap implementation with:

• workspace scaffolding for all planned crates
• crate-backed PDB, mmCIF, and BinaryCIF parsing with gzip input support
• canonical structure normalization
• residue, atom, and interface graph construction (GraphML export)
• structural primitives: solvent accessible surface area (Shrake-Rupley), DSSP-style secondary structure, backbone dihedrals, optimal superposition/RMSD (Kabsch, with optional sequence-alignment correspondence), and typed interactions (disulfides, salt bridges, hydrogen bonds, cation-pi, pi-pi stacking, hydrophobic contacts)
• configurable ligand identification (LigandFilter with default denylist and CLI overrides) and protein–ligand features: binding-site residues, cross-boundary interaction counts, and ligand SASA
• protein–protein interface metrics (BSA, interface patch area, Lawrence–Colman shape complementarity) with structure-level aggregates in featurize and per chain-pair JSONL via interfaces; distance cutoffs via --interface-distance, --interface-area-distance, and --interface-sc-distance
• structure quality checks (Ramachandran favored/allowed/outlier, steric clashes, missing backbone) with structure-level aggregates in featurize and per-residue JSONL via quality; clash threshold via --clash-overlap
• multi-structure compare: pairwise RMSD matrix and feature deltas vs a reference (compare), with flexible reference selection and JSON or CSV output
• basic and graph-derived feature extraction, with parallel batch featurize via --jobs / -j
• JSONL and Parquet feature export
• DuckDB-backed SQL querying over feature Parquet (build with --features duckdb)
• optional SQLite/JSONL provenance
• CLI entrypoints for parse, featurize, compare, interfaces, ligands, quality, graph, query, rmsd, residues, and provenance

Querying is gated behind a Cargo feature because it bundles DuckDB:

cargo build -p structscope-cli --features duckdb
structscope query <features.parquet|out-dir> --sql "SELECT * FROM features"

Install

From crates.io (builds from source):

cargo install structscope-cli

Prebuilt Linux x86_64 binaries are attached to GitHub Releases (structscope-*-x86_64-unknown-linux-gnu.tar.gz).

Feature records are exposed to SQL as a features table.

Per-ligand JSONL output:

structscope ligands complex.cif.gz --ligand-include HEM,NAG --binding-distance 4.0

Current limitations:

• the eBPF guard crate is scaffolded only
• parse reports raw hetero residue count as ligands=; featurize uses the filtered ligand definition (see Changelog)

Documentation

• CLI usage — commands and examples
• Architecture — crate layout
• Changelog

Citation

If you use structscope in academic work, please cite the repository (entry subject to change while WIP):

@software{structscope2026,
  author    = {Amirabadi, Danial Gharaie},
  title     = {{structscope}: Rust-native structural bioinformatics toolkit},
  year      = {2026},
  publisher = {GitHub},
  url       = {https://github.com/Danialgharaie/structscope},
  version   = {0.4.1},
  note      = {Work in progress. APIs and output schemas may change between releases.}
}

See also CITATION.bib.