Keyboard shortcuts

Press ← or → to navigate between chapters

Press S or / to search in the book

Press ? to show this help

Press Esc to hide this help

Changelog

All notable changes to this project are documented here. This project follows Keep a Changelog conventions.

[Unreleased]

[0.4.1] - 2026-06-11

Added

  • GitHub Release Linux x86_64 binary (structscope-*-x86_64-unknown-linux-gnu.tar.gz) on version tags.
  • crates.io publishing for workspace crates (cargo install structscope-cli).

[0.4.0] - 2026-06-11

Added

  • Multi-structure compare: pairwise RMSD matrix (CA atoms with sequence alignment by default) and numeric feature deltas against a chosen reference.
  • CLI command:
    • compare <input> — compare two or more structures from a file or directory; prints JSON to stdout or writes matrix.json + deltas.jsonl (or matrix.csv + deltas.csv with --format csv) to --out.
  • Reference selection (first match wins): --reference, --reference-by min:field|max:field, --auto-reference (lowest Ramachandran outliers, clashes, missing backbone), else first input.
  • --delta-fields to restrict feature delta columns; --atoms, --align, and --local for RMSD correspondence (same semantics as rmsd).
  • Ligand, interface, and quality flags shared with featurize.

[0.3.1] - 2026-06-11

Added

  • Golden fixtures and regression tests for structure quality metrics (tests/fixtures/quality/, quality_golden.rs).

[0.3.0] - 2026-06-11

Added

  • Structure quality metrics: MolProbity-style Ramachandran classification (favored / allowed / outlier, with Gly/Pro regions), steric clash detection (heavy atoms, configurable VdW overlap), and missing backbone atom checks (N, CA, C, O) over canonical and common variant residues.
  • CLI command:
    • quality <input> — per-residue quality records as JSONL (problems only by default; --all-residues for full output).
  • Structure-level quality aggregates in featurize: quality_residue_count, Ramachandran counts, clash_pair_count, and missing_backbone_residue_count.
  • --clash-overlap flag on featurize and quality (default 0.4 Å).

[0.2.0] - 2026-06-11

Added

  • Parallel execution support for structscope featurize using Rayon, allowing high-performance concurrent parsing and feature extraction controlled via a new --jobs / -j CLI flag.
  • B-factor (temperature factor) support: extended core Atom model, parsed B-factors from PDB, mmCIF, and BinaryCIF, and computed structure-level (bfactor_mean, bfactor_std, bfactor_min, bfactor_max) and residue-level statistics.
  • Advanced geometric interaction detectors: cation-pi, parallel and perpendicular pi-pi stacking, and hydrophobic carbon-carbon contacts.
  • Enhanced contact graphs: integrated chemical/geometric interactions as prioritized edges overlaying standard distance contacts.
  • New contact graph formats: added custom exporters for GML and node-link JSON formats, with automatic file extension matching.
  • Thread-safe background event and provenance logging architecture using a message-passing channel (mpsc) to safely write events to SQLite and JSONL from worker threads.
  • BinaryCIF (.bcif / .bcif.gz) parsing: a hand-written MessagePack-based decoder covering all seven column encodings (ByteArray, IntegerPacking, RunLength, Delta, FixedPoint, IntervalQuantization, StringArray) and value masks. structscope now ingests PDB, mmCIF, and BinaryCIF.
  • Structural primitives computed directly from coordinates:
    • Solvent accessible surface area (Shrake-Rupley), per-atom and total.
    • Relative solvent accessibility (RSA), per residue, normalised by residue-type maxima (Tien et al. 2013).
    • DSSP-style secondary structure (Kabsch-Sander hydrogen bonds).
    • Backbone dihedrals (phi/psi/omega).
    • Optimal superposition and RMSD (quaternion/Kabsch).
    • Typed interactions: disulfides, salt bridges, hydrogen bonds.
  • Sequence alignment primitive (Needleman-Wunsch) for residue correspondence.
  • CLI commands:
    • rmsd <reference> <mobile> — optimal-superposition RMSD over matched atoms (--atoms ca|backbone|all), with --align for sequence-based correspondence between structures of different lengths.
    • residues <input> — per-residue features (SASA, RSA, secondary structure, dihedrals) as JSONL.
    • ligands <input> — per-ligand features (SASA, binding-site residues, protein–ligand interaction counts) as JSONL.
  • Protein–ligand features: configurable ligand filter (default excludes water and common ions), structure-level protein–ligand interaction counts, binding-site residue count, and ligand SASA.
  • Protein–protein interface metrics: buried surface area (BSA), interface patch area, and Lawrence–Colman shape complementarity per contacting chain pair.
  • CLI command:
    • interfaces <input> — per chain-pair interface features (BSA, area, shape complementarity, contact and residue counts) as JSONL.
  • Structure-level interface aggregates and largest-interface fields in featurize: interface_pair_count, total and max BSA/area/SC, and largest-interface chain IDs.
  • Structure-level features: sasa_total, helix/strand/coil_residue_count, disulfide/salt_bridge/hydrogen_bond_count, buried/exposed_residue_count, ligand_sasa_total, ligand_sasa_mean, binding_site_residue_count, protein_ligand_hbond_count, protein_ligand_salt_bridge_count, protein_ligand_hydrophobic_count, protein_ligand_contact_count.

Changed

  • Breaking: ligand_count in featurize now uses the filtered ligand definition (hetero residues minus the default denylist and CLI overrides), not the raw hetero residue count.

Notes

  • All primitives emit raw quantities; downstream interpretation is left to the user. Per-residue and per-atom detail is exposed as library functions.