v0.4.1

chore: release v0.4.1

v0.4.0

Multi-structure comparison (Slice D).

Added

• Pairwise RMSD matrix with sequence-aligned CA atoms by default
• Feature deltas vs reference (all numeric featurize fields; --delta-fields to narrow)
• CLI: compare <input> with JSON/CSV output to stdout or --out
• Reference modes: --reference, --auto-reference, --reference-by min|max:field, or first input
• Shared ligand/interface/quality flags from featurize
• Golden fixtures for compare regression tests

See CHANGELOG.md for full details.

v0.3.1

Quality golden fixtures and version alignment.

Added

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

Fixed

• Workspace Cargo.toml version aligned with release tags

See CHANGELOG.md for full details.

v0.3.0

Structure quality metrics (Slice C).

Added

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

See CHANGELOG.md for full details.

v0.2.0

Protein–ligand and protein–protein interface features (Slices A & B).

Added

• Parallel featurize via --jobs / -j
• B-factor parsing and statistics
• Advanced interactions: cation-pi, pi-pi stacking, hydrophobic contacts
• GML and JSON graph export formats
• BinaryCIF parsing
• Structural primitives: SASA, RSA, DSSP secondary structure, dihedrals, RMSD (Kabsch), typed interactions
• CLI: rmsd, residues, ligands, interfaces
• Protein–ligand features with configurable LigandFilter
• Protein–protein interface metrics (BSA, patch area, Lawrence–Colman SC)

Changed

• Breaking: ligand_count in featurize uses filtered ligand definition

See CHANGELOG.md for full details.