Analysis

Structural analysis lives in molex::analysis (source: src/analysis/). All analysis functions operate on entity-level types (&[Atom], &[ResidueBackbone]).

Secondary structure (analysis::ss)

DSSP-based secondary structure classification.

use molex::analysis::{detect_dssp, resolve_ss, SSType};

// Full DSSP: detect H-bonds, then classify
let (ss_types, hbonds) = detect_dssp(&backbone_residues);
// ss_types: Vec<SSType> -- one per residue (Helix, Sheet, or Coil)
// hbonds: Vec<HBond> -- backbone H-bond pairs that produced the assignment

// With optional override (e.g. from mmCIF annotation)
let ss = resolve_ss(Some(&override_ss), &backbone_residues);
// Falls back to DSSP if override is None

SSType is a Q3 classification:

pub enum SSType { Helix, Sheet, Coil }

Each variant has a .color() method returning an RGB [f32; 3] for rendering.

Short isolated segments (1-residue helix/sheet runs) are automatically merged to Coil by merge_short_segments.

SS from string

analysis::ss::from_string parses secondary structure strings (e.g. "HHHCCCEEE") into Vec<SSType>.

Bond detection (analysis::bonds)

Covalent bonds

use molex::analysis::{infer_bonds, InferredBond, BondOrder, DEFAULT_TOLERANCE};

let bonds: Vec<InferredBond> = infer_bonds(atoms, tolerance);
// InferredBond { atom_a: usize, atom_b: usize, order: BondOrder }
// BondOrder: Single, Double, Triple, Aromatic

Distance-based inference using element covalent radii with a configurable tolerance (default: DEFAULT_TOLERANCE).

Hydrogen bonds

use molex::analysis::detect_hbonds;

let hbonds: Vec<HBond> = detect_hbonds(&backbone_residues);
// HBond { donor: usize, acceptor: usize } -- residue indices

DSSP-style backbone N-H…O=C hydrogen bond detection using electrostatic energy criteria.

Disulfide bonds

use molex::analysis::{detect_disulfide_bonds, DisulfideBond};

let disulfides: Vec<DisulfideBond> = detect_disulfide_bonds(atoms);

Detects CYS SG-SG bonds by distance.

Bounding box (analysis::aabb)

use molex::analysis::Aabb;

let aabb = Aabb::from_positions(&positions)?;
aabb.center();   // Vec3 -- geometric center
aabb.extents();  // Vec3 -- size along each axis
aabb.radius();   // f32 -- bounding sphere radius

let merged = aabb.union(&other_aabb);
let combined = Aabb::from_aabbs(&[aabb1, aabb2, aabb3])?;

Also available directly on entities: entity.aabb().