Secondary Structure

The secondary_structure module classifies protein residues into helix, sheet, coil, and turn based on backbone geometry.

SSType

pub enum SSType {
    Helix,   // alpha-helix (H)
    Sheet,   // beta-strand (E)
    Coil,    // unstructured (C)
    Turn,    // hydrogen-bonded turn (T)
}

Implements From<char> for Q8-style single-letter codes and Display for the reverse mapping.

DSSP algorithm (dssp submodule)

The primary classification method. Computes hydrogen bond energies from backbone N-H…O=C geometry and assigns secondary structure based on the standard DSSP criteria.

use molex::secondary_structure::dssp;

// From a MoleculeEntity
let ss: Vec<SSType> = dssp::from_entity(&entity);

// From a Q8 string (e.g., from PDB HELIX/SHEET records)
let ss: Vec<SSType> = dssp::from_string("HHHHCCCEEEECCC");

Auto-detection (auto submodule)

Fallback method using dihedral angle (phi/psi) ranges when full DSSP is not needed:

use molex::secondary_structure::auto::detect;

let ss: Vec<SSType> = detect(&backbone_residues);

Resolution and override

The resolve() function merges DSSP output with optional per-entity Q8 overrides:

use molex::secondary_structure::{resolve, DetectionInput};

let input = DetectionInput { entity, override_q8: Some("HHHCCCEEE") };
let ss = resolve(&input);

This is the entry point used by viso’s scene metadata pipeline.