cyanea-struct 0.1.0

Protein and nucleic acid 3D structures for the Cyanea bioinformatics ecosystem
Documentation

cyanea-struct

Protein and nucleic acid 3D structure analysis: parsing, geometry, secondary structure, superposition, and validation.

What's Inside

  • PDB parsing -- ATOM/HETATM records into Structure/Chain/Residue/Atom hierarchy
  • mmCIF parsing -- PDBx/mmCIF format with loop_ construct handling
  • Geometry -- distances, bond angles, dihedral angles, center of mass, RMSD
  • Secondary structure -- simplified and full DSSP assignment from backbone dihedrals
  • Kabsch superposition -- optimal rotation/translation alignment with RMSD
  • Contact maps -- CA-only and all-atom (minimum distance) residue contact matrices
  • Ramachandran validation -- phi/psi classification (favored/allowed/outlier/glycine/proline)
  • B-factor analysis -- per-residue/per-chain statistics, flexibility Z-scores

Quick Start

[dependencies]
cyanea-struct = "0.1"

use cyanea_struct::{parse_pdb, kabsch, assign_secondary_structure};

let structure = parse_pdb(pdb_text).unwrap();
let chain = &structure.chains[0];
let ss = assign_secondary_structure(chain).unwrap();

println!("{} residues, {} chains", chain.residues.len(), structure.chains.len());

Feature Flags

Flag Default Description
std Yes Standard library support (file I/O)
wasm No WASM target marker
serde No Serialize/Deserialize derives
parallel No Rayon parallelism

Modules

Module Description
types Point3D, Atom, Residue, Chain, Structure
pdb PDB format parser
mmcif mmCIF/PDBx format parser
geometry Distance, angle, dihedral, center of mass, RMSD
secondary DSSP-based secondary structure assignment
superposition Kabsch optimal alignment
contact Contact map computation (CA and all-atom)
ramachandran Ramachandran region validation
analysis B-factor statistics and flexibility scoring

See Also