Crate cyanea_struct 

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

• PDB parsing — Read macromolecular structure files with pdb::parse_pdb
• mmCIF parsing — Read PDBx/mmCIF files with mmcif::parse_mmcif
• Coordinate geometry — Distance, angle, dihedral, RMSD in geometry
• Secondary structure — Simplified and full DSSP assignment in secondary
• Superposition — Kabsch structural alignment in superposition
• Contact maps — Residue-residue contact analysis in contact
• Ramachandran — Backbone dihedral validation in ramachandran
• B-factor analysis — Flexibility scoring in analysis

Quick start

use cyanea_struct::pdb::parse_pdb;
use cyanea_struct::types::Structure;
use cyanea_core::Summarizable;

let pdb_text = "\
HEADER                                                        1TST
ATOM      1  N   ALA A   1       1.000   2.000   3.000  1.00  0.00           N
ATOM      2  CA  ALA A   1       2.000   2.000   3.000  1.00  0.00           C
ATOM      3  C   ALA A   1       3.000   2.000   3.000  1.00  0.00           C
ATOM      4  O   ALA A   1       3.000   3.000   3.000  1.00  0.00           O
TER
END
";

let structure = parse_pdb(pdb_text).unwrap();
assert_eq!(structure.chain_count(), 1);
assert!(structure.summary().contains("1TST"));

Re-exports

pub use analysis::chain_bfactors;

pub use analysis::flexibility_score;

pub use analysis::residue_bfactors;

pub use analysis::BFactorStats;

pub use contact::compute_contact_map;

pub use contact::compute_contact_map_allatom;

pub use contact::ContactMap;

pub use geometry::angle;

pub use geometry::angle_points;

pub use geometry::center_of_mass;

pub use geometry::dihedral;

pub use geometry::dihedral_points;

pub use geometry::distance;

pub use mmcif::parse_mmcif;

pub use pdb::parse_pdb;

pub use ramachandran::ramachandran_report;

pub use ramachandran::validate_ramachandran;

pub use ramachandran::RamachandranRegion;

pub use secondary::assign_secondary_structure;

pub use secondary::backbone_dihedrals;

pub use secondary::dssp;

pub use secondary::DsspAssignment;

pub use secondary::DsspState;

pub use secondary::SecondaryStructure;

pub use secondary::SecondaryStructureAssignment;

pub use superposition::kabsch;

pub use superposition::kabsch_points;

pub use superposition::SuperpositionResult;

pub use types::Atom;

pub use types::Chain;

pub use types::Point3D;

pub use types::Residue;

pub use types::Structure;

Modules

analysis

B-factor analysis for macromolecular structures.

contact

Residue-residue contact maps.

geometry

Coordinate geometry: distances, angles, dihedrals, RMSD.

mmcif

mmCIF/PDBx format parser.

pdb

PDB format parser.

ramachandran

Ramachandran plot validation.

secondary

Secondary structure assignment using DSSP-like algorithms.

superposition

Structural superposition via the Kabsch algorithm.

types

Core types for macromolecular 3D structure representation.