PDBRust

A fast Rust library for parsing and analyzing PDB and mmCIF protein structure files.

Installation

[dependencies]
pdbrust = "0.2"

With optional features:

[dependencies]
pdbrust = { version = "0.2", features = ["filter", "descriptors", "rcsb"] }

Quick Start

use pdbrust::{parse_pdb_file, PdbStructure};

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let structure = parse_pdb_file("protein.pdb")?;

    println!("Atoms: {}", structure.atoms.len());
    println!("Chains: {:?}", structure.get_chain_ids());

    Ok(())
}

Features

Examples

Filter and Clean Structures

use pdbrust::parse_pdb_file;

let structure = parse_pdb_file("protein.pdb")?;

// Extract CA coordinates
let ca_coords = structure.get_ca_coords(None);

// Chain operations with fluent API
let chain_a = structure
    .remove_ligands()
    .keep_only_chain("A")
    .keep_only_ca();

Compute Structural Descriptors

let structure = parse_pdb_file("protein.pdb")?;

let rg = structure.radius_of_gyration();
let max_dist = structure.max_ca_distance();
let composition = structure.aa_composition();

// Or get everything at once
let descriptors = structure.structure_descriptors();

Download from RCSB PDB

use pdbrust::rcsb::{download_structure, rcsb_search, SearchQuery, FileFormat};

// Download a structure
let structure = download_structure("1UBQ", FileFormat::Pdb)?;

// Search RCSB
let query = SearchQuery::new()
    .with_text("kinase")
    .with_organism("Homo sapiens")
    .with_resolution_max(2.0);

let results = rcsb_search(&query, 10)?;

Performance

Benchmarks against equivalent Python code show 40-260x speedups for in-memory operations:

Documentation

• API Documentation
• Examples

License

MIT