PDBRust

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

Installation

[dependencies]
pdbrust = "0.3"

With optional features:

[dependencies]
pdbrust = { version = "0.3", features = ["filter", "descriptors", "rcsb", "gzip"] }

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

Feature	Description
`filter`	Filter atoms, extract chains, remove ligands, clean structures
`descriptors`	Radius of gyration, amino acid composition, geometric metrics
`quality`	Structure quality assessment (altlocs, missing residues, etc.)
`summary`	Combined quality + descriptors in one call
`rcsb`	Search and download structures from RCSB PDB
`gzip`	Parse gzip-compressed files (.ent.gz, .pdb.gz, .cif.gz)
`parallel`	Parallel processing with Rayon

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();

Parse Gzip-Compressed Files

use pdbrust::parse_gzip_pdb_file;

// Parse gzip-compressed PDB files from the PDB archive
let structure = parse_gzip_pdb_file("pdb1ubq.ent.gz")?;
println!("Atoms: {}", structure.atoms.len());

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)?;

Common Workflows

See the examples/ directory for complete working code:

Workflow	Example	Features Used
Load, clean, analyze, export	analysis_workflow.rs	filter, descriptors, quality, summary
Filter and clean structures	filtering_demo.rs	filter
Search and download from RCSB	rcsb_workflow.rs	rcsb, descriptors
Process multiple files	batch_processing.rs	descriptors, summary

Run examples with:

cargo run --example analysis_workflow --features "filter,descriptors,quality,summary"
cargo run --example filtering_demo --features "filter"
cargo run --example rcsb_workflow --features "rcsb,descriptors"
cargo run --example batch_processing --features "descriptors,summary"

For a complete getting started guide, see docs/GETTING_STARTED.md.

Performance

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

Operation	Speedup
Parsing	2-3x
get_ca_coords	240x
max_ca_distance	260x
radius_of_gyration	100x

Full PDB Archive Validation

PDBRust has been validated against the entire Protein Data Bank:

Metric	Value
Total Structures Tested	230,655
Success Rate	100%
Failed Parses	0
Total Atoms Parsed	2,057,302,767
Processing Rate	~92 files/sec
Largest Structure	2ku2 (1,290,100 atoms)

Run the full benchmark yourself:

cargo run --release --example full_pdb_benchmark \
    --features "gzip,parallel,descriptors,quality,summary" \
    -- /path/to/pdb/archive --output-dir ./results

Documentation

Citation

If you use PDBRust in your research, please cite:

@software{pdbrust,
  author = {Fooladi, Hosein},
  title = {PDBRust: A High-Performance Rust Library for PDB/mmCIF Parsing and Analysis},
  year = {2025},
  url = {https://github.com/HFooladi/pdbrust},
  version = {0.3.0}
}

Or in text format:

Fooladi, H. (2025). PDBRust: A High-Performance Rust Library for PDB/mmCIF Parsing and Analysis. https://github.com/HFooladi/pdbrust

License

MIT

pdbrust 0.3.0