BioForge

BioForge is a pure-Rust toolkit for automated preparation of biological macromolecules. It reads experimental structures (PDB/mmCIF), reconciles them with high-quality residue templates, repairs missing atoms, assigns hydrogens and termini, builds topologies, and optionally solvates the system with water and ions—all without leaving the Rust type system.

Highlights

• Template-driven accuracy – Curated TOML templates for standard amino acids, nucleotides, and water guarantee reproducible coordinates, charges, and bonding.
• High performance – Multithreaded processing (via rayon) handles million-atom systems in milliseconds; single-pass parsing, in-place mutation, and zero-copy serialization minimize overhead.
• Rich structure model – Lightweight Atom, Residue, Chain, and Structure types backed by nalgebra make geometric operations trivial.
• Format interoperability – Buffered readers/writers for PDB, mmCIF, and MOL2 plus error types that surface precise parsing diagnostics.
• Preparation pipeline – Cleaning, repairing, protonating, solvation, coordinate transforms, and topology reconstruction share a common ops::Error so workflows compose cleanly.
• WebAssembly support – Full-featured WASM bindings for modern JavaScript bundlers (Vite, webpack, Rollup); ideal for browser-based molecular viewers and web applications.
• Rust-first ergonomics – No FFI, no global mutable state beyond the lazily-loaded template store, and edition 2024 guarantees modern language features.

Processing Pipeline

Load → Clean → Repair → Hydrogenate → Solvate → Topology → Write

1. Load – io::read_pdb_structure or io::read_mmcif_structure parses coordinates with IoContext alias resolution.
2. Clean – ops::clean_structure removes waters, ions, hetero residues, or arbitrary residue names via CleanConfig.
3. Repair – ops::repair_structure realigns residues to templates and rebuilds missing heavy atoms (OXT on C-termini, OP3 on 5'-phosphorylated nucleic acids).
4. Hydrogenate – ops::add_hydrogens infers protonation states (configurable pH and histidine strategy) and reconstructs hydrogens from template anchors.
5. Solvate – ops::solvate_structure creates a periodic box, packs water on a configurable lattice, and swaps molecules for ions to satisfy a target charge.
6. Topology – ops::TopologyBuilder emits bond connectivity with peptide-link detection, nucleic backbone connectivity, and disulfide heuristics.
7. Write – io::write_pdb_structure / io::write_mmcif_structure serialize the processed structure; write_*_topology helpers emit CONECT or struct_conn records.

Quick Start

For CLI Users

Install the latest BioForge CLI binary from the releases page or via cargo:

cargo install bio-forge

Once the bioforge binary is installed, you can repair a structure in a single step:

bioforge repair -i input.pdb -o repaired.pdb

Explore the complete preparation pipeline in the user manual and browse the examples directory for runnable walkthroughs.

For Library Developers (Rust)

BioForge is also available as a library crate. Add it to your Cargo.toml dependencies:

[dependencies]
bio-forge = "0.3.1"

Example: Preparing a PDB Structure

use std::{fs::File, io::{BufReader, BufWriter}};

use bio_forge::{
    io::{
        read_pdb_structure,
        write_pdb_structure,
        write_pdb_topology,
        IoContext,
    },
    ops::{
        add_hydrogens, clean_structure, repair_structure, solvate_structure,
        CleanConfig, HydroConfig, SolvateConfig, TopologyBuilder,
    },
};

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let ctx = IoContext::new_default();
    let input = BufReader::new(File::open("input.pdb")?);
    let mut structure = read_pdb_structure(input, &ctx)?;

    clean_structure(&mut structure, &CleanConfig::water_only())?;
    repair_structure(&mut structure)?;
    add_hydrogens(&mut structure, &HydroConfig::default())?;
    solvate_structure(&mut structure, &SolvateConfig::default())?;

    let topology = TopologyBuilder::new().build(structure.clone())?;

    write_pdb_structure(BufWriter::new(File::create("prepared.pdb")?), &structure)?;
    write_pdb_topology(BufWriter::new(File::create("prepared-topology.pdb")?), &topology)?;
    Ok(())
}

Prefer mmCIF? Swap in read_mmcif_structure / write_mmcif_structure. Need to process ligands? Parse them via io::read_mol2_template and feed the resulting Template into TopologyBuilder::add_hetero_template.

For Library Developers (JavaScript/TypeScript)

Install via npm:

npm install bio-forge-wasm

Prepare a structure with the following code:

import { Structure } from "bio-forge-wasm";

const pdb = await fetch("https://files.rcsb.org/view/1UBQ.pdb").then((r) =>
  r.text()
);
const structure = Structure.fromPdb(pdb);

structure.clean({ removeWater: true });
structure.repair();
structure.addHydrogens({ hisStrategy: "network" });

const topology = structure.toTopology();
console.log(`Bonds: ${topology.bondCount}`);

Documentation

Resource	Description
CLI Manual	Command-line usage and options
JS/TS API	WebAssembly bindings reference
Rust API	Library documentation
Architecture	Internal design and algorithms
Examples	Runnable walkthroughs

License

This project is licensed under the MIT License - see the LICENSE file for details.