EnzymeML-Rust

This is the official EnzymeML Rust library.

Warning

The library is currently under development and is not yet ready for production use.

Installation

cargo install enzymeml

Examples

Create an EnzymeML document

use enzymeml::prelude::*;

let mut enzmldoc = EnzymeMLDocumentBuilder::default();

    // Create small molecules
    let substrate = SmallMoleculeBuilder::default()
        .id("s1")
        .name("Substrate")
        .build()?;
    let product = SmallMoleculeBuilder::default()
        .id("s2")
        .name("Product")
        .build()?;

    enzmldoc.to_small_molecules(substrate);
    enzmldoc.to_small_molecules(product);

    // Create a reaction
    let reaction = build_reaction!(
        "r1",
        "Reaction",
        true,
        "s1" => -1.0,
        "s2" => 1.0
    );

    enzmldoc.to_reactions(reaction);
    
    // Create an equation
    let equation = EquationBuilder::default()
        .species_id("s1")
        .equation("v_max * s1 / (k_m + s1)")
        .build()?;
    
    enzmldoc.to_equations(equation);
    
    // Serialize the document
    let enzmldoc = enzmldoc.build()?;
    let serialized = serde_json::to_string_pretty(&enzmldoc)?;
    
    println!("{}", serialized);

Deserialize an EnzymeML document

use enzymeml::prelude::*;
use std::path::Path;

let path = Path::new("model.md");
let enzmldoc: EnzymeMLDocument = serde_json::from_reader(std::fs::File::open(path)?)?;

println!("{:#?}", enzmldoc);