A parser for SBML

This is a parser for the Systems Biology Markup Language (SBML): * Standalone Rust library * Python API

Example

rust let example=r#"<?xml version="1.0" encoding="UTF-8"?> <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2"> <model timeUnits="second" extentUnits="mole" substanceUnits="mole"> </model> </sbml>"#; let result = parse_document(example);

Getting started

Rust

Add it to your Cargo.toml with no default features to avoid all PyO3 nuisances.

toml [dependencies.rust_sbml] version = "0.3.0" default_features=false

Python

It has only been tested on Linux.

Using pip

shell pip install rust_sbml

From source

Clone the repository. shell git clone https://github.com/carrascomj/rust_sbml.git You need maturin for building it. shell python -m pip install maturin * Build locally shell maturin build --release pip install . * Build on virtualenv (no pip install required) shell # --release can be omitted to speed up compilation time maturin develop --release

Having it installed, you can use it as a normal Python package.

```python from rust_sbml import Model

sbml = Model("examples/EcoliCore.xml") reaction = sbml.getListOfReactions()[0] print(reaction.getListOfReactants()) ```

Milestone

• [x] getListOfSpecies() (id, name)
• [x] getListOfCompartments() (id, name)
• [x] getListOfReactions() (id, name)
  • [x] .getListOfReactants() (id, name)
  • [x] .getListOfProducts() (id, name)
• [x] Capable of retrieving FBC bounds.
• [x] Published to pypi
• [ ] Kinetic Laws.
• [ ] Metadata.
• [x] Test suite with python calls.
• [x] Test suite with libsbml comparison trough cobrapy.