A parser for SBML
Project description
A parser for SBML
This is a parser for the Systems Biology Markup Language (SBML):
Example
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.
[dependencies.rust_sbml]
version = "0.3.0"
default_features=false
Python
It has only been tested on Linux.
Using pip
pip install rust_sbml
From source
Clone the repository.
git clone https://github.com/carrascomj/rust_sbml.git
You need maturin for building it.
python -m pip install maturin
- Build locally
maturin build --release pip install .
- Build on virtualenv (no pip install required)
# --release can be omitted to speed up compilation time maturin develop --release
Having it installed, you can use it as a normal Python package.
from rust_sbml import Model
sbml = Model("examples/EcoliCore.xml")
reaction = sbml.getListOfReactions()[0]
print(reaction.getListOfReactants())
Milestone
-
getListOfSpecies()
(id, name) -
getListOfCompartments()
(id, name) -
getListOfReactions()
(id, name)-
.getListOfReactants()
(id, name) - .
getListOfProducts()
(id, name)
-
- Capable of retrieving FBC bounds.
- Published to pypi
- Kinetic Laws.
- Metadata.
- Test suite with python calls.
- Test suite with libsbml comparison trough cobrapy.
Project details
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