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

For example,

use rust_sbml::Model;

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 = Model::parse(example);
println!("{:?}", result.unwrap());

See write_to_file.rs for an example on serializing to a file.

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())

Milestones

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.

Structs

Compartment	A compartment in SBML represents a bounded space in which species are located.
Constraint	The Constraint object is a mechanism for stating the assumptions under which a model is designed to operate.
InitialAssignment	InitialAssigments provide a way to declare initial values that must be computed (using a MathML expression).
Model	Abstraction over the SBML specification. It traverses each top-level listOF_ and provides `HashMaps<id, object>` instead. In addition the model units are gathered in an `ModelUnits` struct.
ModelRaw	SBML model as defined in the SBML Level 3 Version 2 core.
ModelUnits	Bucket struct to hold all units defined on the top level of `ModelRaw`.
Objective	The Flux Balance Constraints package of SBML defines extensions for the model, including the FBC Objective.
Parameter	A Parameter is used in SBML to define a symbol associated with a value; this symbol can then be used in mathematical formulas in a model.
Reaction	A reaction in SBML represents any kind of process that can change the quantity of one or more species in a model. Examples of such processes can include transformation, transport, molecular interactions, and more.
Species	A species in SBML refers to a pool of entities that
SpeciesReference	Provide a way for reactions to define species as products and reactants.
Unit	A Unit object represents a reference to a (possibly transformed) base unit (see UnitSIdRef).

Enums

UnitSId
UnitSIdRef	SBML provides predefined base units, gathered in `UnitSId`. Alternatively, one can use arbitrary `CustomUnit`s.

Functions

PyInit_rust_sbml ^⚠	This autogenerated function is called by the python interpreter when importing the module.
parse_document	Shortcut to `Model::parse`.

Crate rust_sbml[−][src]

Getting started

Rust