Crate rust_sbml

Source
Expand description

Parser for the Systems Biology Markup Language (SBML):

§Getting started

§Rust

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

[dependencies.rust_sbml]
version = "0.7.0"
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, with naive mathml tailored for SBML.
  • Metadata, with naive rdf tailored for SBML.
  • Test suite with python calls.
  • Test suite with libsbml comparison trough cobrapy.

Modules§

mathml
rdf

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.
FunctionDefinition
The FunctionDefinition object associates an identifier with a function definition. This identifier can then be4 used as the function called in subsequent MathML apply elements.
InitialAssignment
InitialAssigments provide a way to declare initial values that must be computed (using a MathML expression).
Message
A XML <message> node.
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§

Rule
Rules provide additional ways to define the values of variables in a model, their relationships, and the dynamical behaviors of those variables. Rules enable the encoding of relationships that cannot be expressed using Reactions alone nor by an InitialAssignment.
UnitSId
UnitSIdRef
SBML provides predefined base units, gathered in UnitSId. Alternatively, one can use arbitrary CustomUnits.

Functions§

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