Crate rust_sbml[−][src]
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 = "0.3.0"
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 |
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
|
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 |
Functions
PyInit_rust_sbml⚠ | This autogenerated function is called by the python interpreter when importing the module. |
parse_document | Shortcut to |