Crate rust_sbml[−][src]
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)
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
Structs
A compartment in SBML represents a bounded space in which species are located.
The Constraint object is a mechanism for stating the assumptions under which a model is designed to operate.
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.
InitialAssigments provide a way to declare initial values that must be computed (using a MathML expression).
A XML <message>
node.
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.
SBML model as defined in the SBML Level 3 Version 2 core.
Bucket struct to hold all units defined on the top level of
ModelRaw
.
The Flux Balance Constraints package of SBML defines extensions for the model, including the FBC Objective.
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.
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.
A species in SBML refers to a pool of entities that
Provide a way for reactions to define species as products and reactants.
A Unit object represents a reference to a (possibly transformed) base unit (see UnitSIdRef).
Enums
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 Reaction
s alone nor by
an InitialAssignment
.
SBML provides predefined base units, gathered in UnitSId
.
Alternatively, one can use arbitrary CustomUnit
s.
Functions
This autogenerated function is called by the python interpreter when importing the module.
Shortcut to Model::parse
.