A parser for SBML
Project description
rust_sbml
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 = "0.6.0"
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.
- (Missing) Metadata.
- Test suite with python calls.
- Test suite with libsbml comparison trough cobrapy.
License
Licensed under either of
- Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
- MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)
at your option.
Contribution
Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.
README.md is automatically generated on CI using cargo-readme. Please, modify README.tpl or lib.rs instead (check the github worflow for more details).
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
Hashes for rust_sbml-0.6.1-cp39-none-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 23b7fd36f557f23440a6f4122b22a799b6cbb5663988caf7387cd4dd5cf4eb8a |
|
MD5 | 6d97529155d1e91dcc322768bb7bcf10 |
|
BLAKE2b-256 | c0a3f796adac7fb45e9bcb73ce10d271b372974ba224df55455398661f55dd27 |
Hashes for rust_sbml-0.6.1-cp39-cp39-macosx_10_7_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | e0286325dd78b7001b39b75bc36b0c42af40d8b0b2047efd750ccf1b96dfdf15 |
|
MD5 | 62a7f7d2d9b834d54d1b375a2e695ceb |
|
BLAKE2b-256 | ca283501ae1f62cefb96664bf2ad13322ee1ff829f86dd57bc793b1bed1e5aec |
Hashes for rust_sbml-0.6.1-cp38-none-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d7994a8dfc1d28b1722812943081e8c0554e6d8a97cb2294985537020c1f7972 |
|
MD5 | 9337e0c8ee15883031f9101338b9d390 |
|
BLAKE2b-256 | 4bca858e6348ae73e4cb7d3ae42e992b9da4f82b292c6fcde179f70fef217134 |
Hashes for rust_sbml-0.6.1-cp38-cp38-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ea0fbb93a0357a16429bbcc2cce1f4489756c0243793ccd633c8e6ea6e39dc3b |
|
MD5 | a703200a18d74c42ae364e87a5863172 |
|
BLAKE2b-256 | d01d2f0b3d1d67524220a2c8a358a86e105ec23f205cee8be4432fdb45a839fc |
Hashes for rust_sbml-0.6.1-cp38-cp38-macosx_10_7_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f298f66525edc9ba58dba560235359974858555e072f62c72013d4fddd11eb7b |
|
MD5 | ece386b043f28867631fbcb553c04ba4 |
|
BLAKE2b-256 | 889dcd5db5c6f0b9df8cc8e0e42397cd51f665ba743afdfca000a81d94c0bf15 |
Hashes for rust_sbml-0.6.1-cp37-none-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 10a08dcaf36c821f3df01be7eec2c7de0105233c947a5a702ddb174430337c1a |
|
MD5 | fab7146e811a50c975c2e20902a7f40d |
|
BLAKE2b-256 | d835c9dca61da8b1c4ef34b6091575e900ccb769ed06d3c6a4c585ba860aaa38 |
Hashes for rust_sbml-0.6.1-cp37-cp37m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4fea576646031d60e9b6641e2f88f2946f5235afa7ca839e697b7b32881272ea |
|
MD5 | a88c89139540411ccd815d3c4cb7d172 |
|
BLAKE2b-256 | 814a8c1b4a02b59c30d37d64b0d8f5163ae2cfc29968e2d723a79d58332e49d6 |
Hashes for rust_sbml-0.6.1-cp37-cp37m-macosx_10_7_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f2be624002ca2727b19edd83560440f90710db5585e10b1160dd0b68b832b331 |
|
MD5 | 4827821a9fee0078b1cf55f3f77bf1af |
|
BLAKE2b-256 | db244431c1a10f1e3c2fa51d3a3f0ce7fb0171c936f2c0623c44a1a64e756af1 |
Hashes for rust_sbml-0.6.1-cp36-none-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1ef967cdd4be2558486758d8a0496277a3ca36e98de9aa7008e8e981cc327ce0 |
|
MD5 | 119d99c2da40e6126a59de974ddee88b |
|
BLAKE2b-256 | ad58a46f3f190e0dbcfc92a9998117a2194d69527798bf59ea968e2a9a945574 |
Hashes for rust_sbml-0.6.1-cp36-cp36m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8d3c1b86344c2a0bb2404db62b3dd3d9077be4af1da4d86c0bbd5fadbb2b3a2a |
|
MD5 | 4887102710f2474c26875c4689d006cc |
|
BLAKE2b-256 | db5763547d4f79b6d3dde135a3e993418aa1772d567ac25cd2ac11db6e2be745 |
Hashes for rust_sbml-0.6.1-cp36-cp36m-macosx_10_7_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c60f951699fca5cf62e7398b0eeec75015431a418751a9dccf9247f46722b21f |
|
MD5 | 235e02997d427307daedfeea08db5d00 |
|
BLAKE2b-256 | 5dc5088d9c9b3b5c19d1dd3e170a32843c70c7eeca46899c5dce79a3d068c032 |