chemlite

Defines chemical compounds, reactions, pathways

Name	Downloads	Version	Platforms

Description

chemlite provides classes to deal with chemical compounds, reactions and metabolic pathways.

Install

From Conda

[sudo] conda install -c conda-forge -c chemlite

Use

Compound

from chemlite import Compound

c = Compound(id='test_cmpd')

The code above creates an empty compound. The following fields can be filled and accessed either at build time or later on:

• smiles
• inchi
• inchikey
• formula
• name
• infos

Reaction

from chemlite import Reaction

r = Reaction(id='test_rxn')

The code above creates an empty reaction. The following fields can be filled and accessed either at build time or later on:

• ec_numbers
• reactants
• products
• infos

The following methods are also available:

• get_smiles()
• add_reactant()
• add_product()

Pathway

from chemlite import Pathway

p = Pathway(id='test_path')

The code above creates an empty reaction. The following fields can be filled and accessed either at build time or later on:

• id
• species
• reactions

The following methods are also available:

• add_compound()
• add_reaction()
• del_reaction()
• Pathway.net_reaction()

Tests

Please follow instructions below ti run tests:

cd tests
pytest -v

For further tests and development tools, a CI toolkit is provided in ci folder (see ci/README.md).

Authors

• Joan Hérisson

Acknowledgments

• Thomas Duigou

Licence

chemlite is released under the MIT licence. See the LICENCE file for details.