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dAMN

Artificial Metabolic Networks

Name Downloads Version Platforms
Conda Recipe Conda Downloads Conda Version Conda Platforms

Description

damn Hybrid Neural Network Framework for Dynamic Flux Balance Analysis (dFBA).

Install

From Conda

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

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Use

Compound

from damn 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()

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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

  • Ramiz Khaled

Acknowledgments

  • Thomas Duigou
  • Danilo Dursoniah
  • Joan Hérisson

Licence

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