├── .github └── workflows │ └── ci.yml ├── .gitignore ├── LICENSE.txt ├── README.rst ├── docs ├── Model_computation (RBApy.core).pdf ├── Model_construction (RBApy.prerba).pdf ├── Parameter_estimation (RBApy.estim) - Text-S6.pdf ├── XML_format (RBApy.xml).pdf └── xml_tutorial.ipynb ├── rba ├── __init__.py ├── _authors.py ├── _version.py ├── cli │ ├── __init__.py │ ├── generate_rba_model.py │ └── solve_rba_model.py ├── core │ ├── __init__.py │ ├── constraint_blocks.py │ ├── constraint_matrix.py │ ├── density.py │ ├── enzymes.py │ ├── functions.py │ ├── metabolism.py │ ├── parameter_vector.py │ ├── parameters.py │ ├── processes.py │ ├── solver.py │ ├── species.py │ └── targets.py ├── estim │ ├── kapp.cfg │ ├── kapp.py │ ├── nonenz_per_compartment.cfg │ ├── nonenz_per_compartment.py │ ├── prot_per_compartment.cfg │ ├── prot_per_compartment.py │ └── utils.py ├── model.py ├── prerba │ ├── __init__.py │ ├── curation_data.py │ ├── default_data.py │ ├── default_processes.py │ ├── default_targets.py │ ├── enzyme.py │ ├── fasta_parser.py │ ├── macromolecule.py │ ├── manual_annotation.py │ ├── model_builder.py │ ├── pipeline_parameters.py │ ├── protein_data.py │ ├── protein_export.py │ ├── sbml_data.py │ ├── uniprot_data.py │ ├── uniprot_importer.py │ ├── user_data.py │ └── user_machinery.py ├── utils │ ├── __init__.py │ ├── efficiencies.py │ └── results.py └── xml │ ├── __init__.py │ ├── common.py │ ├── density.py │ ├── enzymes.py │ ├── macromolecules.py │ ├── metabolism.py │ ├── parameters.py │ ├── processes.py │ └── targets.py ├── sample_input ├── data │ ├── chaperones.fasta │ ├── ribosome.fasta │ ├── sample.xml │ └── trnas.fasta └── params.in ├── sample_input_small ├── data │ ├── chaperones.fasta │ ├── ribosome.fasta │ ├── sbml.xml │ └── trnas.fasta └── params.in ├── setup.cfg ├── setup.py └── tests ├── test_cli.py ├── test_tutorial.py └── utils ├── efficiencies.tsv └── test_inject_efficiencies.py /.github/workflows/ci.yml: 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