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