LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
cpp/CMakeLists.txt
cpp/cmake/OptimizeArchitectureFlags.cmake
cpp/externals/CMakeLists.txt
cpp/externals/dynamic_bitset/LICENSE.txt
cpp/externals/dynamic_bitset/README.md
cpp/externals/dynamic_bitset/dynamic_bitset.hpp
cpp/externals/gurobi/CMakeLists.txt
cpp/include/eigen-hash.h
cpp/include/flux_constraints.h
cpp/include/flux_space.h
cpp/include/lrucache.hpp
cpp/include/python_helper.h
cpp/include/steady_state_free_energies_descriptor.h
cpp/include/steady_state_verifier.h
cpp/include/thermodynamic_constraints.h
cpp/include/thermodynamic_space.h
cpp/include/utilities.h
cpp/include/loggers/matlab_progress_logger.h
cpp/include/loggers/orthants_logger.h
cpp/include/loggers/python_progress_logger.h
cpp/include/settings/free_energy_sampling_settings.h
cpp/include/settings/uniform_flux_sampling_settings.h
cpp/python/CMakeLists.txt
cpp/python/common_python_bindings.cpp
cpp/python/common_python_bindings.h
cpp/python/python_bindings.cpp
cpp/python/tfs_python_bindings.cpp
cpp/python/tfs_python_bindings.h
cpp/python/us_python_bindings.cpp
cpp/python/us_python_bindings.h
docs/conf.py
examples/benchmark_tfs_core.py
examples/benchmark_uniform_iJO1366.py
examples/benchmark_uniform_iML1515.py
pta/README.md
pta/__init__.py
pta/commons.py
pta/concentrations_prior.py
pta/constants.py
pta/flux_space.py
pta/model_assessment.py
pta/pmo.py
pta/thermodynamic_space.py
pta/utils.py
pta.egg-info/PKG-INFO
pta.egg-info/SOURCES.txt
pta.egg-info/dependency_links.txt
pta.egg-info/not-zip-safe
pta.egg-info/requires.txt
pta.egg-info/top_level.txt
pta/data/__init__.py
pta/data/concentration_priors/M9_aerobic.csv
pta/data/concentration_priors/M9_anaerobic.csv
pta/data/concentration_priors/__init__.py
pta/data/concentration_priors/ecoli_M9_ac.csv
pta/data/concentration_priors/ecoli_M9_cofactors.csv
pta/data/concentration_priors/ecoli_M9_fru.csv
pta/data/concentration_priors/ecoli_M9_gal.csv
pta/data/concentration_priors/ecoli_M9_glc.csv
pta/data/concentration_priors/ecoli_M9_glcn.csv
pta/data/concentration_priors/ecoli_M9_glyc.csv
pta/data/concentration_priors/ecoli_M9_pyr.csv
pta/data/concentration_priors/ecoli_M9_specific.csv
pta/data/concentration_priors/ecoli_M9_succ.csv
pta/data/concentration_priors/ecoli_M9_unspecific.csv
pta/data/models/__init__.py
pta/data/models/e_coli_core.xml
pta/data/models/iJO1366.xml
pta/data/models/iML1515.xml
pta/data/models/phosphohexoses.xml
pta/sampling/__init__.py
pta/sampling/commons.py
pta/sampling/convergence_manager.py
pta/sampling/primitives.py
pta/sampling/tfs.py
pta/sampling/uniform.py
tests/conftest.py
tests/test_assessment.py
tests/test_concentrations_prior.py
tests/test_pmo.py
tests/test_tfs.py
tests/test_thermodynamic_space.py
tests/test_uniform_sampling.py
tests/test_utils.py
utilities/create_phosphoexoses_model.py
venv/bin/activate_this.py