LICENSE-gsl-2.5.txt
LICENSE-libgomp.txt
LICENSE-liblbfgs-1.10.txt
LICENSE.txt
MANIFEST.in
README.rst
setup.cfg
setup.py
bioen/__init__.py
bioen/fileio.py
bioen/version.py
bioen.egg-info/PKG-INFO
bioen.egg-info/SOURCES.txt
bioen.egg-info/dependency_links.txt
bioen.egg-info/entry_points.txt
bioen.egg-info/not-zip-safe
bioen.egg-info/requires.txt
bioen.egg-info/top_level.txt
bioen/analyze/__init__.py
bioen/analyze/procedure.py
bioen/analyze/run_bioen.py
bioen/analyze/utils.py
bioen/analyze/observables/__init__.py
bioen/analyze/observables/observables.py
bioen/analyze/observables/cd_data/__init__.py
bioen/analyze/observables/cd_data/cd_data.py
bioen/analyze/observables/deer/__init__.py
bioen/analyze/observables/deer/deer.py
bioen/analyze/observables/generic/__init__.py
bioen/analyze/observables/generic/generic.py
bioen/analyze/observables/scattering/__init__.py
bioen/analyze/observables/scattering/scattering.py
bioen/analyze/show_plot/__init__.py
bioen/analyze/show_plot/show_plot.py
bioen/optimize/__init__.py
bioen/optimize/common.py
bioen/optimize/forces.py
bioen/optimize/log_weights.py
bioen/optimize/minimize.py
bioen/optimize/unused_code.py
bioen/optimize/util.py
bioen/optimize/config/bioen_optimize.yaml
bioen/optimize/ext/__init__.py
bioen/optimize/ext/_clang-format
bioen/optimize/ext/c_bioen.pyx
bioen/optimize/ext/c_bioen_common.c
bioen/optimize/ext/c_bioen_common.h
bioen/optimize/ext/c_bioen_error.c
bioen/optimize/ext/c_bioen_error.h
bioen/optimize/ext/c_bioen_kernels_forces.c
bioen/optimize/ext/c_bioen_kernels_forces.h
bioen/optimize/ext/c_bioen_kernels_logw.c
bioen/optimize/ext/c_bioen_kernels_logw.h
bioen/optimize/ext/ompmagic.h
doc/conf.py
doc/fileio.rst
doc/index.rst
doc/modules.rst
doc/redesign.rst
doc/_build/_dummy
doc/_static/_dummy
doc/_templates/_dummy
img/bioen.png
img/bioen_logo.png
img/bioen_logo_480.png
scripts/build_documentation.sh
scripts/build_packages.sh
scripts/requirements_cp310-cp310.txt
scripts/requirements_cp311-cp311.txt
scripts/requirements_cp312-cp312.txt
scripts/requirements_cp36-cp36m.txt
scripts/requirements_cp37-cp37m.txt
scripts/requirements_cp38-cp38.txt
scripts/requirements_cp39-cp39.txt
scripts/setup_develop_home.sh
scripts/setup_install_home.sh
scripts/update_git_hash.py
scripts/upload_wheels_gitlab.sh
test/CD_data/run_bioen_cd.sh
test/CD_data/thetas.dat
test/CD_data/data/conf1-cd.dat
test/CD_data/data/conf10-cd.dat
test/CD_data/data/conf2-cd.dat
test/CD_data/data/conf3-cd.dat
test/CD_data/data/conf4-cd.dat
test/CD_data/data/conf5-cd.dat
test/CD_data/data/conf6-cd.dat
test/CD_data/data/conf7-cd.dat
test/CD_data/data/conf8-cd.dat
test/CD_data/data/conf9-cd.dat
test/CD_data/data/exp-cd-error.dat
test/CD_data/data/exp-cd.dat
test/CD_data/data/models-cd.dat
test/deer/run_bioen_deer.sh
test/deer/thetas.dat
test/deer/data/conf0-319-259-deer.dat
test/deer/data/conf1-319-259-deer.dat
test/deer/data/conf2-319-259-deer.dat
test/deer/data/conf3-319-259-deer.dat
test/deer/data/conf4-319-259-deer.dat
test/deer/data/conf5-319-259-deer.dat
test/deer/data/conf6-319-259-deer.dat
test/deer/data/conf7-319-259-deer.dat
test/deer/data/conf8-319-259-deer.dat
test/deer/data/conf9-319-259-deer.dat
test/deer/data/exp-319-259-deer.dat
test/deer/data/exp-error.dat
test/deer/data/moddepth-deer.dat
test/deer/data/models-deer.dat
test/generic/run_bioen.sh
test/generic/thetas.dat
test/generic/data/exp-generic.dat
test/generic/data/models-generic.dat
test/generic/data/sim-distance_1-generic.dat
test/generic/data/sim-noe_1-generic.dat
test/generic/data/sim-noe_2-generic.dat
test/generic/data/sim-pre_1-generic.dat
test/generic/data/sim-r2-J1JNCA-generic.dat
test/optimize/run.sh
test/optimize/test_error_opt_forces.py
test/optimize/test_error_opt_logw.py
test/optimize/test_fileio_forces.py
test/optimize/test_fileio_logw.py
test/optimize/test_fileio_units.py
test/optimize/test_find_opt_analytical_grad_forces.py
test/optimize/test_find_opt_analytical_grad_logw.py
test/optimize/test_forces_reproducibility.py
test/optimize/test_func_gradient_forces.py
test/optimize/test_func_gradient_logw.py
test/optimize/test_logw_reproducibility.py
test/optimize/data/data_16x15.h5
test/optimize/data/data_16x15.pkl
test/optimize/data/data_16x15.ref
test/optimize/data/data_16x15.ref.h5
test/optimize/data/data_M64xN64.pkl
test/optimize/data/data_deer_test_forces_M808xN10.h5
test/optimize/data/data_deer_test_forces_M808xN10.pkl
test/optimize/data/data_deer_test_forces_M808xN10.ref
test/optimize/data/data_deer_test_forces_M808xN10.ref.h5
test/optimize/data/data_deer_test_logw_M808xN10.h5
test/optimize/data/data_deer_test_logw_M808xN10.pkl
test/optimize/data/data_deer_test_logw_M808xN10.ref
test/optimize/data/data_deer_test_logw_M808xN10.ref.h5
test/optimize/data/data_forces_M64xN64.h5
test/optimize/data/data_forces_M64xN64.pkl
test/optimize/data/data_forces_M64xN64.ref
test/optimize/data/data_forces_M64xN64.ref.h5
test/optimize/data/data_potra_part_1_logw_M808xN80.h5
test/optimize/data/data_potra_part_1_logw_M808xN80.pkl
test/optimize/data/data_potra_part_1_logw_M808xN80.ref
test/optimize/data/data_potra_part_1_logw_M808xN80.ref.h5
test/optimize/data/data_potra_part_2_logw_M205xN10.h5
test/optimize/data/data_potra_part_2_logw_M205xN10.pkl
test/optimize/data/data_potra_part_2_logw_M205xN10.ref
test/optimize/data/data_potra_part_2_logw_M205xN10.ref.h5
test/optimize/data/data_potra_part_2_logw_M808xN10.h5
test/optimize/data/data_potra_part_2_logw_M808xN10.pkl
test/optimize/data/data_potra_part_2_logw_M808xN10.ref
test/optimize/data/data_potra_part_2_logw_M808xN10.ref.h5
test/scattering/run_bioen_saxs.sh
test/scattering/thetas.dat
test/scattering/data/lyz-exp.dat
test/scattering/data/lyz0-sim-saxs.dat
test/scattering/data/lyz1-sim-saxs.dat
test/scattering/data/lyz2-sim-saxs.dat
test/scattering/data/lyz3-sim-saxs.dat
test/scattering/data/lyz4-sim-saxs.dat
test/scattering/data/lyz_sim.dat
test/scattering/data/models-saxs.dat
third-party/README.txt
third-party/download_dependencies.sh
third-party/install_dependencies.sh