CITATION.bib
LICENSE.txt
MANIFEST.in
README.md
installation.md
pyproject.toml
images/0_qDNA_logo.png
images/1BNA_1.png
images/1BNA_2.png
images/1BNA_3.png
images/1_CT_EET.png
images/2_qDNA_structure.png
images/5_GUI.png
qDNA/__init__.py
qDNA/defaults.yaml
qDNA/legacy.py
qDNA/qDNA-default.mplstyle
qDNA.egg-info/PKG-INFO
qDNA.egg-info/SOURCES.txt
qDNA.egg-info/dependency_links.txt
qDNA.egg-info/requires.txt
qDNA.egg-info/top_level.txt
qDNA/data/qDNA.log
qDNA/data/color_palettes/matplotlib.json
qDNA/data/color_palettes/nature.json
qDNA/data/color_palettes/seaborn.json
qDNA/data/lcao_params/HKS.json
qDNA/data/lcao_params/MMTS.json
qDNA/data/lcao_params/MSF.json
qDNA/data/lcao_params/SN.json
qDNA/data/lcao_params/SN_all.json
qDNA/data/raw/data_paper/dipole_7bp_J0.5.json
qDNA/data/raw/data_paper/dipole_7bp_J0.json
qDNA/data/raw/data_paper/dipole_7bp_J1.json
qDNA/data/raw/data_paper/lifetime_4bp_relax0.01.json
qDNA/data/raw/data_paper/lifetime_4bp_relax0.02.json
qDNA/data/raw/data_paper/lifetime_4bp_relax0.05.json
qDNA/data/raw/data_paper/lifetime_7bp_J0.5.json
qDNA/data/raw/data_paper/lifetime_7bp_J0.json
qDNA/data/raw/data_paper/lifetime_7bp_J1.json
qDNA/data/raw/figures_paper/Fig_1.pdf
qDNA/data/raw/figures_paper/Fig_2.pdf
qDNA/data/raw/figures_paper/Fig_3.pdf
qDNA/data/raw/figures_paper/Fig_3a.pdf
qDNA/data/raw/figures_paper/Fig_3b.pdf
qDNA/data/raw/figures_paper/Fig_4.pdf
qDNA/data/raw/figures_paper/Fig_5a.pdf
qDNA/data/raw/figures_paper/Fig_5b.pdf
qDNA/data/raw/figures_paper/Fig_6.pdf
qDNA/data/raw/figures_paper/Fig_7.pdf
qDNA/data/raw/figures_paper/Fig_8a.pdf
qDNA/data/raw/figures_paper/Fig_8b.pdf
qDNA/data/raw/figures_paper/Fig_S1.pdf
qDNA/data/raw/figures_paper/Fig_S2.pdf
qDNA/data/raw/figures_paper/Fig_S3a.pdf
qDNA/data/raw/figures_paper/Fig_S3b.pdf
qDNA/data/raw/figures_paper/Fig_S4.pdf
qDNA/data/raw/figures_paper/Fig_S5.pdf
qDNA/data/raw/figures_tutorials/FMO_energy_level.png
qDNA/data/raw/figures_tutorials/Fig_1.png
qDNA/data/raw/figures_tutorials/Fig_2.png
qDNA/data/raw/figures_tutorials/base_translation_rotation.png
qDNA/data/tb_params/1BNA_ELM.json
qDNA/data/tb_params/Bittner2007_ELM.json
qDNA/data/tb_params/Endres2002_WM.json
qDNA/data/tb_params/Hawke2010_ELM.json
qDNA/data/tb_params/Hawke2010_LM.json
qDNA/data/tb_params/Hawke2010_WM.json
qDNA/data/tb_params/Kordas2025_FC.json
qDNA/data/tb_params/Mantela2021_WM.json
qDNA/data/tb_params/Simserides2014_WM.json
qDNA/data/tb_params/Simserides2024_ELM.json
qDNA/data/tb_params/Simserides2024_FELM.json
qDNA/data/tb_params/meth_ELM.json
qDNA/data/tb_params/unmeth_ELM.json
qDNA/dynamics/__init__.py
qDNA/dynamics/dm_analysis.py
qDNA/dynamics/me_solver.py
qDNA/dynamics/reduced_dm.py
qDNA/environment/__init__.py
qDNA/environment/deph_ops.py
qDNA/environment/lind_diss.py
qDNA/environment/observables.py
qDNA/environment/relax_ops.py
qDNA/environment/therm_ops.py
qDNA/environment/therm_rates.py
qDNA/evaluation/__init__.py
qDNA/evaluation/eq_states.py
qDNA/evaluation/evaluation.py
qDNA/gui/__init__.py
qDNA/gui/advanced_frame.py
qDNA/gui/fasta_window.py
qDNA/gui/gui_utils.py
qDNA/gui/initial_frame.py
qDNA/gui/lind_diss_frame.py
qDNA/gui/me_solver_frame.py
qDNA/gui/options_frame.py
qDNA/gui/pdb_window.py
qDNA/gui/plot_options_frame.py
qDNA/gui/plotting_window.py
qDNA/gui/qdna_app.py
qDNA/gui/scrollable_console_frame.py
qDNA/gui/tb_ham_frame.py
qDNA/hamiltonian/__init__.py
qDNA/hamiltonian/dna_seq.py
qDNA/hamiltonian/ham_analysis.py
qDNA/hamiltonian/tb_ham.py
qDNA/hamiltonian/tb_matrices.py
qDNA/io/__init__.py
qDNA/io/defaults.py
qDNA/io/helpers.py
qDNA/io/io_json.py
qDNA/io/io_mpl.py
qDNA/io/io_pdb.py
qDNA/io/io_tb_params.py
qDNA/io/io_xyz.py
qDNA/io/io_yaml.py
qDNA/lcao/__init__.py
qDNA/lcao/component.py
qDNA/lcao/monomer.py
qDNA/lcao/oligomer.py
qDNA/lcao/slater_koster.py
qDNA/model/__init__.py
qDNA/model/tb_basis.py
qDNA/model/tb_config.py
qDNA/model/tb_model.py
qDNA/utils/__init__.py
qDNA/utils/check_input.py
qDNA/utils/decorators.py
qDNA/utils/helpers.py
qDNA/utils/logging.py
qDNA/utils/unit_converter.py
qDNA/visualization/__init__.py
qDNA/visualization/plot_base_frequency.py
qDNA/visualization/visualization.py
requirements/dev-requirements.txt
requirements/doc-requirements.txt
requirements/requirements.txt