CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
Dockerfile
LICENSE
MANIFEST.in
Makefile
README.md
build_standalone.py
build_standalone_linux.py
build_standalone_windows.py
compose.yaml
hbat-web.py
hbat.icns
hbat.ico
hbat.png
hbat.svg
hbat_cli.py
hbat_gui.py
pyproject.toml
pytest.ini
requirements-dev.txt
requirements.txt
.github/workflows/cleanup-prereleases.yml
.github/workflows/coverage.yml
.github/workflows/joss-paper.yml
.github/workflows/release.yml
.github/workflows/test.yml
conda/meta.yaml
docs/Makefile
docs/requirements.txt
docs/source/cli.rst
docs/source/conf.py
docs/source/development.rst
docs/source/hbat.bib
docs/source/index.rst
docs/source/installation.rst
docs/source/license.rst
docs/source/logic.rst
docs/source/parameters.rst
docs/source/pdbfixing.rst
docs/source/presets.rst
docs/source/quickstart.rst
docs/source/references.rst
docs/source/web.rst
docs/source/_static/custom.css
docs/source/_static/light-theme.css
docs/source/api/index.rst
docs/source/api/ccd/ccd_analyzer.rst
docs/source/api/ccd/constants_generator.rst
docs/source/api/ccd/generate_ccd_constants.rst
docs/source/api/ccd/index.rst
docs/source/api/cli/index.rst
docs/source/api/constants/app.rst
docs/source/api/constants/atomic_data.rst
docs/source/api/constants/index.rst
docs/source/api/constants/misc.rst
docs/source/api/constants/parameters.rst
docs/source/api/constants/pdb_constants.rst
docs/source/api/core/index.rst
docs/source/api/core/interactions.rst
docs/source/api/core/np_analyzer.rst
docs/source/api/core/np_vector.rst
docs/source/api/core/pdb_fixer.rst
docs/source/api/core/pdb_parser.rst
docs/source/api/core/structure.rst
docs/source/api/examples/index.rst
docs/source/api/gui/index.rst
docs/source/api/utilities/atom_utils.rst
docs/source/api/utilities/graphviz_utils.rst
docs/source/api/utilities/index.rst
example_pdb_files/1CRN.cif
example_pdb_files/1bhl.pdb
example_pdb_files/1crn.pdb
example_pdb_files/1gai.pdb
example_pdb_files/1luc.pdb
example_pdb_files/1ubi.pdb
example_pdb_files/2cdg.pdb
example_pdb_files/2izf.pdb
example_pdb_files/4X21.cif
example_pdb_files/4hhb.pdb
example_pdb_files/4jsv.pdb
example_pdb_files/4laz.pdb
example_pdb_files/4ub7.pdb
example_pdb_files/4x21.pdb
example_pdb_files/6RSA.cif
example_pdb_files/6rsa.pdb
example_pdb_files/7nwd.pdb
example_presets/drug_design_strict.hbat
example_presets/high_resolution.hbat
example_presets/low_resolution.hbat
example_presets/membrane_proteins.hbat
example_presets/nmr_structures.hbat
example_presets/standard_resolution.hbat
example_presets/strong_interactions_only.hbat
example_presets/weak_interactions_permissive.hbat
hbat/__init__.py
hbat/_version.py
hbat/ccd/__init__.py
hbat/ccd/ccd_analyzer.py
hbat/ccd/constants_generator.py
hbat/ccd/generate_ccd_constants.py
hbat/cli/__init__.py
hbat/cli/main.py
hbat/constants/__init__.py
hbat/constants/app.py
hbat/constants/atomic_data.py
hbat/constants/misc.py
hbat/constants/parameters.py
hbat/constants/pdb_constants.py
hbat/constants/residue_bonds.py
hbat/core/__init__.py
hbat/core/analysis.py
hbat/core/analyzer.py
hbat/core/app_config.py
hbat/core/atom_classifier.py
hbat/core/interactions.py
hbat/core/np_analyzer.py
hbat/core/np_vector.py
hbat/core/pdb_fixer.py
hbat/core/pdb_parser.py
hbat/core/structure.py
hbat/export/__init__.py
hbat/export/results.py
hbat/gui/__init__.py
hbat/gui/base_graph_renderer.py
hbat/gui/chain_visualization_window.py
hbat/gui/export_manager.py
hbat/gui/geometry_cutoffs_dialog.py
hbat/gui/graphviz_preferences_dialog.py
hbat/gui/graphviz_renderer.py
hbat/gui/main_window.py
hbat/gui/matplotlib_renderer.py
hbat/gui/pdb_fixing_dialog.py
hbat/gui/preset_manager_dialog.py
hbat/gui/results_panel.py
hbat/server/README.md
hbat/server/SESSION.md
hbat/server/__init__.py
hbat/server/__main__.py
hbat/server/app.py
hbat/server/session.py
hbat/server/components/__init__.py
hbat/server/components/parameter_panel.py
hbat/server/components/results_panel.py
hbat/server/components/upload_panel.py
hbat/server/static/favicon.ico
hbat/server/static/hbat.svg
hbat/utilities/__init__.py
hbat/utilities/atom_utils.py
hbat/utilities/graphviz_utils.py
hbat/visualization/README.md
hbat/visualization/__init__.py
hbat/visualization/chain_graph.py
hbat/visualization/graphviz_dot_helper.py
hbat/visualization/minimal_pdb_extractor.py
hbat/visualization/notebook.py
hbat/visualization/pymol3d.py
hbat/visualization/pymol_exporter.py
notebooks/01_analyze_6rsa_with_visualization.ipynb
notebooks/02_halogen_bonds_4x21.ipynb
notebooks/03_pdbfixer_vs_openbabel_comparison.ipynb
notebooks/README.md
notebooks/requirements.txt
paper/paper.bib
paper/paper.md
paper/images/4x21-7-co-chain.png
paper/images/6rsa-network-hbonds.pdf
paper/images/6rsa_A_ALA_20_to_A_TYR_25_pi.png
paper/images/hbat-gui.png
paper/images/hbat-web.png
paper/images/overall-workflow-graphviz.pdf
paper/images/overall-workflow-graphviz.png
tests/README.md
tests/__init__.py
tests/conftest.py
tests/run_tests.py
tests/cli/__init__.py
tests/cli/test_cli_main.py
tests/cli/test_cli_output_formats.py
tests/e2e/__init__.py
tests/e2e/test_cli_cif_workflows.py
tests/e2e/test_cli_workflows.py
tests/e2e/test_complete_workflow.py
tests/e2e/test_complete_workflows.py
tests/e2e/test_graphviz_workflows.py
tests/e2e/test_gui_workflows.py
tests/e2e/test_ligand_water_bridge_workflows.py
tests/e2e/test_visualization_workflows.py
tests/gui/__init__.py
tests/gui/test_gui_components.py
tests/integration/__init__.py
tests/integration/test_analyzer_components.py
tests/integration/test_cif_bond_connectivity.py
tests/integration/test_cif_edge_cases.py
tests/integration/test_cif_parsing.py
tests/integration/test_cif_pdb_fixing.py
tests/integration/test_cli_input_validation.py
tests/integration/test_cli_integration.py
tests/integration/test_format_equivalence.py
tests/integration/test_graphviz_renderer.py
tests/integration/test_molecular_validation.py
tests/integration/test_new_interaction_analyzers.py
tests/integration/test_pdb_parsing.py
tests/performance/__init__.py
tests/performance/test_ccd_performance.py
tests/performance/test_performance_workflows.py
tests/unit/__init__.py
tests/unit/test_carbonyl_carbonyl.py
tests/unit/test_chain_graph.py
tests/unit/test_cli_parsing.py
tests/unit/test_graphviz_dot_helper.py
tests/unit/test_graphviz_utils.py
tests/unit/test_gui_components.py
tests/unit/test_halogen_bonds.py
tests/unit/test_interactions.py
tests/unit/test_n_pi_interactions.py
tests/unit/test_parameters.py
tests/unit/test_pi_pi_stacking.py
tests/unit/test_scrollable_canvas.py
tests/unit/test_structures.py
tests/unit/test_vector_math.py