LICENSE
README.md
pyproject.toml
setup.py
benchmark/benchmark_subcomplexes.py
ioNERDSS.egg-info/PKG-INFO
ioNERDSS.egg-info/SOURCES.txt
ioNERDSS.egg-info/dependency_links.txt
ioNERDSS.egg-info/requires.txt
ioNERDSS.egg-info/top_level.txt
ionerdss/__init__.py
ionerdss/api.py
ionerdss/util.py
ionerdss/analysis/__init__.py
ionerdss/analysis/api.py
ionerdss/analysis/core/__init__.py
ionerdss/analysis/core/simulation.py
ionerdss/analysis/core/types.py
ionerdss/analysis/io/__init__.py
ionerdss/analysis/io/loader.py
ionerdss/analysis/io/parser.py
ionerdss/analysis/legacy/__init__.py
ionerdss/analysis/legacy/interface.py
ionerdss/analysis/processing/__init__.py
ionerdss/analysis/processing/transitions.py
ionerdss/analysis/visualization/__init__.py
ionerdss/analysis/visualization/config.py
ionerdss/analysis/visualization/plots.py
ionerdss/gillespie_simulation/__init__.py
ionerdss/gillespie_simulation/adaptive_rates.py
ionerdss/gillespie_simulation/helpers.py
ionerdss/gillespie_simulation/simple_gillespie.py
ionerdss/model/PlatonicSolids.py
ionerdss/model/ProAffinity_GNN_inference.py
ionerdss/model/__init__.py
ionerdss/model/proaffinity_predictor.py
ionerdss/model/components/instances.py
ionerdss/model/components/reactions.py
ionerdss/model/components/registry.py
ionerdss/model/components/system.py
ionerdss/model/components/types.py
ionerdss/model/components/units.py
ionerdss/model/components/docs/crosslink_diagram.py
ionerdss/model/components/docs/pipeline_flowchart.py
ionerdss/model/graph_based/complexes/__init__.py
ionerdss/model/graph_based/complexes/conversion.py
ionerdss/model/graph_based/complexes/examples.py
ionerdss/model/graph_based/complexes/graphize.py
ionerdss/model/graph_based/complexes/subcomplexes.py
ionerdss/model/graph_based/reactions/__init__.py
ionerdss/model/graph_based/reactions/dimer.py
ionerdss/model/graph_based/reactions/transformation.py
ionerdss/model/graph_based/symmetry/__init__.py
ionerdss/model/graph_based/symmetry/grid.py
ionerdss/model/graph_based/symmetry/pointgroup.py
ionerdss/model/graph_based/symmetry/utils.py
ionerdss/model/pdb/__init__.py
ionerdss/model/pdb/api.py
ionerdss/model/pdb/chain_grouping.py
ionerdss/model/pdb/coarse_graining.py
ionerdss/model/pdb/file_manager.py
ionerdss/model/pdb/hyperparameters.py
ionerdss/model/pdb/interface_naming.py
ionerdss/model/pdb/main.py
ionerdss/model/pdb/nerdss_exporter.py
ionerdss/model/pdb/parser.py
ionerdss/model/pdb/ring_regularizer.py
ionerdss/model/pdb/system_builder.py
ionerdss/model/pdb/template_builder.py
ionerdss/model/pdb/visualizer.py
ionerdss/model/platonic_solids/geometry.py
ionerdss/model/platonic_solids/solids.py
ionerdss/model/spherical_assembly/__init__.py
ionerdss/model/spherical_assembly/core.py
ionerdss/model/spherical_assembly/geometry.py
ionerdss/model/spherical_assembly/output_test.py
ionerdss/model/spherical_assembly/legacy/_pdb.py
ionerdss/model/spherical_assembly/legacy/chain_int.py
ionerdss/model/spherical_assembly/legacy/gagReshape.py
ionerdss/model/titrate/parms_titrator.py
ionerdss/nerdss_guis/__init__.py
ionerdss/nerdss_guis/gui.py
ionerdss/nerdss_guis/nerdss.py
ionerdss/nerdss_guis/gen/__init__.py
ionerdss/nerdss_guis/gen/advanced_options_parse_pdb.py
ionerdss/nerdss_guis/gen/mainwindow.py
ionerdss/nerdss_guis/gen/modify_parameters.py
ionerdss/nerdss_guis/gen/mplwidget.py
ionerdss/nerdss_guis/gen/nerdss_install.py
ionerdss/nerdss_guis/gen/pdb_movie_player.py
ionerdss/nerdss_guis/gen/plot_complex.py
ionerdss/nerdss_guis/gen/plot_copy_num.py
ionerdss/nerdss_simulation/__init__.py
ionerdss/nerdss_simulation/simulation.py
ionerdss/ode/__init__.py
ionerdss/ode/ode_pipeline.py
ionerdss/ode/reaction_ode_solver.py
ionerdss/ode/reaction_string_parser.py
ionerdss/ode/system_ode_generator.py
ionerdss/simularium_converter/simularium_converter.py
ionerdss/utils/__init__.py
ionerdss/utils/angles.py
ionerdss/utils/bond_geometry.py
ionerdss/utils/coords.py
ionerdss/utils/diffusion_constant.py
ionerdss/utils/inertia_tensors.py
ionerdss/utils/rigid_transform.py
ionerdss/utils/rotations.py
ionerdss/utils/steric_clash.py
ionerdss/utils/string_similarity.py
ionerdss/utils/vectors.py
tests/graph_based/test_reactions_generation_pipeline.py
tests/graph_based/test_subcomplexes_extraction.py
tests/graph_based/test_symmetry_group_identification.py
tests/integration/__init__.py
tests/unit/analysis/test_api.py
tests/unit/analysis/test_io.py
tests/unit/analysis/test_processing.py
tests/unit/gillespie_simulation/test_simple_gillespie.py
tests/unit/model/test_platonic_solids.py
tests/unit/model/components/test_instances.py
tests/unit/model/components/test_reactions.py
tests/unit/model/components/test_reference_coordinates.py
tests/unit/model/components/test_registry.py
tests/unit/model/components/test_types.py
tests/unit/model/components/test_units.py
tests/unit/model/pdb/test_chain_grouping.py
tests/unit/model/pdb/test_coarse_graining.py
tests/unit/model/pdb/test_file_manager.py
tests/unit/model/pdb/test_hyperparameters.py
tests/unit/model/pdb/test_nerdss_exporter.py
tests/unit/model/pdb/test_parser.py
tests/unit/model/pdb/test_ring_regularizer.py
tests/unit/model/pdb/test_template_builder.py
tests/unit/model/pdb/test_visualizer.py
tests/unit/ode_solver/test_ode_solver.py
tests/unit/utils/test_angles.py
tests/unit/utils/test_bond_geometry.py
tests/unit/utils/test_coords.py
tests/unit/utils/test_diffusion_constants.py
tests/unit/utils/test_inertia_tensors.py
tests/unit/utils/test_rigid_transform.py
tests/unit/utils/test_rotations.py
tests/unit/utils/test_steric_clash.py
tests/unit/utils/test_string_similarity.py