.gitignore
.readthedocs.yml
LICENSE
README.rst
justfile
pyproject.toml
.github/pull_request_template.md
.github/workflows/publish_release.yml
.github/workflows/tests.yml
docs/Makefile
docs/environment.yml
docs/source/cage_analysis.rst
docs/source/cage_optimisation.rst
docs/source/calculators.rst
docs/source/conf.py
docs/source/helpers.rst
docs/source/index.rst
docs/source/modules.rst
docs/source/molecular.rst
docs/source/optimizers.rst
docs/source/video_tutorials.rst
docs/source/_static/openmm_opt_file.mol
docs/source/_static/stko.png
docs/source/_templates/class.rst
docs/source/_templates/module.rst
examples/aligner_example.py
examples/basic_example.py
examples/cage_analysis_example.py
examples/cage_openmm_example.py
examples/calculators_example.py
examples/gulp_test_example.py
examples/mdanalysis_example.py
examples/molecule_splitter_example.py
examples/obabel_example.py
examples/openmm_example.py
examples/orca_example.py
examples/shape_example.py
examples/testable_example.py
examples/topology_extraction_example.py
examples/torsion_example.py
examples/zmatrix_example.py
examples/aligner_directory/aligned_0.mol
examples/aligner_directory/aligned_1.mol
examples/aligner_directory/aligned_2.mol
examples/aligner_directory/aligned_3.mol
examples/aligner_directory/aligned_4.mol
examples/aligner_directory/aligned_5.mol
examples/aligner_directory/init_0.mol
examples/aligner_directory/init_1.mol
examples/aligner_directory/init_2.mol
examples/aligner_directory/init_3.mol
examples/aligner_directory/init_4.mol
examples/aligner_directory/init_5.mol
examples/aligner_directory/unaligned_0.mol
examples/aligner_directory/unaligned_1.mol
examples/aligner_directory/unaligned_2.mol
examples/aligner_directory/unaligned_3.mol
examples/aligner_directory/unaligned_4.mol
examples/aligner_directory/unaligned_5.mol
examples/cage_openmm_example_directory/opt_cage.mol
examples/cage_openmm_example_directory/unopt_cage.mol
examples/cage_openmm_example_directory/md_optimisation/trajectory_data.dat
examples/cage_openmm_example_directory/md_optimisation/trajectory_structures.pdb
examples/cage_output/apdcage.mol
examples/cage_output/apdcage_0.mol
examples/cage_output/apdcage_1.mol
examples/cage_output/apdcage_10.mol
examples/cage_output/apdcage_11.mol
examples/cage_output/apdcage_2.mol
examples/cage_output/apdcage_3.mol
examples/cage_output/apdcage_4.mol
examples/cage_output/apdcage_5.mol
examples/cage_output/apdcage_6.mol
examples/cage_output/apdcage_7.mol
examples/cage_output/apdcage_8.mol
examples/cage_output/apdcage_9.mol
examples/openmm_example_directory/ff_opt_cage.mol
examples/openmm_example_directory/ffrest_opt_cage.mol
examples/openmm_example_directory/ffunrest_opt_cage.mol
examples/openmm_example_directory/md_opt_cage.mol
examples/openmm_example_directory/unopt_cage.mol
examples/openmm_example_directory/md_optimisation/trajectory_data.dat
examples/openmm_example_directory/md_optimisation/trajectory_structures.pdb
examples/orca_output_directory/orca_e1_dir/input_structure.xyz
examples/orca_output_directory/orca_e1_dir/orca_energy.output
examples/orca_output_directory/orca_e1_dir/orca_input.inp
examples/orca_output_directory/orca_e2_dir/input_structure.xyz
examples/orca_output_directory/orca_e2_dir/orca_energy.output
examples/orca_output_directory/orca_e2_dir/orca_input.inp
examples/orca_output_directory/orca_e3_dir/input_structure.xyz
examples/orca_output_directory/orca_e3_dir/orca_input.inp
examples/output_directory/bb1.mol
examples/output_directory/bb2.mol
examples/output_directory/obabel_axle_opt.mol
examples/output_directory/obabel_axle_unopt.mol
examples/output_directory/obabel_bb1_opt.mol
examples/output_directory/obabel_bb1_unopt.mol
examples/output_directory/obabel_bb2_opt.mol
examples/output_directory/obabel_bb2_unopt.mol
examples/output_directory/obabel_bb3_opt.mol
examples/output_directory/obabel_bb3_unopt.mol
examples/output_directory/obabel_cage2_opt.mol
examples/output_directory/obabel_cage2_unopt.mol
examples/output_directory/obabel_cage_opt.mol
examples/output_directory/obabel_cage_unopt.mol
examples/output_directory/obabel_cycle_opt.mol
examples/output_directory/obabel_cycle_unopt.mol
examples/output_directory/obabel_hg_complex_opt.mol
examples/output_directory/obabel_hg_complex_unopt.mol
examples/output_directory/obabel_m_iron_oct_delta_opt.mol
examples/output_directory/obabel_m_iron_oct_delta_unopt.mol
examples/output_directory/obabel_m_moc_opt.mol
examples/output_directory/obabel_m_moc_unopt.mol
examples/output_directory/obabel_polymer_opt.mol
examples/output_directory/obabel_polymer_unopt.mol
examples/output_directory/obabel_rotaxane_opt.mol
examples/output_directory/obabel_rotaxane_unopt.mol
examples/output_directory/poly_etkdg.mol
examples/output_directory/poly_mmff.mol
examples/output_directory/poly_uff.mol
examples/output_directory/polymer.mol
examples/output_directory/tg_cage.mol
examples/output_directory/tg_info.pdb
examples/output_directory/tors_test_bb1.mol
examples/output_directory/tors_test_polymer.mol
examples/output_directory/example_xtb_out/charges
examples/output_directory/example_xtb_out/det_control.in
examples/output_directory/example_xtb_out/energy.output
examples/output_directory/example_xtb_out/input_structure.xyz
examples/output_directory/example_xtb_out/wbo
examples/output_directory/example_xtb_out/xtbrestart
examples/output_directory/example_xtb_out/xtbtopo.mol
examples/splitter_output_directory/original.mol
examples/splitter_output_directory/original2.mol
examples/splitter_output_directory/reconstructed.mol
examples/splitter_output_directory/splits2_0.mol
examples/splitter_output_directory/splits2_0.xyz
examples/splitter_output_directory/splits2_1.mol
examples/splitter_output_directory/splits2_1.xyz
examples/splitter_output_directory/splits2_2.mol
examples/splitter_output_directory/splits2_2.xyz
examples/splitter_output_directory/splits2_3.mol
examples/splitter_output_directory/splits2_3.xyz
examples/splitter_output_directory/splits2_4.mol
examples/splitter_output_directory/splits2_4.xyz
examples/splitter_output_directory/splits2_5.mol
examples/splitter_output_directory/splits2_5.xyz
examples/splitter_output_directory/splits2_6.mol
examples/splitter_output_directory/splits2_6.xyz
examples/splitter_output_directory/splits2_7.mol
examples/splitter_output_directory/splits2_7.xyz
examples/splitter_output_directory/splits2_8.mol
examples/splitter_output_directory/splits2_8.xyz
examples/splitter_output_directory/splits_0.mol
examples/splitter_output_directory/splits_0.xyz
examples/splitter_output_directory/splits_1.mol
examples/splitter_output_directory/splits_1.xyz
examples/splitter_output_directory/transform2_0.mol
examples/splitter_output_directory/transform2_1.mol
examples/splitter_output_directory/transform2_2.mol
examples/splitter_output_directory/transform2_3.mol
examples/splitter_output_directory/transform2_4.mol
examples/splitter_output_directory/transform2_5.mol
examples/splitter_output_directory/transform2_6.mol
examples/splitter_output_directory/transform2_7.mol
examples/splitter_output_directory/transform2_8.mol
examples/splitter_output_directory/transform_0.mol
examples/splitter_output_directory/transform_1.mol
src/stko/__init__.py
src/stko/_version.py
src/stko/functional_groups.py
src/stko/molecule_analysis.py
src/stko/py.typed
src/stko.egg-info/PKG-INFO
src/stko.egg-info/SOURCES.txt
src/stko.egg-info/dependency_links.txt
src/stko.egg-info/requires.txt
src/stko.egg-info/top_level.txt
src/stko/_internal/__init__.py
src/stko/_internal/types.py
src/stko/_internal/calculators/__init__.py
src/stko/_internal/calculators/open_babel_calculators.py
src/stko/_internal/calculators/openmm_calculators.py
src/stko/_internal/calculators/orca_calculators.py
src/stko/_internal/calculators/planarity_calculators.py
src/stko/_internal/calculators/rdkit_calculators.py
src/stko/_internal/calculators/rmsd_calculators.py
src/stko/_internal/calculators/shape_calculators.py
src/stko/_internal/calculators/torsion_calculators.py
src/stko/_internal/calculators/utilities.py
src/stko/_internal/calculators/xtb_calculators.py
src/stko/_internal/calculators/extractors/__init__.py
src/stko/_internal/calculators/extractors/orca_extractor.py
src/stko/_internal/calculators/extractors/utilities.py
src/stko/_internal/calculators/extractors/xtb_extractor.py
src/stko/_internal/calculators/geometry_analysis/__init__.py
src/stko/_internal/calculators/geometry_analysis/geometry.py
src/stko/_internal/calculators/results/__init__.py
src/stko/_internal/calculators/results/energy_results.py
src/stko/_internal/calculators/results/orca_results.py
src/stko/_internal/calculators/results/planarity_results.py
src/stko/_internal/calculators/results/rmsd_results.py
src/stko/_internal/calculators/results/shape_results.py
src/stko/_internal/calculators/results/torsion_results.py
src/stko/_internal/calculators/results/xtb_results.py
src/stko/_internal/molecular/__init__.py
src/stko/_internal/molecular/atoms/__init__.py
src/stko/_internal/molecular/atoms/dummy_atom.py
src/stko/_internal/molecular/atoms/positioned_atom.py
src/stko/_internal/molecular/constructed/__init__.py
src/stko/_internal/molecular/constructed/constructed_analysis.py
src/stko/_internal/molecular/conversion/__init__.py
src/stko/_internal/molecular/conversion/md_analysis.py
src/stko/_internal/molecular/conversion/z_matrix.py
src/stko/_internal/molecular/decompose/__init__.py
src/stko/_internal/molecular/decompose/decompose_moc.py
src/stko/_internal/molecular/functional_groups/__init__.py
src/stko/_internal/molecular/functional_groups/three_site.py
src/stko/_internal/molecular/molecule_modifiers/__init__.py
src/stko/_internal/molecular/molecule_modifiers/molecule_splitter.py
src/stko/_internal/molecular/molecule_modifiers/molecule_transformer.py
src/stko/_internal/molecular/networkx/__init__.py
src/stko/_internal/molecular/networkx/network.py
src/stko/_internal/molecular/periodic/__init__.py
src/stko/_internal/molecular/periodic/unitcell.py
src/stko/_internal/molecular/periodic/utilities.py
src/stko/_internal/molecular/subgroup_analysis/__init__.py
src/stko/_internal/molecular/subgroup_analysis/subgroup_analyser.py
src/stko/_internal/molecular/subgroup_analysis/three_site_analysis.py
src/stko/_internal/molecular/topology_extractor/__init__.py
src/stko/_internal/molecular/topology_extractor/topology_extractor.py
src/stko/_internal/molecular/topology_extractor/topology_info.py
src/stko/_internal/molecular/torsion/__init__.py
src/stko/_internal/molecular/torsion/torsion.py
src/stko/_internal/molecular/torsion/torsion_info.py
src/stko/_internal/optimizers/__init__.py
src/stko/_internal/optimizers/aligner.py
src/stko/_internal/optimizers/collapser.py
src/stko/_internal/optimizers/gulp.py
src/stko/_internal/optimizers/macromodel.py
src/stko/_internal/optimizers/open_babel.py
src/stko/_internal/optimizers/openmm.py
src/stko/_internal/optimizers/optimizers.py
src/stko/_internal/optimizers/rdkit.py
src/stko/_internal/optimizers/utilities.py
src/stko/_internal/optimizers/xtb.py
src/stko/_internal/utilities/__init__.py
src/stko/_internal/utilities/exceptions.py
src/stko/_internal/utilities/utilities.py
tests/__init__.py
tests/calculators/__init__.py
tests/calculators/geometry/__init__.py
tests/calculators/geometry/case_data.py
tests/calculators/geometry/conftest.py
tests/calculators/geometry/test_calculate_angles.py
tests/calculators/geometry/test_calculate_bonds.py
tests/calculators/geometry/test_calculate_torsions.py
tests/calculators/geometry/test_get_avg_centroid_distance.py
tests/calculators/geometry/test_get_max_diamter.py
tests/calculators/geometry/test_get_metal_centroid_metal_angle.py
tests/calculators/geometry/test_get_metal_distances.py
tests/calculators/geometry/test_get_min_atom_atom.py
tests/calculators/geometry/test_get_min_centroid_distance.py
tests/calculators/geometry/test_get_radius_gyration.py
tests/calculators/openbabel/__init__.py
tests/calculators/openbabel/conftest.py
tests/calculators/openbabel/test_obabel_calculators.py
tests/calculators/planarity/__init__.py
tests/calculators/planarity/conftest.py
tests/calculators/planarity/test_planarity_calculators.py
tests/calculators/pore/__init__.py
tests/calculators/pore/case_data.py
tests/calculators/pore/conftest.py
tests/calculators/rmsd/__init__.py
tests/calculators/rmsd/conftest.py
tests/calculators/rmsd/test_rmsd_calculators.py
tests/calculators/torsion/__init__.py
tests/calculators/torsion/test_torsion_calculators.py
tests/molecular/__init__.py
tests/molecular/atoms/__init__.py
tests/molecular/atoms/utilities.py
tests/molecular/atoms/dummy_atom/__init__.py
tests/molecular/atoms/dummy_atom/case_data.py
tests/molecular/atoms/dummy_atom/conftest.py
tests/molecular/atoms/dummy_atom/test_clone.py
tests/molecular/atoms/dummy_atom/test_get_atomic_number.py
tests/molecular/atoms/dummy_atom/test_get_charge.py
tests/molecular/atoms/dummy_atom/test_get_id.py
tests/molecular/atoms/positioned_atom/__init__.py
tests/molecular/atoms/positioned_atom/case_data.py
tests/molecular/atoms/positioned_atom/conftest.py
tests/molecular/atoms/positioned_atom/test_clone.py
tests/molecular/atoms/positioned_atom/test_get_atomic_number.py
tests/molecular/atoms/positioned_atom/test_get_charge.py
tests/molecular/atoms/positioned_atom/test_get_id.py
tests/molecular/atoms/positioned_atom/test_get_position.py
tests/molecular/atoms/positioned_atom/test_repr.py
tests/molecular/atoms/positioned_atom/test_with_id.py
tests/molecular/constructed/__init__.py
tests/molecular/constructed/case_data.py
tests/molecular/constructed/conftest.py
tests/molecular/constructed/test_get_building_block_atom_ids.py
tests/molecular/constructed/test_get_building_block_centroids.py
tests/molecular/decompose/__init__.py
tests/molecular/decompose/case_data.py
tests/molecular/decompose/conftest.py
tests/molecular/decompose/test_decomposemoc.py
tests/molecular/functional_group/__init__.py
tests/molecular/functional_group/case_data.py
tests/molecular/functional_group/conftest.py
tests/molecular/functional_group/test_threesite.py
tests/molecular/mdanalysis/__init__.py
tests/molecular/mdanalysis/conftest.py
tests/molecular/mdanalysis/test_universe.py
tests/molecular/subgroup/__init__.py
tests/molecular/subgroup/case_data.py
tests/molecular/subgroup/conftest.py
tests/molecular/subgroup/test_subgroup_analysis.py
tests/molecular/threesite/__init__.py
tests/molecular/threesite/case_data.py
tests/molecular/threesite/conftest.py
tests/molecular/threesite/test_get_adjecent_positions.py
tests/molecular/threesite/test_get_binder_adjacent_torsion.py
tests/molecular/threesite/test_get_binder_angles.py
tests/molecular/threesite/test_get_binder_binder_angle.py
tests/molecular/threesite/test_get_binder_centroid_angle.py
tests/molecular/threesite/test_get_binder_distance.py
tests/molecular/z_matrix/__init__.py
tests/molecular/z_matrix/case_data.py
tests/molecular/z_matrix/conftest.py
tests/molecular/z_matrix/test_zmatrix.py
tests/optimizers/__init__.py
tests/optimizers/utilities.py
tests/optimizers/aligner/__init__.py
tests/optimizers/aligner/conftest.py
tests/optimizers/aligner/test_aligner.py
tests/optimizers/gulp/__init__.py
tests/optimizers/gulp/conftest.py
tests/optimizers/gulp/test_gulp.py
tests/optimizers/gulp/test_uff_assign_ff.py
tests/optimizers/gulp/fixtures/conformer.xyz
tests/optimizers/gulp/fixtures/gulp_MD.trg
tests/optimizers/gulp/fixtures/gulp_MD_template.xyz
tests/optimizers/maeextractor/__init__.py
tests/optimizers/maeextractor/case_data.py
tests/optimizers/maeextractor/conftest.py
tests/optimizers/maeextractor/test-out.maegz
tests/optimizers/maeextractor/test_maeextractor.py
tests/optimizers/optimizer/__init__.py
tests/optimizers/optimizer/conftest.py
tests/optimizers/optimizer/test_optimizers.py
tests/optimizers/rdkit/__init__.py
tests/optimizers/rdkit/conftest.py
tests/optimizers/rdkit/test_rdkit_optimizers.py