.gitignore
.readthedocs.yml
LICENSE
README.rst
justfile
mypy.ini
pyproject.toml
uv.lock
.github/pull_request_template.md
.github/workflows/publish_release.yml
.github/workflows/tests.yml
docs/Makefile
docs/source/cage_analysis.rst
docs/source/calculators.rst
docs/source/conf.py
docs/source/index.rst
docs/source/modules.rst
docs/source/molecular.rst
docs/source/optimizers.rst
docs/source/using_topology_for_opt.rst
docs/source/video_tutorials.rst
docs/source/_static/logo.png
docs/source/_static/new_stko_logo_dec2025.pdf
docs/source/_static/new_stko_logo_dec2025.svg
docs/source/_static/openmm_opt_file.mol
docs/source/_static/opt_complex.mol
docs/source/_static/sidebar_logo.png
docs/source/_static/sidebar_logo.svg
docs/source/_static/stko.png
docs/source/_static/unopt_hgcomplex.mol
docs/source/_templates/class.rst
docs/source/_templates/module.rst
examples/basic_example.py
examples/cage_analysis_example.py
examples/calculators_example.py
examples/intermediates_example.py
examples/optwrite_example.py
examples/shape_example.py
examples/testable_example.py
examples/topology_extraction_example.py
examples/torsion_example.py
examples/zmatrix_example.py
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/optwrite_output/etkdg_out.mol
examples/optwrite_output/mmff_out.mol
examples/optwrite_output/uff_out.mol
examples/out_intermediates/idx0_3x3FG+2x2FG.mol
examples/out_intermediates/idx1_1x3FG.mol
examples/out_intermediates/idx2_1x2FG.mol
examples/out_intermediates/idx3_2x3FG+3x2FG.mol
examples/out_intermediates/idx4_2x3FG+2x2FG.mol
examples/out_intermediates/idx5_1x3FG+1x2FG.mol
examples/out_intermediates/idx6_2x3FG+3x2FG.mol
examples/out_intermediates/idx7_2x3FG+1x2FG.mol
examples/out_intermediates/idx8_1x3FG+2x2FG.mol
examples/out_intermediates/idx9_1x3FG+3x2FG.mol
examples/output_directory/bb1.mol
examples/output_directory/bb2.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
src/stko/__init__.py
src/stko/_version.py
src/stko/functional_groups.py
src/stko/molecular_utilities.py
src/stko/molecule_analysis.py
src/stko/py.typed
src/stko/topology_functions.py
src/stko/_internal/__init__.py
src/stko/_internal/internal_types.py
src/stko/_internal/calculators/__init__.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/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/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/molecular/__init__.py
src/stko/_internal/molecular/molecular_utilities.py
src/stko/_internal/molecular/atoms/__init__.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/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/intermediates/__init__.py
src/stko/_internal/molecular/intermediates/unreacted.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/collapser.py
src/stko/_internal/optimizers/gfnff.py
src/stko/_internal/optimizers/optimizers.py
src/stko/_internal/optimizers/rdkit.py
src/stko/_internal/optimizers/utilities.py
src/stko/_internal/utilities/__init__.py
src/stko/_internal/utilities/exceptions.py
src/stko/_internal/utilities/utilities.py
src/stko_lite.egg-info/PKG-INFO
src/stko_lite.egg-info/SOURCES.txt
src/stko_lite.egg-info/dependency_links.txt
src/stko_lite.egg-info/requires.txt
src/stko_lite.egg-info/scm_file_list.json
src/stko_lite.egg-info/scm_version.json
src/stko_lite.egg-info/top_level.txt
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_properties.py
tests/calculators/geometry/test_calculate_torsions.py
tests/calculators/geometry/geom_jsons/case_data0_angles.json
tests/calculators/geometry/geom_jsons/case_data0_bonds.json
tests/calculators/geometry/geom_jsons/case_data0_properties.json
tests/calculators/geometry/geom_jsons/case_data0_torsions.json
tests/calculators/geometry/geom_jsons/case_data1_angles.json
tests/calculators/geometry/geom_jsons/case_data1_bonds.json
tests/calculators/geometry/geom_jsons/case_data1_properties.json
tests/calculators/geometry/geom_jsons/case_data1_torsions.json
tests/calculators/geometry/geom_jsons/case_data2_angles.json
tests/calculators/geometry/geom_jsons/case_data2_bonds.json
tests/calculators/geometry/geom_jsons/case_data2_properties.json
tests/calculators/geometry/geom_jsons/case_data2_torsions.json
tests/calculators/planarity/__init__.py
tests/calculators/planarity/conftest.py
tests/calculators/planarity/test_planarity_calculators.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/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/constructed/centroid_jsons/case_data0.json
tests/molecular/constructed/centroid_jsons/case_data1.json
tests/molecular/constructed/centroid_jsons/case_data2.json
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/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_threesite_properties.py
tests/molecular/threesite/property_jsons/case_data0_properties.json
tests/molecular/threesite/property_jsons/case_data1_properties.json
tests/molecular/threesite/property_jsons/case_data2_properties.json
tests/molecular/threesite/property_jsons/case_data3_properties.json
tests/molecular/utilities/__init__.py
tests/molecular/utilities/conftest.py
tests/molecular/utilities/test_merge_molecules.py
tests/molecular/utilities/test_seperate_molecules.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/gfnff/__init__.py
tests/optimizers/gfnff/conftest.py
tests/optimizers/gfnff/test_gfnff.py
tests/optimizers/gfnff/test_lbfgs.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