.dockerignore
.gitattributes
.gitignore
.pre-commit-config.yaml
AGENTS.md
CITATION.cff
Dockerfile
Dockerfile.bohrium
LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
.github/workflows/publish-ghcr.yml
.github/workflows/publish-pypi.yml
.github/workflows/unit-tests.yml
docs/api_reference.md
docs/architecture.md
docs/tutorials.md
examples/BRCRIM10.cif
examples/DAI-4.cif
examples/DAP-7.cif
examples/MAP.cif
examples/SUXRUA.cif
molcrys_kit/__init__.py
molcrys_kit.egg-info/PKG-INFO
molcrys_kit.egg-info/SOURCES.txt
molcrys_kit.egg-info/dependency_links.txt
molcrys_kit.egg-info/requires.txt
molcrys_kit.egg-info/top_level.txt
molcrys_kit/analysis/__init__.py
molcrys_kit/analysis/charge.py
molcrys_kit/analysis/chemical_env.py
molcrys_kit/analysis/formula_moiety.py
molcrys_kit/analysis/interactions.py
molcrys_kit/analysis/packing_shell.py
molcrys_kit/analysis/shape.py
molcrys_kit/analysis/species.py
molcrys_kit/analysis/stoichiometry.py
molcrys_kit/analysis/disorder/__init__.py
molcrys_kit/analysis/disorder/diagnostics.py
molcrys_kit/analysis/disorder/edge_priority.py
molcrys_kit/analysis/disorder/graph.py
molcrys_kit/analysis/disorder/info.py
molcrys_kit/analysis/disorder/process.py
molcrys_kit/analysis/disorder/solver.py
molcrys_kit/constants/__init__.py
molcrys_kit/constants/atomic_masses.json
molcrys_kit/constants/atomic_radii.json
molcrys_kit/constants/config.py
molcrys_kit/io/__init__.py
molcrys_kit/io/cif.py
molcrys_kit/io/output.py
molcrys_kit/io/xyz.py
molcrys_kit/operations/__init__.py
molcrys_kit/operations/builders.py
molcrys_kit/operations/defects.py
molcrys_kit/operations/desolvation.py
molcrys_kit/operations/hydrogen_completion.py
molcrys_kit/operations/molecule_manipulation.py
molcrys_kit/operations/perturbation.py
molcrys_kit/operations/rotation.py
molcrys_kit/operations/surface.py
molcrys_kit/structures/__init__.py
molcrys_kit/structures/atom.py
molcrys_kit/structures/crystal.py
molcrys_kit/structures/molecule.py
molcrys_kit/structures/polyhedra.py
molcrys_kit/utils/__init__.py
molcrys_kit/utils/geometry.py
notebook/molcryskit.ipynb
notebook/polyhedra_gallery.ipynb
notebook/example/H_lacking_structures/IBPRAC_ibuprofen.cif
notebook/example/H_lacking_structures/MAP.cif
notebook/example/disordered_structures/DAN-2.cif
notebook/example/disordered_structures/DAP-4.cif
notebook/example/disordered_structures/PAP-H4.cif
notebook/example/disordered_structures/TILPEN.cif
notebook/example/disordered_structures/TILPEN01.cif
notebook/example/disordered_structures/TILPEN02.cif
notebook/example/disordered_structures/TILPEN03.cif
notebook/example/slab-benchmark/PETN_PERYTN10.cif
notebook/example/slab-benchmark/beta-HMX_OCHTET12.cif
paper/README.md
paper/csd_statistics/README.md
paper/csd_statistics/csd_statistics.py
paper/csd_statistics/plot_csd_results.py
paper/csd_statistics/results/csd_statistics_summary.json
paper/qm9_benchmark/README.md
paper/qm9_benchmark/plot_qm9_analysis.py
paper/qm9_benchmark/validate_hybridization_qm9_real.py
paper/qm9_benchmark/results/qm9_real_raw.json
paper/qm9_benchmark/results/qm9_statistics.json
paper/slab_benchmark/README.md
paper/slab_benchmark/multi_system_benchmark.py
paper/slab_benchmark/plot_benchmark.py
paper/slab_benchmark/bohrium_submit/submit_bohrium.py
paper/slab_benchmark/results/multi_system_benchmark.json
paper/slab_benchmark/slab_examples/Acetaminophen_HXACAN.cif
paper/slab_benchmark/slab_examples/DAP-M4.cif
paper/slab_benchmark/slab_examples/beta-HMX_OCHTET12.cif
scripts/diagnose_valence.py
scripts/docker-test.sh
scripts/docker_smoke_test.py
scripts/dump_disorder_modes.py
scripts/identify_molecules.py
scripts/process_disordered_structures.py
scripts/repro_implicit_nh4.py
scripts/test_defect.py
scripts/test_desolvation.py
scripts/test_h_completion.py
scripts/test_topological_slab.py
scripts/visualize_disorder_graphs.py
scripts/visualize_disorder_partialgraphs.py
tests/conftest.py
tests/test_cif_parsing.py
tests/data/test_full_coords.cif
tests/data/cif/1-HTP.cif
tests/data/cif/Acetaminophen_HXACAN.cif
tests/data/cif/BRCRIM10.cif
tests/data/cif/DAC-4.cif
tests/data/cif/DACMOR.cif
tests/data/cif/DAI-4.cif
tests/data/cif/DAI-X1.cif
tests/data/cif/DAN-2.cif
tests/data/cif/DAP-4.cif
tests/data/cif/DAP-7.cif
tests/data/cif/DAP-O4.cif
tests/data/cif/GICVUJ03.cif
tests/data/cif/ISATIN.cif
tests/data/cif/MAF-4.cif
tests/data/cif/MAP.cif
tests/data/cif/NatComm-1.cif
tests/data/cif/PAP-4.cif
tests/data/cif/PAP-H4.cif
tests/data/cif/PAP-M5.cif
tests/data/cif/PETN_PERYTN10.cif
tests/data/cif/SUXRUA.cif
tests/data/cif/TILPEN.cif
tests/data/cif/ZIF-4.cif
tests/data/cif/ZIF-8.cif
tests/data/cif/ammonium_sp_explicit_hm4.cif
tests/data/cif/anhydrousCaffeine2_CGD_2007_7_1406.cif
tests/data/cif/anhydrousCaffeine_CGD_2007_7_1406.cif
tests/data/cif/phenethylammonium_sp_p21m.cif
tests/dev/test_phase1_io.py
tests/unit/README.md
tests/unit/test_analysis.py
tests/unit/test_constants.py
tests/unit/test_disorder.py
tests/unit/test_disorder_regression.py
tests/unit/test_disorder_repair.py
tests/unit/test_formula_moiety.py
tests/unit/test_geometry.py
tests/unit/test_hydrogen_completion_regression.py
tests/unit/test_io_cif.py
tests/unit/test_io_output.py
tests/unit/test_molecule_manipulation.py
tests/unit/test_operations.py
tests/unit/test_packing_shell.py
tests/unit/test_polyhedra.py
tests/unit/test_shape.py
tests/unit/test_slab_terminations.py
tests/unit/test_sp_completion.py
tests/unit/test_special_positions.py
tests/unit/test_structures.py
tests/unit/test_topological_slab_script.py
tests/unit/test_unwrap.py