├── .gitignore ├── .readthedocs.yaml ├── .scrutinizer.yml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── make.bat ├── objects.inv ├── objs.txt ├── requirements.txt └── source │ ├── Description_of_AMD_PDD.rst │ ├── Disorder.rst │ ├── Miscellaneous.rst │ ├── Reading_cifs.rst │ ├── Reading_from_the_CSD.rst │ ├── Using_AMD.rst │ ├── Using_PDD.rst │ ├── _build │ └── doctrees │ │ ├── Description_of_AMD_PDD.doctree │ │ ├── Get_Started.doctree │ │ ├── Miscellaneous.doctree │ │ ├── Reading_cifs.doctree │ │ ├── Reading_from_the_CSD.doctree │ │ ├── Using_AMDs.doctree │ │ ├── Using_PDDs.doctree │ │ ├── amd.calculate.doctree │ │ ├── amd.compare.doctree │ │ ├── amd.io.doctree │ │ ├── amd.periodicset.doctree │ │ ├── amd.utils.doctree │ │ ├── environment.pickle │ │ ├── images │ │ ├── 238ee994f8325644a377715b303a1fd5cce0c2c5 │ │ │ └── build.png │ │ ├── 3cd1adf8e0ac99e0da863a5b667daf11847b6e07 │ │ │ └── average-minimum-distance.svg │ │ ├── 648504b14f0b557d4d89e50de07082c6828e0547 │ │ │ └── average-minimum-distance.svg │ │ ├── 7b0ed7c913d6b1f544e97168f735528d2fb878d6 │ │ │ └── average-minimum-distance.svg │ │ └── e2e030c632e78e79afb1a1aa1a0db4210dc19b3e │ │ │ └── 533e6db8fa4b36a6c830782e84cb29aadae1ce9d.svg │ │ └── index.doctree │ ├── amd.calculate.rst │ ├── amd.compare.rst │ ├── amd.io.rst │ ├── amd.periodicset.rst │ ├── amd.utils.rst │ ├── conf.py │ └── index.rst ├── examples ├── CaCO3.cif └── guide.ipynb ├── pyproject.toml ├── requirements.txt ├── src └── amd │ ├── __init__.py │ ├── _emd.py │ ├── _nearest_neighbors.py │ ├── _types.py │ ├── atomic_masses.json │ ├── atomic_numbers.json │ ├── calculate.py │ ├── compare.py │ ├── globals_.py │ ├── io.py │ ├── periodicset.py │ ├── reconstruct.py │ └── utils.py └── tests ├── conftest.py ├── data ├── CSD_families.pkl ├── CSD_families_cdm.npz ├── T2-alpha-solvent.cif ├── T2_experimental.cif ├── T2_experimental.pkl ├── T2_experimental_cdm.npz ├── cubic.cif ├── cubic.pkl ├── eq_sites_test.cif └── regenerate_data.py ├── test_CSDReader.py ├── test_CifReader.py ├── test_calculate.py ├── test_compare.py └── test_utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /.scrutinizer.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/.scrutinizer.yml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/README.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/objects.inv -------------------------------------------------------------------------------- /docs/objs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/objs.txt -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /docs/source/Description_of_AMD_PDD.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/Description_of_AMD_PDD.rst -------------------------------------------------------------------------------- /docs/source/Disorder.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/Disorder.rst -------------------------------------------------------------------------------- /docs/source/Miscellaneous.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/Miscellaneous.rst -------------------------------------------------------------------------------- /docs/source/Reading_cifs.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/Reading_cifs.rst -------------------------------------------------------------------------------- /docs/source/Reading_from_the_CSD.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/Reading_from_the_CSD.rst -------------------------------------------------------------------------------- /docs/source/Using_AMD.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/Using_AMD.rst -------------------------------------------------------------------------------- /docs/source/Using_PDD.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/Using_PDD.rst -------------------------------------------------------------------------------- /docs/source/_build/doctrees/Description_of_AMD_PDD.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/Description_of_AMD_PDD.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/Get_Started.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/Get_Started.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/Miscellaneous.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/Miscellaneous.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/Reading_cifs.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/Reading_cifs.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/Reading_from_the_CSD.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/Reading_from_the_CSD.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/Using_AMDs.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/Using_AMDs.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/Using_PDDs.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/Using_PDDs.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/amd.calculate.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/amd.calculate.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/amd.compare.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/amd.compare.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/amd.io.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/amd.io.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/amd.periodicset.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/amd.periodicset.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/amd.utils.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/amd.utils.doctree -------------------------------------------------------------------------------- /docs/source/_build/doctrees/environment.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/environment.pickle -------------------------------------------------------------------------------- /docs/source/_build/doctrees/images/238ee994f8325644a377715b303a1fd5cce0c2c5/build.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/images/238ee994f8325644a377715b303a1fd5cce0c2c5/build.png -------------------------------------------------------------------------------- /docs/source/_build/doctrees/images/3cd1adf8e0ac99e0da863a5b667daf11847b6e07/average-minimum-distance.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/images/3cd1adf8e0ac99e0da863a5b667daf11847b6e07/average-minimum-distance.svg -------------------------------------------------------------------------------- /docs/source/_build/doctrees/images/648504b14f0b557d4d89e50de07082c6828e0547/average-minimum-distance.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/images/648504b14f0b557d4d89e50de07082c6828e0547/average-minimum-distance.svg -------------------------------------------------------------------------------- /docs/source/_build/doctrees/images/7b0ed7c913d6b1f544e97168f735528d2fb878d6/average-minimum-distance.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/images/7b0ed7c913d6b1f544e97168f735528d2fb878d6/average-minimum-distance.svg -------------------------------------------------------------------------------- /docs/source/_build/doctrees/images/e2e030c632e78e79afb1a1aa1a0db4210dc19b3e/533e6db8fa4b36a6c830782e84cb29aadae1ce9d.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/images/e2e030c632e78e79afb1a1aa1a0db4210dc19b3e/533e6db8fa4b36a6c830782e84cb29aadae1ce9d.svg -------------------------------------------------------------------------------- /docs/source/_build/doctrees/index.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/_build/doctrees/index.doctree -------------------------------------------------------------------------------- /docs/source/amd.calculate.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/amd.calculate.rst -------------------------------------------------------------------------------- /docs/source/amd.compare.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/amd.compare.rst -------------------------------------------------------------------------------- /docs/source/amd.io.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/amd.io.rst -------------------------------------------------------------------------------- /docs/source/amd.periodicset.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/amd.periodicset.rst -------------------------------------------------------------------------------- /docs/source/amd.utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/amd.utils.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /examples/CaCO3.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/examples/CaCO3.cif -------------------------------------------------------------------------------- /examples/guide.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/examples/guide.ipynb -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/pyproject.toml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/requirements.txt -------------------------------------------------------------------------------- /src/amd/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/__init__.py -------------------------------------------------------------------------------- /src/amd/_emd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/_emd.py -------------------------------------------------------------------------------- /src/amd/_nearest_neighbors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/_nearest_neighbors.py -------------------------------------------------------------------------------- /src/amd/_types.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/_types.py -------------------------------------------------------------------------------- /src/amd/atomic_masses.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/atomic_masses.json -------------------------------------------------------------------------------- /src/amd/atomic_numbers.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/atomic_numbers.json -------------------------------------------------------------------------------- /src/amd/calculate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/calculate.py -------------------------------------------------------------------------------- /src/amd/compare.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/compare.py -------------------------------------------------------------------------------- /src/amd/globals_.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/globals_.py -------------------------------------------------------------------------------- /src/amd/io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/io.py -------------------------------------------------------------------------------- /src/amd/periodicset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/periodicset.py -------------------------------------------------------------------------------- /src/amd/reconstruct.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/reconstruct.py -------------------------------------------------------------------------------- /src/amd/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/src/amd/utils.py -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/data/CSD_families.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/CSD_families.pkl -------------------------------------------------------------------------------- /tests/data/CSD_families_cdm.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/CSD_families_cdm.npz -------------------------------------------------------------------------------- /tests/data/T2-alpha-solvent.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/T2-alpha-solvent.cif -------------------------------------------------------------------------------- /tests/data/T2_experimental.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/T2_experimental.cif -------------------------------------------------------------------------------- /tests/data/T2_experimental.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/T2_experimental.pkl -------------------------------------------------------------------------------- /tests/data/T2_experimental_cdm.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/T2_experimental_cdm.npz -------------------------------------------------------------------------------- /tests/data/cubic.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/cubic.cif -------------------------------------------------------------------------------- /tests/data/cubic.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/cubic.pkl -------------------------------------------------------------------------------- /tests/data/eq_sites_test.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/eq_sites_test.cif -------------------------------------------------------------------------------- /tests/data/regenerate_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/data/regenerate_data.py -------------------------------------------------------------------------------- /tests/test_CSDReader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/test_CSDReader.py -------------------------------------------------------------------------------- /tests/test_CifReader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/test_CifReader.py -------------------------------------------------------------------------------- /tests/test_calculate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/test_calculate.py -------------------------------------------------------------------------------- /tests/test_compare.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/test_compare.py -------------------------------------------------------------------------------- /tests/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwiddo/average-minimum-distance/HEAD/tests/test_utils.py --------------------------------------------------------------------------------