├── .github └── workflows │ └── test_and_deploy.yml ├── .gitignore ├── CONTRIB.rst ├── LICENSE.rst ├── MANIFEST.in ├── README.rst ├── doc ├── api.rst ├── cli.rst ├── conf.py ├── figure_scripts │ ├── api.py │ ├── cover_structure.py │ ├── fragments.py │ ├── molecules │ │ ├── benzene.sdf │ │ ├── isobutylene.sdf │ │ ├── propane.sdf │ │ └── toluene.sdf │ ├── rotation_freedom.py │ └── util.py ├── images │ ├── api_01.png │ ├── api_02.png │ ├── api_03.png │ ├── api_04.png │ ├── cover_structure.png │ └── cover_structure.svg ├── index.rst ├── intro.rst ├── issues.rst └── static │ ├── assets │ ├── hydride_icon.svg │ ├── hydride_icon_32p.png │ ├── hydride_logo.png │ └── hydride_logo.svg │ ├── fonts.css │ ├── fonts │ ├── LICENSE │ ├── crete-round-v13-latin-italic.woff │ ├── crete-round-v13-latin-italic.woff2 │ ├── crete-round-v13-latin-regular.woff │ ├── crete-round-v13-latin-regular.woff2 │ ├── fira-sans-v15-latin-italic.woff │ ├── fira-sans-v15-latin-italic.woff2 │ ├── fira-sans-v15-latin-regular.woff │ └── fira-sans-v15-latin-regular.woff2 │ └── hydride.css ├── prot_variants.msgpack ├── pyproject.toml ├── setup.py ├── src └── hydride │ ├── __init__.py │ ├── add.py │ ├── charge.py │ ├── cli.py │ ├── fragments.py │ ├── names.py │ └── relax.pyx └── tests ├── __init__.py ├── conftest.py ├── data ├── 1gya.bcif ├── 1l2y.bcif ├── 2rtg.bcif ├── TYR.mol └── TYR.sdf ├── test_add.py ├── test_charge.py ├── test_cli.py ├── test_fragments.py ├── test_names.py ├── test_relax.py └── util.py /.github/workflows/test_and_deploy.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/.github/workflows/test_and_deploy.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/.gitignore -------------------------------------------------------------------------------- /CONTRIB.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/CONTRIB.rst -------------------------------------------------------------------------------- /LICENSE.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/LICENSE.rst -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/README.rst -------------------------------------------------------------------------------- /doc/api.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/api.rst -------------------------------------------------------------------------------- /doc/cli.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/cli.rst -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/conf.py -------------------------------------------------------------------------------- /doc/figure_scripts/api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/figure_scripts/api.py -------------------------------------------------------------------------------- /doc/figure_scripts/cover_structure.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/figure_scripts/cover_structure.py -------------------------------------------------------------------------------- /doc/figure_scripts/fragments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/figure_scripts/fragments.py -------------------------------------------------------------------------------- /doc/figure_scripts/molecules/benzene.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/figure_scripts/molecules/benzene.sdf -------------------------------------------------------------------------------- /doc/figure_scripts/molecules/isobutylene.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/figure_scripts/molecules/isobutylene.sdf -------------------------------------------------------------------------------- /doc/figure_scripts/molecules/propane.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/figure_scripts/molecules/propane.sdf -------------------------------------------------------------------------------- /doc/figure_scripts/molecules/toluene.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/figure_scripts/molecules/toluene.sdf -------------------------------------------------------------------------------- /doc/figure_scripts/rotation_freedom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/figure_scripts/rotation_freedom.py -------------------------------------------------------------------------------- /doc/figure_scripts/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/figure_scripts/util.py -------------------------------------------------------------------------------- /doc/images/api_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/images/api_01.png -------------------------------------------------------------------------------- /doc/images/api_02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/images/api_02.png -------------------------------------------------------------------------------- /doc/images/api_03.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/images/api_03.png -------------------------------------------------------------------------------- /doc/images/api_04.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/images/api_04.png -------------------------------------------------------------------------------- /doc/images/cover_structure.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/images/cover_structure.png -------------------------------------------------------------------------------- /doc/images/cover_structure.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/images/cover_structure.svg -------------------------------------------------------------------------------- /doc/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/index.rst -------------------------------------------------------------------------------- /doc/intro.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/intro.rst -------------------------------------------------------------------------------- /doc/issues.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/issues.rst -------------------------------------------------------------------------------- /doc/static/assets/hydride_icon.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/assets/hydride_icon.svg -------------------------------------------------------------------------------- /doc/static/assets/hydride_icon_32p.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/assets/hydride_icon_32p.png -------------------------------------------------------------------------------- /doc/static/assets/hydride_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/assets/hydride_logo.png -------------------------------------------------------------------------------- /doc/static/assets/hydride_logo.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/assets/hydride_logo.svg -------------------------------------------------------------------------------- /doc/static/fonts.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts.css -------------------------------------------------------------------------------- /doc/static/fonts/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts/LICENSE -------------------------------------------------------------------------------- /doc/static/fonts/crete-round-v13-latin-italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts/crete-round-v13-latin-italic.woff -------------------------------------------------------------------------------- /doc/static/fonts/crete-round-v13-latin-italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts/crete-round-v13-latin-italic.woff2 -------------------------------------------------------------------------------- /doc/static/fonts/crete-round-v13-latin-regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts/crete-round-v13-latin-regular.woff -------------------------------------------------------------------------------- /doc/static/fonts/crete-round-v13-latin-regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts/crete-round-v13-latin-regular.woff2 -------------------------------------------------------------------------------- /doc/static/fonts/fira-sans-v15-latin-italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts/fira-sans-v15-latin-italic.woff -------------------------------------------------------------------------------- /doc/static/fonts/fira-sans-v15-latin-italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts/fira-sans-v15-latin-italic.woff2 -------------------------------------------------------------------------------- /doc/static/fonts/fira-sans-v15-latin-regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts/fira-sans-v15-latin-regular.woff -------------------------------------------------------------------------------- /doc/static/fonts/fira-sans-v15-latin-regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/fonts/fira-sans-v15-latin-regular.woff2 -------------------------------------------------------------------------------- /doc/static/hydride.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/doc/static/hydride.css -------------------------------------------------------------------------------- /prot_variants.msgpack: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/prot_variants.msgpack -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/pyproject.toml -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/setup.py -------------------------------------------------------------------------------- /src/hydride/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/src/hydride/__init__.py -------------------------------------------------------------------------------- /src/hydride/add.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/src/hydride/add.py -------------------------------------------------------------------------------- /src/hydride/charge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/src/hydride/charge.py -------------------------------------------------------------------------------- /src/hydride/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/src/hydride/cli.py -------------------------------------------------------------------------------- /src/hydride/fragments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/src/hydride/fragments.py -------------------------------------------------------------------------------- /src/hydride/names.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/src/hydride/names.py -------------------------------------------------------------------------------- /src/hydride/relax.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/src/hydride/relax.pyx -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/data/1gya.bcif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/data/1gya.bcif -------------------------------------------------------------------------------- /tests/data/1l2y.bcif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/data/1l2y.bcif -------------------------------------------------------------------------------- /tests/data/2rtg.bcif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/data/2rtg.bcif -------------------------------------------------------------------------------- /tests/data/TYR.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/data/TYR.mol -------------------------------------------------------------------------------- /tests/data/TYR.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/data/TYR.sdf -------------------------------------------------------------------------------- /tests/test_add.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/test_add.py -------------------------------------------------------------------------------- /tests/test_charge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/test_charge.py -------------------------------------------------------------------------------- /tests/test_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/test_cli.py -------------------------------------------------------------------------------- /tests/test_fragments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/test_fragments.py -------------------------------------------------------------------------------- /tests/test_names.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/test_names.py -------------------------------------------------------------------------------- /tests/test_relax.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/test_relax.py -------------------------------------------------------------------------------- /tests/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biotite-dev/hydride/HEAD/tests/util.py --------------------------------------------------------------------------------