├── .devcontainer ├── Dockerfile └── devcontainer.json ├── .git_archival.txt ├── .gitattributes ├── .github ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── ci.yaml │ └── docs.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── Makefile ├── README.md ├── devtools └── envs │ └── base.yaml ├── docs ├── development.md ├── examples ├── index.md ├── javascripts │ └── mathjax.js └── scripts │ └── gen_ref_pages.py ├── examples ├── README.md ├── compute-energy.ipynb ├── conformer-minimization.ipynb ├── md-simulations.ipynb └── parameter-gradients.ipynb ├── mkdocs.yml ├── pyproject.toml └── smee ├── __init__.py ├── _constants.py ├── _models.py ├── converters ├── __init__.py ├── openff │ ├── __init__.py │ ├── _openff.py │ ├── nonbonded.py │ └── valence.py └── openmm │ ├── __init__.py │ ├── _ff.py │ ├── _openmm.py │ ├── nonbonded.py │ └── valence.py ├── geometry.py ├── mm ├── __init__.py ├── _config.py ├── _fe.py ├── _mm.py ├── _ops.py ├── _reporters.py └── _utils.py ├── potentials ├── __init__.py ├── _potentials.py ├── nonbonded.py └── valence.py ├── py.typed ├── tests ├── __init__.py ├── conftest.py ├── convertors │ ├── __init__.py │ ├── openff │ │ ├── __init__.py │ │ ├── test_nonbonded.py │ │ ├── test_openff.py │ │ └── test_valence.py │ └── openmm │ │ ├── __init__.py │ │ ├── test_ff.py │ │ └── test_openmm.py ├── data │ └── de-ff.offxml ├── mm │ ├── __init__.py │ ├── conftest.py │ ├── test_fe.py │ ├── test_mm.py │ ├── test_ops.py │ └── test_reporters.py ├── potentials │ ├── __init__.py │ ├── conftest.py │ ├── test_nonbonded.py │ ├── test_potentials.py │ └── test_valence.py ├── test_geometry.py ├── test_models.py ├── test_utils.py └── utils.py └── utils.py /.devcontainer/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/.devcontainer/Dockerfile -------------------------------------------------------------------------------- /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/.devcontainer/devcontainer.json -------------------------------------------------------------------------------- /.git_archival.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/.git_archival.txt -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | .git_archival.txt export-subst 2 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/.github/PULL_REQUEST_TEMPLATE.md -------------------------------------------------------------------------------- /.github/workflows/ci.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/.github/workflows/ci.yaml -------------------------------------------------------------------------------- /.github/workflows/docs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/.github/workflows/docs.yaml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/README.md -------------------------------------------------------------------------------- /devtools/envs/base.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/devtools/envs/base.yaml -------------------------------------------------------------------------------- /docs/development.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/docs/development.md -------------------------------------------------------------------------------- /docs/examples: -------------------------------------------------------------------------------- 1 | ../examples -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- 1 | --8<-- "README.md" 2 | -------------------------------------------------------------------------------- /docs/javascripts/mathjax.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/docs/javascripts/mathjax.js -------------------------------------------------------------------------------- /docs/scripts/gen_ref_pages.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/docs/scripts/gen_ref_pages.py -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/examples/README.md -------------------------------------------------------------------------------- /examples/compute-energy.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/examples/compute-energy.ipynb -------------------------------------------------------------------------------- /examples/conformer-minimization.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/examples/conformer-minimization.ipynb -------------------------------------------------------------------------------- /examples/md-simulations.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/examples/md-simulations.ipynb -------------------------------------------------------------------------------- /examples/parameter-gradients.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/examples/parameter-gradients.ipynb -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/mkdocs.yml -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/pyproject.toml -------------------------------------------------------------------------------- /smee/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/__init__.py -------------------------------------------------------------------------------- /smee/_constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/_constants.py -------------------------------------------------------------------------------- /smee/_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/_models.py -------------------------------------------------------------------------------- /smee/converters/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/__init__.py -------------------------------------------------------------------------------- /smee/converters/openff/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/openff/__init__.py -------------------------------------------------------------------------------- /smee/converters/openff/_openff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/openff/_openff.py -------------------------------------------------------------------------------- /smee/converters/openff/nonbonded.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/openff/nonbonded.py -------------------------------------------------------------------------------- /smee/converters/openff/valence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/openff/valence.py -------------------------------------------------------------------------------- /smee/converters/openmm/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/openmm/__init__.py -------------------------------------------------------------------------------- /smee/converters/openmm/_ff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/openmm/_ff.py -------------------------------------------------------------------------------- /smee/converters/openmm/_openmm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/openmm/_openmm.py -------------------------------------------------------------------------------- /smee/converters/openmm/nonbonded.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/openmm/nonbonded.py -------------------------------------------------------------------------------- /smee/converters/openmm/valence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/converters/openmm/valence.py -------------------------------------------------------------------------------- /smee/geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/geometry.py -------------------------------------------------------------------------------- /smee/mm/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/mm/__init__.py -------------------------------------------------------------------------------- /smee/mm/_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/mm/_config.py -------------------------------------------------------------------------------- /smee/mm/_fe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/mm/_fe.py -------------------------------------------------------------------------------- /smee/mm/_mm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/mm/_mm.py -------------------------------------------------------------------------------- /smee/mm/_ops.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/mm/_ops.py -------------------------------------------------------------------------------- /smee/mm/_reporters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/mm/_reporters.py -------------------------------------------------------------------------------- /smee/mm/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/mm/_utils.py -------------------------------------------------------------------------------- /smee/potentials/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/potentials/__init__.py -------------------------------------------------------------------------------- /smee/potentials/_potentials.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/potentials/_potentials.py -------------------------------------------------------------------------------- /smee/potentials/nonbonded.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/potentials/nonbonded.py -------------------------------------------------------------------------------- /smee/potentials/valence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/potentials/valence.py -------------------------------------------------------------------------------- /smee/py.typed: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /smee/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /smee/tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/conftest.py -------------------------------------------------------------------------------- /smee/tests/convertors/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /smee/tests/convertors/openff/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /smee/tests/convertors/openff/test_nonbonded.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/convertors/openff/test_nonbonded.py -------------------------------------------------------------------------------- /smee/tests/convertors/openff/test_openff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/convertors/openff/test_openff.py -------------------------------------------------------------------------------- /smee/tests/convertors/openff/test_valence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/convertors/openff/test_valence.py -------------------------------------------------------------------------------- /smee/tests/convertors/openmm/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /smee/tests/convertors/openmm/test_ff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/convertors/openmm/test_ff.py -------------------------------------------------------------------------------- /smee/tests/convertors/openmm/test_openmm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/convertors/openmm/test_openmm.py -------------------------------------------------------------------------------- /smee/tests/data/de-ff.offxml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/data/de-ff.offxml -------------------------------------------------------------------------------- /smee/tests/mm/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /smee/tests/mm/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/mm/conftest.py -------------------------------------------------------------------------------- /smee/tests/mm/test_fe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/mm/test_fe.py -------------------------------------------------------------------------------- /smee/tests/mm/test_mm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/mm/test_mm.py -------------------------------------------------------------------------------- /smee/tests/mm/test_ops.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/mm/test_ops.py -------------------------------------------------------------------------------- /smee/tests/mm/test_reporters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/mm/test_reporters.py -------------------------------------------------------------------------------- /smee/tests/potentials/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /smee/tests/potentials/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/potentials/conftest.py -------------------------------------------------------------------------------- /smee/tests/potentials/test_nonbonded.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/potentials/test_nonbonded.py -------------------------------------------------------------------------------- /smee/tests/potentials/test_potentials.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/potentials/test_potentials.py -------------------------------------------------------------------------------- /smee/tests/potentials/test_valence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/potentials/test_valence.py -------------------------------------------------------------------------------- /smee/tests/test_geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/test_geometry.py -------------------------------------------------------------------------------- /smee/tests/test_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/test_models.py -------------------------------------------------------------------------------- /smee/tests/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/test_utils.py -------------------------------------------------------------------------------- /smee/tests/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/tests/utils.py -------------------------------------------------------------------------------- /smee/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimonBoothroyd/smee/HEAD/smee/utils.py --------------------------------------------------------------------------------