├── .dockerignore ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── feature_request.md │ └── user_story.md └── workflows │ ├── black.yml │ ├── ci-integration.yml │ └── deploy-docker.yml ├── .gitignore ├── .readthedocs.yaml ├── CITATION.cff ├── LICENSE ├── NOTICE ├── README.md ├── alchemiscale ├── __init__.py ├── base │ ├── __init__.py │ ├── api.py │ └── client.py ├── cli.py ├── cli_utils.py ├── compression.py ├── compute │ ├── __init__.py │ ├── api.py │ ├── client.py │ ├── manager.py │ ├── service.py │ └── settings.py ├── interface │ ├── __init__.py │ ├── api.py │ └── client.py ├── migrations │ └── v03_to_v04.py ├── models.py ├── security │ ├── __init__.py │ ├── auth.py │ └── models.py ├── settings.py ├── storage │ ├── __init__.py │ ├── cypher.py │ ├── models.py │ ├── objectstore.py │ ├── statestore.py │ └── subgraph.py ├── strategist │ ├── __init__.py │ ├── service.py │ └── settings.py ├── tests │ ├── __init__.py │ ├── integration │ │ ├── __init__.py │ │ ├── compute │ │ │ ├── __init__.py │ │ │ ├── client │ │ │ │ ├── __init__.py │ │ │ │ ├── conftest.py │ │ │ │ ├── test_compute_client.py │ │ │ │ ├── test_compute_manager.py │ │ │ │ ├── test_compute_manager_client.py │ │ │ │ └── test_compute_service.py │ │ │ ├── conftest.py │ │ │ ├── test_compute_api.py │ │ │ └── utils.py │ │ ├── conftest.py │ │ ├── interface │ │ │ ├── __init__.py │ │ │ ├── client │ │ │ │ ├── __init__.py │ │ │ │ ├── conftest.py │ │ │ │ └── test_client.py │ │ │ ├── conftest.py │ │ │ ├── test_api.py │ │ │ └── utils.py │ │ ├── storage │ │ │ ├── __init__.py │ │ │ ├── test_objectstore.py │ │ │ ├── test_statestore.py │ │ │ └── utils.py │ │ ├── strategist │ │ │ ├── __init__.py │ │ │ └── test_strategist_service.py │ │ ├── test_cli.py │ │ └── utils.py │ └── unit │ │ ├── __init__.py │ │ ├── compute │ │ └── test_settings.py │ │ ├── conftest.py │ │ ├── test_base_api.py │ │ ├── test_client_params.py │ │ ├── test_cypher.py │ │ ├── test_models.py │ │ ├── test_security.py │ │ ├── test_storage_models.py │ │ ├── test_utils.py │ │ └── test_validators.py ├── utils.py └── validators.py ├── devtools ├── conda-envs │ ├── alchemiscale-client.yml │ ├── alchemiscale-compute.yml │ ├── alchemiscale-server.yml │ ├── docs.yml │ └── test.yml └── configs │ ├── strategist-settings.yaml │ └── synchronous-compute-settings.yaml ├── docker ├── alchemiscale-compute │ └── Dockerfile └── alchemiscale-server │ ├── .env.template │ ├── .env.testing │ ├── Dockerfile │ ├── README.md │ └── docker-compose.yml ├── docs ├── .nojekyll ├── CHANGELOG.rst ├── Makefile ├── api.rst ├── api │ ├── base.rst │ ├── cli.rst │ ├── compute.rst │ ├── interface.rst │ ├── models.rst │ ├── security.rst │ ├── settings.rst │ ├── storage.rst │ └── strategist.rst ├── assets │ ├── logo │ │ └── logo_full_horizontal_inverted.png │ └── system-architecture.png ├── compute.rst ├── conf.py ├── deployment.rst ├── development.rst ├── index.rst ├── make.bat ├── operations.rst ├── tutorials │ ├── demo │ │ ├── Alchemiscale Demo.ipynb │ │ ├── ligands.sdf │ │ ├── ligands.yml │ │ └── protein.pdb │ └── index.rst └── user_guide │ ├── getting_started.rst │ ├── handling_errors.rst │ ├── index.rst │ └── strategy_automation.rst ├── news ├── TEMPLATE.rst └── driver-notifications.rst ├── pyproject.toml └── rever.xsh /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | fah_alchemy/_version.py export-subst 2 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/.github/ISSUE_TEMPLATE/feature_request.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/user_story.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/.github/ISSUE_TEMPLATE/user_story.md -------------------------------------------------------------------------------- /.github/workflows/black.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/.github/workflows/black.yml -------------------------------------------------------------------------------- /.github/workflows/ci-integration.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/.github/workflows/ci-integration.yml -------------------------------------------------------------------------------- /.github/workflows/deploy-docker.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/.github/workflows/deploy-docker.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/CITATION.cff -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/LICENSE -------------------------------------------------------------------------------- /NOTICE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/NOTICE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/README.md -------------------------------------------------------------------------------- /alchemiscale/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/__init__.py -------------------------------------------------------------------------------- /alchemiscale/base/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/base/api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/base/api.py -------------------------------------------------------------------------------- /alchemiscale/base/client.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/base/client.py -------------------------------------------------------------------------------- /alchemiscale/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/cli.py -------------------------------------------------------------------------------- /alchemiscale/cli_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/cli_utils.py -------------------------------------------------------------------------------- /alchemiscale/compression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/compression.py -------------------------------------------------------------------------------- /alchemiscale/compute/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/compute/__init__.py -------------------------------------------------------------------------------- /alchemiscale/compute/api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/compute/api.py -------------------------------------------------------------------------------- /alchemiscale/compute/client.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/compute/client.py -------------------------------------------------------------------------------- /alchemiscale/compute/manager.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/compute/manager.py -------------------------------------------------------------------------------- /alchemiscale/compute/service.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/compute/service.py -------------------------------------------------------------------------------- /alchemiscale/compute/settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/compute/settings.py -------------------------------------------------------------------------------- /alchemiscale/interface/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/interface/__init__.py -------------------------------------------------------------------------------- /alchemiscale/interface/api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/interface/api.py -------------------------------------------------------------------------------- /alchemiscale/interface/client.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/interface/client.py -------------------------------------------------------------------------------- /alchemiscale/migrations/v03_to_v04.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/migrations/v03_to_v04.py -------------------------------------------------------------------------------- /alchemiscale/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/models.py -------------------------------------------------------------------------------- /alchemiscale/security/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/security/auth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/security/auth.py -------------------------------------------------------------------------------- /alchemiscale/security/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/security/models.py -------------------------------------------------------------------------------- /alchemiscale/settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/settings.py -------------------------------------------------------------------------------- /alchemiscale/storage/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/storage/cypher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/storage/cypher.py -------------------------------------------------------------------------------- /alchemiscale/storage/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/storage/models.py -------------------------------------------------------------------------------- /alchemiscale/storage/objectstore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/storage/objectstore.py -------------------------------------------------------------------------------- /alchemiscale/storage/statestore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/storage/statestore.py -------------------------------------------------------------------------------- /alchemiscale/storage/subgraph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/storage/subgraph.py -------------------------------------------------------------------------------- /alchemiscale/strategist/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/strategist/__init__.py -------------------------------------------------------------------------------- /alchemiscale/strategist/service.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/strategist/service.py -------------------------------------------------------------------------------- /alchemiscale/strategist/settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/strategist/settings.py -------------------------------------------------------------------------------- /alchemiscale/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/tests/integration/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/client/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/client/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/compute/client/conftest.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/client/test_compute_client.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/compute/client/test_compute_client.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/client/test_compute_manager.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/compute/client/test_compute_manager.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/client/test_compute_manager_client.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/compute/client/test_compute_manager_client.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/client/test_compute_service.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/compute/client/test_compute_service.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/compute/conftest.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/test_compute_api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/compute/test_compute_api.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/compute/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/compute/utils.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/conftest.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/interface/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/tests/integration/interface/client/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/tests/integration/interface/client/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/interface/client/conftest.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/interface/client/test_client.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/interface/client/test_client.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/interface/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/interface/conftest.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/interface/test_api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/interface/test_api.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/interface/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/interface/utils.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/storage/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/tests/integration/storage/test_objectstore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/storage/test_objectstore.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/storage/test_statestore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/storage/test_statestore.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/storage/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/storage/utils.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/strategist/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/tests/integration/strategist/test_strategist_service.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/strategist/test_strategist_service.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/test_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/test_cli.py -------------------------------------------------------------------------------- /alchemiscale/tests/integration/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/integration/utils.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alchemiscale/tests/unit/compute/test_settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/compute/test_settings.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/conftest.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/test_base_api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/test_base_api.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/test_client_params.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/test_client_params.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/test_cypher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/test_cypher.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/test_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/test_models.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/test_security.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/test_security.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/test_storage_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/test_storage_models.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/test_utils.py -------------------------------------------------------------------------------- /alchemiscale/tests/unit/test_validators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/tests/unit/test_validators.py -------------------------------------------------------------------------------- /alchemiscale/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/utils.py -------------------------------------------------------------------------------- /alchemiscale/validators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/alchemiscale/validators.py -------------------------------------------------------------------------------- /devtools/conda-envs/alchemiscale-client.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/devtools/conda-envs/alchemiscale-client.yml -------------------------------------------------------------------------------- /devtools/conda-envs/alchemiscale-compute.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/devtools/conda-envs/alchemiscale-compute.yml -------------------------------------------------------------------------------- /devtools/conda-envs/alchemiscale-server.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/devtools/conda-envs/alchemiscale-server.yml -------------------------------------------------------------------------------- /devtools/conda-envs/docs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/devtools/conda-envs/docs.yml -------------------------------------------------------------------------------- /devtools/conda-envs/test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/devtools/conda-envs/test.yml -------------------------------------------------------------------------------- /devtools/configs/strategist-settings.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/devtools/configs/strategist-settings.yaml -------------------------------------------------------------------------------- /devtools/configs/synchronous-compute-settings.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/devtools/configs/synchronous-compute-settings.yaml -------------------------------------------------------------------------------- /docker/alchemiscale-compute/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docker/alchemiscale-compute/Dockerfile -------------------------------------------------------------------------------- /docker/alchemiscale-server/.env.template: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docker/alchemiscale-server/.env.template -------------------------------------------------------------------------------- /docker/alchemiscale-server/.env.testing: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docker/alchemiscale-server/.env.testing -------------------------------------------------------------------------------- /docker/alchemiscale-server/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docker/alchemiscale-server/Dockerfile -------------------------------------------------------------------------------- /docker/alchemiscale-server/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docker/alchemiscale-server/README.md -------------------------------------------------------------------------------- /docker/alchemiscale-server/docker-compose.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docker/alchemiscale-server/docker-compose.yml -------------------------------------------------------------------------------- /docs/.nojekyll: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/CHANGELOG.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/CHANGELOG.rst -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/api.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api.rst -------------------------------------------------------------------------------- /docs/api/base.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api/base.rst -------------------------------------------------------------------------------- /docs/api/cli.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api/cli.rst -------------------------------------------------------------------------------- /docs/api/compute.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api/compute.rst -------------------------------------------------------------------------------- /docs/api/interface.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api/interface.rst -------------------------------------------------------------------------------- /docs/api/models.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api/models.rst -------------------------------------------------------------------------------- /docs/api/security.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api/security.rst -------------------------------------------------------------------------------- /docs/api/settings.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api/settings.rst -------------------------------------------------------------------------------- /docs/api/storage.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api/storage.rst -------------------------------------------------------------------------------- /docs/api/strategist.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/api/strategist.rst -------------------------------------------------------------------------------- /docs/assets/logo/logo_full_horizontal_inverted.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/assets/logo/logo_full_horizontal_inverted.png -------------------------------------------------------------------------------- /docs/assets/system-architecture.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/assets/system-architecture.png -------------------------------------------------------------------------------- /docs/compute.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/compute.rst -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/deployment.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/deployment.rst -------------------------------------------------------------------------------- /docs/development.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/development.rst -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/operations.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/operations.rst -------------------------------------------------------------------------------- /docs/tutorials/demo/Alchemiscale Demo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/tutorials/demo/Alchemiscale Demo.ipynb -------------------------------------------------------------------------------- /docs/tutorials/demo/ligands.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/tutorials/demo/ligands.sdf -------------------------------------------------------------------------------- /docs/tutorials/demo/ligands.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/tutorials/demo/ligands.yml -------------------------------------------------------------------------------- /docs/tutorials/demo/protein.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/tutorials/demo/protein.pdb -------------------------------------------------------------------------------- /docs/tutorials/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/tutorials/index.rst -------------------------------------------------------------------------------- /docs/user_guide/getting_started.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/user_guide/getting_started.rst -------------------------------------------------------------------------------- /docs/user_guide/handling_errors.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/user_guide/handling_errors.rst -------------------------------------------------------------------------------- /docs/user_guide/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/user_guide/index.rst -------------------------------------------------------------------------------- /docs/user_guide/strategy_automation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/docs/user_guide/strategy_automation.rst -------------------------------------------------------------------------------- /news/TEMPLATE.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/news/TEMPLATE.rst -------------------------------------------------------------------------------- /news/driver-notifications.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/news/driver-notifications.rst -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/pyproject.toml -------------------------------------------------------------------------------- /rever.xsh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/HEAD/rever.xsh --------------------------------------------------------------------------------