.gitignore
LICENSE
MANIFEST.in
Makefile
README.md
pyproject.toml
update_license_header.py
.github/workflows/docs.yml
.github/workflows/pythonpublish.yml
docs/Makefile
docs/getversion.py
docs/make.bat
docs/source/.gitignore
docs/source/conf.py
docs/source/index.md
docs/source/installation.md
docs/source/llms-full.txt
docs/source/explanation/apps-and-manifests.md
docs/source/explanation/architecture.md
docs/source/explanation/artifacts-and-files.md
docs/source/explanation/executable-directory.md
docs/source/explanation/index.md
docs/source/explanation/job-lifecycle.md
docs/source/howto/check-job-status.md
docs/source/howto/index.md
docs/source/howto/install-apps-for-a-cluster.md
docs/source/howto/list-and-inspect-apps.md
docs/source/howto/log-in-to-the-http-backend.md
docs/source/howto/pass-input-files-to-an-app.md
docs/source/howto/run-an-app-locally.md
docs/source/howto/run-an-app-on-slurm.md
docs/source/howto/run-built-in-app-tests.md
docs/source/howto/run-many-jobs-on-one-gpu.md
docs/source/howto/select-an-app-version.md
docs/source/howto/switch-between-docker-and-apptainer.md
docs/source/howto/update-installed-apps.md
docs/source/howto/use-app-artifacts.md
docs/source/reference/cli.md
docs/source/reference/environment-variables.md
docs/source/reference/index.md
docs/source/tutorials/01-first-app-run.md
docs/source/tutorials/02-using-app-versions-and-tests.md
docs/source/tutorials/03-running-on-slurm.md
docs/source/tutorials/index.md
playmolecule/__init__.py
playmolecule/_appfiles.py
playmolecule/_cli.py
playmolecule/_config.py
playmolecule/_devutils.py
playmolecule/_dynamicfunction.py
playmolecule/_protocols.py
playmolecule/_public_api.py
playmolecule/_tests.py
playmolecule/_update.py
playmolecule/_validation.py
playmolecule/logging.ini
playmolecule.egg-info/PKG-INFO
playmolecule.egg-info/SOURCES.txt
playmolecule.egg-info/dependency_links.txt
playmolecule.egg-info/entry_points.txt
playmolecule.egg-info/requires.txt
playmolecule.egg-info/top_level.txt
playmolecule/_backends/__init__.py
playmolecule/_backends/_docker.py
playmolecule/_backends/_http.py
playmolecule/_backends/_local.py
playmolecule/_backends/_slurm.py
playmolecule/apps/__init__.py
playmolecule/share/apptainer_run.sh
playmolecule/share/docker_run.sh
tests/3ptb.pdb
tests/conftest.py
tests/test_backends.py
tests/test_docker_backend.py
tests/test_http_backend.py
tests/test_local_backend.py
tests/test_playmolecule.py
tests/test_pmbackend.py
tests/test_playmolecule/apptainer_run.sh
tests/test_playmolecule/acellera-protocols/protocols/__init__.py
tests/test_playmolecule/acellera-protocols/protocols/crypticscout/__init__.py
tests/test_playmolecule/acellera-protocols/protocols/crypticscout/v1/__init__.py
tests/test_playmolecule/acellera-protocols/protocols/crypticscout/v1/crypticscout.py
tests/test_playmolecule/acellera-protocols/protocols/crypticscout/v1/files/tutorials/my_tutorial.ipynb
tests/test_playmolecule/apps/proteinprepare/v1/ProteinPrepare_v1.json
tests/test_playmolecule/apps/proteinprepare/v1/run.sh
tests/test_playmolecule/apps/proteinprepare/v1/files/datasets/3ptb.pdb
tests/test_playmolecule/apps/proteinprepare/v1/files/tests/3ptb.pdb
tests/test_playmolecule/apps/proteinprepare/v1/files/tests/587HG92V.pdb
tests/test_playmolecule/apps/proteinprepare/v1/files/tests/reprepare.pickle
tests/test_playmolecule/apps/proteinprepare/v1/files/tests/web_content.pickle
tests/test_playmolecule/apps/proteinprepare/v1/files/tutorials/learn_this_app.ipynb
tests/test_playmolecule/apps/proteinpreparenew/v1/ProteinPrepareNew_v1.json
tests/test_playmolecule/apps/proteinpreparenew/v1/run.sh
tests/test_playmolecule/apps/proteinpreparenew/v1/files/datasets/3ptb.pdb
tests/test_playmolecule/apps/proteinpreparenew/v1/files/tests/3ptb.pdb
tests/test_playmolecule/apps/proteinpreparenew/v1/files/tests/587HG92V.pdb
tests/test_playmolecule/apps/proteinpreparenew/v1/files/tests/reprepare.pickle
tests/test_playmolecule/apps/proteinpreparenew/v1/files/tests/web_content.pickle
tests/test_playmolecule/apps/proteinpreparenew/v1/files/tutorials/learn_this_app.ipynb
tests/test_playmolecule/apps/proteinpreparenew/v2/ProteinPrepareNew_v1.json
tests/test_playmolecule/apps/proteinpreparenew/v2/run.sh
tests/test_playmolecule/apps/proteinpreparenew/v2/files/datasets/3ptb.pdb
tests/test_playmolecule/apps/proteinpreparenew/v2/files/tests/3ptb.pdb
tests/test_playmolecule/apps/proteinpreparenew/v2/files/tests/587HG92V.pdb
tests/test_playmolecule/apps/proteinpreparenew/v2/files/tests/reprepare.pickle
tests/test_playmolecule/apps/proteinpreparenew/v2/files/tests/web_content.pickle
tests/test_playmolecule/apps/proteinpreparenew/v2/files/tutorials/learn_this_app.ipynb
tests/test_playmolecule/datasets/3ptb.pdb
tests/test_playmolecule/datasets/datasets.json