.dockerignore
.gitignore
.pre-commit-config.yaml
CLAUDE.md
Dockerfile
LICENSE
README.md
pyproject.toml
.github/workflows/docker-build.yml
.github/workflows/format.yml
.github/workflows/publish.yml
.github/workflows/test.yml
scripts/download_weights.sh
src/graphrelax/__init__.py
src/graphrelax/_version.py
src/graphrelax/chain_gaps.py
src/graphrelax/cli.py
src/graphrelax/config.py
src/graphrelax/designer.py
src/graphrelax/idealize.py
src/graphrelax/pipeline.py
src/graphrelax/relaxer.py
src/graphrelax/resfile.py
src/graphrelax/structure_io.py
src/graphrelax/utils.py
src/graphrelax/weights.py
src/graphrelax.egg-info/PKG-INFO
src/graphrelax.egg-info/SOURCES.txt
src/graphrelax.egg-info/dependency_links.txt
src/graphrelax.egg-info/entry_points.txt
src/graphrelax.egg-info/requires.txt
src/graphrelax.egg-info/top_level.txt
src/graphrelax/LigandMPNN/__init__.py
src/graphrelax/LigandMPNN/data_utils.py
src/graphrelax/LigandMPNN/model_utils.py
src/graphrelax/LigandMPNN/sc_utils.py
src/graphrelax/LigandMPNN/openfold/__init__.py
src/graphrelax/LigandMPNN/openfold/config.py
src/graphrelax/LigandMPNN/openfold/data/__init__.py
src/graphrelax/LigandMPNN/openfold/data/data_transforms.py
src/graphrelax/LigandMPNN/openfold/np/__init__.py
src/graphrelax/LigandMPNN/openfold/np/protein.py
src/graphrelax/LigandMPNN/openfold/np/residue_constants.py
src/graphrelax/LigandMPNN/openfold/np/relax/__init__.py
src/graphrelax/LigandMPNN/openfold/np/relax/amber_minimize.py
src/graphrelax/LigandMPNN/openfold/np/relax/cleanup.py
src/graphrelax/LigandMPNN/openfold/np/relax/relax.py
src/graphrelax/LigandMPNN/openfold/np/relax/utils.py
src/graphrelax/LigandMPNN/openfold/resources/__init__.py
src/graphrelax/LigandMPNN/openfold/resources/stereo_chemical_props.txt
src/graphrelax/LigandMPNN/openfold/utils/__init__.py
src/graphrelax/LigandMPNN/openfold/utils/feats.py
src/graphrelax/LigandMPNN/openfold/utils/loss.py
src/graphrelax/LigandMPNN/openfold/utils/rigid_utils.py
src/graphrelax/LigandMPNN/openfold/utils/tensor_utils.py
tests/conftest.py
tests/test_chain_gaps.py
tests/test_cli.py
tests/test_cli_integration.py
tests/test_config.py
tests/test_designer_integration.py
tests/test_designer_unit.py
tests/test_idealize.py
tests/test_pipeline_integration.py
tests/test_relaxer_integration.py
tests/test_resfile.py
tests/test_structure_io.py
tests/test_utils.py
tests/test_weights.py
tests/data/small_peptide.pdb