.gitattributes
.gitignore
LICENSE
README.md
environment.yml
logo.svg
pyproject.toml
pytest.ini
setup.py
examples/01_profiles.ipynb
examples/02_scoring.ipynb
examples/03_evaluation.ipynb
scripts/README.md
scripts/conditional_evaluation.py
scripts/conditional_evaluation.sh
scripts/consistency_benchmark.py
scripts/consistency_benchmark.sh
scripts/consistency_evaluation.py
scripts/consistency_evaluation.sh
scripts/docking_evaluation.py
scripts/docking_evaluation.sh
scripts/docking_screen.py
scripts/docking_screen.sh
shepherd_score/__init__.py
shepherd_score/alignment.py
shepherd_score/alignment_jax.py
shepherd_score/conformer_generation.py
shepherd_score/container.py
shepherd_score/extract_profiles.py
shepherd_score/generate_point_cloud.py
shepherd_score/objective.py
shepherd_score/visualize.py
shepherd_score.egg-info/PKG-INFO
shepherd_score.egg-info/SOURCES.txt
shepherd_score.egg-info/dependency_links.txt
shepherd_score.egg-info/requires.txt
shepherd_score.egg-info/top_level.txt
shepherd_score/alignment_utils/__init__.py
shepherd_score/alignment_utils/pca.py
shepherd_score/alignment_utils/pca_jax.py
shepherd_score/alignment_utils/pca_np.py
shepherd_score/alignment_utils/se3.py
shepherd_score/alignment_utils/se3_jax.py
shepherd_score/alignment_utils/se3_np.py
shepherd_score/evaluations/__init__.py
shepherd_score/evaluations/docking.py
shepherd_score/evaluations/evaluate/__init__.py
shepherd_score/evaluations/evaluate/_pipeline_eval_single.py
shepherd_score/evaluations/evaluate/evals.py
shepherd_score/evaluations/evaluate/pipelines.py
shepherd_score/evaluations/pdbs/1iep.pdbqt
shepherd_score/evaluations/pdbs/3eml.pdbqt
shepherd_score/evaluations/pdbs/3ny8.pdbqt
shepherd_score/evaluations/pdbs/4rlu.pdbqt
shepherd_score/evaluations/pdbs/4unn.pdbqt
shepherd_score/evaluations/pdbs/5mo4.pdbqt
shepherd_score/evaluations/pdbs/7l11.pdbqt
shepherd_score/evaluations/pdbs/README.md
shepherd_score/evaluations/utils/__init__.py
shepherd_score/evaluations/utils/convert_data.py
shepherd_score/evaluations/utils/interactions.py
shepherd_score/pharm_utils/__init__.py
shepherd_score/pharm_utils/pharmacophore.py
shepherd_score/pharm_utils/pharmvec.py
shepherd_score/pharm_utils/smarts_features.fdef
shepherd_score/score/__init__.py
shepherd_score/score/constants.py
shepherd_score/score/electrostatic_scoring.py
shepherd_score/score/electrostatic_scoring_jax.py
shepherd_score/score/electrostatic_scoring_np.py
shepherd_score/score/gaussian_overlap.py
shepherd_score/score/gaussian_overlap_jax.py
shepherd_score/score/gaussian_overlap_np.py
shepherd_score/score/pharmacophore_scoring.py
shepherd_score/score/pharmacophore_scoring_jax.py
shepherd_score/score/pharmacophore_scoring_np.py
tests/__init__.py
tests/test_alignment.py
tests/test_alignment_utils.py
tests/test_electrostatic_scoring.py
tests/test_gaussian_overlap.py
tests/test_parallel.py
tests/test_pharmacophore_scoring.py