LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
alphapulldown/create_individual_features.py
alphapulldown/run_multimer_jobs.py
alphapulldown/analysis_pipeline/create_notebook.py
src/af2plots/__init__.py
src/af2plots/plotter.py
src/alphafold/__init__.py
src/alphafold/run_alphafold.py
src/alphafold/common/__init__.py
src/alphafold/common/confidence.py
src/alphafold/common/protein.py
src/alphafold/common/protein_test.py
src/alphafold/common/residue_constants.py
src/alphafold/common/residue_constants_test.py
src/alphafold/data/__init__.py
src/alphafold/data/feature_processing.py
src/alphafold/data/mmcif_parsing.py
src/alphafold/data/msa_identifiers.py
src/alphafold/data/msa_pairing.py
src/alphafold/data/parsers.py
src/alphafold/data/pipeline.py
src/alphafold/data/pipeline_multimer.py
src/alphafold/data/templates.py
src/alphafold/data/tools/__init__.py
src/alphafold/data/tools/hhblits.py
src/alphafold/data/tools/hhsearch.py
src/alphafold/data/tools/hmmbuild.py
src/alphafold/data/tools/hmmsearch.py
src/alphafold/data/tools/jackhmmer.py
src/alphafold/data/tools/kalign.py
src/alphafold/data/tools/utils.py
src/alphafold/model/__init__.py
src/alphafold/model/all_atom.py
src/alphafold/model/all_atom_multimer.py
src/alphafold/model/all_atom_test.py
src/alphafold/model/common_modules.py
src/alphafold/model/config.py
src/alphafold/model/data.py
src/alphafold/model/features.py
src/alphafold/model/folding.py
src/alphafold/model/folding_multimer.py
src/alphafold/model/layer_stack.py
src/alphafold/model/layer_stack_test.py
src/alphafold/model/lddt.py
src/alphafold/model/lddt_test.py
src/alphafold/model/mapping.py
src/alphafold/model/model.py
src/alphafold/model/modules.py
src/alphafold/model/modules_multimer.py
src/alphafold/model/prng.py
src/alphafold/model/prng_test.py
src/alphafold/model/quat_affine.py
src/alphafold/model/quat_affine_test.py
src/alphafold/model/r3.py
src/alphafold/model/utils.py
src/alphafold/model/geometry/__init__.py
src/alphafold/model/geometry/rigid_matrix_vector.py
src/alphafold/model/geometry/rotation_matrix.py
src/alphafold/model/geometry/struct_of_array.py
src/alphafold/model/geometry/test_utils.py
src/alphafold/model/geometry/utils.py
src/alphafold/model/geometry/vector.py
src/alphafold/model/tf/__init__.py
src/alphafold/model/tf/data_transforms.py
src/alphafold/model/tf/input_pipeline.py
src/alphafold/model/tf/protein_features.py
src/alphafold/model/tf/protein_features_test.py
src/alphafold/model/tf/proteins_dataset.py
src/alphafold/model/tf/shape_helpers.py
src/alphafold/model/tf/shape_helpers_test.py
src/alphafold/model/tf/shape_placeholders.py
src/alphafold/model/tf/utils.py
src/alphafold/notebooks/__init__.py
src/alphafold/notebooks/notebook_utils.py
src/alphafold/notebooks/notebook_utils_test.py
src/alphafold/relax/__init__.py
src/alphafold/relax/amber_minimize.py
src/alphafold/relax/amber_minimize_test.py
src/alphafold/relax/cleanup.py
src/alphafold/relax/cleanup_test.py
src/alphafold/relax/relax.py
src/alphafold/relax/relax_test.py
src/alphafold/relax/utils.py
src/alphafold/relax/utils_test.py
src/alphapulldown/__init__.py
src/alphapulldown/create_individual_features.py
src/alphapulldown/objects.py
src/alphapulldown/plot_pae.py
src/alphapulldown/predict_structure.py
src/alphapulldown/run_multimer_jobs.py
src/alphapulldown/utils.py
src/alphapulldown.egg-info/PKG-INFO
src/alphapulldown.egg-info/SOURCES.txt
src/alphapulldown.egg-info/dependency_links.txt
src/alphapulldown.egg-info/requires.txt
src/alphapulldown.egg-info/top_level.txt
src/analysis_pipeline/__init__.py
src/analysis_pipeline/af2_3dmol.py
src/analysis_pipeline/calculate_mpdockq.py
src/analysis_pipeline/create_notebook.py
src/analysis_pipeline/get_good_inter_pae.py
src/analysis_pipeline/utils.py
test/test_image.py
test/test_pip.py