LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
./alphafold/run_alphafold.py
./alphapulldown/analysis_pipeline/create_notebook.py
./alphapulldown/analysis_pipeline/get_good_inter_pae.py
./alphapulldown/scripts/convert_to_modelcif.py
./alphapulldown/scripts/create_individual_features.py
./alphapulldown/scripts/generate_crosslink_pickle.py
./alphapulldown/scripts/prepare_seq_names.py
./alphapulldown/scripts/rename_colab_search_a3m.py
./alphapulldown/scripts/run_multimer_jobs.py
./alphapulldown/scripts/run_structure_prediction.py
./alphapulldown/scripts/truncate_pickles.py
AlphaLink2/unifold/__init__.py
AlphaLink2/unifold/alphalink_inference.py
AlphaLink2/unifold/config.py
AlphaLink2/unifold/dataset.py
AlphaLink2/unifold/dataset_inference.py
AlphaLink2/unifold/homo_search.py
AlphaLink2/unifold/inference.py
AlphaLink2/unifold/inference_symmetry.py
AlphaLink2/unifold/loss.py
AlphaLink2/unifold/model.py
AlphaLink2/unifold/task.py
AlphaLink2/unifold/data/__init__.py
AlphaLink2/unifold/data/data_ops.py
AlphaLink2/unifold/data/msa_pairing.py
AlphaLink2/unifold/data/msa_subsampling.py
AlphaLink2/unifold/data/process.py
AlphaLink2/unifold/data/process_multimer.py
AlphaLink2/unifold/data/protein.py
AlphaLink2/unifold/data/residue_constants.py
AlphaLink2/unifold/data/utils.py
AlphaLink2/unifold/losses/__init__.py
AlphaLink2/unifold/losses/auxillary.py
AlphaLink2/unifold/losses/chain_align.py
AlphaLink2/unifold/losses/fape.py
AlphaLink2/unifold/losses/geometry.py
AlphaLink2/unifold/losses/utils.py
AlphaLink2/unifold/losses/violation.py
AlphaLink2/unifold/modules/__init__.py
AlphaLink2/unifold/modules/alphafold.py
AlphaLink2/unifold/modules/attentions.py
AlphaLink2/unifold/modules/auxillary_heads.py
AlphaLink2/unifold/modules/common.py
AlphaLink2/unifold/modules/confidence.py
AlphaLink2/unifold/modules/embedders.py
AlphaLink2/unifold/modules/evoformer.py
AlphaLink2/unifold/modules/featurization.py
AlphaLink2/unifold/modules/flash_attention.py
AlphaLink2/unifold/modules/frame.py
AlphaLink2/unifold/modules/structure_module.py
AlphaLink2/unifold/modules/template.py
AlphaLink2/unifold/modules/triangle_multiplication.py
AlphaLink2/unifold/msa/__init__.py
AlphaLink2/unifold/msa/mmcif.py
AlphaLink2/unifold/msa/msa_identifiers.py
AlphaLink2/unifold/msa/parsers.py
AlphaLink2/unifold/msa/pipeline.py
AlphaLink2/unifold/msa/templates.py
AlphaLink2/unifold/msa/utils.py
AlphaLink2/unifold/symmetry/__init__.py
AlphaLink2/unifold/symmetry/assemble.py
AlphaLink2/unifold/symmetry/config.py
AlphaLink2/unifold/symmetry/dataset.py
AlphaLink2/unifold/symmetry/geometry_utils.py
AlphaLink2/unifold/symmetry/loss.py
AlphaLink2/unifold/symmetry/model.py
AlphaLink2/unifold/symmetry/modules.py
ColabFold/colabfold/__init__.py
ColabFold/colabfold/batch.py
ColabFold/colabfold/citations.py
ColabFold/colabfold/colabfold.py
ColabFold/colabfold/download.py
ColabFold/colabfold/pdb.py
ColabFold/colabfold/plot.py
ColabFold/colabfold/relax.py
ColabFold/colabfold/utils.py
alphafold/run_alphafold.py
alphafold/alphafold/__init__.py
alphafold/alphafold/version.py
alphafold/alphafold/common/__init__.py
alphafold/alphafold/common/confidence.py
alphafold/alphafold/common/confidence_test.py
alphafold/alphafold/common/mmcif_metadata.py
alphafold/alphafold/common/protein.py
alphafold/alphafold/common/protein_test.py
alphafold/alphafold/common/residue_constants.py
alphafold/alphafold/common/residue_constants_test.py
alphafold/alphafold/common/stereo_chemical_props.txt
alphafold/alphafold/data/__init__.py
alphafold/alphafold/data/feature_processing.py
alphafold/alphafold/data/mmcif_parsing.py
alphafold/alphafold/data/msa_identifiers.py
alphafold/alphafold/data/msa_pairing.py
alphafold/alphafold/data/parsers.py
alphafold/alphafold/data/pipeline.py
alphafold/alphafold/data/pipeline_multimer.py
alphafold/alphafold/data/templates.py
alphafold/alphafold/data/tools/__init__.py
alphafold/alphafold/data/tools/hhblits.py
alphafold/alphafold/data/tools/hhsearch.py
alphafold/alphafold/data/tools/hmmbuild.py
alphafold/alphafold/data/tools/hmmsearch.py
alphafold/alphafold/data/tools/jackhmmer.py
alphafold/alphafold/data/tools/kalign.py
alphafold/alphafold/data/tools/utils.py
alphafold/alphafold/model/__init__.py
alphafold/alphafold/model/all_atom.py
alphafold/alphafold/model/all_atom_multimer.py
alphafold/alphafold/model/all_atom_test.py
alphafold/alphafold/model/common_modules.py
alphafold/alphafold/model/config.py
alphafold/alphafold/model/data.py
alphafold/alphafold/model/features.py
alphafold/alphafold/model/folding.py
alphafold/alphafold/model/folding_multimer.py
alphafold/alphafold/model/layer_stack.py
alphafold/alphafold/model/layer_stack_test.py
alphafold/alphafold/model/lddt.py
alphafold/alphafold/model/lddt_test.py
alphafold/alphafold/model/mapping.py
alphafold/alphafold/model/model.py
alphafold/alphafold/model/modules.py
alphafold/alphafold/model/modules_multimer.py
alphafold/alphafold/model/prng.py
alphafold/alphafold/model/prng_test.py
alphafold/alphafold/model/quat_affine.py
alphafold/alphafold/model/quat_affine_test.py
alphafold/alphafold/model/r3.py
alphafold/alphafold/model/utils.py
alphafold/alphafold/model/geometry/__init__.py
alphafold/alphafold/model/geometry/rigid_matrix_vector.py
alphafold/alphafold/model/geometry/rotation_matrix.py
alphafold/alphafold/model/geometry/struct_of_array.py
alphafold/alphafold/model/geometry/test_utils.py
alphafold/alphafold/model/geometry/utils.py
alphafold/alphafold/model/geometry/vector.py
alphafold/alphafold/model/tf/__init__.py
alphafold/alphafold/model/tf/data_transforms.py
alphafold/alphafold/model/tf/input_pipeline.py
alphafold/alphafold/model/tf/protein_features.py
alphafold/alphafold/model/tf/protein_features_test.py
alphafold/alphafold/model/tf/proteins_dataset.py
alphafold/alphafold/model/tf/shape_helpers.py
alphafold/alphafold/model/tf/shape_helpers_test.py
alphafold/alphafold/model/tf/shape_placeholders.py
alphafold/alphafold/model/tf/utils.py
alphafold/alphafold/notebooks/__init__.py
alphafold/alphafold/notebooks/notebook_utils.py
alphafold/alphafold/notebooks/notebook_utils_test.py
alphafold/alphafold/relax/__init__.py
alphafold/alphafold/relax/amber_minimize.py
alphafold/alphafold/relax/amber_minimize_test.py
alphafold/alphafold/relax/cleanup.py
alphafold/alphafold/relax/cleanup_test.py
alphafold/alphafold/relax/relax.py
alphafold/alphafold/relax/relax_test.py
alphafold/alphafold/relax/utils.py
alphafold/alphafold/relax/utils_test.py
alphafold3/src/alphafold3/__init__.py
alphafold3/src/alphafold3/build_data.py
alphafold3/src/alphafold3/version.py
alphafold3/src/alphafold3/structure/__init__.py
alphafold3/src/alphafold3/structure/bioassemblies.py
alphafold3/src/alphafold3/structure/bonds.py
alphafold3/src/alphafold3/structure/chemical_components.py
alphafold3/src/alphafold3/structure/mmcif.py
alphafold3/src/alphafold3/structure/parsing.py
alphafold3/src/alphafold3/structure/sterics.py
alphafold3/src/alphafold3/structure/structure.py
alphafold3/src/alphafold3/structure/structure_tables.py
alphafold3/src/alphafold3/structure/table.py
alphafold3/src/alphafold3/structure/test_utils.py
alphapulldown/__init__.py
alphapulldown/entry_points.py
alphapulldown/objects.py
alphapulldown.egg-info/PKG-INFO
alphapulldown.egg-info/SOURCES.txt
alphapulldown.egg-info/dependency_links.txt
alphapulldown.egg-info/requires.txt
alphapulldown.egg-info/top_level.txt
alphapulldown/analysis_pipeline/af2_3dmol.py
alphapulldown/analysis_pipeline/calculate_mpdockq.py
alphapulldown/analysis_pipeline/create_notebook.py
alphapulldown/analysis_pipeline/get_good_inter_pae.py
alphapulldown/analysis_pipeline/pdb_analyser.py
alphapulldown/analysis_pipeline/utils.py
alphapulldown/analysis_pipeline/af2plots/af2plots/__main__.py
alphapulldown/analysis_pipeline/af2plots/af2plots/plotter.py
alphapulldown/analysis_pipeline/af2plots/af2plots/version.py
alphapulldown/folding_backend/__init__.py
alphapulldown/folding_backend/alphafold3_backend.py
alphapulldown/folding_backend/alphafold_backend.py
alphapulldown/folding_backend/alphalink_backend.py
alphapulldown/folding_backend/folding_backend.py
alphapulldown/folding_backend/unifold_backend.py
alphapulldown/scripts/convert_to_modelcif.py
alphapulldown/scripts/create_individual_features.py
alphapulldown/scripts/generate_crosslink_pickle.py
alphapulldown/scripts/prepare_seq_names.py
alphapulldown/scripts/rename_colab_search_a3m.py
alphapulldown/scripts/run_multimer_jobs.py
alphapulldown/scripts/run_structure_prediction.py
alphapulldown/scripts/split_jobs_into_clusters.py
alphapulldown/scripts/truncate_pickles.py
alphapulldown/utils/__init__.py
alphapulldown/utils/calculate_rmsd.py
alphapulldown/utils/create_combinations.py
alphapulldown/utils/create_custom_template_db.py
alphapulldown/utils/distogram_parser.py
alphapulldown/utils/file_handling.py
alphapulldown/utils/modelling_setup.py
alphapulldown/utils/multimeric_template_utils.py
alphapulldown/utils/plotting.py
alphapulldown/utils/post_modelling.py
alphapulldown/utils/remove_clashes_low_plddt.py
alphapulldown/utils/save_meta_data.py
test/test_create_monomeric_objects.py
test/test_create_multimeric_objects.py
test/test_create_multimeric_template_features.py
test/test_custom_db.py
test/test_features.py
test/test_features_with_templates.py
test/test_get_good_inter_pae.py
test/test_mmseqs.py
test/test_modelcif.py
test/test_multimeric_objects.py
test/test_parse_fold.py
test/test_pdb_analyser.py
test/test_post_prediction.py
test/test_predictions_slurm.py
test/test_python_imports.py
test/test_remove_clashes_low_plddt.py