1 file changed
+1
-1
lines changedSubmodule alphafold3 updated 47 files
- README.md+2-2
- docker/Dockerfile+6-2
- docs/input.md+231-77
- docs/installation.md+51-15
- docs/known_issues.md+9-30
- docs/output.md+32-2
- docs/performance.md+25-12
- run_alphafold.py+97-63
- run_alphafold_data_test.py+3-3
- run_alphafold_test.py+21-9
- src/alphafold3/.github/workflows/ci.yaml+38
- src/alphafold3/common/folding_input.py+437-152
- src/alphafold3/constants/chemical_components.py+16-8
- src/alphafold3/data/featurisation.py+6-1
- src/alphafold3/data/parsers.py+1-1
- src/alphafold3/data/pipeline.py+24-11
- src/alphafold3/data/templates.py+3-1
- src/alphafold3/data/tools/rdkit_utils.py+22
- src/alphafold3/jax/gated_linear_unit/matmul_ext.py+7-6
- src/alphafold3/model/atom_layout/atom_layout.py+10-40
- src/alphafold3/model/components/base_model.py-62
- src/alphafold3/model/confidence_types.py+4-4
- src/alphafold3/model/confidences.py+12-8
- src/alphafold3/model/data3.py+2-4
- src/alphafold3/model/features.py+117-106
- src/alphafold3/model/model.py+57-344
- src/alphafold3/model/model_config.py+1-1
- src/alphafold3/model/network/atom_cross_attention.py+1-1
- src/alphafold3/model/network/confidence_head.py+2-2
- src/alphafold3/model/network/diffusion_head.py+3-3
- src/alphafold3/model/network/diffusion_transformer.py
- src/alphafold3/model/network/distogram_head.py
- src/alphafold3/model/network/evoformer.py+347
- src/alphafold3/model/network/featurization.py
- src/alphafold3/model/network/modules.py+1-1
- src/alphafold3/model/network/template_modules.py+1-1
- src/alphafold3/model/pipeline/pipeline.py+4-4
- src/alphafold3/model/post_processing.py+13-3
- src/alphafold3/test_data/alphafold_run_outputs/run_alphafold_test_output_bucket_1024.pkl
- src/alphafold3/test_data/alphafold_run_outputs/run_alphafold_test_output_bucket_default.pkl
- src/alphafold3/test_data/featurised_example.json+4-4
- src/alphafold3/test_data/featurised_example.pkl
- src/alphafold3/test_data/miniature_databases/pdb_mmcif/5y2e.cif+562
- src/alphafold3/test_data/miniature_databases/pdb_mmcif/6s61.cif+3.3k
- src/alphafold3/test_data/miniature_databases/pdb_mmcif/6ydw.cif+2.5k
- src/alphafold3/test_data/miniature_databases/pdb_mmcif/7rye.cif+893
- src/alphafold3/test_data/model_config.json+2-1
0 commit comments