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Update alphafold3
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@DimaMolod
DimaMolod committed Jan 16, 2025
1 parent a4b4135 commit d4fd6c6
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2 changes: 1 addition & 1 deletion alphafold3
Submodule alphafold3 updated 47 files
+2 −2 README.md
+6 −2 docker/Dockerfile
+231 −77 docs/input.md
+51 −15 docs/installation.md
+9 −30 docs/known_issues.md
+32 −2 docs/output.md
+25 −12 docs/performance.md
+97 −63 run_alphafold.py
+3 −3 run_alphafold_data_test.py
+21 −9 run_alphafold_test.py
+38 −0 src/alphafold3/.github/workflows/ci.yaml
+437 −152 src/alphafold3/common/folding_input.py
+16 −8 src/alphafold3/constants/chemical_components.py
+6 −1 src/alphafold3/data/featurisation.py
+1 −1 src/alphafold3/data/parsers.py
+24 −11 src/alphafold3/data/pipeline.py
+3 −1 src/alphafold3/data/templates.py
+22 −0 src/alphafold3/data/tools/rdkit_utils.py
+7 −6 src/alphafold3/jax/gated_linear_unit/matmul_ext.py
+10 −40 src/alphafold3/model/atom_layout/atom_layout.py
+0 −62 src/alphafold3/model/components/base_model.py
+4 −4 src/alphafold3/model/confidence_types.py
+12 −8 src/alphafold3/model/confidences.py
+2 −4 src/alphafold3/model/data3.py
+117 −106 src/alphafold3/model/features.py
+57 −344 src/alphafold3/model/model.py
+1 −1 src/alphafold3/model/model_config.py
+1 −1 src/alphafold3/model/network/atom_cross_attention.py
+2 −2 src/alphafold3/model/network/confidence_head.py
+3 −3 src/alphafold3/model/network/diffusion_head.py
+0 −0 src/alphafold3/model/network/diffusion_transformer.py
+0 −0 src/alphafold3/model/network/distogram_head.py
+347 −0 src/alphafold3/model/network/evoformer.py
+0 −0 src/alphafold3/model/network/featurization.py
+1 −1 src/alphafold3/model/network/modules.py
+1 −1 src/alphafold3/model/network/template_modules.py
+4 −4 src/alphafold3/model/pipeline/pipeline.py
+13 −3 src/alphafold3/model/post_processing.py
+ − 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
+4 −4 src/alphafold3/test_data/featurised_example.json
+ − src/alphafold3/test_data/featurised_example.pkl
+562 −0 src/alphafold3/test_data/miniature_databases/pdb_mmcif/5y2e.cif
+3,293 −0 src/alphafold3/test_data/miniature_databases/pdb_mmcif/6s61.cif
+2,467 −0 src/alphafold3/test_data/miniature_databases/pdb_mmcif/6ydw.cif
+893 −0 src/alphafold3/test_data/miniature_databases/pdb_mmcif/7rye.cif
+2 −1 src/alphafold3/test_data/model_config.json

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