Sync draco-postproc updates from AFCDB toolkit#26
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Sync the AFDB-Integration-Kit folder from the internal AFCDB draco-postproc branch. Includes the new GPU interface analysis pipeline, ipSAE C++ implementation, manifest tooling, ModelPDB generator, UniProt batching scripts, validation parallelization, and updated examples / Nextflow workflows. The internal slurm-scaling/, mock_data/, and assets/ directories are intentionally excluded from this sync. The vendored Eigen 3.4.0 tree under afdb_integration_kit/ipsae/deps/ is also excluded; the ipSAE Makefile now fetches Eigen on demand.
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| # Get raw arrays | ||
| res_name_raw = arr.res_name | ||
| atom_name_all = arr.atom_name |
| # Get raw arrays | ||
| res_name_raw = arr.res_name | ||
| atom_name_all = arr.atom_name | ||
| chain_all = arr.chain_id |
| res_name_raw = arr.res_name | ||
| atom_name_all = arr.atom_name | ||
| chain_all = arr.chain_id | ||
| res_id_all = arr.res_id.astype(np.int32, copy=False) |
| atom_name_all = arr.atom_name | ||
| chain_all = arr.chain_id | ||
| res_id_all = arr.res_id.astype(np.int32, copy=False) | ||
| coord_all = arr.coord |
| return # already materialized or built directly | ||
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| p = result._protein | ||
| n_res = p.n_residues |
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| # Move to device | ||
| coords_t = torch.tensor(coords_valid, dtype=torch.float32, device=device) | ||
| vdw_t = torch.tensor(vdw_valid, dtype=torch.float32, device=device) |
| valid = ca_mask_flat | ||
| ca_valid = ca_flat[valid] | ||
| chain_valid = chain_flat[valid] | ||
| res_id_valid = res_id_flat[valid] |
| chain_flat = chain_ids.reshape(B * N) | ||
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| protein_idx = torch.arange(B, device=device).repeat_interleave(N) | ||
| res_idx = torch.arange(N, device=device).repeat(B) |
| logger.debug(f"Directory scan found {len(file_map)} matched pairs", indent=1) | ||
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| # Split into found / missing | ||
| model_id_set = set(model_ids) |
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| # Create symlinks for PDB files and meta JSON files in the same directory | ||
| # ipsae_cpp expects *-model_v1.pdb and *-meta_v1.json pairs | ||
| start = time.time() |
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Summary
Syncs the
AFDB-Integration-Kit/folder from the internal AFCDBdraco-postprocbranch into this repository. Touches 86 files with the new tooling developed downstream:afdb_integration_kit/gpu/(clash detection, interface analysis, batch driver, schema)afdb_integration_kit/ipsae/(Makefile now auto-fetches Eigen; no vendored dependency tree)afdb_integration_kit/manifest/batch_convert_colabfold.py,batch_export_metadata.py,batch_export_modelcif_input.py,batch_ipsae.py,batch_validate_assets.py) and new ModelCIF templatesvalidators/_parallel.py)uv.lockupdatesIntentionally excluded
slurm-scaling/— internal HPC orchestration code, not relevant upstreammock_data/— bulky local fixturesassets/— internal pipeline diagramsafdb_integration_kit/ipsae/deps/eigen-3.4.0/— Eigen is now fetched on demand by the Makefile rather than vendoredTest plan
makebuildsipsae_cppfrom a clean checkout (verifying the Eigen auto-fetch step)make checkreports missing Eigen prior tomake depstests/still passworkflow/end_to_end_with_validation_multibatch.nfruns on the example inputs