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Major refactor - #118
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Major refactor#118
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OleinikovasV
added
bug
14 tasks done
…tion Published CIGAR shards omit alignment scores, so Scorer.load_alignments reads the matching exports/protein_similarity_scores shard. prefetch only downloaded the CIGAR shards, so reconstruct_similarity_scores failed on a lazily populated cache. Register the score shard as a release path and fetch it when include_protein_scores=True (used by ligand reconstruction only).
- drop the PLINDER_RELEASE=2026-07 / PLINDER_RELEASE_NUMBER=1 overrides so notebooks use the default release and download lazily from R2 - remove the notebook execution skip list - install docs builds with uv sync --locked --extra docs into the Conda env (OpenStructure and MMseqs2 are needed by the evaluation and search notebooks)
…numbers Custom-scoring alignments keep their CIGAR column but are already mapped to query/target residue numbers. load_alignments only checked for decoded positions, so it tried to decode them, which needs a release chain lookup the custom scorer doesn't have (ValueError: CIGAR alignments require a chain lookup). Found by executing docs/examples/custom_scoring.ipynb.
CI now tests the dependency set users get from pip, catching upstream breakage early rather than through a lockfile that must be refreshed.
…lease-date-prefix # Conflicts: # src/plinder/core/release.py
- make_sub_dbs now also builds monomer databases whenever holo is built; when no monomer chains exist (e.g. the end-to-end test entry) linclust segfaults on the empty database. Skip monomer databases with no chains; downstream bundling already treats them as optional. - check query_batch_index is not None so mypy can narrow the batch slice.
The end-to-end entry has monomer chains, but none are selected into the MMseqs sub-database, so the chain-count check in make_sub_dbs never fired and linclust still crashed. Check the selected database instead and skip clustering an empty monomer universe; revert the earlier chain-count check.
- README, getting-started and migration pages now point at 2026-09 on plinderdata.org instead of 2024-06/v2 and the release-number layout - regenerate the release tree in docs/dataset.md from the published manifest (adds protein_clusters, ligand_pocket_residues, apo/interface_apo CIGARs and the manifest; drops ligand_archives/manifest.json and per-fragment ligand_scores) - document the manifest builder's prefix argument and the publish order / Cache-Control needed for manifest updates
- directory downloads drop cached Parquet files the release no longer lists, so dataset readers never mix removed fragments (e.g. the 290 old ligand_scores files removed from 2026-09) with their replacements - skipping an empty monomer sub-database also retires an earlier build, so a stale monomer target is never published as current - custom scoring treats monomer search databases as optional per backend, and public_release no longer requires monomer artifacts, matching the pipeline - monomer chain masks cast fillna results to bool for pandas 3 - build_r2_manifest skips a root folder placeholder; clarify its prefix argument
Serve the 2026-09 release from Cameo and execute all docs notebooks against it
Remove the Metaflow runners, legacy configs, and graph tests. Keep the ingest config examples under scripts/slurm and document supported set-cover commands. Allow compound residue-table joins with shared base identifiers, use unique atomic SDF extraction files, finalize empty ligand 3D plans, preserve metadata-only weekly updates on resume, and validate mapping drops against the protein plan. These changes leave hosted release artifacts and scientific calculations intact. Validation: 248 tests passed; 15 tests needing native Foldseek/MMseqs executables were excluded. All pre-commit checks and Slurm command checks passed. Mypy reports the same 158 existing errors as the original PR head in the local environment.
tjduigna
approved these changes
Oct 9, 2026
This was referenced Oct 9, 2026
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Reduce external dependencies to reduce support conflicts - eliminates explicit use of
Adds:
Bugfixes:
8q5i__1__1.GA__1.ZBmissing DNA complex #61Closes:
Features:
Entry.from_custom_cif_filefrom_custom_cif_filefrom RNPOther changes:
Changing License to Apache-2.0
Redefined systems: merging upon shared pocket residues (min 3), only artifacts added by 4A cutoff (like before), any polymer < 12 units is considered ligand (based on mmseqs search limit)
uses biotite
bt_infoas the source truth for CCD ligand definition, to generate smiles, etcIngests and collates protein–protein interfaces alongside ligand systems.
Adds PRODIGY interaction and affinity annotations.
Calculates and exports whole-interface and chain-side similarity scores.
Adds representative clustering for whole and half interfaces.
Supports interface-only repair and resumable ingest.
Preserves chains discovered during interface processing in shared sidecars.
Parallelizes interface collation and enforces a shared interface-residue cutoff
Uses pinder test cases to ensure correct functionality