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feat(drug-discovery): Ligand list file for >100 ligands across tools; Admet batch_size - #653
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…batch_size Admet, Metabolism, Docking and SecondaryPharmacology now build ligand inputs through ligand_list_file.py: inline up to INLINE_LIGAND_CAP (100), else upload a Ligand list file and send ligands_file (+ ligands_count where the tool takes it). from_dto rehydrates either form. ADMET_/METABOLISM_ caps merge into INLINE_LIGAND_CAP. SecondaryPharmacology ligand-ml above the cap now syncs ligands first: preflight requires id on every file row (validate_secondary_pharma.py). Admet(batch_size=...) sends batchSize (ligands per workflow pod, min 50) on file and project runs. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
… example Docking._build_tool_inputs now uploads a Ligand list file above the inline cap; SecondaryPharmacology._ligands_from_inputs downloads ligands_file. The Admet bulk example passes batch_size explicitly. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
ASinanSaglam
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October 5, 2026 19:36
ASinanSaglam
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sg-s
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Oct 5, 2026
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Summary
src/drug_discovery/ligand_list_file.py: one inline-vs-file path for Admet, Metabolism, Docking, SecondaryPharmacology (>100 ligands → UFA Ligand list file +ligands_file/ligands_count);from_dtorehydrates both.id, which preflight rejects; now syncs above the cap.Admet(batch_size=...): setsbatchSize(ligands per pod, min 50) on file/project runs.Test plan
uv run pytest tests --env local -p no:xdist: 1643 passed, 1 failed (test_pairwise_pose_rmsd_lv0, fails on main too)test_secondary_pharma_make_inputs_ligand_ml_above_cap_uses_synced_file,test_admet_batch_size_sent_on_workflow_paths_onlybatch_size=50→ 3 chunk pods🤖 Generated with Claude Code