Reverso

bontojr/Reverso

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Author	SHA1	Message	Date
Junior B.	907a39aaba	Capture structure-track deps + pose entrypoint - gpu/modal_app.py: add the `pose` local entrypoint used for the HDAC2 pose-RMSD validation (run: `modal run gpu/modal_app.py::pose`). - pyproject [structure] extra: add the deps we actually use locally (gemmi, spyrmsd, meeko, modal) for reproducibility; document the non-pip tools (Vina binary, open-babel) and that Boltz/cuequivariance are Modal-image-only. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-24 19:56:40 +02:00
Junior B.	817bcda7dc	Structure-binding track: scaffold + ligand-retrieval baseline Start the structure-based binding branch (PLAN §12), baseline-first. - src/binding.py: validated RDKit ligand retrieval (morgan_fp, tanimoto, retrieve_nearest = the §12.9 engine) + dock() stub documenting the blocked ARM-Mac toolchain - scripts/binding_ligand_baseline.py: 300 drugs vs known binders - docs/structure_binding_notes.md: status, toolchain blocker, next steps - pyproject: [structure] extra (rdkit); data/raw/structures/ for PDBs Step-0 finding: retrieval engine VALIDATED on in-set classes (decitabine->azacitidine 0.62; vorinostat->scriptaid/belinostat) but the distinctive binders voxelotor/mitapivat have no analog in our 300-drug set (Tanimoto ~0.2). Needs (a) bigger library, (b) real docking (§12.3), which is blocked on the ARM-Mac docking toolchain (§12.6 pitfall 4). Structures 5E83 (Hb+voxelotor) and 8XFD (PKR+mitapivat) fetched. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-23 23:53:27 +02:00
Junior B.	b731478f5d	Scaffold Reverso MVP pipeline structure Set up the project skeleton per PLAN.md §4: - src/ package: identifiers, disease, drugs, scoring, provenance with pydantic schemas and confidence-tier logic (working); data-pull/compute functions stubbed per their build week - 5 starter notebooks (01-05) with PLAN-referenced steps - tests/test_scoring.py: tier-assignment tests pass; scoring reference test xfail until Week 3 - docs/: recovery_test_report, data_sources, known_limitations skeletons - pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README - data/ tree preserved via .gitkeep; raw/processed/results gitignored Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-23 20:20:09 +02:00

Author

SHA1

Message

Date

Junior B.

907a39aaba

Capture structure-track deps + pose entrypoint

- gpu/modal_app.py: add the `pose` local entrypoint used for the HDAC2
  pose-RMSD validation (run: `modal run gpu/modal_app.py::pose`).
- pyproject [structure] extra: add the deps we actually use locally
  (gemmi, spyrmsd, meeko, modal) for reproducibility; document the non-pip
  tools (Vina binary, open-babel) and that Boltz/cuequivariance are
  Modal-image-only.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-06-24 19:56:40 +02:00

Junior B.

817bcda7dc

Structure-binding track: scaffold + ligand-retrieval baseline

Start the structure-based binding branch (PLAN §12), baseline-first.

- src/binding.py: validated RDKit ligand retrieval (morgan_fp, tanimoto,
  retrieve_nearest = the §12.9 engine) + dock() stub documenting the
  blocked ARM-Mac toolchain
- scripts/binding_ligand_baseline.py: 300 drugs vs known binders
- docs/structure_binding_notes.md: status, toolchain blocker, next steps
- pyproject: [structure] extra (rdkit); data/raw/structures/ for PDBs

Step-0 finding: retrieval engine VALIDATED on in-set classes
(decitabine->azacitidine 0.62; vorinostat->scriptaid/belinostat) but the
distinctive binders voxelotor/mitapivat have no analog in our 300-drug
set (Tanimoto ~0.2). Needs (a) bigger library, (b) real docking (§12.3),
which is blocked on the ARM-Mac docking toolchain (§12.6 pitfall 4).
Structures 5E83 (Hb+voxelotor) and 8XFD (PKR+mitapivat) fetched.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-06-23 23:53:27 +02:00

Junior B.

b731478f5d

Scaffold Reverso MVP pipeline structure

Set up the project skeleton per PLAN.md §4:
- src/ package: identifiers, disease, drugs, scoring, provenance
  with pydantic schemas and confidence-tier logic (working);
  data-pull/compute functions stubbed per their build week
- 5 starter notebooks (01-05) with PLAN-referenced steps
- tests/test_scoring.py: tier-assignment tests pass; scoring
  reference test xfail until Week 3
- docs/: recovery_test_report, data_sources, known_limitations skeletons
- pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README
- data/ tree preserved via .gitkeep; raw/processed/results gitignored

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-06-23 20:20:09 +02:00

3 Commits