Reverso/gpu/modal_app.py

"""Ephemeral GPU runner for AF3-class co-folding (PLAN §12, docs/gpu_plan.md).

Serverless: `modal run gpu/modal_app.py` provisions a GPU, runs Phase 1, releases the GPU — zero
idle cost. Model weights cache in a persistent Volume so we never re-pay GPU time to re-download.

Phase 1 (positive-control recovery test, §12.4): co-fold each known binder + a couple of negative
controls against each sickle target and rank by Boltz-2 predicted affinity. The known binder
should win its own target — the test Vina couldn't pass on metal/covalent/allosteric modes.
Affinity ranking avoids the receptor-alignment that pose-RMSD would need (a later refinement).

Setup (one-time): `pip install modal && modal token new`.
Run: `modal run gpu/modal_app.py`.

Helpers below the GPU function run locally (no GPU) and are import-safe for testing.
"""

from __future__ import annotations

import json
import subprocess
from pathlib import Path

import modal

app = modal.App("reverso-binding")

image = (
    modal.Image.debian_slim(python_version="3.12")
    .apt_install("git", "wget")
    # Boltz-2 needs NVIDIA cuequivariance kernels (cuda 12) for inference, plus rdkit/numpy.
    .pip_install("boltz", "cuequivariance-torch", "cuequivariance-ops-torch-cu12", "rdkit", "numpy")
)
weights = modal.Volume.from_name("reverso-binding-weights", create_if_missing=True)
WEIGHTS = "/weights"

# target -> (PDB id, crystal-ligand resname, drug name, cofactor/metal CCD codes to co-fold).
# The cofactors are the binding-mode determinants Vina couldn't model: HDAC2 needs the catalytic
# Zn (vorinostat chelates it), PKR the allosteric FBP + Mg, hemoglobin the heme. Co-folding them
# in as CCD ligands is the whole point of the AF3-class pivot. The same cofactors are present when
# co-folding the negatives into that target, for a fair comparison.
TARGETS = {
    "hemoglobin": ("5E83", "5L7", "voxelotor", ["HEM"]),
    "PKR": ("8XFD", "WV2", "mitapivat", ["FBP", "MG"]),
    "HDAC2": ("4LXZ", "SHH", "vorinostat", ["ZN"]),
}
NEGATIVES = ["caffeine", "hydroxyurea"]

# Honest limitation: hemoglobin's voxelotor site sits at the tetramer centre and the bond is
# covalent (Schiff base) — a single-chain + heme model only approximates it, so Hb is the weak
# case. HDAC2 (Zn chelation) and PKR (allosteric + cofactor) are the real tests of whether
# co-folding handles the modes classical docking could not.


# --------------------------------------------------------------------------- local helpers (CPU)

def fetch_pdb(pdb: str, struct_dir: Path = Path("data/raw/structures")) -> Path:
    """Return a local PDB path, downloading from RCSB if absent (keeps the GPU run self-contained)."""
    import requests
    p = struct_dir / f"{pdb}.pdb"
    if not p.exists():
        p.parent.mkdir(parents=True, exist_ok=True)
        p.write_bytes(requests.get(f"https://files.rcsb.org/download/{pdb}.pdb", timeout=60).content)
    return p


def binding_chain_sequence(pdb: str, lig_resname: str) -> str:
    """One-letter sequence of the protein chain nearest the crystal ligand (the binding chain)."""
    import gemmi
    st = gemmi.read_structure(str(fetch_pdb(pdb)))
    model = st[0]
    lig_atoms = [a.pos for ch in model for res in ch if res.name == lig_resname for a in res]
    if not lig_atoms:
        raise ValueError(f"ligand {lig_resname} not found in {pdb}")
    lig_center = gemmi.Position(
        sum(p.x for p in lig_atoms) / len(lig_atoms),
        sum(p.y for p in lig_atoms) / len(lig_atoms),
        sum(p.z for p in lig_atoms) / len(lig_atoms),
    )
    best, best_d = None, 1e9
    for ch in model:
        poly = ch.get_polymer()
        if len(poly) < 20:
            continue
        d = min((a.pos.dist(lig_center) for res in ch for a in res), default=1e9)
        if d < best_d:
            best, best_d = poly, d
    if best is None:
        raise ValueError(f"no protein chain in {pdb}")
    return gemmi.one_letter_code(best.extract_sequence()).upper().replace("X", "")


def pubchem_smiles(name: str) -> str:
    import requests
    for prop in ("SMILES", "ConnectivitySMILES", "IsomericSMILES", "CanonicalSMILES"):
        try:
            d = requests.get(f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{name}"
                             f"/property/{prop}/JSON", timeout=30).json()["PropertyTable"]["Properties"][0]
            if prop in d:
                return d[prop]
        except Exception:
            continue
    raise ValueError(f"no SMILES for {name}")


def build_boltz_yaml(protein_seq: str, ligand_smiles: str, cofactor_ccds: list[str] | None = None) -> str:
    """Boltz-2 YAML: protein + the drug ligand (affinity binder) + any cofactor/metal CCD ligands.

    Cofactors/ions are added as `ligand` entries referencing their CCD code (e.g. ZN, MG, FBP,
    HEM) so the model places the metal/cofactor that defines the binding mode. Affinity is
    predicted on the drug ligand L only.
    """
    lines = ["version: 1", "sequences:",
             "  - protein:", "      id: A", f"      sequence: {protein_seq}",
             "  - ligand:", "      id: L", f"      smiles: '{ligand_smiles}'"]
    for i, ccd in enumerate(cofactor_ccds or []):
        lines += ["  - ligand:", f"      id: M{i}", f"      ccd: {ccd}"]
    lines += ["properties:", "  - affinity:", "      binder: L"]
    return "\n".join(lines) + "\n"


# ------------------------------------------------------------------------------- GPU function

# max_containers=1: run the inputs serially on one warm container so the weights download ONCE
# (no concurrent-download race that corrupts the checkpoint) and are reused for the rest.
@app.function(gpu="L4", image=image, volumes={WEIGHTS: weights}, timeout=3600, max_containers=1)
def cofold(label: str, protein_seq: str, ligand_smiles: str, cofactor_ccds: list[str]) -> dict:
    """Co-fold one complex (protein + drug + cofactors) on the GPU; return affinity + P(binder).

    Weights persist on the mounted Volume (HF_HOME/boltz --cache under /weights), so run 2+ skips
    the download. GPU is released the moment this returns.
    """
    import os
    os.environ["HF_HOME"] = f"{WEIGHTS}/hf"
    boltz_cache = f"{WEIGHTS}/boltz"
    os.makedirs(boltz_cache, exist_ok=True)
    weights.reload()

    work = Path("/tmp") / label
    work.mkdir(parents=True, exist_ok=True)
    (work / "in.yaml").write_text(build_boltz_yaml(protein_seq, ligand_smiles, cofactor_ccds))
    out = work / "out"
    try:
        subprocess.run(
            ["boltz", "predict", str(work / "in.yaml"), "--use_msa_server",
             "--cache", boltz_cache, "--out_dir", str(out), "--output_format", "pdb"],
            check=True,
        )
    finally:
        weights.commit()  # persist downloaded weights/CCD even if this run fails, so retries skip it

    # Affinity is written to a JSON under out/predictions/<name>/; parse defensively (keys vary).
    aff = {"affinity_pred_value": None, "affinity_probability_binary": None}
    for jf in out.rglob("affinity*.json"):
        data = json.loads(jf.read_text())
        for k in aff:
            if k in data:
                aff[k] = data[k]
        break
    cif = next(out.rglob("*_model_0.pdb"), None) or next(out.rglob("*.pdb"), None)
    return {"label": label, "affinity": aff["affinity_pred_value"],
            "prob_binder": aff["affinity_probability_binary"],
            "structure": cif.read_text() if cif else None}


# ------------------------------------------------------------------------------- driver (local)

@app.local_entrypoint()
def pose() -> None:
    """Save the predicted HDAC2/vorinostat complex for local pose-RMSD validation.

    Run: `modal run gpu/modal_app.py::pose`. Weights are cached, so this is one fast GPU call.
    The returned PDB (protein + vorinostat + Zn) is scored locally against 4LXZ by
    scripts/pose_rmsd.py (align predicted protein to crystal, compare ligand).
    """
    target = "HDAC2"
    pdb, res, drug, cofactors = TARGETS[target]
    seq = binding_chain_sequence(pdb, res)
    r = cofold.remote(f"{target}_{drug}_pose", seq, pubchem_smiles(drug), cofactors)
    out = Path("data/processed/binding"); out.mkdir(parents=True, exist_ok=True)
    if r.get("structure"):
        dest = out / f"{target}_{drug}_pred.pdb"
        dest.write_text(r["structure"])
        print(f"saved {dest}; affinity={r['affinity']}, P(binder)={r['prob_binder']}")
    else:
        print("no structure returned")


@app.local_entrypoint()
def main() -> None:
    """Fan out one GPU call per (target, ligand) pair; tabulate affinities; positive-control test."""
    jobs = []  # (label, protein_seq, smiles, cofactor_ccds)
    for target, (pdb, res, drug, cofactors) in TARGETS.items():
        seq = binding_chain_sequence(pdb, res)
        for lig in [drug, *NEGATIVES]:
            jobs.append((f"{target}_{lig}", seq, pubchem_smiles(lig), cofactors))
    cofactor_summary = {t: c[3] for t, c in TARGETS.items()}
    print(f"co-folding {len(jobs)} complexes ({len(TARGETS)} targets x {1+len(NEGATIVES)} ligands); "
          f"cofactors per target: {cofactor_summary}")

    results = list(cofold.starmap(jobs))
    by = {r["label"]: r for r in results}

    print(f"\n{'target':12s}{'ligand':14s}{'affinity':>10s}{'P(binder)':>11s}")
    out_rows = []
    for target, (pdb, res, drug, cofactors) in TARGETS.items():
        prob = {}  # rank by P(binder): unambiguous (higher = more likely a binder). Boltz
        for lig in [drug, *NEGATIVES]:   # affinity_pred_value is ~log(IC50) (lower=stronger) -- sign
            r = by.get(f"{target}_{lig}", {})           # is version-dependent, so don't rank on it.
            a, p = r.get("affinity"), r.get("prob_binder")
            if p is not None:
                prob[lig] = p
            print(f"{target:12s}{lig:14s}{(f'{a:.2f}' if a is not None else 'NA'):>10s}"
                  f"{(f'{p:.2f}' if p is not None else 'NA'):>11s}")
            out_rows.append({"target": target, "ligand": lig, "affinity": a, "prob_binder": p,
                             "is_known_binder": lig == drug})
        if prob:
            best = max(prob, key=prob.get)  # highest P(binder)
            print(f"  -> {target}: best P(binder) = {best} (known = {drug}) "
                  f"{'PASS' if best == drug else 'FAIL'}\n")

    outdir = Path("data/processed/binding"); outdir.mkdir(parents=True, exist_ok=True)
    import csv
    with (outdir / "phase1_affinity.csv").open("w", newline="") as f:
        w = csv.DictWriter(f, fieldnames=["target", "ligand", "affinity", "prob_binder", "is_known_binder"])
        w.writeheader(); w.writerows(out_rows)
    print(f"wrote {outdir/'phase1_affinity.csv'}")