Optimize nupack service startup and compute

nupack/app.py

@@ -0,0 +1,64 @@
+from fastapi import FastAPI
+from pydantic import BaseModel
+from typing import List
+from nupack import Model, Strand, Tube, SetSpec, tube_analysis
+
+app = FastAPI()
+
+class ModelInput(BaseModel):
+    material: str = "rna"
+    ensemble: str = "stacking"
+    celsius: float = 37
+    sodium: float = 1.0
+    magnesium: float = 0.0
+
+class StrandInput(BaseModel):
+    name: str
+    sequence: str
+    concentration: float
+    unit: str = "uM"
+
+class TubeInput(BaseModel):
+    name: str = "tube1"
+    max_size: int = 2
+
+class AnalysisPayload(BaseModel):
+    model: ModelInput
+    strands: List[StrandInput]
+    tube: TubeInput
+
+def unit_to_molar(value: float, unit: str) -> float:
+    mapping = {"M": 1, "mM": 1e-3, "uM": 1e-6, "nM": 1e-9, "pM": 1e-12}
+    return value * mapping[unit]
+
+@app.get("/health")
+def health():
+    return {"status": "ok"}
+
+@app.post("/run")
+def run(payload: AnalysisPayload):
+    model = Model(
+        material=payload.model.material,
+        ensemble=payload.model.ensemble,
+        celsius=payload.model.celsius,
+        sodium=payload.model.sodium,
+        magnesium=payload.model.magnesium,
+    )
+
+    strands = {}
+    for s in payload.strands:
+        obj = Strand(s.sequence, name=s.name)
+        strands[obj] = unit_to_molar(s.concentration, s.unit)
+
+    tube = Tube(
+        strands=strands,
+        complexes=SetSpec(max_size=payload.tube.max_size),
+        name=payload.tube.name,
+    )
+
+    result = tube_analysis(tubes=[tube], model=model)
+
+    return {
+        "status": "success",
+        "result": str(result)
+    }