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be36a29 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 | """SWISS-MODEL homology modelling endpoints — proxies to the SMR Repository API."""
import logging
from typing import Any
from fastapi import APIRouter, HTTPException
from pydantic import BaseModel, Field
import httpx
logger = logging.getLogger(__name__)
router = APIRouter(prefix="/api/swissmodel", tags=["swissmodel"])
SMR_BASE = "https://swissmodel.expasy.org/repository"
class SwissModelRequest(BaseModel):
accession: str = Field(..., description="UniProt accession (e.g. P07900)")
class ModelInfo(BaseModel):
template: str | None = None
provider: str | None = None
method: str | None = None
coverage: float | None = None
oligo_state: str | None = None
from_res: int | None = None
to_res: int | None = None
created_date: str | None = None
coordinates_url: str | None = None
qmean_score: float | None = None
ligands: list[dict[str, Any]] = []
complex_with: list[dict[str, Any]] = []
class SwissModelResponse(BaseModel):
accession: str
sequence: str = ""
sequence_length: int = 0
models: list[ModelInfo]
experimental: list[ModelInfo]
@router.post("/repository", response_model=SwissModelResponse)
async def query_repository(body: SwissModelRequest):
accession = body.accession.strip().upper()
if not accession:
raise HTTPException(status_code=400, detail="Accession is required")
try:
async with httpx.AsyncClient(timeout=30) as client:
resp = await client.get(f"{SMR_BASE}/uniprot/{accession}.json")
if resp.status_code == 404:
raise HTTPException(status_code=404, detail=f"No SWISS-MODEL data for {accession}")
resp.raise_for_status()
data = resp.json()
except httpx.HTTPStatusError:
raise
except Exception as e:
logger.exception("SWISS-MODEL request failed for %s", accession)
raise HTTPException(status_code=500, detail=f"SWISS-MODEL request failed: {e}")
result = data.get("result", {})
structures = result.get("structures", [])
sequence = result.get("sequence", "")
models: list[ModelInfo] = []
experimental: list[ModelInfo] = []
for s in structures:
info = ModelInfo(
template=s.get("template"),
provider=s.get("provider"),
method=s.get("method"),
coverage=s.get("coverage"),
oligo_state=s.get("oligo-state"),
from_res=s.get("from"),
to_res=s.get("to"),
created_date=s.get("created_date"),
coordinates_url=s.get("coordinates"),
)
if s.get("ligand_chains"):
for lc in s["ligand_chains"]:
for lig in lc.get("ligands", []):
info.ligands.append({
"hetid": lig.get("hetid", ""),
"description": lig.get("description", ""),
})
if s.get("in_complex_with"):
for chain_id, partners in s["in_complex_with"].items():
for p in partners:
info.complex_with.append({
"chain": chain_id,
"uniprot_ac": p.get("uniprot_ac", ""),
"description": p.get("description", ""),
})
if s.get("provider") == "PDB":
experimental.append(info)
else:
models.append(info)
return SwissModelResponse(
accession=accession,
sequence=sequence,
sequence_length=len(sequence),
models=models,
experimental=experimental,
)
@router.get("/coordinates/{accession}")
async def get_coordinates(accession: str):
accession = accession.strip().upper()
try:
async with httpx.AsyncClient(timeout=30) as client:
resp = await client.get(f"{SMR_BASE}/uniprot/{accession}.pdb")
resp.raise_for_status()
return {"accession": accession, "pdb": resp.text}
except Exception as e:
raise HTTPException(status_code=500, detail=f"Failed to fetch coordinates: {e}")
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