feat: implemented surge - structure generator

Dockerfile

@@ -13,6 +13,10 @@ RUN apt-get update && \
     apt-get update -y && \
     apt-get install -y openjdk-11-jre
 
+RUN wget -O surge "https://github.com/StructureGenerator/surge/releases/download/v1.0/surge-linux-v1.0"
+RUN chmod +x surge
+RUN mv surge /usr/bin
+
 RUN conda install -c conda-forge python>=PYTHON_VERSION
 RUN conda install -c conda-forge rdkit>=RDKIT_VERSION
 RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION
@@ -41,4 +45,4 @@ RUN pip3 install --no-cache-dir chembl_structure_pipeline --no-deps
 
 COPY ./app /code/app
 
-CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "80", "--workers", "4"]
+CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "80", "--workers", "4"]

app/main.py

@@ -2,7 +2,7 @@
 from fastapi.responses import RedirectResponse
 from fastapi_versioning import VersionedFastAPI
 
-from .routers import chem, converters, depict, ocsr
+from .routers import chem, converters, depict, tools  # , ocsr
 from fastapi.middleware.cors import CORSMiddleware
 
 from prometheus_fastapi_instrumentator import Instrumentator
@@ -35,7 +35,8 @@
 app.include_router(chem.router)
 app.include_router(converters.router)
 app.include_router(depict.router)
-app.include_router(ocsr.router)
+app.include_router(tools.router)
+# app.include_router(ocsr.router)
 
 app = VersionedFastAPI(
     app,

app/modules/tools/surge.py

@@ -0,0 +1,20 @@
+from subprocess import Popen, PIPE
+
+
+def generateStructures(mf: str):
+    """This function uses the sugar removal utility and checks
+    whether a molecule has ring or linear sugars
+    Args:
+        smiles (string): SMILES string given by the user.
+    Returns:
+        (boolean): True or false values whtehr or not molecule has sugar.
+    """
+    smiles = []
+    process = Popen(
+        ["surge", "-P", "-T", "-B1,2,3,4,5,7,9", "-t0", "-f0", "-S", mf],
+        stdout=PIPE,
+        stderr=PIPE,
+    )
+    for line in iter(process.stdout.readline, b""):
+        smiles.append(line.decode("utf-8").rstrip())
+    return smiles

app/routers/tools.py

@@ -0,0 +1,24 @@
+from fastapi import APIRouter
+from app.modules.tools.surge import generateStructures
+
+router = APIRouter(
+    prefix="/tools",
+    tags=["tools"],
+    dependencies=[],
+    responses={404: {"description": "Not found"}},
+)
+
+
+@router.get("/")
+async def tools_index():
+    return {"module": "tools", "message": "Successful", "status": 200}
+
+
+@router.get("/generate-structures")
+async def Generate_Structures(molecular_formula: str):
+    """
+    Extract chemical structure depictions and convert them into SMILES using DECIMER:
+
+    - **Images**: required (query)
+    """
+    return generateStructures(molecular_formula)