基于raiz和sqlmodel-rdkit-example代码, 开发SQLite数据库RDKit cartridge (ChemicaLite) ORM.
conda create -n test python=3.9
conda activate test
conda install rdkit chemicalite -c conda-forge
pip install git+https://github.com/iuhgnor/chemicalite-orm.git-
创建数据库
from sqlalchemy import Integer, String from sqlalchemy.orm import Mapped, declarative_base, mapped_column from chemicalite_orm.search import enable_chem_search from chemicalite_orm.types import Mol DATABASE_URL = "sqlite:///chemicalite.db" engine = create_engine(DATABASE_URL, echo=True) @event.listens_for(engine, "connect") def load_chemicalite(dbapi_conn, connection_record): dbapi_conn.enable_load_extension(True) dbapi_conn.load_extension("chemicalite") Base = declarative_base() @enable_chem_search(mol_col="molecule", id_col="id", fp_bits=2048, fp_radius=2) class Compound(Base): # type: ignore __tablename__ = "compound" id: Mapped[int] = mapped_column(Integer, primary_key=True) name: Mapped[str] = mapped_column(String, nullable=False) smiles: Mapped[str] = mapped_column(String, nullable=False) molecule: Mapped[Mol] = mapped_column(Mol, nullable=False) Base.metadata.create_all(engine) SessionLocal = sessionmaker(bind=engine)
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插入数据
with SessionLocal() as session: for i, smiles in enumerate(mols): compound = Compound( name=f"mol_{i}", smiles=smiles, molecule=Chem.MolFromSmiles(smiles), ) session.add(compound) session.commit()
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检索数据
with SessionLocal() as session: stmt = select(Compound).where(Compound.name == "mol_1") result = session.execute(stmt).scalars().first() mol = result.molecule mol
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子结构查询
with SessionLocal() as session: stmt = select(Compound).where(Compound.has_substructure("c1ccccc1")) results = session.execute(stmt).scalars().all() mols = [r.molecule for r in results[:10]] Draw.MolsToGridImage(mols, molsPerRow=5)
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相似性查询
with SessionLocal() as session: stmt = select(Compound).where(Compound.similarity_to("c1ccnnc1", 0.1)) results = session.execute(stmt).scalars().all() mols = [r.molecule for r in results[:10]] Draw.MolsToGridImage(mols, molsPerRow=5)