我想利用smiles式（或者其他方法，目前我只有结构式）输出化合物官能团类型及数量

Question

希望可以批量处理，输出化合物的官能团（如羧基、氨基、特殊原子P等）

Answer 1

解决方案如下

from rdkit import Chem
from rdkit.Chem import FunctionalGroups

smiles_list = ['CCO', 'CC(=O)O', 'C1=CC=CC=C1N', 'C[P@@](C)(O)O'] #给定SMILES并转化为Mol对象
mols = [Chem.MolFromSmiles(smile) for smile in smiles_list]

FGHierarchyNodes = FunctionalGroups.BuildFuncGroupHierarchy() #获取已定义的官能团节点对象并转为tuples
functional_groups = []
for FGhierarchy in FGHierarchyNodes:
    functional_groups.append((FGhierarchy.name, FGhierarchy.smarts))

#基于官能团Smarts进行子结构搜索，并输出结果
for mol in mols:
    counts = {}  
    for (name, smarts) in functional_groups:
        matches = mol.GetSubstructMatches(Chem.MolFromSmarts(smarts))
        count = len(matches)
        if count > 0:
            counts[name] = count
    
    for name,count in counts.items():
        print("Molecule: {}".format(Chem.MolToSmiles(mol)))
        print(f"{name}: {count}")
        print('\n')