RDKit建化合物库-拼接

from rdkit import Chem
# 函数一：获取marker邻居原子的indexdef get_neiid_bysymbol(mol, marker):
    try:
        for atom in mol.GetAtoms():
            if atom.GetSymbol() == marker:
                neighbors = atom.GetNeighbors()
                if len(neighbors) > 1:
                    print('Cannot process more than one neighbor, will only return one of them')
                atom_nb = neighbors[0]
                return atom_nb.GetIdx()
    except Exception as e:
        print(e)
        return None
# 函数二：获取marker原子的indexdef get_id_bysymbol(mol, marker):
    for atom in mol.GetAtoms():
        if atom.GetSymbol() == marker:
            return atom.GetIdx()
# 示例
mol = Chem.MolFromSmiles('CCBr')
marker = 'Br'
# 获取标记原子邻居的索引
nei_idx = get_neiid_bysymbol(mol, marker)print(f"Neighbor Index: {nei_idx}")
# 获取标记原子的索引
marker_idx = get_id_bysymbol(mol, marker)print(f"Marker Index: {marker_idx}")