计算片段在多个分子中出现的次数

要计算分子片段在多个分子中出现的次数，您可以修改上面的代码，将统计分子片段出现次数的部分提取出来，并计算所有分子中分子片段的总出现次数。代码如下：

from rdkit import Chem

# 读取分子文件并转换为 RDKit 分子对象
with open('path/to/smi/file', 'r') as f:
    smiles = f.readlines()
smiles = [s.strip() for s in smiles]
mols = [Chem.MolFromSmiles(smi) for smi in smiles]

# 读取分子片段文件并转换为 RDKit 分子对象
with open('path/to/submol/file', 'r') as f:
    submol_smarts = f.readlines()
submol_smarts = [s.strip() for s in submol_smarts]
submols = [Chem.MolFromSmarts(sma) for sma in submol_smarts]

# 计算分子片段出现的次数
count_dict = {}
for submol_idx, submol in enumerate(submols):
    count = 0
    for mol in mols:
        if mol.HasSubstructMatch(submol):
            count += 1
    count_dict[submol_idx] = count

# 计算分子片段在多个分子中出现的频率
freq_dict = {}
for idx, mol in enumerate(mols):
    freq_dict[idx] = {}
    atoms_num = mol.GetNumAtoms()
    for submol_idx, submol in enumerate(submols):
        if mol.HasSubstructMatch(submol):
            submol_atoms_num = submol.GetNumAtoms()
            freq = count_dict[submol_idx] / (atoms_num - submol_atoms_num + 1)
            freq_dict[idx][submol_idx] = freq

# 输出结果
for idx, freqs in freq_dict.items():
    print(f'分子{idx}中各片段出现的频率：')
    for submol_idx, freq in freqs.items():
        print(f'片段{submol_idx}: {freq:.3f}')

这将输出一个字典，其中键为每个分子的索引（从 0 开始），值为一个字典，该字典的键为每个分子片段的索引（从 0 开始），值为该分子片段在多个分子中出现的频率。