当前位置：首页 > article >正文

Biopython从pdb文件中提取蛋白质链的信息

article 2025/3/15 12:16:10

使用Biopython的PDB模块可以方便地解析PDB文件并提取你需要的信息。下面是一个示例代码，用于提取PDB文件中的链名称、序列和长度：

示例代码

from Bio import PDB

# 读取PDB文件
pdb_file = "/Users/zhengxueming/Downloads/1a0h.pdb"
parser = PDB.PDBParser(QUIET=True)
structure = parser.get_structure("protein", pdb_file)

# 初始化保存信息的列表
chain_info = []

# 遍历所有模型、链和残基
for model in structure:
    for chain in model:
        chain_id = chain.id
        sequence = []
        for residue in chain:
            # 检查是否是标准氨基酸
            if PDB.is_aa(residue):
                sequence.append(PDB.Polypeptide.three_to_one(residue.resname))
        # 提取链的序列和长度
        seq_str = ''.join(sequence)
        chain_length = len(sequence)
        chain_info.append((chain_id, chain_length, seq_str))

# 打印链的信息
for chain_id, chain_length, seq_str in chain_info:
    print(f"链ID: {chain_id}, 长度: {chain_length}, 序列: {seq_str}")

查看全文

http://www.kler.cn/a/297333.html