从PDB中除去杂原子 [英] Remove heteroatoms from PDB

问题描述

必须删除pdb文件中的杂原子.这是代码，但不适用于我的测试PDB 1C4R.

The heteroatoms from pdb file has to be removed. Here is the code but it did not work with my test PDB 1C4R.

for model in structure:
    for chain in model:
        for reisdue in chain:
            id = residue.id
            if id[0] != ' ':
                chain.detach_child(id)
        if len(chain) == 0:
            model.detach_child(chain.id)

有什么建议吗?

推荐答案

杂原子不应成为链的一部分.但是您可以知道残基是否为具有以下特征的杂原子:

The heteroatoms shouldn't be part of the chain. But you can know if a residue is a heteroatom with:

pdb = PDBParser().get_structure("1C4R", "1C4R.pdb")

for residue in pdb.get_residues():
    tags = residue.get_full_id()

    # tags contains a tuple with (Structure ID, Model ID, Chain ID, (Residue ID))
    # Residue ID is a tuple with (*Hetero Field*, Residue ID, Insertion Code)

    # Thus you're interested in the Hetero Field, that is empty if the residue
    # is not a hetero atom or have some flag if it is (W for waters, H, etc.)

    if tags[3][0] != " ":
        # The residue is a heteroatom
    else:
        # It is not

您还可以通过以下方式获取残基的ID(没有前三个字段):

You can also get the id of the residue (without the three first fields) with:

tags = residue.id

# or het_flag,_ ,_ = residue.id

if tags[0] != " ":
    # The residue is a heteroatom
else:
    # It is not

我正在添加指向相关文档的链接: http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf

I'm adding a link to the relevant documentation: http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf

主题位于第8页，什么是残基ID?".报价:

The subject is in the page 8, "What is a residue id?". Quoting:

由于笨拙的PDB格式，这有点复杂.残基id是一个元组 包含三个元素:

This is a bit more complicated, due to the clumsy PDB format. A residue id is a tuple with three elements:

• 杂种标记:这是"H_"加上杂种残基的名称(例如"H_GLC" 如果是葡萄糖分子，则为"W"；如果是水分子，则为"W".

• The hetero-flag: this is ’H_’ plus the name of the hetero-residue (eg. ’H_GLC’ in the case of a glucose molecule), or ’W’ in the case of a water molecule.

---

要添加评论并继续:

---

To add comments in and resume:

from Bio.PDB import PDBParser, PDBIO, Select

class NonHetSelect(Select):
    def accept_residue(self, residue):
        return 1 if residue.id[0] == " " else 0

pdb = PDBParser().get_structure("1C4R", "1C4R.pdb")
io = PDBIO()
io.set_structure(pdb)
io.save("non_het.pdb", NonHetSelect())

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