Question

在下面的代码中，我使用DSSP库解析了pdb和计算的二级结构。在解析和存储值之后，我重新编号了残差编号，但我没有修改_pdb和_dssp个实例。重新编号后，它还会重新编号以前指定的_dssp值，就像您在我评论的输出中看到的那样。我认为这是参考操作的效果。我想在重新编号后避免_dssp值的更改，因为我没有明确修改_dssp。如何避免这种类型的操作？

class PDBModify:

  _pdb = None
  _dssp = None

  def parse(self, pdbid, pdbfile):
    pdbparser = PDBParser(PERMISSIVE=1)
    structure = pdbparser.get_structure(pdbid, pdbfile)
    self._pdb = structure[0]
    self._dssp = DSSP(structure[0], pdbfile)

  def delete_n_dump(self, rsds, map_rsds):
    current = self._pdb
    for chain in current:
      for residue in list(chain):
        if not residue.id[1] in rsds:
          chain.detach_child(residue.id)
        else:
          residue.id = (' ', map_rsds[residue.id[1]], ' ')

    write_pdb = PDBIO()
    write_pdb.set_structure(current)
    write_pdb.save("./3chy_md.pdb")

if __name__=="__main__":
  map_rsds = {15:200, 20: 201, 25:202, 26:203, 30:204, 34:205, 35:206, 36:207}
  rsds = [15, 20, 25, 26, 30, 34, 35, 36]

  pdbmodify = PDBModify()
  pdbmodify.parse('3chy', './3chy.pdb')  # parsing pdb and computing ss
  print "before "
  for item in pdbmodify._dssp:  # initial call
    print item
  pdbmodify.delete_n_dump(rsds, map_rsds)  # renumber the residue id
  print "after "
  for item in pdbmodify._dssp:  # second call 
    print item

输出：

before
(<Residue ALA het=  resseq=2 icode= >, '-', 65, 0.6132075471698113, 360.0, 127.6)
...
(<Residue SER het=  resseq=15 icode= >, 'H', 73, 0.5615384615384615, -60.0, -33.4)
...

after 
(<Residue ALA het=  resseq=2 icode= >, '-', 65, 0.6132075471698113, 360.0, 127.6)
...
(<Residue SER het=  resseq=200 icode= >, 'H', 73, 0.5615384615384615, -60.0, -33.4) # residue number is changed here why?
...

Answer 1

您使用structure[0]和self._pdb指向同一self._dssp个对象

self._pdb = structure[0]
self._dssp = DSSP(structure[0], pdbfile)

如果要取消关联它们，可以使用copy.copy或copy.deepcopy（取决于structure[0]是否是一个简单的对象，如列表，只需要浅层副本或复杂的，就像列表一样。）

例如：

import copy
self._pdb = copy.deepcopy(structure[0])
self._dssp = DSSP(structure[0], pdbfile)

使用biopython重新编号pdb残留数的后效应

1 个答案: