Biopython:reseq与pdb-fi不匹配

Question

我有一个PDB文件，我需要提取它的剩余序列号（resseqs）。根据对PDB文件（粘贴在下面）前几行的手动检查，我认为resseqs应该是{}。然而，Biopython的^{}模块提出了其他建议（输出也附在下面）。我想知道这是一个Biopython错误，还是我在理解PDB格式时有问题。在

ATOM      1  N   GLY A  22      78.171  89.858  59.231  1.00 21.24           N  
ATOM      2  CA  GLY A  22      79.174  88.827  58.999  1.00 20.87           C  
ATOM      3  C   GLY A  22      80.438  89.415  58.391  1.00 21.89           C  
ATOM      4  O   GLY A  22      80.362  90.202  57.440  1.00 23.18           O  
ATOM      5  N   LEU A  23      81.588  89.069  58.972  1.00 21.51           N  
ATOM      6  CA  LEU A  23      82.895  89.555  58.527  1.00 20.80           C  
ATOM      7  C   LEU A  23      83.288  89.020  57.162  1.00 22.41           C  
ATOM      8  O   LEU A  23      82.889  87.923  56.788  1.00 22.93           O  
ATOM      9  CB  LEU A  23      83.973  89.232  59.560  1.00 20.97           C  
ATOM     10  CG  LEU A  23      84.225  87.818  60.062  1.00 13.32           C  
ATOM     11  CD1 LEU A  23      85.448  87.888  60.939  1.00 15.24           C  
ATOM     12  CD2 LEU A  23      83.035  87.258  60.829  1.00 12.21           C

我用来提取resseq的代码：

^{pr2}$

Answer 1

来自Bio.PDB.Entity.get_full_id的文档

def get_full_id(self):
    """Return the full id.

    The full id is a tuple containing all id's starting from
    the top object (Structure) down to the current object. A full id for
    a Residue object e.g. is something like:

    ("1abc", 0, "A", (" ", 10, "A"))

    This corresponds to:

    Structure with id "1abc"
    Model with id 0
    Chain with id "A"
    Residue with id (" ", 10, "A")

    The Residue id indicates that the residue is not a hetero-residue
    (or a water) because it has a blank hetero field, that its sequence
    identifier is 10 and its insertion code "A".
    """
    # The function implementation below here ...

我假设你是在链的原子上迭代，而不是残基，这样就得到了每个Atom而不是Residue的完整id。在

如果您将示例残留物保存在一个名为struct.pdb的文件中，并运行下面的代码，您将得到正确的ids

^{pr2}$