Question

我使用biopython找到两个残基的C alpha原子之间的距离，并且我不断收到错误。这是我的代码和错误：

```

>>> from Bio.PDB.mmtf import MMTFParser
>>> structure = MMTFParser.get_structure_from_url('4mne')
/Library/Python/2.7/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 0.
  PDBConstructionWarning)
/Library/Python/2.7/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 0.
  PDBConstructionWarning)
/Library/Python/2.7/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 0.
  PDBConstructionWarning)
/Library/Python/2.7/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain F is discontinuous at line 0.
  PDBConstructionWarning)
/Library/Python/2.7/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain H is discontinuous at line 0.
  PDBConstructionWarning)
/Library/Python/2.7/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 0.
  PDBConstructionWarning)
/Library/Python/2.7/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 0.
  PDBConstructionWarning)
/Library/Python/2.7/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain G is discontinuous at line 0.
  PDBConstructionWarning)
>>> for c in structure.get_chains():
...     if c.get_id() == 'B':
...             chain = c
...
>>> chain
<Chain id=B>
>>> CAatoms = [a for a in chain.get_atoms() if a.id == 'CA']
>>> for a in CAatoms:
...     for b in CAatoms:
...             distance = a-b
...
Traceback (most recent call last):
  File "<stdin>", line 3, in <module>
  File "/Library/Python/2.7/site-packages/Bio/PDB/Atom.py", line 124, in __sub__
    diff = self.coord - other.coord
TypeError: unsupported operand type(s) for -: 'list' and 'list'
>>>

```

这是否与＆＃34; get_structure_from_url＆＃34;有关？ MMTFParser的方法？我已经用PDBParser（）。get_structure尝试了这个，它工作得很好。

Answer 1

Biopython的原子类有一个自定义减法方法。

来自source code：

for i, name in enumerate(files):
    os.rename(os.path.join(path, name), os.path.join(path, '{}.mp4'.format(names[i])))

~~对于MMTFParser，此功能似乎缺失，但您可以轻松自行完成。~~

MMTFParser将坐标作为列表（def __sub__(self, other): """Calculate distance between two atoms. :param other: the other atom :type other: L{Atom} Examples -------- >>> distance = atom1 - atom2 """ diff = self.coord - other.coord return numpy.sqrt(numpy.dot(diff, diff))，line 53）读取，这与PDBParser不同，PDBParser将坐标读取为Numpy数组（init_atom(str(atom_name), [x, y, z] ...，line 187）。

为了获得距离，您可以将坐标列表转换为Numpy数组，然后计算距离。

coord = numpy.array((x, y, z), "f")

Biopython：MMTFParser无法找到原子之间的距离

1 个答案: