使用BioPython读取.pdb文件的整个目录 [英] Reading an entire directory of .pdb files using BioPython
问题描述
我最近受命用python编写程序,以从.pdb(蛋白质数据库)的蛋白质中找到距每种金属2埃以内的原子.这是我为此编写的脚本.
I was recently tasked to write a program in python to find atoms within 2 angstroms distance from every metal in a protein from a .pdb (Protein Data Bank). This is the script I wrote for it.
from Bio.PDB import *
parser = PDBParser(PERMISSIVE=True)
def print_coordinates(list):
neighborList = list
for y in neighborList:
print " ", y.get_coord()
structure_id = '5m6n'
fileName = '5m6n.pdb'
structure = parser.get_structure(structure_id, fileName)
atomList = Selection.unfold_entities(structure, 'A')
ns = NeighborSearch(atomList)
for x in structure.get_atoms():
if x.name == 'ZN' or x.name == 'FE' or x.name == 'CU' or x.name == 'MG' or x.name == 'CA' or x.name == 'MN':
center = x.get_coord()
neighbors = ns.search(center,2.0)
neighborList = Selection.unfold_entities(neighbors, 'A')
print x.get_id(), ': ', neighborList
print_coordinates(neighborList)
else:
continue
但这仅适用于单个.pdb文件,我希望能够读取它们的整个目录.由于直到现在我一直只使用Java,所以我不太确定如何在Python 2.7中做到这一点.我的想法是,将脚本放入try catch语句中,并在其中进行while循环,然后在到达末尾时引发异常,但这就是我在Java中的处理方式,不确定如何用Python完成.所以我很想听听任何人可能有的任何想法或示例代码.
But this is only for a single .pdb file, I would like to be able to read an entire directory of them. Since I've only been using Java until now, I am not entirely sure how I would be able to do this in Python 2.7. An idea I have is that I would put the script in a try catch statement and in it, a while loop, then throw an exception when it reaches the end, but that's how I would've done in Java, not sure how I would do it in Python. So I would love to hear any idea or sample code anyone might have.
推荐答案
您的代码中有一些冗余,例如,这样做是相同的:
You have some redundancies in your code, for instance this does the same:
from Bio.PDB import *
parser = PDBParser(PERMISSIVE=True)
def print_coordinates(neighborList):
for y in neighborList:
print " ", y.get_coord()
structure_id = '5m6n'
fileName = '5m6n.pdb'
structure = parser.get_structure(structure_id, fileName)
metals = ['ZN', 'FE', 'CU', 'MG', 'CA', 'MN']
atomList = [atom for atom in structure.get_atoms() if atom.name in metals]
ns = NeighborSearch(Selection.unfold_entities(structure, 'A'))
for atom in atomList:
neighbors = ns.search(atom.coord, 2)
print("{0}: {1}").format(atom.name, neighbors)
print_coordinates(neighborList)
要回答您的问题,您可以使用glob
模块获取所有pdb文件的列表,并将代码嵌套在对所有文件进行迭代的for
循环中.假设您的pdb文件位于/home/pdb_files/
:
To answer your question, you can get a list of all your pdb files using the glob
module and nest your code on a for
loop iterating over all files. Supposing your pdb files are at /home/pdb_files/
:
from Bio.PDB import *
from glob import glob
parser = PDBParser(PERMISSIVE=True)
pdb_files = glob('/home/pdb_files/*')
def print_coordinates(neighborList):
for y in neighborList:
print " ", y.get_coord()
for fileName in pdb_files:
structure_id = fileName.rsplit('/', 1)[1][:-4]
structure = parser.get_structure(structure_id, fileName)
# The rest of your code
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