3

我有成千上万个这样的文件，我想提取与原子 ['CG', 'CD1', 'CD2', 'CE1', 'CE2', ' CZ'],

ATOM      1  CG  TOLU    1      -0.437  -0.756   1.802  1.00  1.99      PRO0
ATOM      2  HG  TOLU    1      -0.689  -1.123   2.786  1.00  0.00      PRO0
ATOM      3  CD1 TOLU    1       0.041  -1.623   0.811  1.00  1.99      PRO0
ATOM      4  HD1 TOLU    1       0.331  -2.603   1.162  1.00  0.00      PRO0
ATOM      5  CD2 TOLU    1      -0.692   0.547   1.352  1.00  1.99      PRO0
ATOM      6  HD2 TOLU    1      -1.131   1.264   2.030  1.00  0.00      PRO0
ATOM      7  CE1 TOLU    1       0.246  -1.276  -0.504  1.00  1.99      PRO0
ATOM      8  HE1 TOLU    1       0.596  -2.073  -1.144  1.00  0.00      PRO0
ATOM      9  CE2 TOLU    1      -0.331   0.991   0.063  1.00  1.99      PRO0
ATOM     10  HE2 TOLU    1      -0.565   2.030  -0.117  1.00  0.00      PRO0
ATOM     11  CZ  TOLU    1       0.136   0.076  -0.919  1.00  1.99      PRO0
ATOM     12  CT  TOLU    1       0.561   0.474  -2.282  1.00  0.00      PRO0
ATOM     13  H11 TOLU    1       0.529  -0.410  -2.955  1.00  0.00      PRO0
ATOM     14  H12 TOLU    1       1.574   0.930  -2.294  1.00  0.00      PRO0
ATOM     15  H13 TOLU    1      -0.203   1.165  -2.699  1.00  0.00      PRO0
ATOM     16  CG  TOLU    2       5.140   1.762  -1.390  1.00  1.99      PRO0
ATOM     17  HG  TOLU    2       5.815   1.717  -2.231  1.00  0.00      PRO0
ATOM     18  CD1 TOLU    2       4.578   0.647  -0.862  1.00  1.99      PRO0
ATOM     19  HD1 TOLU    2       4.835  -0.329  -1.246  1.00  0.00      PRO0
ATOM     20  CD2 TOLU    2       4.786   3.044  -0.824  1.00  1.99      PRO0
ATOM     21  HD2 TOLU    2       5.184   3.982  -1.181  1.00  0.00      PRO0
ATOM     22  CE1 TOLU    2       3.734   0.667   0.248  1.00  1.99      PRO0
ATOM     23  HE1 TOLU    2       3.131  -0.167   0.574  1.00  0.00      PRO0
ATOM     24  CE2 TOLU    2       4.042   3.068   0.321  1.00  1.99      PRO0
ATOM     25  HE2 TOLU    2       3.753   3.969   0.841  1.00  0.00      PRO0
ATOM     26  CZ  TOLU    2       3.465   1.886   0.893  1.00  1.99      PRO0
ATOM     27  CT  TOLU    2       2.501   1.806   2.157  1.00  0.00      PRO0
ATOM     28  H11 TOLU    2       2.361   0.712   2.283  1.00  0.00      PRO0
ATOM     29  H12 TOLU    2       1.490   2.181   1.890  1.00  0.00      PRO0
ATOM     30  H13 TOLU    2       2.845   2.513   2.943  1.00  0.00      PRO0
TER
END

请注意，每个提到的原子都有两行。因此，我认为两个有 12 个键的字典最适合我的目标，就像这样

{1: {'CG':(0,0,0), 'CD1':(0,0,0), 'CD2':(0,0,0), 'CE1':(0,0,0), 'CE2':(0,0,0), 'CZ':(0,0,0)},
2: {'CG':(0,0,0), 'CD1':(0,0,0), 'CD2':(0,0,0), 'CE1':(0,0,0), 'CE2':(0,0,0), 'CZ':(0,0,0)}}

其中第一个键 (1, 2) 指的是第 5 列。

你能告诉我一种读取文件并将每个值元组分配到字典中正确位置的可靠方法吗？我可以使用多个 if 条件来做到这一点，但我认为必须有更好的方法（也许使用 numpy）

4

2 回答 2

5

One way to parse the file is numpy.genfromtxt():

keys = set(['CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ'])
data = numpy.genfromtxt("input", usecols=(2, 4, 5, 6, 7), 
                        dtype=["S3", "i", "d", "d", "d"], skip_footer=2)
data = [row for row in data if row[0] in keys]

After this, data will be

[('CG', 1, -0.437, -0.756, 1.802),
 ('CD1', 1, 0.041, -1.623, 0.811),
 ('CD2', 1, -0.692, 0.547, 1.352),
 ('CE1', 1, 0.246, -1.276, -0.504),
 ('CE2', 1, -0.331, 0.991, 0.063),
 ('CZ', 1, 0.136, 0.076, -0.919),
 ('CG', 2, 5.14, 1.762, -1.39),
 ('CD1', 2, 4.578, 0.647, -0.862),
 ('CD2', 2, 4.786, 3.044, -0.824),
 ('CE1', 2, 3.734, 0.667, 0.248),
 ('CE2', 2, 4.042, 3.068, 0.321),
 ('CZ', 2, 3.465, 1.886, 0.893)]

It's easy to put the data in whatever dictionary format you need now.

于 2013-08-16T16:05:00.013 回答
2

这将完成工作：

atmlist = ['CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ']
def Read_PDB(filename):
   coord={r:{k:(0,0,0) for k in atmlist} for r in [0,1]}
   try:
      f = open(filename, 'r')
   except IOError as err:
      print ("I/O error({0}): {1}".format(err.errno, err.strerror))
      quit()

   for line in f:
      for at in atmlist:
         if (line.find(at) == 13):
            line = line.strip()
            temp = line.split()
            crd = (float(temp[5]), float(temp[6]), float(temp[7]))
            coord[int(temp[4])-1][at] = crd;

   return coord`
于 2013-08-16T18:01:01.493 回答