Python(numpy)读取混合格式的文本文件 [英] Python (numpy) read a text file with mixed format
问题描述
我有成千上万个这样的文件，我想为与原子['CG'，'CD1'，'CD2'，'CE1'，'CE2' '，'CZ']，
I have thousands of files like this, and I want to extract the values of columns 6,7,8 for the rows corresponding to atoms ['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，我认为两个具有12个键的字典最适合我的目标，例如
and notice that there exist two rows for each of the mentioned atoms. Therefore, I think two dictionaries with 12 keys would best fit my goal, like this
{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)}}
第一个键(1、2)指向第5列.
Where the first keys (1, 2) refer to the 5th column.
您能告诉我一种健壮的方法来读取文件并将每个值的元组分配给字典中的正确位置吗?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)
Can you tell me a robust way to read the file and assign each tuple of values to its correct place in the dictionary? I can do it with multiple if conditions, but I thought there must be a better way (maybe with numpy)
推荐答案
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`
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