Hi,
I have file 1: cur.itp
1 CH3 1 CUR C1 1 0.066 15.0350
2 OA 1 CUR O1 1 -0.183 15.9994
3 C 1 CUR C2 1 0.126 12.0110
4 CR1 1 CUR C3 1 -0.020 12.0110
5 HC 1 CUR H31 1 0.011 1.0080
6 C 1 CUR C7 2 0.137 12.0110
7 OA 1 CUR O2 2 -0.175 15.9994
8 H 1 CUR H22 2 0.038 1.0080
9 CR1 1 CUR C6 3 -0.025 12.0110
10 HC 1 CUR H61 3 0.009 1.0080
11 CR1 1 CUR C5 3 -0.025 12.0110
12 HC 1 CUR H51 3 0.009 1.0080
13 C 1 CUR C4 3 -0.041 12.0110
14 C 1 CUR C8 3 -0.012 13.0190
15 C 1 CUR C9 3 -0.013 13.0190
16 C 1 CUR C10 3 0.304 12.0110
17 OA 1 CUR O6 3 -0.234 15.9994
18 H 1 CUR H62 3 0.028 1.0080
19 C 1 CUR C11 4 0.000 13.0190
20 C 1 CUR C12 5 0.304 12.0110
21 OA 1 CUR O3 5 -0.234 15.9994
22 H 1 CUR H32 5 0.028 1.0080
23 C 1 CUR C13 5 -0.012 13.0190
24 C 1 CUR C14 5 -0.012 13.0190
25 C 1 CUR C15 5 -0.041 12.0110
26 CR1 1 CUR C20 5 -0.026 12.0110
27 HC 1 CUR H20 5 0.009 1.0080
28 CR1 1 CUR C16 5 -0.025 12.0110
29 HC 1 CUR H16 5 0.009 1.0080
30 CR1 1 CUR C17 6 -0.018 12.0110
31 HC 1 CUR H17 6 0.012 1.0080
32 C 1 CUR C18 6 0.140 12.0110
33 OA 1 CUR O5 6 -0.172 15.9994
34 H 1 CUR H52 6 0.038 1.0080
35 C 1 CUR C19 7 0.123 12.0110
36 OA 1 CUR O4 7 -0.187 15.9994
37 CH3 1 CUR C21 7 0.064 15.0350
and file 2: procesed.pdb
ATOM 1 H52 CUR 1 33.502 30.958 -9.831 -0.71 -0.23
H
ATOM 2 H32 CUR 1 34.440 28.421 -3.916 0.00 0.09
H
ATOM 3 H22 CUR 1 31.110 22.839 1.886 -0.18 0.12
H
ATOM 4 H51 CUR 1 29.829 27.375 1.674 -0.21 -0.00
H
ATOM 5 H31 CUR 1 33.510 26.681 -0.511 -0.27 -0.02
H
ATOM 6 H6 CUR 1 29.459 24.909 1.878 -0.23 -0.01
H
ATOM 7 H17 CUR 1 35.217 29.440 -7.832 -0.21 0.01
H
ATOM 8 H20 CUR 1 30.338 28.778 -6.812 -0.06 -0.01
H
ATOM 9 H16 CUR 1 34.487 28.652 -5.564 -0.18 -0.00
H
ATOM 10 C21 CUR 1 30.599 28.677 -10.410 -0.06 -0.05
C
ATOM 11 O4 CUR 1 30.948 29.625 -9.382 -0.04 0.04
O
ATOM 12 C19 CUR 1 31.790 29.357 -8.323 -0.10 -0.00
C
ATOM 13 C20 CUR 1 31.394 28.922 -7.039 -0.06 -0.01
C
ATOM 14 C15 CUR 1 32.371 28.675 -6.051 -0.08 0.00
C
ATOM 15 C16 CUR 1 33.744 28.855 -6.335 -0.18 -0.00
C
ATOM 16 C17 CUR 1 34.160 29.295 -7.609 -0.21 0.01
C
ATOM 17 C18 CUR 1 33.174 29.543 -8.587 -0.20 0.02
C
ATOM 18 C14 CUR 1 31.931 28.137 -4.836 -0.06 0.00
C
ATOM 19 C13 CUR 1 31.827 29.048 -3.599 -0.03 -0.01
C
ATOM 20 C12 CUR 1 33.154 29.408 -2.909 -0.04 -0.03
C
ATOM 21 O3 CUR 1 34.199 28.542 -2.995 0.00 0.09
O
ATOM 22 C11 CUR 1 33.102 30.386 -1.736 -0.14 -0.02
C
ATOM 23 C10 CUR 1 31.707 30.606 -1.152 -0.30 -0.04
C
ATOM 24 O6 CUR 1 31.139 31.683 -1.277 -0.38 0.05
O
ATOM 25 C9 CUR 1 31.046 29.377 -0.519 -0.35 -0.04
C
ATOM 26 C8 CUR 1 31.923 28.547 0.425 -0.29 0.01
C
ATOM 27 C4 CUR 1 31.681 27.171 0.558 -0.27 0.01
C
ATOM 28 C3 CUR 1 32.636 26.289 0.009 -0.27 -0.02
C
ATOM 29 C2 CUR 1 32.451 24.894 0.139 -0.24 -0.02
C
ATOM 30 C7 CUR 1 31.296 24.423 0.823 -0.22 -0.02
C
ATOM 31 C6 CUR 1 30.341 25.296 1.368 -0.23 -0.01
C
ATOM 32 C5 CUR 1 30.547 26.678 1.242 -0.21 -0.00
C
ATOM 33 O1 CUR 1 33.288 23.913 -0.343 -0.69 0.04
O
ATOM 34 C1 CUR 1 34.646 24.135 -0.767 -0.21 -0.06
C
ATOM 35 O2 CUR 1 31.119 23.072 0.955 -0.18 0.12
O
ATOM 36 O5 CUR 1 33.561 30.000 -9.813 -0.71 -0.23
O
Now I wish the file 2 filed 3 output as the order of the file 1 field 2,
namely will be,
ATOM 10 C21 CUR 1 30.599 28.677 -10.410 -0.06 -0.05
C
ATOM 11 O4 CUR 1 30.948 29.625 -9.382 -0.04 0.04
O
namely rearrange it.
I wrote a failed python script,
hope someone can give me some advice,
#!/bin/python
mapping={}
for line in open("cur.itp").readlines():
parts=line.strip().split()
if len(parts)==8:
mapping[parts[4]]=parts[0]
origs=open("processedpdb").read().split()
print " ".join([mapping[orig] for orig in origs])
the last sentence I even don't know what I am doing. sorry.
--
Best Regards,
lina
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