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Full Discussion: Data manipulating script. Please HELP!
Top Forums Shell Programming and Scripting Data manipulating script. Please HELP! Post 302927916 by liuzhencc on Sunday 7th of December 2014 09:34:08 AM
Old 12-07-2014
Data manipulating script. Please HELP!
Dear friends,

I'm struggling to preparing a bunch of gromacs input files, say manually. It's really a time-consuming work without any techniques. I suppose that it could be done by a smart script automatically. But I lack some basic knowledge on scripting. Please help!

My original input looks like,(only show the first 10 lines, there are a few hundreds of thousands of lines in the input file)
Code:
ATOM      1  C1  C20 P   1       1.000   1.540   0.000  1.00  0.00           C    
ATOM      2  C2  C20 P   1       2.456   2.041   0.000  1.00  0.00           C    
ATOM      7  C1  C20 P   1       2.456   3.581   0.000  1.00  0.00           C    
ATOM      8  C2  C20 P   1       3.912   4.083  -0.000  1.00  0.00           C    
ATOM     13  C1  C20 P   1       3.912   5.623  -0.000  1.00  0.00           C    
ATOM     14  C2  C20 P   1       5.368   6.124  -0.000  1.00  0.00           C    
ATOM     19  C1  C20 P   1       5.368   7.664  -0.000  1.00  0.00           C    
ATOM     20  C2  C20 P   1       6.824   8.165  -0.000  1.00  0.00           C    
ATOM     25  C1  C20 P   1       6.824   9.705  -0.000  1.00  0.00           C    
ATOM     26  C2  C20 P   1       8.280  10.207  -0.000  1.00  0.00           C

The output file needs to be modified into the following format,
Code:
ATOM      1  CM  ETH P   1       1.000   1.540   0.000  1.00  0.00           C  
ATOM      2  CD  ETH P   1       2.456   2.041   0.000  1.00  0.00           C  
ATOM      3  CM  ETH P   2       2.456   3.581   0.000  1.00  0.00           C  
ATOM      4  CD  ETH P   2       3.912   4.083  -0.000  1.00  0.00           C  
ATOM      5  CM  ETH P   3       3.912   5.623  -0.000  1.00  0.00           C  
ATOM      6  CD  ETH P   3       5.368   6.124  -0.000  1.00  0.00           C  
ATOM      7  CM  ETH P   4       5.368   7.664  -0.000  1.00  0.00           C  
ATOM      8  CD  ETH P   4       6.824   8.165  -0.000  1.00  0.00           C  
ATOM      9  CM  ETH P   5       6.824   9.705  -0.000  1.00  0.00           C  
ATOM     10  CD  ETH P   5       8.280  10.207  -0.000  1.00  0.00           C 
TER 11 
CONECT    1    
CONECT    2    1    3
CONECT    3    2    4
CONECT    4    3    5
CONECT    5    4    6
CONECT    6    5    7
CONECT    7    6    8
CONECT    8    7    9
CONECT    9    8   10
CONECT   10    9

Clearly to say, the script would do:
1. there are 12 columns in each line, keep $1, $5, $7-$12 with no change;
2. ignore the original data in $2, fill with series line number;
3. ignore the original data in $3, fill with series CM CD in the alternative sequence; or just replace C1 with CM and replace C2 with CD;
4. ignore the original data in $4, fill with "ETH"; or simply replace C20 with "ETH"
5. ignore the original data in $6, fill with series 1 1 2 2 3 3 .... up to $(line number)/2;
6. at the end of the output, add some new lines start with "TER LineNum+1";
7. the following line should start with CONECT and fill with three-column numbers of 1-10, 1-9, and 3-10 as shown in the above output sample.


I hope I have already made myself clear in explaining the function of this script. Please do me a favor. All you help will be greatly appreciated. Thank you in advanced!

ZHEN
from Shanghai, China.
Last edited by liuzhencc; 12-07-2014 at 10:52 AM..
 

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