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Data manipulating script. Please HELP!

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Top Forums Shell Programming and Scripting Data manipulating script. Please HELP!
# 1  
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..
# 2  
Old 12-07-2014
OK Zhen. That seems straightforward. Do you need the formatting preserved or would this do?
Code:
awk '
  END { 
    print "TER",NR+1
    for(i=1; i<=NR; i++) print "CONNECT", i, (i==1?x:i-1),(i==NR?x:i+1)
  }

  { 
    $2=NR
    sub(1,"M",$3)
    sub(2,"D",$3)
    $4="ETH"
    $5=int((NR+1)/2)
  }
  1
' OFS='\t' file

These 2 Users Gave Thanks to Scrutinizer For This Post:
liuzhencc naresh7590
# 3  
Old 12-08-2014
Thank you very much, Scrutinizer! it works like a charm! As you metioned, if each column could be printed with format, it'll look much tidy. So, would you please add some function to this script to get the output in the following format?

Code:
ATOM      10       CD      ETH         P        5        8.280      10.207    -0.000     1.00      0.00       C 
(10s%)  (10d%) (10s%) (10s%) (10s%) (10d%) (10.3f%) (10.3f%) (10.3f%) (5.2f%) (5.2f%)  (10s%)

and the new added lines in the following format,
Code:
CONNECT	999	998	1000
CONNECT	1000	999	1001
CONNECT	1001	1000	1002
(10s%)           (10d%)  (10d%)  (10d%)

# 4  
Old 12-08-2014
Hi,
just replace the last
Code:
1

with
Code:
{printf "%10s%10d%10s%10s%10s%10d%10.3f%10.3f%10.3f%5.2f%5.2f%10s\n",$1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}

and remove
Code:
OFS='\t'

Last edited by Scrutinizer; 12-08-2014 at 02:55 AM..
This User Gave Thanks to Scrutinizer For This Post:
liuzhencc
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