[SOLVED] Replacing columns in a file

vjramana · 03-20-2011, 08:04 PM

I am doing some operation on a file which represents a molecular system in PDB file format.

The format of the file which I am operating now is as below and this represents only one PDB file:

Code:

REMARKS
ATOM      1  O22 DDM     1       5.844   4.178   7.821  0.00  0.00
ATOM      2  H62 DDM     1       6.423   4.054   8.578  0.00  0.00
ATOM      3  C22 DDM     1       6.606   4.907   6.827  0.00  0.00
TER
ATOM    163  O22 DDM     3       3.758  10.266   8.321  0.00  0.00
ATOM    164  H62 DDM     3       4.450  10.757   8.770  0.00  0.00
ATOM    165  C22 DDM     3       3.346  10.797   7.028  0.00  0.00
TER
ATOM    325  O22 DDM     5       8.310   1.239  14.788  0.00  0.00
ATOM    326  H62 DDM     5       8.858   0.914  15.507  0.00  0.00
ATOM    327  C22 DDM     5       9.143   2.061  13.825  0.00  0.00
TER
END

Basically I want to change the sequence of the numbers in the second and fifth column.
To achive this I generated two seperate files which contain the number in the sequence of.

Quote:

1
2
3

4
5
6

7
8
9

and

Quote:

1
1
1

2
2
2

3
3
3

Now I am trying to replace the first sequence in the second column and the second sequence in the fifth column and finally get the format as below:

Code:

REMARKS
ATOM      1  O22 DDM     1       5.844   4.178   7.821  0.00  0.00
ATOM      2  H62 DDM     1       6.423   4.054   8.578  0.00  0.00
ATOM      3  C22 DDM     1       6.606   4.907   6.827  0.00  0.00
TER
ATOM      4  O22 DDM     2       3.758  10.266   8.321  0.00  0.00
ATOM      5  H62 DDM     2       4.450  10.757   8.770  0.00  0.00
ATOM      6  C22 DDM     2       3.346  10.797   7.028  0.00  0.00
TER
ATOM      7  O22 DDM     3       8.310   1.239  14.788  0.00  0.00
ATOM      8  H62 DDM     3       8.858   0.914  15.507  0.00  0.00
ATOM      9  C22 DDM     3       9.143   2.061  13.825  0.00  0.00
TER
END

I want to do this for each PDB file. But I need some help on how to replace this columns file after file.

I really appreciate any help to achieve this.

Vijay

quanta · 03-20-2011, 10:53 PM

Something like this:

Code:

$ paste 1.txt 2.txt input.txt | awk '{ print $3,$1,$5,$6,$2,$8,$9,$10,$11,$12 }'

but you should use printf to keep the formatting as original file.

grail · 03-21-2011, 07:30 AM

Code:

awk 'FNR==1{i++;j=0}FILENAME != "input.txt"{if(!/^$/)_[i,j++]=$0;next}/ATOM/{$2 = _[1,j];$5 = _[2,j++]}1' 1.txt 2.txt input.txt