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how I can add a constant to a field without changing the file format

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Top Forums Shell Programming and Scripting how I can add a constant to a field without changing the file format
# 1  
Old 05-26-2010
how I can add a constant to a field without changing the file format
Hi, I need to edit a file Protein Data Bank (pdb) and then open that file with the program VMD but when I edit the file with awk, it changes pdb format and the VMD program can not read it.
I need to subtract 34 to field 6 ($ 6).
this is a pdb file :
Code:
ATOM    918  N   GLY B 103     -11.855   8.675 -11.404  1.00  0.00           N  
ATOM    919  CA  GLY B 103     -13.297   8.831 -11.189  1.00  0.00           C  
ATOM    920  C   GLY B 103     -13.977   7.468 -11.253  1.00  0.00           C  
ATOM    921  O   GLY B 103     -14.817   7.213 -12.116  1.00  0.00           O  
ATOM    922  H   GLY B 103     -11.342   7.827 -11.132  1.00  0.00           H  
ATOM    923  HA2 GLY B 103     -13.483   9.303 -10.207  1.00  0.00           H  
ATOM    924  HA3 GLY B 103     -13.734   9.500 -11.952  1.00  0.00           H  
ATOM    925  N   MET B 104     -13.601   6.588 -10.332  1.00  0.00           N  
ATOM    926  CA  MET B 104     -14.127   5.222 -10.341  1.00  0.00           C  
ATOM    927  C   MET B 104     -15.232   5.094  -9.286  1.00  0.00           C  
ATOM    928  O   MET B 104     -16.396   4.872  -9.620  1.00  0.00           O  
ATOM    929  CB  MET B 104     -12.929   4.298 -10.093  1.00  0.00           C  
ATOM    930  CG  MET B 104     -13.316   2.824 -10.092  1.00  0.00           C  
ATOM    931  SD  MET B 104     -14.028   2.373 -11.684  1.00  0.00           S  
ATOM    932  CE  MET B 104     -14.384   0.636 -11.368  1.00  0.00           C  
ATOM    933  H   MET B 104     -12.859   6.880  -9.688  1.00  0.00           H  
ATOM    934  HA  MET B 104     -14.557   4.991 -11.333  1.00  0.00           H  
ATOM    935  HB2 MET B 104     -12.161   4.469 -10.870  1.00  0.00           H  
ATOM    936  HB3 MET B 104     -12.447   4.551  -9.131  1.00  0.00           H  
ATOM    937  HG2 MET B 104     -12.421   2.209  -9.894  1.00  0.00           H  
ATOM    938  HG3 MET B 104     -14.041   2.627  -9.283  1.00  0.00           H  
ATOM    939  HE1 MET B 104     -15.076   0.527 -10.513  1.00  0.00           H  
ATOM    940  HE2 MET B 104     -14.852   0.168 -12.252  1.00  0.00           H  
ATOM    941  HE3 MET B 104     -13.456   0.082 -11.135  1.00  0.00           H

when I try with this script:
Code:
#!/bin/bash

awk  '$6= $6 - 34'  > pba10.

I get this

Code:
ATOM 918 N GLY B 69 -11.855 8.675 -11.404 1.00 0.00 N
ATOM 919 CA GLY B 69 -13.297 8.831 -11.189 1.00 0.00 C
ATOM 920 C GLY B 69 -13.977 7.468 -11.253 1.00 0.00 C
ATOM 921 O GLY B 69 -14.817 7.213 -12.116 1.00 0.00 O
ATOM 922 H GLY B 69 -11.342 7.827 -11.132 1.00 0.00 H
ATOM 923 HA2 GLY B 69 -13.483 9.303 -10.207 1.00 0.00 H
ATOM 924 HA3 GLY B 69 -13.734 9.500 -11.952 1.00 0.00 H
ATOM 925 N MET B 70 -13.601 6.588 -10.332 1.00 0.00 N
ATOM 926 CA MET B 70 -14.127 5.222 -10.341 1.00 0.00 C
ATOM 927 C MET B 70 -15.232 5.094 -9.286 1.00 0.00 C
ATOM 928 O MET B 70 -16.396 4.872 -9.620 1.00 0.00 O
ATOM 929 CB MET B 70 -12.929 4.298 -10.093 1.00 0.00 C
ATOM 930 CG MET B 70 -13.316 2.824 -10.092 1.00 0.00 C
ATOM 931 SD MET B 70 -14.028 2.373 -11.684 1.00 0.00 S
ATOM 932 CE MET B 70 -14.384 0.636 -11.368 1.00 0.00 C
ATOM 933 H MET B 70 -12.859 6.880 -9.688 1.00 0.00 H
ATOM 934 HA MET B 70 -14.557 4.991 -11.333 1.00 0.00 H
ATOM 935 HB2 MET B 70 -12.161 4.469 -10.870 1.00 0.00 H
ATOM 936 HB3 MET B 70 -12.447 4.551 -9.131 1.00 0.00 H
ATOM 937 HG2 MET B 70 -12.421 2.209 -9.894 1.00 0.00 H
ATOM 938 HG3 MET B 70 -14.041 2.627 -9.283 1.00 0.00 H
ATOM 939 HE1 MET B 70 -15.076 0.527 -10.513 1.00 0.00 H
ATOM 940 HE2 MET B 70 -14.852 0.168 -12.252 1.00 0.00 H
ATOM 941 HE3 MET B 70 -13.456 0.082 -11.135 1.00 0.00 H

and thist pdb file can not read by VMD, i have tried replacing the spaces with a "\t" but the result is not good
# 2  
Old 05-26-2010
Looks like you're working with a fixed-width format on the input file, but not accounting for it on the way out. The awk util will assume you FS=' ' but won't necessarily count them on the output...whitespace is counted as one, hence the output shifting on you.

Are you familiar with the control file or file layout for the .pdb file? You can process things according to substr() or even printf() with much more better results...
# 3  
Old 05-26-2010
thanks for your help, another suggestion?
# 4  
Old 05-26-2010
Does this work?:
Code:
$ awk '{X = $6 - 34; sub($6, X)}1' file

# 5  
Old 05-26-2010
I'm guessing at field defs here, but something like-a-dis:
Code:
$ awk '{printf "%-4s%7d  %-4s%-4s%-2s%3.d\n",$1,$2,$3,$4,$5,($6-34)}' Edit8
ATOM    918  N   GLY B  69
ATOM    919  CA  GLY B  69
ATOM    920  C   GLY B  69
ATOM    921  O   GLY B  69
ATOM    922  H   GLY B  69
ATOM    923  HA2 GLY B  69
ATOM    924  HA3 GLY B  69
ATOM    925  N   MET B  70
ATOM    926  CA  MET B  70
ATOM    927  C   MET B  70
ATOM    928  O   MET B  70
ATOM    929  CB  MET B  70
ATOM    930  CG  MET B  70
ATOM    931  SD  MET B  70
ATOM    932  CE  MET B  70
ATOM    933  H   MET B  70
ATOM    934  HA  MET B  70
ATOM    935  HB2 MET B  70
ATOM    936  HB3 MET B  70
ATOM    937  HG2 MET B  70
ATOM    938  HG3 MET B  70
ATOM    939  HE1 MET B  70
ATOM    940  HE2 MET B  70
ATOM    941  HE3 MET B  70

or, if you prefer concise and/or succinct...scottn posted something short and sweet. Only seems to shift $6 just a tad left...
Code:
$ awk '{X = $6 - 34; sub($6, X)}1' Edit8
ATOM    918  N   GLY B 69     -11.855   8.675 -11.404  1.00  0.00           N
ATOM    919  CA  GLY B 69     -13.297   8.831 -11.189  1.00  0.00           C
ATOM    920  C   GLY B 69     -13.977   7.468 -11.253  1.00  0.00           C
ATOM    921  O   GLY B 69     -14.817   7.213 -12.116  1.00  0.00           O
ATOM    922  H   GLY B 69     -11.342   7.827 -11.132  1.00  0.00           H
ATOM    923  HA2 GLY B 69     -13.483   9.303 -10.207  1.00  0.00           H
ATOM    924  HA3 GLY B 69     -13.734   9.500 -11.952  1.00  0.00           H
ATOM    925  N   MET B 70     -13.601   6.588 -10.332  1.00  0.00           N
ATOM    926  CA  MET B 70     -14.127   5.222 -10.341  1.00  0.00           C
ATOM    927  C   MET B 70     -15.232   5.094  -9.286  1.00  0.00           C
ATOM    928  O   MET B 70     -16.396   4.872  -9.620  1.00  0.00           O
ATOM    929  CB  MET B 70     -12.929   4.298 -10.093  1.00  0.00           C
ATOM    930  CG  MET B 70     -13.316   2.824 -10.092  1.00  0.00           C
ATOM    931  SD  MET B 70     -14.028   2.373 -11.684  1.00  0.00           S
ATOM    932  CE  MET B 70     -14.384   0.636 -11.368  1.00  0.00           C
ATOM    933  H   MET B 70     -12.859   6.880  -9.688  1.00  0.00           H
ATOM    934  HA  MET B 70     -14.557   4.991 -11.333  1.00  0.00           H
ATOM    935  HB2 MET B 70     -12.161   4.469 -10.870  1.00  0.00           H
ATOM    936  HB3 MET B 70     -12.447   4.551  -9.131  1.00  0.00           H
ATOM    937  HG2 MET B 70     -12.421   2.209  -9.894  1.00  0.00           H
ATOM    938  HG3 MET B 70     -14.041   2.627  -9.283  1.00  0.00           H
ATOM    939  HE1 MET B 70     -15.076   0.527 -10.513  1.00  0.00           H
ATOM    940  HE2 MET B 70     -14.852   0.168 -12.252  1.00  0.00           H
ATOM    941  HE3 MET B 70     -13.456   0.082 -11.135  1.00  0.00           H

# 6  
Old 05-26-2010
Quote:
Originally Posted by curleb
I'm guessing at field defs here, but something like-a-dis:
Code:
$ awk '{printf "%-4s%7d  %-4s%-4s%-2s%3.d\n",$1,$2,$3,$4,$5,($6-34)}' Edit8
ATOM    918  N   GLY B  69
ATOM    919  CA  GLY B  69
ATOM    920  C   GLY B  69
ATOM    921  O   GLY B  69
ATOM    922  H   GLY B  69
ATOM    923  HA2 GLY B  69
ATOM    924  HA3 GLY B  69
ATOM    925  N   MET B  70
ATOM    926  CA  MET B  70
ATOM    927  C   MET B  70
ATOM    928  O   MET B  70
ATOM    929  CB  MET B  70
ATOM    930  CG  MET B  70
ATOM    931  SD  MET B  70
ATOM    932  CE  MET B  70
ATOM    933  H   MET B  70
ATOM    934  HA  MET B  70
ATOM    935  HB2 MET B  70
ATOM    936  HB3 MET B  70
ATOM    937  HG2 MET B  70
ATOM    938  HG3 MET B  70
ATOM    939  HE1 MET B  70
ATOM    940  HE2 MET B  70
ATOM    941  HE3 MET B  70

or, if you prefer concise and/or succinct...scottn posted something short and sweet. Only seems to shift $6 just a tad left...
Code:
$ awk '{X = $6 - 34; sub($6, X)}1' Edit8
ATOM    918  N   GLY B 69     -11.855   8.675 -11.404  1.00  0.00           N
ATOM    919  CA  GLY B 69     -13.297   8.831 -11.189  1.00  0.00           C
ATOM    920  C   GLY B 69     -13.977   7.468 -11.253  1.00  0.00           C
ATOM    921  O   GLY B 69     -14.817   7.213 -12.116  1.00  0.00           O
ATOM    922  H   GLY B 69     -11.342   7.827 -11.132  1.00  0.00           H
ATOM    923  HA2 GLY B 69     -13.483   9.303 -10.207  1.00  0.00           H
ATOM    924  HA3 GLY B 69     -13.734   9.500 -11.952  1.00  0.00           H
ATOM    925  N   MET B 70     -13.601   6.588 -10.332  1.00  0.00           N
ATOM    926  CA  MET B 70     -14.127   5.222 -10.341  1.00  0.00           C
ATOM    927  C   MET B 70     -15.232   5.094  -9.286  1.00  0.00           C
ATOM    928  O   MET B 70     -16.396   4.872  -9.620  1.00  0.00           O
ATOM    929  CB  MET B 70     -12.929   4.298 -10.093  1.00  0.00           C
ATOM    930  CG  MET B 70     -13.316   2.824 -10.092  1.00  0.00           C
ATOM    931  SD  MET B 70     -14.028   2.373 -11.684  1.00  0.00           S
ATOM    932  CE  MET B 70     -14.384   0.636 -11.368  1.00  0.00           C
ATOM    933  H   MET B 70     -12.859   6.880  -9.688  1.00  0.00           H
ATOM    934  HA  MET B 70     -14.557   4.991 -11.333  1.00  0.00           H
ATOM    935  HB2 MET B 70     -12.161   4.469 -10.870  1.00  0.00           H
ATOM    936  HB3 MET B 70     -12.447   4.551  -9.131  1.00  0.00           H
ATOM    937  HG2 MET B 70     -12.421   2.209  -9.894  1.00  0.00           H
ATOM    938  HG3 MET B 70     -14.041   2.627  -9.283  1.00  0.00           H
ATOM    939  HE1 MET B 70     -15.076   0.527 -10.513  1.00  0.00           H
ATOM    940  HE2 MET B 70     -14.852   0.168 -12.252  1.00  0.00           H
ATOM    941  HE3 MET B 70     -13.456   0.082 -11.135  1.00  0.00           H

Ah.. good point Smilie
# 7  
Old 05-26-2010
Code:
$ cat data.pdb
ATOM    918  N   GLY B 103     -11.855   8.675 -11.404  1.00  0.00           N  
ATOM    919  CA  GLY B 103     -13.297   8.831 -11.189  1.00  0.00           C  
ATOM    920  C   GLY B 103     -13.977   7.468 -11.253  1.00  0.00           C  
ATOM    921  O   GLY B 103     -14.817   7.213 -12.116  1.00  0.00           O  
ATOM    922  H   GLY B 103     -11.342   7.827 -11.132  1.00  0.00           H  
ATOM    923  HA2 GLY B 103     -13.483   9.303 -10.207  1.00  0.00           H  
ATOM    924  HA3 GLY B 103     -13.734   9.500 -11.952  1.00  0.00           H  
ATOM    925  N   MET B 104     -13.601   6.588 -10.332  1.00  0.00           N  
ATOM    926  CA  MET B 104     -14.127   5.222 -10.341  1.00  0.00           C  
ATOM    927  C   MET B 104     -15.232   5.094  -9.286  1.00  0.00           C  
ATOM    928  O   MET B 104     -16.396   4.872  -9.620  1.00  0.00           O  
ATOM    929  CB  MET B 104     -12.929   4.298 -10.093  1.00  0.00           C  
ATOM    930  CG  MET B 104     -13.316   2.824 -10.092  1.00  0.00           C  
ATOM    931  SD  MET B 104     -14.028   2.373 -11.684  1.00  0.00           S  
ATOM    932  CE  MET B 104     -14.384   0.636 -11.368  1.00  0.00           C  
ATOM    933  H   MET B 104     -12.859   6.880  -9.688  1.00  0.00           H  
ATOM    934  HA  MET B 104     -14.557   4.991 -11.333  1.00  0.00           H  
ATOM    935  HB2 MET B 104     -12.161   4.469 -10.870  1.00  0.00           H  
ATOM    936  HB3 MET B 104     -12.447   4.551  -9.131  1.00  0.00           H  
ATOM    937  HG2 MET B 104     -12.421   2.209  -9.894  1.00  0.00           H  
ATOM    938  HG3 MET B 104     -14.041   2.627  -9.283  1.00  0.00           H  
ATOM    939  HE1 MET B 104     -15.076   0.527 -10.513  1.00  0.00           H  
ATOM    940  HE2 MET B 104     -14.852   0.168 -12.252  1.00  0.00           H  
ATOM    941  HE3 MET B 104     -13.456   0.082 -11.135  1.00  0.00           H
$ ./modpdb.pl
ATOM    918  N   GLY B 69      -11.855   8.675 -11.404  1.00  0.00           N
ATOM    919  CA  GLY B 69      -13.297   8.831 -11.189  1.00  0.00           C
ATOM    920  C   GLY B 69      -13.977   7.468 -11.253  1.00  0.00           C
ATOM    921  O   GLY B 69      -14.817   7.213 -12.116  1.00  0.00           O
ATOM    922  H   GLY B 69      -11.342   7.827 -11.132  1.00  0.00           H
ATOM    923  HA2 GLY B 69      -13.483   9.303 -10.207  1.00  0.00           H
ATOM    924  HA3 GLY B 69      -13.734   9.500 -11.952  1.00  0.00           H
ATOM    925  N   MET B 70      -13.601   6.588 -10.332  1.00  0.00           N
ATOM    926  CA  MET B 70      -14.127   5.222 -10.341  1.00  0.00           C
ATOM    927  C   MET B 70      -15.232   5.094  -9.286  1.00  0.00           C
ATOM    928  O   MET B 70      -16.396   4.872  -9.620  1.00  0.00           O
ATOM    929  CB  MET B 70      -12.929   4.298 -10.093  1.00  0.00           C
ATOM    930  CG  MET B 70      -13.316   2.824 -10.092  1.00  0.00           C
ATOM    931  SD  MET B 70      -14.028   2.373 -11.684  1.00  0.00           S
ATOM    932  CE  MET B 70      -14.384   0.636 -11.368  1.00  0.00           C
ATOM    933  H   MET B 70      -12.859   6.880  -9.688  1.00  0.00           H
ATOM    934  HA  MET B 70      -14.557   4.991 -11.333  1.00  0.00           H
ATOM    935  HB2 MET B 70      -12.161   4.469 -10.870  1.00  0.00           H
ATOM    936  HB3 MET B 70      -12.447   4.551  -9.131  1.00  0.00           H
ATOM    937  HG2 MET B 70      -12.421   2.209  -9.894  1.00  0.00           H
ATOM    938  HG3 MET B 70      -14.041   2.627  -9.283  1.00  0.00           H
ATOM    939  HE1 MET B 70      -15.076   0.527 -10.513  1.00  0.00           H
ATOM    940  HE2 MET B 70      -14.852   0.168 -12.252  1.00  0.00           H
ATOM    941  HE3 MET B 70      -13.456   0.082 -11.135  1.00  0.00           H
$

Code:
#!/usr/bin/perl

use strict;
use warnings;

my @array;
my $infile='data.pdb';

open(IN,$infile) or die "Error opening input file $infile: $!\n";
while (<IN>) {
chomp;
$_ =~ s/\s+/ /g;
push @array, "$_\n";
}
close(IN);

foreach (@array) {
chomp;
my @arr=split(/ /);
$arr[5]=$arr[5]-34;
printf("%-7s %-4s %-3s %-3s %-1s %-7s %7s %7s %7s %5s %5s %11s\n", @arr);
}

You could simply redirect the output to a new file, instead of having it printed on the terminal:
Code:
$ ./modpdb.pl > newdata.pdb

Last edited by pseudocoder; 05-26-2010 at 07:47 PM.. Reason: optimized code, got rid of a half ton of $arr[0] $arr[1] ,....
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10. Shell Programming and Scripting

Changing particular field in fixed width file

I have a fixed width file and i need to change 36th field to "G" in for about random 20 records? How can I do it? (4 Replies)
Discussion started by: dsravan
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