File1 is an hard formatted pdb file containing protein coordinates:
ATOM 1 N MET A 1 -37.809 27.446 34.618 1.00 43.34 N
ATOM 2 CA MET A 1 -37.480 26.307 33.746 1.00 43.34 C
ATOM 3 C MET A 1 -36.495 25.493 34.556 1.00 43.34 C
ATOM 4 CB MET A 1 -36.919 26.801 32.394 1.00 43.34 C
ATOM 5 O MET A 1 -35.346 25.898 34.661 1.00 43.34 O
ATOM 6 CG MET A 1 -36.980 25.729 31.301 1.00 43.34 C
ATOM 7 SD MET A 1 -35.977 26.080 29.826 1.00 43.34 S
ATOM 8 CE MET A 1 -36.833 27.479 29.055 1.00 43.34 C
ATOM 9 N GLU A 2 -36.991 24.516 35.314 1.00 37.48 N
ATOM 10 CA GLU A 2 -36.090 23.617 36.039 1.00 37.48 C
ATOM 11 C GLU A 2 -35.250 22.852 35.010 1.00 37.48 C
ATOM 12 CB GLU A 2 -36.860 22.659 36.957 1.00 37.48 C
ATOM 13 O GLU A 2 -35.776 22.534 33.938 1.00 37.48 O
ATOM 14 CG GLU A 2 -37.467 23.407 38.153 1.00 37.48 C
..............................................................................
..............................................................................
..............................................................................
ATOM 981 N CYS A 123 -15.659 -7.164 13.998 1.00 90.53 N
ATOM 982 CA CYS A 123 -16.801 -7.332 13.106 1.00 90.53 C
ATOM 983 C CYS A 123 -17.894 -8.234 13.699 1.00 90.53 C
ATOM 984 CB CYS A 123 -16.321 -7.886 11.757 1.00 90.53 C
ATOM 985 O CYS A 123 -18.918 -8.425 13.046 1.00 90.53 O
ATOM 986 SG CYS A 123 -15.266 -6.683 10.904 1.00 90.53 S
ATOM 987 N GLY A 124 -17.679 -8.840 14.874 1.00 90.37 N
ATOM 988 CA GLY A 124 -18.641 -9.764 15.474 1.00 90.37 C
ATOM 989 C GLY A 124 -18.851 -11.029 14.637 1.00 90.37 C
ATOM 990 O GLY A 124 -19.970 -11.514 14.513 1.00 90.37 O
ATOM 991 N SER A 125 -17.793 -11.536 13.996 1.00 92.09 N
ATOM 992 CA SER A 125 -17.837 -12.749 13.159 1.00 92.09 C
ATOM 993 C SER A 125 -17.220 -13.976 13.833 1.00 92.09 C
ATOM 994 CB SER A 125 -17.117 -12.481 11.840 1.00 92.09 C
ATOM 995 O SER A 125 -17.538 -15.108 13.459 1.00 92.09 O
ATOM 996 OG SER A 125 -17.831 -11.523 11.084 1.00 92.09 O
....................... plus many more lines .................................
File2 is a list of representative lines obtained from fields 3,4, and 5 of the above
pdb file. To keep all simple, let's consider just to lines:
GLU A 2
GLY A 124
The desired output is:
ATOM 1 N MET A 1 -37.809 27.446 34.618 1.00 43.34 N
ATOM 2 CA MET A 1 -37.480 26.307 33.746 1.00 43.34 C
ATOM 3 C MET A 1 -36.495 25.493 34.556 1.00 43.34 C
ATOM 4 CB MET A 1 -36.919 26.801 32.394 1.00 43.34 C
ATOM 5 O MET A 1 -35.346 25.898 34.661 1.00 43.34 O
ATOM 6 CG MET A 1 -36.980 25.729 31.301 1.00 43.34 C
ATOM 7 SD MET A 1 -35.977 26.080 29.826 1.00 43.34 S
ATOM 8 CE MET A 1 -36.833 27.479 29.055 1.00 43.34 C
ATOM 9 N GLU A 2 -36.991 24.516 35.314 1.00 00.00 N
ATOM 10 CA GLU A 2 -36.090 23.617 36.039 1.00 00.00 C
ATOM 11 C GLU A 2 -35.250 22.852 35.010 1.00 00.00 C
ATOM 12 CB GLU A 2 -36.860 22.659 36.957 1.00 00.00 C
ATOM 13 O GLU A 2 -35.776 22.534 33.938 1.00 00.00 O
ATOM 14 CG GLU A 2 -37.467 23.407 38.153 1.00 00.00 C
..............................................................................
..............................................................................
..............................................................................
ATOM 981 N CYS A 123 -15.659 -7.164 13.998 1.00 90.53 N
ATOM 982 CA CYS A 123 -16.801 -7.332 13.106 1.00 90.53 C
ATOM 983 C CYS A 123 -17.894 -8.234 13.699 1.00 90.53 C
ATOM 984 CB CYS A 123 -16.321 -7.886 11.757 1.00 90.53 C
ATOM 985 O CYS A 123 -18.918 -8.425 13.046 1.00 90.53 O
ATOM 986 SG CYS A 123 -15.266 -6.683 10.904 1.00 90.53 S
ATOM 987 N GLY A 124 -17.679 -8.840 14.874 1.00 00.00 N
ATOM 988 CA GLY A 124 -18.641 -9.764 15.474 1.00 00.00 C
ATOM 989 C GLY A 124 -18.851 -11.029 14.637 1.00 00.00 C
ATOM 990 O GLY A 124 -19.970 -11.514 14.513 1.00 00.00 O
ATOM 991 N SER A 125 -17.793 -11.536 13.996 1.00 92.09 N
ATOM 992 CA SER A 125 -17.837 -12.749 13.159 1.00 92.09 C
ATOM 993 C SER A 125 -17.220 -13.976 13.833 1.00 92.09 C
ATOM 994 CB SER A 125 -17.117 -12.481 11.840 1.00 92.09 C
ATOM 995 O SER A 125 -17.538 -15.108 13.459 1.00 92.09 O
ATOM 996 OG SER A 125 -17.831 -11.523 11.084 1.00 92.09 O
i.e. a modified pdb with 00.00 in the 11th field if a File1's line contain a
File2 occurrence.
I already know how to do that with Bash while-read and awk but because these tools
change the format and require reformatting and/or specify the output format, in this
particular case dealing with hundreds of files they are not practical.
In order to avoid these problems I decided to look for a solution based on sed.
I got a working solution if I explicitly give a single search pattern. i.e. the
following code works:
digits=00.00
sed "/GLU A 2/s/\(.\{61\}\)\(.\{5\}\)/\1$digits/" File1.pdb > out.pdb
but the following does not (the File1 lines are unchanged) and I did not manage
to figure out why:
digits=00.00
while read pattern; do
sed "/$pattern/s/\(.\{61\}\)\(.\{5\}\)/\1$digits/" File1.pdb > out.pdb ;
done < File2.txt
Sorry for the lengthy message. Thanks in advance for any help.
#anubhava:
using my real data this is what happen at the first substitution site:
ATOM 293 CE1 HIS A 38 -18.278 19.735 13.486 1.00 67.94 C
ATOM 294 NE2 HIS A 38 -18.518 18.594 14.144 1.00 67.94 N
ATOM 295 N GLY A 39 -13.836 00.00 9.206 1.00 71.50 N
ATOM 296 CA GLY A 39 -12.628 00.00 8.447 1.00 71.50 C
ATOM 297 C GLY A 39 -11.358 00.00 9.286 1.00 71.50 C
ATOM 298 O GLY A 39 -11.411 18.636 10.344 1.00 00.00 O
ATOM 299 N PRO A 40 -10.180 17.577 8.797 1.00 71.93 N
ATOM 300 CA PRO A 40 -8.908 17.719 9.520 1.00 71.93 C
ATOM 301 C PRO A 40 -8.580 19.169 9.912 1.00 71.93 C
In this case the site is /GLY A 39/. As you can see there is a shift in some lines and unwanted substitutions in the 8th field.
Strange enough such problems occur only for the first replacement i.e. the remaning output is just perfect. Thanks.
Using sed in a while loop which reads file 2 line by line, you can target only lines matches those found in file2 and carry out the sub on those lines where;
s/\(.*\)[0-9]\{2\}\.[0-9]\{2\}\([[:space:]]\+.*$\)/ - Group everything up to the last digits that matches the pattern and retain to be returned with back reference \1. Exclude the number matched in the pattern and once again group everything else after from the space to the end of the line and return with back-reference \2
$ cat file1
ATOM 1 N MET A 1 -37.809 27.446 34.618 1.00 43.34 N
ATOM 2 CA MET A 1 -37.480 26.307 33.746 1.00 43.34 C
ATOM 3 C MET A 1 -36.495 25.493 34.556 1.00 43.34 C
ATOM 4 CB MET A 1 -36.919 26.801 32.394 1.00 43.34 C
ATOM 5 O MET A 1 -35.346 25.898 34.661 1.00 43.34 O
ATOM 6 CG MET A 1 -36.980 25.729 31.301 1.00 43.34 C
ATOM 7 SD MET A 1 -35.977 26.080 29.826 1.00 43.34 S
ATOM 8 CE MET A 1 -36.833 27.479 29.055 1.00 43.34 C
ATOM 9 N GLU A 2 -36.991 24.516 35.314 1.00 37.48 N
ATOM 10 CA GLU A 2 -36.090 23.617 36.039 1.00 37.48 C
ATOM 11 C GLU A 2 -35.250 22.852 35.010 1.00 37.48 C
ATOM 12 CB GLU A 2 -36.860 22.659 36.957 1.00 37.48 C
ATOM 13 O GLU A 2 -35.776 22.534 33.938 1.00 37.48 O
ATOM 14 CG GLU A 2 -37.467 23.407 38.153 1.00 37.48 C
ATOM 981 N CYS A 123 -15.659 -7.164 13.998 1.00 90.53 N
ATOM 982 CA CYS A 123 -16.801 -7.332 13.106 1.00 90.53 C
ATOM 983 C CYS A 123 -17.894 -8.234 13.699 1.00 90.53 C
ATOM 984 CB CYS A 123 -16.321 -7.886 11.757 1.00 90.53 C
ATOM 985 O CYS A 123 -18.918 -8.425 13.046 1.00 90.53 O
ATOM 986 SG CYS A 123 -15.266 -6.683 10.904 1.00 90.53 S
ATOM 987 N GLY A 124 -17.679 -8.840 14.874 1.00 90.37 N
ATOM 988 CA GLY A 124 -18.641 -9.764 15.474 1.00 90.37 C
ATOM 989 C GLY A 124 -18.851 -11.029 14.637 1.00 90.37 C
ATOM 990 O GLY A 124 -19.970 -11.514 14.513 1.00 90.37 O
ATOM 991 N SER A 125 -17.793 -11.536 13.996 1.00 92.09 N
ATOM 992 CA SER A 125 -17.837 -12.749 13.159 1.00 92.09 C
ATOM 993 C SER A 125 -17.220 -13.976 13.833 1.00 92.09 C
ATOM 994 CB SER A 125 -17.117 -12.481 11.840 1.00 92.09 C
ATOM 995 O SER A 125 -17.538 -15.108 13.459 1.00 92.09 O
ATOM 996 OG SER A 125 -17.831 -11.523 11.084 1.00 92.09 O
$ while read -r line; do sed -i.bak "/$line/s/\(.*\)[0-9]\{2\}\.[0-9]\{2\}\([[:space:]]\+.*$\)/\100.00\2/" file1; done < file2
$ cat file1
ATOM 1 N MET A 1 -37.809 27.446 34.618 1.00 43.34 N
ATOM 2 CA MET A 1 -37.480 26.307 33.746 1.00 43.34 C
ATOM 3 C MET A 1 -36.495 25.493 34.556 1.00 43.34 C
ATOM 4 CB MET A 1 -36.919 26.801 32.394 1.00 43.34 C
ATOM 5 O MET A 1 -35.346 25.898 34.661 1.00 43.34 O
ATOM 6 CG MET A 1 -36.980 25.729 31.301 1.00 43.34 C
ATOM 7 SD MET A 1 -35.977 26.080 29.826 1.00 43.34 S
ATOM 8 CE MET A 1 -36.833 27.479 29.055 1.00 43.34 C
ATOM 9 N GLU A 2 -36.991 24.516 35.314 1.00 00.00 N
ATOM 10 CA GLU A 2 -36.090 23.617 36.039 1.00 00.00 C
ATOM 11 C GLU A 2 -35.250 22.852 35.010 1.00 00.00 C
ATOM 12 CB GLU A 2 -36.860 22.659 36.957 1.00 00.00 C
ATOM 13 O GLU A 2 -35.776 22.534 33.938 1.00 00.00 O
ATOM 14 CG GLU A 2 -37.467 23.407 38.153 1.00 00.00 C
ATOM 981 N CYS A 123 -15.659 -7.164 13.998 1.00 90.53 N
ATOM 982 CA CYS A 123 -16.801 -7.332 13.106 1.00 90.53 C
ATOM 983 C CYS A 123 -17.894 -8.234 13.699 1.00 90.53 C
ATOM 984 CB CYS A 123 -16.321 -7.886 11.757 1.00 90.53 C
ATOM 985 O CYS A 123 -18.918 -8.425 13.046 1.00 90.53 O
ATOM 986 SG CYS A 123 -15.266 -6.683 10.904 1.00 90.53 S
ATOM 987 N GLY A 124 -17.679 -8.840 14.874 1.00 00.00 N
ATOM 988 CA GLY A 124 -18.641 -9.764 15.474 1.00 00.00 C
ATOM 989 C GLY A 124 -18.851 -11.029 14.637 1.00 00.00 C
ATOM 990 O GLY A 124 -19.970 -11.514 14.513 1.00 00.00 O
ATOM 991 N SER A 125 -17.793 -11.536 13.996 1.00 92.09 N
ATOM 992 CA SER A 125 -17.837 -12.749 13.159 1.00 92.09 C
ATOM 993 C SER A 125 -17.220 -13.976 13.833 1.00 92.09 C
ATOM 994 CB SER A 125 -17.117 -12.481 11.840 1.00 92.09 C
ATOM 995 O SER A 125 -17.538 -15.108 13.459 1.00 92.09 O
ATOM 996 OG SER A 125 -17.831 -11.523 11.084 1.00 92.09 O
awk suites this role better:
awk 'FNR==NR {a[$1,$2,$3]; next} ($4,$5,$6) in a {$11="00.00"} 1' file2 file1 | column -t
ATOM 1 N MET A 1 -37.809 27.446 34.618 1.00 43.34 N
ATOM 2 CA MET A 1 -37.480 26.307 33.746 1.00 43.34 C
ATOM 3 C MET A 1 -36.495 25.493 34.556 1.00 43.34 C
ATOM 4 CB MET A 1 -36.919 26.801 32.394 1.00 43.34 C
ATOM 5 O MET A 1 -35.346 25.898 34.661 1.00 43.34 O
ATOM 6 CG MET A 1 -36.980 25.729 31.301 1.00 43.34 C
ATOM 7 SD MET A 1 -35.977 26.080 29.826 1.00 43.34 S
ATOM 8 CE MET A 1 -36.833 27.479 29.055 1.00 43.34 C
ATOM 9 N GLU A 2 -36.991 24.516 35.314 1.00 00.00 N
ATOM 10 CA GLU A 2 -36.090 23.617 36.039 1.00 00.00 C
ATOM 11 C GLU A 2 -35.250 22.852 35.010 1.00 00.00 C
ATOM 12 CB GLU A 2 -36.860 22.659 36.957 1.00 00.00 C
ATOM 13 O GLU A 2 -35.776 22.534 33.938 1.00 00.00 O
ATOM 14 CG GLU A 2 -37.467 23.407 38.153 1.00 00.00 C
ATOM 981 N CYS A 123 -15.659 -7.164 13.998 1.00 90.53 N
ATOM 982 CA CYS A 123 -16.801 -7.332 13.106 1.00 90.53 C
ATOM 983 C CYS A 123 -17.894 -8.234 13.699 1.00 90.53 C
ATOM 984 CB CYS A 123 -16.321 -7.886 11.757 1.00 90.53 C
ATOM 985 O CYS A 123 -18.918 -8.425 13.046 1.00 90.53 O
ATOM 986 SG CYS A 123 -15.266 -6.683 10.904 1.00 90.53 S
ATOM 987 N GLY A 124 -17.679 -8.840 14.874 1.00 00.00 N
ATOM 988 CA GLY A 124 -18.641 -9.764 15.474 1.00 00.00 C
ATOM 989 C GLY A 124 -18.851 -11.029 14.637 1.00 00.00 C
ATOM 990 O GLY A 124 -19.970 -11.514 14.513 1.00 00.00 O
ATOM 991 N SER A 125 -17.793 -11.536 13.996 1.00 92.09 N
ATOM 992 CA SER A 125 -17.837 -12.749 13.159 1.00 92.09 C
ATOM 993 C SER A 125 -17.220 -13.976 13.833 1.00 92.09 C
ATOM 994 CB SER A 125 -17.117 -12.481 11.840 1.00 92.09 C
ATOM 995 O SER A 125 -17.538 -15.108 13.459 1.00 92.09 O
ATOM 996 OG SER A 125 -17.831 -11.523 11.084 1.00 92.09 O
Used column -t for tabular output display only.
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I currently have a text file that starts like this,
ATOM 277 N DOPC 3 2.637 5.546 17.667 1.00 0.00 MEMB
ATOM 278 C12 DOPC 3 2.869 5.398 19.176 1.00 0.00 MEMB
ATOM 279 H12A DOPC 3 3.729 6.005 19.418 1.00 0.00 MEMB
ATOM 280 H12B DOPC 3 3.176 4.394 19.427 1.00 0.00 MEMB
ATOM 281 C13 DOPC 3 1.352 4.873 17.275 1.00 0.00 MEMB
ATOM 282 H13A DOPC 3 1.380 5.091 16.217 1.00 0.00 MEMB
ATOM 283 H13B DOPC 3 1.415 3.810 17.452 1.00 0.00 MEMB
ATOM 284 H13C DOPC 3 0.491 5.261 17.799 1.00 0.00 MEMB
ATOM 285 C14 DOPC 3 3.791 4.845 16.976 1.00 0.00 MEMB
ATOM 286 H14A DOPC 3 4.692 4.989 17.554 1.00 0.00 MEMB
ATOM 287 H14B DOPC 3 3.563 3.790 17.025 1.00 0.00 MEMB
ATOM 288 H14C DOPC 3 3.875 5.097 15.930 1.00 0.00 MEMB
ATOM 289 C15 DOPC 3 2.627 6.991 17.324 1.00 0.00 MEMB
ATOM 290 H15A DOPC 3 1.812 7.530 17.785 1.00 0.00 MEMB
.
.
I'm wondering if there is any way using sed or awk to reorder the lines so that the ordering goes from [1,2,3...14...] to [1,2,5,9,13,3,4,6,7,8,10,11,12,14...] just by simply using their unique line number?
Here is the desired output,
ATOM 277 N DOPC 3 2.637 5.546 17.667 1.00 0.00 MEMB
ATOM 278 C12 DOPC 3 2.869 5.398 19.176 1.00 0.00 MEMB
ATOM 281 C13 DOPC 3 1.352 4.873 17.275 1.00 0.00 MEMB
ATOM 285 C14 DOPC 3 3.791 4.845 16.976 1.00 0.00 MEMB
ATOM 289 C15 DOPC 3 2.627 6.991 17.324 1.00 0.00 MEMB
ATOM 279 H12A DOPC 3 3.729 6.005 19.418 1.00 0.00 MEMB
ATOM 280 H12B DOPC 3 3.176 4.394 19.427 1.00 0.00 MEMB
ATOM 284 H13C DOPC 3 0.491 5.261 17.799 1.00 0.00 MEMB
ATOM 286 H14A DOPC 3 4.692 4.989 17.554 1.00 0.00 MEMB
ATOM 287 H14B DOPC 3 3.563 3.790 17.025 1.00 0.00 MEMB
ATOM 288 H14C DOPC 3 3.875 5.097 15.930 1.00 0.00 MEMB
ATOM 290 H15A DOPC 3 1.812 7.530 17.785 1.00 0.00 MEMB
.
.
Thanks!
In awk:
$ awk -v order="1,2,5,9,13,3,4,6,7,8,10,11,12,13,14" '{
a[NR]=$0 # hash records to a with NR as index
}
END {
n=split(order,o,/,/) # split the given order to a mapping
for(i=1;i<=n;i++) { # iterate the map indexes
print a[o[i]] # output
# delete a[o[i]] # uncomment these
}
# for(i=1;i<=NR;i++) # to print any leftovers
# if(i in a) # that were not in the order list
# print a[i]
}' file
Use this Perl one-liner:
perl -ne 'push #a, $_; END { print $a[$_-1] for ( 1,2,5,9,13,3,4,6,7,8,10,11,12,13,14, 15..($#a+1) ); }' in_file > out_file
The Perl one-liner uses these command line flags:
-e : Tells Perl to look for code in-line, instead of in a file.
-n : Loop over the input one line at a time, assigning it to $_ by default.
push #a, $_; : Add to the array #a (which is empty initially) the current line as the next element.
$#a : The index of the last element of the array #a.
END { ... } : After all input lines have been read, execute the code inside the block. Here, print the lines in the specified order.
I am trying to print only predefined sequence (ATOM Name) but not getting expected output. I want to print input file as per following expected output. Chain ID may be A to H.
Code:
my $OutputDir = 'C:\test_result_file';
open my $dir, "Document1.txt" or die "Failed to open Document1.txt:$!";
chomp(my #files = <$dir>);
foreach my $file (#files) {
my $win_len = 4;
my #window = ();
my $prev_chain = "";
open my $input, $file or die "failed to open $file: $!\n";
open my $output, '>', "$OutputDir/$file" or die "failed to open $OutputDir/$file.pdb: $!\n";
while (<$input>) {
my ($atom_name, $chain) = (split)[2, 4];
next unless $atom_name =~ /\b(?:C4B|O4B|C1B|C2B|O4B|C1B|C2B|C3B|C1B|C2B|C3B|C4B|C2B|C3B|C4B|O4B|C3B|C4B|O4B|C1B)\b/;
if ($chain eq $prev_chain) {
if (#window == $win_len) {
print_window($output, #window);
shift #window;
}
push #window, $_;
} else {
print_window($output, #window) if #window;
#window = ($_);
$prev_chain = $chain;
}
}
print_window($output, #window) if #window;
}
sub print_window {
my $fh = shift;
print $fh $_ foreach #_;
print $fh "\n";
}
Input File:
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
Expected Output:
A chain:
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
B chain:
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
Description: I want to sort HETATM predefined ATOM name (e.g.: C4B, O4B, C1B, C2B etc.). I have above script so far. So please anyone help me to solve this problem. In my current script I am getting same format but not able to get expected result.
I don't want separate file for A chain and B chain or any chain id. I want to sort ATOM name as per my sequence (Predefined).
My sequence is:
C4B-O4B-C1B-C2B
O4B-C1B-C2B-C3B
C1B-C2B-C3B-C4B
C2B-C3B-C4B-O4B
C3B-C4B-O4B-C1B
e.g., first row: C4B
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
Second row: O4B
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
Third Row: C1B
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
Fourth Row: C2B
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
Fifth Row: O4B
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
Sixth Row: C1B
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
Seventh Row: C2B
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
Eighth Row: C3B
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
.
.
.
so on
same format for B and other chain also.
Its means I need each row multiple times. all off above atom name should be there in input file and chain wise. we need to copy all of above atom name file and then we need to paste as per above sequence.
It seems to me that your error comes from this line:
my ($atom_name, $chain) = (split)[2, 4];
This will put the 3rd column in $atom_name and the 5th one in $chain.
I guess you want:
my ($atom_name, $chain) = (split)[1, 3];
For the first line you'll get:
$atom_name = C4B and $chain = B
I have a folder that contains 200 pdb files.I would like to arrange the atom lines of PDB files in ascending order based on the 6th column. I would like to get in-place editing for each pdb file in the folder. your help would be appreciated.
ATOM 81 N ASN A 248 38.791 -16.708 12.507 1.00 52.04 N
ATOM 82 CA ASN A 248 39.443 -17.018 11.206 1.00 54.49 C
ATOM 422 C SER A 205 70.124 -29.955 8.226 1.00 55.81 C
ATOM 423 O SER A 205 70.901 -29.008 8.438 1.00 46.60 O
ATOM 303 N MET A 231 61.031 -38.086 -3.054 1.00 52.32 N
ATOM 304 CA MET A 231 60.580 -39.074 -4.047 1.00 64.11 C
ATOM 392 C GLU B 65 23.248 10.071 -7.321 1.00 48.26 C
ATOM 393 O GLU B 65 24.465 10.200 -7.158 1.00 46.53 O
ATOM 394 O GLU B 65 24.465 10.200 -7.158 1.00 46.53 O
Desired output
ATOM 392 C GLU B 65 23.248 10.071 -7.321 1.00 48.26 C
ATOM 393 O GLU B 65 24.465 10.200 -7.158 1.00 46.53 O
ATOM 394 O GLU B 65 24.465 10.200 -7.158 1.00 46.53 O
ATOM 422 C SER A 205 70.124 -29.955 8.226 1.00 55.81 C
ATOM 423 O SER A 205 70.901 -29.008 8.438 1.00 46.60 O
ATOM 303 N MET A 231 61.031 -38.086 -3.054 1.00 52.32 N
ATOM 304 CA MET A 231 60.580 -39.074 -4.047 1.00 64.11 C
ATOM 81 N ASN A 248 38.791 -16.708 12.507 1.00 52.04 N
ATOM 82 CA ASN A 248 39.443 -17.018 11.206 1.00 54.49 C
Use sort.
sort -n -k 6 inputfile
-n performs numeric sort, and -k tells to sort via a key.
EDIT: For in-place sorting, use the -o option:
sort -n -k 6 inputfile -o inputfile
I use a hash where its key will be the 6th field plus a counter that increments each line appended at the end. This avoids overwrite duplicated entries and keep stable order. Then use asorti() function to sort by that 6th field and print each line of the original array.
Content of script.awk:
{
++n
data[ $6 _ n ] = $0;
}
END {
asorti( data, mod_data, "#ind_num_asc" )
l = length( data )
for ( i = 1; i <= l; i++ ) {
print data[ mod_data[i] ]
}
}
Run it like:
awk -f script.awk infile
That yields:
ATOM 392 C GLU B 65 23.248 10.071 -7.321 1.00 48.26 C
ATOM 393 O GLU B 65 24.465 10.200 -7.158 1.00 46.53 O
ATOM 394 O GLU B 65 24.465 10.200 -7.158 1.00 46.53 O
ATOM 422 C SER A 205 70.124 -29.955 8.226 1.00 55.81 C
ATOM 423 O SER A 205 70.901 -29.008 8.438 1.00 46.60 O
ATOM 303 N MET A 231 61.031 -38.086 -3.054 1.00 52.32 N
ATOM 304 CA MET A 231 60.580 -39.074 -4.047 1.00 64.11 C
ATOM 81 N ASN A 248 38.791 -16.708 12.507 1.00 52.04 N
ATOM 82 CA ASN A 248 39.443 -17.018 11.206 1.00 54.49 C
I am stuck at 1 point in my project. I am a biomedical science. So, I don't know perl programming much.
I have a file that explains proteins interactions with ligands. The file looks as shown below:
H P L A 82 SER 1290 N --> O12 1668 GSH 106 A 2.90
H P L A 83 SER 1301 N --> O12 1668 GSH 106 A 2.93
N P L A 19 LYS 302 NZ --- O31 1682 GSH 106 A 3.86
N P L A 22 CYS 348 CB --- CB2 1677 GSH 106 A 3.75
N P L A 22 CYS 348 CB --- SG2 1678 GSH 106 A 3.02
N P L A 22 CYS 349 SG --- CB2 1677 GSH 106 A 3.03
N P L A 22 CYS 349 SG --- SG2 1678 GSH 106 A 2.02
N P L A 24 TYR 372 CB --- CG1 1670 GSH 106 A 3.68
Now you can see the are O12 in two rows. Similarly you can see that there are two CB2 as well. These O12 and CB2 are atom symbols. O12 means oxygen 12 in an atom. Now I need to calculate how many different atom symbols are there in file. I have to use perl script to do that. I am reading this file line by line using perl. while (my $line = <MYFILE>) { }; Now, I need to calculate how many different atom symbols are there while reading the file line by line. I hope I am clear enough to explain my problem. Waiting for a kind reply...
How the problem is best solved depends on how your data is delimited. As it looks like fixed width, I'll present that solution first:
use strict;
use warnings;
my %atom;
while (<DATA>) {
my (undef,$atom) = unpack "A34A4 ", $_;
$atom{$atom}++;
}
print scalar keys %atom;
__DATA__
H P L A 82 SER 1290 N --> O12 1668 GSH 106 A 2.90
H P L A 83 SER 1301 N --> O12 1668 GSH 106 A 2.93
N P L A 19 LYS 302 NZ --- O31 1682 GSH 106 A 3.86
N P L A 22 CYS 348 CB --- CB2 1677 GSH 106 A 3.75
N P L A 22 CYS 348 CB --- SG2 1678 GSH 106 A 3.02
N P L A 22 CYS 349 SG --- CB2 1677 GSH 106 A 3.03
N P L A 22 CYS 349 SG --- SG2 1678 GSH 106 A 2.02
N P L A 24 TYR 372 CB --- CG1 1670 GSH 106 A 3.68
Note here that I estimated the offset used by unpack, so you may need to tweak that to fit your data.
If your data is tab-delimited, you'll need to split on tab, or better yet use Text::CSV to parse your data. Basic script is the same:
use Text::CSV;
my $csv = Text::CSV->new({
binary => 1,
sep_char => "\t",
});
my %atom;
while (<DATA>) {
$csv->parse($_);
my $atom = ($csv->fields())[9];
next unless defined $atom;
$atom{$atom}++;
}
You can also use the loop condition while (my $aref = $csv->getline(*DATA)), which is more efficient, but also breaks if your csv data is not consistent.
A simpler and possibly as valid (depending on how complex your data can be) solution is using split:
while (<DATA>) {
my $atom = (split /\t/)[9]; # implicitly splits $_
$atom{$atom}++;
}
If your data is space delimited, simply remove /\t/ from the above.
Note that I assumed all spaces were tabs in your input, so if they are not, my count may need to be tweaked.
In command line (no perl):
cat yourfile | awk '{print $10}' | sort | uniq | wc -l
Works on your input.
Have a look at this Perl Cookbook recipe.
While you're reading the file line by line you want to split/extract the atom symbols and count them in a hash.
use strict;
use warnings;
# open FILE goes here...
my %seen; # we use this to count
while (<FILE>) {
m/--[>-]\s+(\w+)\s/; # fetch the atom symbol after arrow-thing
$seen{$1}++;
}
close FILE;
print scalar keys %seen; # number of unique atom symbols
print join ', ', keys %seen; # List as string
Or in perl:
#!/usr/bin/perl
while(my $line = <DATA>){
my $atom = (split / +/, $line)[9];
$atoms{$atom}++;
}
print "$_: $atoms{$_}\n" for keys %atoms;
__DATA__
H P L A 82 SER 1290 N --> O12 1668 GSH 106 A 2.90
H P L A 83 SER 1301 N --> O12 1668 GSH 106 A 2.93
N P L A 19 LYS 302 NZ --- O31 1682 GSH 106 A 3.86
N P L A 22 CYS 348 CB --- CB2 1677 GSH 106 A 3.75
N P L A 22 CYS 348 CB --- SG2 1678 GSH 106 A 3.02
N P L A 22 CYS 349 SG --- CB2 1677 GSH 106 A 3.03
N P L A 22 CYS 349 SG --- SG2 1678 GSH 106 A 2.02
N P L A 24 TYR 372 CB --- CG1 1670 GSH 106 A 3.68
I have a file which looks like this.
In the Perl code, i am using an array #query = ('A+80', 'A+40', 'A+202', 'B+130', 'B+268', 'B+211', 'A+35');
What I want to do is: for each element of the array, scan the lines in the file shown below and print out something like this:
A+80 - HELIX
A+40 - SHEET
A+202 - HELIX
B+130 - HELIX
B+268 - SHEET
B+211 - SHEET
A+35 - LOOP
The logic behind this output is to extract for each entry in array, the first part i.e. A or B, and the second part, i.e. the number associated with the 1st part. Consider the first entry in the array: A+80. On the third line of the file the number 80 is lying between 78 (the 6th column) and 90 (the 9th column) and also first alphabet A is also matching in both cases. Hence the program prints HELIX for this query.
Consider 2nd element: A+40. The 2nd part i.e the number lies in the range as on this line
SHEET 2 B 3 ARG A 37 VAL A 43 1
i.e. between the numbers listed in columns 7 and 10, and the alphabet matches too. Hence for this entry the output is: SHEET
For other cases, like B+211. THe line given below matches the number and the alphabet associated with it.
SHEET 2 B 3 ARG A 37 VAL A 43 1
Hence the output for this entry is: SHEET
Also, for entries whose alphabet and number associated with it, do not match any of the lines in the file. the code outputs: A+35 - LOOP
What is an efficient way to do this in Perl?
Since I am a beginner with Perl, I am as of now splitting each entry in successive array elements, i.e. for #query, and matching/comparing the alphabet and number to each of the relevant columns in the lines. But somehow am unable to get the output desired.
Please help...
HELIX 1 1 GLY A 9 GLN A 30 1
HELIX 2 2 ASP A 47 ILE A 63 1
HELIX 3 3 GLU A 78 GLU A 90 1
HELIX 4 4 THR A 111 ALA A 117 1
HELIX 5 5 PRO A 120 LYS A 122 5
HELIX 6 6 SER A 129 ARG A 137 1
HELIX 7 7 CYS A 147 THR A 159 1
HELIX 8 8 GLY A 178 ASN A 188 1
HELIX 9 9 LEU A 202 LYS A 208 1
HELIX 10 10 GLY A 224 TRP A 226 5
HELIX 11 11 TYR A 258 GLU A 263 1
HELIX 12 12 VAL A 275 PHE A 294 1
HELIX 13 13 GLY B 9 GLN B 30 1
HELIX 14 14 ASP B 47 ILE B 63 1
HELIX 15 15 GLU B 78 GLU B 90 1
HELIX 16 16 THR B 111 ALA B 117 1
HELIX 17 17 PRO B 120 LYS B 122 5
HELIX 18 18 SER B 129 ARG B 137 1
HELIX 19 19 CYS B 147 THR B 159 1
HELIX 20 20 GLY B 178 TRP B 187 1
HELIX 21 21 LEU B 202 LYS B 208 1
HELIX 22 22 GLY B 224 TRP B 226 5
HELIX 23 23 TYR B 258 GLU B 263 1
HELIX 24 24 GLY B 276 PHE B 294 5
SHEET 1 A 2 GLU A 5 LEU A 7 0
SHEET 2 A 2 PHE A 267 THR A 269 1
SHEET 1 B 3 LYS A 66 LEU A 72 0
SHEET 2 B 3 ARG A 37 VAL A 43 1
SHEET 3 B 3 GLY A 96 VAL A 99 1
SHEET 1 C 4 THR A 191 CYS A 195 0
SHEET 2 C 4 HIS A 167 VAL A 171 1
SHEET 3 C 4 ILE A 211 VAL A 214 1
SHEET 4 C 4 ILE A 232 ASP A 235 1
SHEET 1 D 2 GLU B 5 LEU B 7 0
SHEET 2 D 2 PHE B 267 THR B 269 1
SHEET 1 E 3 LYS B 66 LEU B 72 0
SHEET 2 E 3 ARG B 37 VAL B 43 1
SHEET 3 E 3 GLY B 96 VAL B 99 1
SHEET 1 F 4 THR B 191 CYS B 195 0
SHEET 2 F 4 HIS B 167 VAL B 171 1
SHEET 3 F 4 ILE B 211 VAL B 214 1
SHEET 4 F 4 ILE B 232 ASP B 235 1
SHEET 1 G 2 ASN B 239 PRO B 242 0
SHEET 2 G 2 ARG B 250 VAL B 253 -1
The program below seems to do what you need. It reads data from within the source file using the DATA file handle for convenience: you must arrange to open and read the appropriate data file.
The entirety of the file is read into memory for straightforward access. If the file is enormous (say, hundreds of megabytes) then this approach may be inappropriate and you will have to come back for more help.
The records vary in length, so the algorithm locates the relevant fields relative to the first three-letter field found.
The hash %categories contains all of the required file data. It is indexed by the key letter - A or B here - and the value of each element is an array of anonymous hashes containing the label (column 1), the letter, and the start and end of the range covered by each record.
Building the output is straightforward, and uses map and grep to find the 'label' of all the relevant entries in the hash. If none are found the text "LOOP" is added as a default.
use strict;
use warnings;
my #query = qw/ A+80 A+40 A+202 B+130 B+268 B+211 A+35 /;
my %categories;
while (<DATA>) {
next unless /\S/;
my #data = split;
my #indices = grep $data[$_] =~ /^[A-Z]{3}$/, 0 .. $#data;
my %info;
#info{qw/ label letter start end /} = #data[ 0, $indices[0]+1, $indices[0]+2, $indices[1]+2 ];
push #{ $categories{$info{letter}} }, \%info;
}
for my $item (#query) {
my ($letter, $value) = split /\+/, $item;
my #matches = map $_->{label},
grep { $value >= $_->{start} and $value <= $_->{end} }
#{ $categories{$letter} };
#matches = ('LOOP') unless #matches;
warn qq(Multiple categories for query "$item") unless #matches == 1;
printf "%s - %s\n", $item, $_ for #matches
}
__DATA__
HELIX 1 1 GLY A 9 GLN A 30 1
HELIX 2 2 ASP A 47 ILE A 63 1
HELIX 3 3 GLU A 78 GLU A 90 1
HELIX 4 4 THR A 111 ALA A 117 1
HELIX 5 5 PRO A 120 LYS A 122 5
HELIX 6 6 SER A 129 ARG A 137 1
HELIX 7 7 CYS A 147 THR A 159 1
HELIX 8 8 GLY A 178 ASN A 188 1
HELIX 9 9 LEU A 202 LYS A 208 1
HELIX 10 10 GLY A 224 TRP A 226 5
HELIX 11 11 TYR A 258 GLU A 263 1
HELIX 12 12 VAL A 275 PHE A 294 1
HELIX 13 13 GLY B 9 GLN B 30 1
HELIX 14 14 ASP B 47 ILE B 63 1
HELIX 15 15 GLU B 78 GLU B 90 1
HELIX 16 16 THR B 111 ALA B 117 1
HELIX 17 17 PRO B 120 LYS B 122 5
HELIX 18 18 SER B 129 ARG B 137 1
HELIX 19 19 CYS B 147 THR B 159 1
HELIX 20 20 GLY B 178 TRP B 187 1
HELIX 21 21 LEU B 202 LYS B 208 1
HELIX 22 22 GLY B 224 TRP B 226 5
HELIX 23 23 TYR B 258 GLU B 263 1
HELIX 24 24 GLY B 276 PHE B 294 5
SHEET 1 A 2 GLU A 5 LEU A 7 0
SHEET 2 A 2 PHE A 267 THR A 269 1
SHEET 1 B 3 LYS A 66 LEU A 72 0
SHEET 2 B 3 ARG A 37 VAL A 43 1
SHEET 3 B 3 GLY A 96 VAL A 99 1
SHEET 1 C 4 THR A 191 CYS A 195 0
SHEET 2 C 4 HIS A 167 VAL A 171 1
SHEET 3 C 4 ILE A 211 VAL A 214 1
SHEET 4 C 4 ILE A 232 ASP A 235 1
SHEET 1 D 2 GLU B 5 LEU B 7 0
SHEET 2 D 2 PHE B 267 THR B 269 1
SHEET 1 E 3 LYS B 66 LEU B 72 0
SHEET 2 E 3 ARG B 37 VAL B 43 1
SHEET 3 E 3 GLY B 96 VAL B 99 1
SHEET 1 F 4 THR B 191 CYS B 195 0
SHEET 2 F 4 HIS B 167 VAL B 171 1
SHEET 3 F 4 ILE B 211 VAL B 214 1
SHEET 4 F 4 ILE B 232 ASP B 235 1
SHEET 1 G 2 ASN B 239 PRO B 242 0
SHEET 2 G 2 ARG B 250 VAL B 253 -1
output
A+80 - HELIX
A+40 - SHEET
A+202 - HELIX
B+130 - HELIX
B+268 - SHEET
B+211 - SHEET
A+35 - LOOP