I have a text file as shown below
ATOM 920 CA GLN A 203 39.292 -13.354 17.416 1.00 55.76 C
ATOM 929 CA HIS A 204 38.546 -15.963 14.792 1.00 29.53 C
ATOM 939 CA ASN A 205 39.443 -17.018 11.206 1.00 54.49 C
ATOM 947 CA GLU A 206 41.454 -13.901 10.155 1.00 26.32 C
ATOM 956 CA VAL A 207 43.664 -14.041 13.279 1.00 40.65 C
.
.
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ATOM 963 CA GLU A 208 45.403 -17.443 13.188 1.00 40.25 C
I would like to calculate the distance between two alpha carbon atoms i.e calculate the distance between first and second atom and then between second and third atom and so on..... The distance between two atoms can be expressed as:distance = sqrt((x1-x2)^2+(y1-y2)^2+(z1-z2)^2) .
The columns 7,8 and 9 represents x,y and z co-ordinates respectively.I need to print the distance and the corresponding residue pairs(column 4) as shown below.(the values of distance are not real)
GLN-HIS 4.5
HIS-ASN 3.2
ASN-GLU 2.5
How can I do this calculation with perl or python?
If your data is separated by whitespace, a simple split can do the job. Buffering the lines to compare them to each other sequentially.
use strict;
use warnings;
my @line;
while (<>) {
push @line, $_; # add line to buffer
next if @line < 2; # skip unless buffer is full
print proc(@line), "\n"; # process and print
shift @line; # remove used line
}
sub proc {
my @a = split ' ', shift; # line 1
my @b = split ' ', shift; # line 2
my $x = ($a[6]-$b[6]); # calculate the diffs
my $y = ($a[7]-$b[7]);
my $z = ($a[8]-$b[8]);
my $dist = sprintf "%.1f", # format the number
sqrt($x**2+$y**2+$z**2); # do the calculation
return "$a[3]-$b[3]\t$dist"; # return the string for printing
}
Output (with the sample data):
GLN-HIS 3.8
HIS-ASN 3.8
ASN-GLU 3.9
GLU-VAL 3.8
If your data is tab separated, you can split on /\t/ instead of ' '.