Data Processing.

[biobrain]

I have a file with following Data

Center Coordinates of 1XO2-as.pdb:
x: 14.5813741258741
y: 40.6704615384615
z: 135.904776223776
Center Coordinates of 1JOW-as.pdb:
x: 19.2733255813953
y: 11.2111666666667
z: 133.909627906977
Center Coordinates of 2EUF-as.pdb:
x: 34.6811643356643
y: 37.7362447552448
z: 59.010472027972
Center Coordinates of 1G3N-as.pdb:
x: 20.2044548693587
y: 66.1429441805226
z: 55.9287173396675
Center Coordinates of 1BI8-as.pdb:
x: 48.2399854014598
y: 1.06650547445255
z: 30.224401459854
Center Coordinates of 1BLX-as.pdb:
x: 20.78611
y: -28.36544
z: 66.4986966666667
Center Coordinates of 1BI7-as.pdb:
x: 142.558162601626
y: 49.1458577235773
z: 101.535272357724
Center Coordinates of 2F2C-as.pdb:
x: 34.686520979021
y: 38.0898846153846
z: 59.5178531468532

Now I wish to open 1XO2.pdb, 1JOW.pdb and other files corresponding to 1XO2-as.pdb 1JOW-as.pdb and want to check If there is any coordinate XYZ matching the values given above

 

[MillerH]

ok ....

And what have you tried thus far?

 

[prex1]

Before answering as required by MillerH also consider that we need to know the format of those .pdb files. Also you need to define a resolution for testing the equality of the coordinates: this could be in the form of a value to test the absolute value of the difference of all three coordinates, or a value to test the distance of the points to be compared.

Franco

http://www.xcalcs.com

: Online tools for structural design

http://www.megamag.it

: Magnetic brakes for fun rides

http://www.levitans.com

: Air bearing pads

 

[biobrain]

Thanks a lot, I have solved the problem,

Regards

 

[stevexff]

Wanna post your solution then? This site supports two-way traffic...

Steve

[small]"Every program can be reduced by one instruction, and every program has at least one bug. Therefore, any program can be reduced to one instruction which doesn't work." (Object:erlDesignPatterns)[/small]

 

[biobrain]

Thanks stevexff

I had renamed 1XO2-as.pdb 1JOW-as.pdb etc as 1XO2.pdb.h2o etc

Well .pdb or .h20 is a simple text file.

use strict;

#open the directory and than read all the files with *.pdb
opendir(DIR,"/home/shafiq/Desktop/water") or die "$!";
my @all_pdb_files  = grep {/\.pdb$/} readdir DIR;
close DIR;
open (OUTPUT, ">out");
foreach (@all_pdb_files){

#open the file
open (SP, "$_");
my $filename=$_;
my $count = 0;
my $x_sum = 0;
my $y_sum = 0;
my $z_sum = 0;

if (/^/) {

while (<SP>) {
    chomp;
    my @data = split;
    
    my ($x, $y, $z) = @data[6,7,8];
   # print ("$x  $y  $z \n");
    $x_sum += $x;
    $y_sum += $y;
    $z_sum += $z;
    $count++;
}}

my $x_center = $x_sum / $count;
my $y_center = $y_sum / $count;
my $z_center = $z_sum / $count;
my $x1=$x_center;
my $y1=$y_center;
my $z1=$z_center;
my $x2;
my $y2;
my $z2;
my $d;
#print ("Center Coordinates of $filename\n");
#print ("$x_center $y_center $z_center \n");
open (WATER, "$filename.h2o");
print "$filename\n";
while (<WATER>){
    chomp;
    my @data = split;
    
    my ($number, $x, $y, $z) = @data[4,5,6,7];
    $x2=$x;
    $y2=$y;
    $z2=$z;
$d = sqrt(($x1-$x2)**2+($y1-$y2)**2+($z1-$z2)**2);
print ("water molecule $number $d\n");

}
}