program to calculate distance between 5 atoms Post: 302242149

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Top Forums Shell Programming and Scripting program to calculate distance between 5 atoms Post 302242149 by annie_singh on Wednesday 1st of October 2008 08:45:37 AM

10-01-2008

Registered User

program to calculate distance between 5 atoms

Hello,

I am a beginner with perl. I have a perl program to calculate the distance between 5 atoms or more.

i have an array which looks like this:
6.324 32.707 50.379
5.197 32.618 46.826
4.020 36.132 46.259
7.131 38.210 45.919
6.719 38.935 42.270
2.986 39.221 41.892
-0.269 37.184 41.565

I want to assign these values with Xi(column 1), Yi(column 2)and Zi(column 3). Suppose the first row values are (Xi,Yi,Zi), then the second row values will be (Xj, Yj, Zj) I want to calculate the distance using the formula

$dist = sqrt(($Xi-$Xj)**2+($Yi-$Yj)**2+($Zi-$Zj)**2) between row1/row2, row1/row3, row1/row4 ......so on.... till row6/row7

so its an iterative calculation. probably i shud us a for loop, and another forloop within the previous for loop. i am totally stuck.

till now my perl program looks like this:

open(IN, "/Users/anu/out.pl") or die "$!";
while (my $line = <IN>) {
chomp($line);
my @array = (split (/\s+/, $line))[6, 7, 8];
print "@array\n";
}
close(IN);

I dnt know wat to do..please help

Thank you

annie_singh

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shtool-path

SHTOOL-PATH.TMP(1)					      GNU Portable Shell Tool						SHTOOL-PATH.TMP(1)

NAME

       shtool-path - GNU shtool command dealing with shell path variables

SYNOPSIS

       shtool path [-s|--suppress] [-r|--reverse] [-d|--dirname] [-b|--basename] [-m|--magic] [-p|--path path] str [str ...]

DESCRIPTION

       This command deals with shell $PATH variables. It can find a program through one or more filenames given by one or more str arguments.  It
       prints the absolute filesystem path to the program displayed on "stdout" plus an exit code of 0 if it was really found.

OPTIONS

       The following command line options are available.

       -s, --suppress
	   Supress output. Useful to only test whether a program exists with the help of the return code.

       -r, --reverse
	   Transform a forward path to a subdirectory into a reverse path.

       -d, --dirname
	   Output the directory name of str.

       -b, --basename
	   Output the base name of str.

       -m, --magic
	   Enable advanced magic search for ""perl"" and ""cpp"".

       -p, --path path
	   Search in path. Default is to search in $PATH.

EXAMPLE

	#   shell script
	awk=`shtool path -p "${PATH}:." gawk nawk awk`
	perl=`shtool path -m perl`
	cpp=`shtool path -m cpp`
	revpath=`shtool path -r path/to/subdir`

HISTORY

       The GNU shtool path command was originally written by Ralf S.  Engelschall <rse@engelschall.com> in 1998 for Apache. It was later taken
       over into GNU shtool.

SEE ALSO

       shtool(1), which(1).

18-Jul-2008							   shtool 2.0.8 						SHTOOL-PATH.TMP(1)