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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
Old 10-01-2008
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
 

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TRIM(3) 								 1								   TRIM(3)

trim - Strip whitespace (or other characters) from the beginning and end of a string

SYNOPSIS
string trim (string $str, [string $character_mask = " 0r B"]) DESCRIPTION
This function returns a string with whitespace stripped from the beginning and end of $str. Without the second parameter, trim(3) will strip these characters: o " " (ASCII 32 ( 0x20)), an ordinary space. o " " (ASCII 9 ( 0x09)), a tab. o " " (ASCII 10 ( 0x0A)), a new line (line feed). o " " (ASCII 13 ( 0x0D)), a carriage return. o "" (ASCII 0 ( 0x00)), the NUL-byte. o "x0B" (ASCII 11 ( 0x0B)), a vertical tab. PARAMETERS
o $str - The string that will be trimmed. o $character_mask - Optionally, the stripped characters can also be specified using the $character_mask parameter. Simply list all characters that you want to be stripped. With .. you can specify a range of characters. RETURN VALUES
The trimmed string. EXAMPLES
Example #1 Usage example of trim(3) <?php $text = " These are a few words :) ... "; $binary = "x09Example stringx0A"; $hello = "Hello World"; var_dump($text, $binary, $hello); print " "; $trimmed = trim($text); var_dump($trimmed); $trimmed = trim($text, " ."); var_dump($trimmed); $trimmed = trim($hello, "Hdle"); var_dump($trimmed); $trimmed = trim($hello, 'HdWr'); var_dump($trimmed); // trim the ASCII control characters at the beginning and end of $binary // (from 0 to 31 inclusive) $clean = trim($binary, "x00..x1F"); var_dump($clean); ?> The above example will output: string(32) " These are a few words :) ... " string(16) " Example string " string(11) "Hello World" string(28) "These are a few words :) ..." string(24) "These are a few words :)" string(5) "o Wor" string(9) "ello Worl" string(14) "Example string" Example #2 Trimming array values with trim(3) <?php function trim_value(&$value) { $value = trim($value); } $fruit = array('apple','banana ', ' cranberry '); var_dump($fruit); array_walk($fruit, 'trim_value'); var_dump($fruit); ?> The above example will output: array(3) { [0]=> string(5) "apple" [1]=> string(7) "banana " [2]=> string(11) " cranberry " } array(3) { [0]=> string(5) "apple" [1]=> string(6) "banana" [2]=> string(9) "cranberry" } NOTES
Note Possible gotcha: removing middle characters Because trim(3) trims characters from the beginning and end of a string, it may be confusing when characters are (or are not) removed from the middle. trim('abc', 'bad') removes both 'a' and 'b' because it trims 'a' thus moving 'b' to the beginning to also be trimmed. So, this is why it "works" whereas trim('abc', 'b') seemingly does not. SEE ALSO
ltrim(3), rtrim(3), str_replace(3). PHP Documentation Group TRIM(3)
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