Sponsored Content
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
 

9 More Discussions You Might Find Interesting

1. Programming

Converting distance list to distance matrix in R

Hi power user, I have this type of data (distance list): file1 A B 10 B C 20 C D 50I want output like this # A B C D A 0 10 30 80 B 10 0 20 70 C 30 20 0 50 D 80 70 50 0 Which is a distance matrix I have tried... (0 Replies)
Discussion started by: anjas
0 Replies

2. UNIX for Dummies Questions & Answers

Script producing error, Program to calculate maximum number

Hi folks, Here i have written a shell script to calculate a maximum number from 10 numbers entered on command line. max=0 echo Enter 10 numbers , one at a time for i in 1 2 3 4 5 6 7 8 9 10 do read n max=`expr $max + $n` if --- At this last step there is some problem, it gives error... (5 Replies)
Discussion started by: rits
5 Replies

3. Shell Programming and Scripting

AWK code for finding distances between atoms in two different files

Hi:) I have two separate data files (.xyz) type and I want to see distances between the coordinates of atoms of the two files. For example:- My first files contains 1 1 1 11.50910000 5.17730000 16.49360000 3 1 2 11.21790000 6.36062000 15.60660000 6 1 2 ... (4 Replies)
Discussion started by: ananyob
4 Replies

4. Shell Programming and Scripting

Calculate distance and azimuth

Hi all, I have a data file like this lat lon lat lon 12.000 25.125 14.235 25.012 14.200 81.000 25.584 25.014 45.023 25.365 25.152 35.222 I want to calculate distance and azimuth between this points eg:- 12.000,25.125 and 14.235,25.012 I want to use awk programming... (3 Replies)
Discussion started by: chamara
3 Replies

5. UNIX for Dummies Questions & Answers

How to make a distance matrix

Hi, I'm trying to generate a distance matrix between sample pairs for use in a tree-drawing program (example below). The example below demonstrates what I'd like to get out of the data - essentially, to calculate the proportion of positions where two samples differ. Any help much appreciated!... (1 Reply)
Discussion started by: auburn
1 Replies

6. Shell Programming and Scripting

Calculate age of a file | calculate time difference

Hello, I'm trying to create a shell script (#!/bin/sh) which should tell me the age of a file in minutes... I have a process, which delivers me all 15 minutes a new file and I want to have a monitoring script, which sends me an email, if the present file is older than 20 minutes. To do... (10 Replies)
Discussion started by: worm
10 Replies

7. Shell Programming and Scripting

Program to calculate the operation from file

Hi I have the file has some formulas how to create a program (per, ksh, awk) which calculate the operation and put the result on other file example data of source file - this has separate by ";"... (5 Replies)
Discussion started by: Miguel Gonzalez
5 Replies

8. Shell Programming and Scripting

finding distance between numbers

Hi, I have a file as ABC 1634230,1634284,1634349,1634468 1634272,1634301,1634356,1634534 What I want is to find distance between the numbers.. column 1 is the gene name and column 2 are starts and column 3 are their respective stops for the starts. So what I want is column 3 which has +1... (2 Replies)
Discussion started by: Diya123
2 Replies

9. Shell Programming and Scripting

Calculate average, azimut and distance

Gents, Please i will to get the distance and azimut from 2 coordinates: Usig excel formula i get the correct values, but i will like to do it using awk. Example A 35089.0 50345.016 9 75 1 2101774 77 70 79 483911.6 2380106.9 137.4 1 1 6 1 A 35089.0 50345.01620 75... (8 Replies)
Discussion started by: jiam912
8 Replies
cgbequb.f(3)							      LAPACK							      cgbequb.f(3)

NAME
cgbequb.f - SYNOPSIS
Functions/Subroutines subroutine cgbequb (M, N, KL, KU, AB, LDAB, R, C, ROWCND, COLCND, AMAX, INFO) CGBEQUB Function/Subroutine Documentation subroutine cgbequb (integerM, integerN, integerKL, integerKU, complex, dimension( ldab, * )AB, integerLDAB, real, dimension( * )R, real, dimension( * )C, realROWCND, realCOLCND, realAMAX, integerINFO) CGBEQUB Purpose: CGBEQUB computes row and column scalings intended to equilibrate an M-by-N matrix A and reduce its condition number. R returns the row scale factors and C the column scale factors, chosen to try to make the largest element in each row and column of the matrix B with elements B(i,j)=R(i)*A(i,j)*C(j) have an absolute value of at most the radix. R(i) and C(j) are restricted to be a power of the radix between SMLNUM = smallest safe number and BIGNUM = largest safe number. Use of these scaling factors is not guaranteed to reduce the condition number of A but works well in practice. This routine differs from CGEEQU by restricting the scaling factors to a power of the radix. Baring over- and underflow, scaling by these factors introduces no additional rounding errors. However, the scaled entries' magnitured are no longer approximately 1 but lie between sqrt(radix) and 1/sqrt(radix). Parameters: M M is INTEGER The number of rows of the matrix A. M >= 0. N N is INTEGER The number of columns of the matrix A. N >= 0. KL KL is INTEGER The number of subdiagonals within the band of A. KL >= 0. KU KU is INTEGER The number of superdiagonals within the band of A. KU >= 0. AB AB is DOUBLE PRECISION array, dimension (LDAB,N) On entry, the matrix A in band storage, in rows 1 to KL+KU+1. The j-th column of A is stored in the j-th column of the array AB as follows: AB(KU+1+i-j,j) = A(i,j) for max(1,j-KU)<=i<=min(N,j+kl) LDAB LDAB is INTEGER The leading dimension of the array A. LDAB >= max(1,M). R R is REAL array, dimension (M) If INFO = 0 or INFO > M, R contains the row scale factors for A. C C is REAL array, dimension (N) If INFO = 0, C contains the column scale factors for A. ROWCND ROWCND is REAL If INFO = 0 or INFO > M, ROWCND contains the ratio of the smallest R(i) to the largest R(i). If ROWCND >= 0.1 and AMAX is neither too large nor too small, it is not worth scaling by R. COLCND COLCND is REAL If INFO = 0, COLCND contains the ratio of the smallest C(i) to the largest C(i). If COLCND >= 0.1, it is not worth scaling by C. AMAX AMAX is REAL Absolute value of largest matrix element. If AMAX is very close to overflow or very close to underflow, the matrix should be scaled. INFO INFO is INTEGER = 0: successful exit < 0: if INFO = -i, the i-th argument had an illegal value > 0: if INFO = i, and i is <= M: the i-th row of A is exactly zero > M: the (i-M)-th column of A is exactly zero Author: Univ. of Tennessee Univ. of California Berkeley Univ. of Colorado Denver NAG Ltd. Date: November 2011 Definition at line 161 of file cgbequb.f. Author Generated automatically by Doxygen for LAPACK from the source code. Version 3.4.1 Sun May 26 2013 cgbequb.f(3)
All times are GMT -4. The time now is 01:30 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy