This is supposed to put the contents of nums into decreasing order, however sort does not change the contents of nums. Many sites I read have said to pass by reference, but I don't think I'm dereferencing the argument correctly. Bear with me, this is my first Perl program :)
#! /usr/bin/env perl
sub sort {
my #arr = #_;
my $len = scalar #arr;
for (my $i = 1; $i < $len-1; $i = $i + 1) {
my $max = $i;
for (my $j = $i + 1; $j < $len; $j = $j + 1) {
if ($arr[$j] > $arr[$max]) {
$max = $j
}
}
$temp = $arr[$max];
$arr[$max] = $arr[$i];
$arr[$i] = $temp;
}
}
print "Enter 10 numbers: ";
my $numbers = <STDIN>;
my #nums = split ' ', $numbers;
print "Unsorted: #nums\n";
sort \#nums;
print "Sorted: #nums\n";
#Matt Jacob helped me out with this one. This is what I was looking for.
#! /usr/bin/env perl
sub selection_sort {
my $arr = shift;
my $len = scalar #$arr;
for (my $i = 0; $i < $len-1; $i++) {
my $max = $i;
for (my $j = $i + 1; $j < $len; $j++) {
if (#$arr[$j] > #$arr[$max]) {
$max = $j
}
}
my $temp = #$arr[$max];
#$arr[$max] = #$arr[$i];
#$arr[$i] = $temp;
}
}
print "Enter 10 numbers: ";
my $input = <STDIN>;
my #integers = split ' ', $input;
print "Unsorted: #integers\n";
selection_sort \#integers;
print "Sorted: #integers\n";
When ever I run this bit of code. it doesn't display any output. Anyone see anything wrong?
I am trying to display this in the out put:
A
AA
AAA
AAAB
AAABA
AAABAA
AAABAAA
AAABAAAB
etc.
#!/usr/local/bin/perl
$A = 3;
$B = 1;
$i = 1;
$output = "";
$j = 1;
while ($i <= $ARGV[0]) {
while ($j <= $i) {
if ($A == 0 && $B == 0) {
$A = 3;
$B = 1;
}
if ($A > 0) {
$output.= "A";
$A--;
}
else {
$output.= "B";
$B--;
}
$j++;
}
print($output . "\n");
$i++;
}
It works for me when I run it with a numeric argument (number of lines).
An idea how to simplify the code:
#!/usr/bin/perl
use warnings;
use strict;
my $count = shift;
my $A = 3;
my $B = 1;
my $string = q();
$string .= ('A' x $A) . ('B' x $B) while $count > length $string;
print substr($string, 0, $_), "\n" for 1 .. $count;
It uses a different algorithm - it creates the longest possible string, and then outputs parts of it.
if there is no #ARGV, while ($i <= $ARGV[0]) never runs.
#ARGV is an array of the command line arguments provided when the script is executed. you did not provide any command line arguments. if you had use warnings in effect, you would be warned that $ARGV[0] is uninitialized.
As from ikegami comment. You cann't pass the input at when the program is compile. For example, consider your file name is algo.pl. Can you run your program with
perl algo.pl 10
Here 10 is the input value of the program. In program value is retrieve by the $ARGV[0]
so in your program looks like while ($i <= $ARGV[0]).
If you want pass the several values like perl filename.pl 12 data1 data2In your data retrieve by $ARGV[0] $ARGV[1] $ARGV[2] for more information see here.
If you want pass the input at the time of execution used STDIN
use warnings;
use strict;
my $A = 3;
my $B = 1;
my $i = 1;
my $output = "";
my $j = 1;
print "Enter the value: ";
chomp(my $value = <STDIN>);
while ($i <= $value) {
while ($j <= $i) {
if ($A == 0 && $B == 0) {
$A = 3;
$B = 1;
}
if ($A > 0) {
$output.= "A";
$A--;
}
else {
$output.= "B";
$B--;
}
$j++;
}
print($output . "\n");
$i++;
}
The problem with the following code is only in one function of the code. The problem function is with a comment head and close. This is my first post to StackOverflow so bear with me. The following script has some modules and other functions that I know work by testing them with the problem function commented out but I just cannot seem to get that one function to work. When ran, the script runs until the enviroment kills the execution.
Basically what this program does is takes a PDB file, copies everything out of the PDB file and creates a new one and pastes all of the original input file content into the new file and appends the cavities(coordinates of center of the cavity and the specified probe radius) that the program is supposed to find.
The problem function within the code is supposed to distinguish between a void space within a bound box of the structure and a cavity. Cavities are considered to be a closed space somewhere within the structure. A void space is any space or coordinate within the bounding box of max and min coorindates where there isn't an atom.The cavity must be large enough to fit into a specified probe radius. There is also a specified resolution when searching through the 3D hashtable of coordinates.
Can anyone tell me why my code isn't working. Anything immediate. I have tested and tested and cannot seem to find the error.
Thank you.
#!/usr/bin/perl
# Example 11-6 Extract atomic coordinates from PDB file
use strict;
use warnings;
use BeginPerlBioinfo; # see Chapter 6 about this module
#open file for printing
open(FH,">results.pdb");
open(PDB,"oneAtom.pdb");
while(<PDB>) { print FH $_; }
close(PDB);
# Read in PDB file
my #file = get_file_data('oneAtom.pdb');
# Parse the record types of the PDB file
my %recordtypes = parsePDBrecordtypes(#file);
# Extract the atoms of all chains in the protein
my %atoms = parseATOM ( $recordtypes{'ATOM'} );
#define some variables and get the atom indices stored in atom_numbers array
my #atom_numbers = sort {$a <=> $b} keys %atoms;
my $resolution = 4.;
my $lo = 1000;
my $hi = -1000;
my $p_rad = 1;
my %pass;
#set the grid boundaries
foreach my $l ( #atom_numbers ) {
for my $i (0..2) {
if ( $atoms{$l}[$i] < $lo ) { $lo = $atoms{$l}[$i]; }
if ( $atoms{$l}[$i] > $hi ) { $hi = $atoms{$l}[$i]; }
}
}
$lo = $lo - 2* $resolution;
$hi = $hi + 2* $resolution;
#compute min distance to the pdb structure from each grid point
for ( my $i = $lo ; $i <= $hi ; $i = $i + $resolution ) {
for ( my $j = $lo ; $j <= $hi ; $j = $j + $resolution ) {
for ( my $k = $lo ; $k <= $hi ; $k = $k + $resolution ) {
my $min_dist = 1000000;
foreach my $l ( #atom_numbers ) {
my $distance = sqrt((($atoms{$l}[0]-($i))*($atoms{$l}[0]-($i))) + (($atoms{$l}[1]-($j))*($atoms{$l}[1]-($j))) + (($atoms{$l}[2]-($k))*($atoms{$l}[2]-($k))));
$distance = $distance - ( $p_rad + $atoms{$l}[3] );
if ( $distance < $min_dist ) {
$min_dist = $distance;
}
}
$pass{$i}{$j}{$k} = $min_dist;
if ( $pass{$i}{$j}{$k} > 0 ) {
$pass{$i}{$j}{$k} = 1;
} else { $pass{$i}{$j}{$k} = 0;
}
}
}
}
#define a starting point on the outside of the grid and place first on list of points
#my #point = ();
my $num_cavities = 0;
#define some offsets used to compute neighbors
my %offset = (
1 => [-1*$resolution,0,0],
2 => [1*$resolution,0,0],
3 => [0,-1*$resolution,0],
4 => [0,1*$resolution,0],
5 => [0,0,-1*$resolution],
6 => [0,0,1*$resolution],
);
##########################################################
#function below with problem
##########################################################
my #point = ();
push #point,[$hi,$hi,$hi];
=pod
#do the following while there are points on the list
while ( #point ) {
foreach my $vector ( keys %offset ) { #for each offset vector
my #neighbor = (($point[0][0]+$offset{$vector}[0]),($point[0][1]+$offset{$vector}[1]),($point[0][2]+$offset{$vector}[2])); #compute neighbor point
if ( exists $pass{$neighbor[0]}{$neighbor[1]}{$neighbor[2]} ) { #see if neighbor is in the grid
if ( $pass{$neighbor[0]}{$neighbor[1]}{$neighbor[2]} == 1 ) { #if it is see if its further than the probe radius
push #point,[($point[0][0]+$offset{$vector}[0]),($point[0][1]+$offset{$vector}[1]),($point[0][2]+$offset{$vector}[2])]; #if it is push it onto the list of points
}
}
}
$pass{$point[0][0]}{$point[0][1]}{$point[0][2]} = 0; #eliminate the point just tested from the pass array
shift #point; #move to the next point in the list
}
=cut
##############################################################
# end of problem function
##############################################################
my $grid_ind = $atom_numbers[$#atom_numbers];
for ( my $i = $lo ; $i <= $hi ; $i = $i + $resolution ) {
for ( my $j = $lo ; $j <= $hi ; $j = $j + $resolution ) {
for ( my $k = $lo ; $k <= $hi ; $k = $k + $resolution ) {
if ( $pass{$i}{$j}{$k} == 1 ) {
$grid_ind = $grid_ind + 1;
my $n = sprintf("%5d",$grid_ind);
my $x = sprintf("%7.3f",$i);
my $y = sprintf("%7.3f",$j);
my $z = sprintf("%7.3f",$k);
my $w = sprintf("%6.3f",1);
my $p = sprintf("%6.3f",$p_rad);
print FH "ATOM $n MC CAV $n $x $y $z $w $p \n";
}
}
}
}
close(FH);
exit;
#do the following while there are points on the list
for ( my $i = $lo ; $i <= $hi ; $i = $i + $resolution ) {
for ( my $j = $lo ; $j <= $hi ; $j = $j + $resolution ) {
for ( my $k = $lo ; $k <= $hi ; $k = $k + $resolution ) {
if ( $pass{$i}{$j}{$k} == 1 ) {
push #point,[$i,$j,$k];
$num_cavities++;
while ( #point ) {
foreach my $vector ( keys %offset ) { #for each offset vector
my #neighbor = (($point[0][0]+$offset{$vector}[0]),($point[0][1]+$offset{$vector}[1]),($point[0][2]+$offset{$vector}[2])); #compute neighbor point
if ( exists $pass{$neighbor[0]}{$neighbor[1]}{$neighbor[2]} ) { #see if neighbor is in the grid
if ( $pass{$neighbor[0]}{$neighbor[1]}{$neighbor[2]} == 1 ) { #if it is see if its further than the probe radius
push #point,[($point[0][0]+$offset{$vector}[0]),($point[0][1]+$offset{$vector}[1]),($point[0][2]+$offset{$vector}[2])]; #if it is push it onto the list of points
}
}
}
$pass{$point[0][0]}{$point[0][1]}{$point[0][2]} = 0; #eliminate the point just tested from the pass array
shift #point; #move to the next point in the list
}
}
}
}
}
#print the results
print "\nthe structure has " . $num_cavities . " cavities.\n\n";
#print the point that are left over (these correspond to the cavities)
#for ( my $i = -10 ; $i <= 10 ; $i = $i + $resolution ) {
# for ( my $j = -10 ; $j <= 10 ; $j = $j + $resolution ) {
# for ( my $k = -10 ; $k <= 10 ; $k = $k + $resolution ) {
# print $i . "\t" . $j . "\t" . $k . "\t" . $pass{$i}{$j}{$k} . "\n";
# }
# }
#}
###################################################
# function
###################################################
sub parseATOM {
my($atomrecord) = #_;
use strict;
use warnings;
my %results = ( );
# Turn the scalar into an array of ATOM lines
my(#atomrecord) = split(/\n/, $atomrecord);
foreach my $record (#atomrecord) {
my $number = substr($record, 6, 5); # columns 7-11
my $x = substr($record, 30, 8); # columns 31-38
my $y = substr($record, 38, 8); # columns 39-46
my $z = substr($record, 46, 8); # columns 47-54
my $r = substr($record, 60, 6); # columns 47-54
#my $element = substr($record, 76, 2); # columns 77-78
# $number and $element may have leading spaces: strip them
$number =~ s/\s*//g;
#$element =~ s/\s*//g;
$x =~ s/\s*//g;
$y =~ s/\s*//g;
$z =~ s/\s*//g;
$r =~ s/\s*//g;
# Store information in hash
#$results{$number} = [$x,$y,$z,$element];
$results{$number} = [$x,$y,$z,$r];
}
# Return the hash
return %results;
}
Here's one thing that is almost certainly slowing things down:
$x =~ s/\s*//g;
$y =~ s/\s*//g;
$z =~ s/\s*//g;
$r =~ s/\s*//g;
It is possible for \s* to match an empty string, so you are replacing empty strings with empty strings, for each empty string in the target string.
Change to:
$x =~ s/\s+//g;
$y =~ s/\s+//g;
$z =~ s/\s+//g;
$r =~ s/\s+//g;
You have the following definitions:
my $lo = 1000;
my $hi = -1000;
So when you get to your first for loop, you will set $i to 1000, and then fail the check to see if it is less than -1000.
I'm fairly new to coding in Perl and am used to using C-style for loops. I'm not sure why the following program never prints a value of 4 for $l:
use strict;
use warnings;
my $minL = 4;
for (my $l = $minL; $l > 0; $l--) {
for (my $i = 0; $i + $l < $minL; $i++) {
print "$i $l\n";
}
}
Many thanks in advance.
Your inner for loop has the condition $i + $l < $minL. If $l == $minL, then $i + $l < $minL will be false even if $i is 0, so the loop runs 0 times and never prints anything.
Maybe you wanted to use <= for the condition?
By the way, here is how you could write the same thing (assuming the <= condition) using Perl-style foreach loops:
my $minL = 4;
for my $l (reverse 1 .. $minL) {
for my $i (0 .. $minL - $l) {
print "$i $l\n";
}
}
In the first iteration:
for (my $l = $minL; $l > 0; $l--) {
$l == $minL
for (my $i = 0; $i + $l < $minL; $i++) {
So this block won't run until $l is decremented:
print "$i $l\n";
}
Change your inner loop to:
for (my $i = 0; $i + $l <= $minL; $i++) {
I have a 2d array in Perl. I passed the array to a subroutine and I want to modify all elements of the 2d array then return it and print the array. I have attached my code so far below. The problem I am having is actually changing each individual element and passing the array to a subroutine.
Original Matrix+Code
x y z
CG -3.74900 -4.89100 -3.45400
OD1 -6.45900 -6.29100 -6.08000
OD2 -1.31600 -1.83300 -0.17600
sub translateMatrixOperation
{
my (#translatematrix, $x, $y, $z) = #_;
print "PRINTING FIRST\n";
my $arrsize = scalar #translatematrix;
for(my $i = 0; $i <= $arrsize; $i++)
{
for(my $j = 0; $j <= $arrsize; $j++)
{
if ($j == 0)
{
print "[$i][$j]:$translatematrix[$i][$j]\n";
$_ = $_ - $x;
}
elsif ($j == 1)
{
print "[$i][$j]:$translatematrix[$i][$j]\n";
$_ = $_ - $y;
}
elsif ($j == 2)
{
print "[$i][$j]:$translatematrix[$i][$j]\n";
$_ = $_ - $z;
}
}
}
print "PRINTING\n";
for(my $i = 0; $i <= $arrsize; $i++)
{
for(my $j = 0; $j <= $arrsize; $j++)
{
print "$translatematrix[$i][$j] ";
}
print "\n";
}
# return (\#translatematrix);
}
I want to edit the whole array by adding a constant value to the x values, a constant value to the y values, and a constant to the z. Where did I go wrong?
my (#translatematrix, $x, $y, $z) = #_;
does not make sense as #translatematrix slurps all elements from #_, and should be:
my ($translatematrix, $x, $y, $z) = #_;
where $translatematrix is array reference.
$_ = $_ - $x;
should be more like
$translatematrix->[$i][$j] -= $x;
and also similar logic to $y and $z should be applied.