 #!/usr/bin/perl

use strict;

# sort_mol2_bonds.pl - a script to reorder the listing in a .mol2 @<TRIPOS>BOND
# section so that the following conventions are preserved:
#   1. Atoms on each line are in increasing order (e.g. 1 2 not 2 1)
#   2. The bonds appear in order of ascending atom number
#   3. For bonds involving the same atom in the first position, the bonds appear
#       in order of ascending second atom
#
# Written by: Justin Lemkul ([email protected])
#
# Distributed under the GPL-3.0 license

unless (scalar(@ARGV)==2)
{
    die "Usage: perl sort_mol2_bonds.pl input.mol2 output.mol2\n";
}

my $input = $ARGV[0];
my $output = $ARGV[1];

open(IN, "<$input") || die "Cannot open $input: $!\n";
my @in = <IN>;
close(IN);

# test for header lines that some scripts produce
unless($in[0] =~ /TRIPOS/)
{
    die "Nonstandard header found: $in[0]. Please delete header lines until the TRIPOS molecule definition.\n"; 
}

open(OUT, ">$output") || die "Cannot open $output: $!\n";

# get number of atoms and number of bonds from mol2 file
my @tmp = split(" ", $in[2]);
my $natom = $tmp[0];
my $nbond = $tmp[1];

# check
print "Found $natom atoms in the molecule, with $nbond bonds.\n";

# print out everything up until the bond section
my $i=0;
while (!($in[$i] =~ /BOND/))
{
    print OUT $in[$i];
    $i++;
}

# print the bond section header line to output
print OUT $in[$i];
$i++;

# read in the bonds and sort them
my $bondfmt = "%6d%6d%6d%5s\n";
my @tmparray; 

# sort the bonds - e.g. the one that has the
# lowest atom number in the first position and then the
# lowest atom number in the second position (swap if necessary)
for (my $j=0; $j<$nbond; $j++)
{
    my @tmp = split(" ", $in[$i+$j]);
    # parse atom numbers
    my $ai = $tmp[1];
    my $aj = $tmp[2];
    # reorder if second atom number < first
    if ($aj < $ai)
    {
        $ai = $tmp[2];
        $aj = $tmp[1];
    }
    # store new lines in a temporary array
    $tmparray[$j] = sprintf($bondfmt, $tmp[0], $ai, $aj, $tmp[3]); 
}

# loop over tmparray to find each atom number
my $nbond = 0;
for (my $x=1; $x<=$natom; $x++)
{
    my @bondarray;
    my $ntmp = scalar(@tmparray);
    for (my $b=0; $b<$ntmp; $b++)
    {
        my @tmp = split(" ", $tmparray[$b]);
        if ($tmp[1] == $x)
        {
            push(@bondarray, $tmparray[$b]);
            splice(@tmparray, $b, 1);
            $ntmp--;
            $b--;
        }
    }

    if (scalar(@bondarray) > 0) # some atoms will only appear in $aj, not $ai
    {
        my $nbondarray = scalar(@bondarray);
        if ($nbondarray > 1)
        {
            # loop over all bonds, find the one with lowest $aj
            # and then print it
            for (my $y=0; $y<$nbondarray; $y++)
            {
                my @tmp2 = split(" ", $bondarray[$y]);
                my $tmpatom = $tmp[2];
                my $lowindex = 0;
                if ($tmp2[2] < $tmpatom)
                {
                    $lowindex = $y; 
                }
                my $keep = splice(@bondarray, $lowindex, 1);
                $y--;
                $nbondarray--;
                my @sorted = split(" ", $keep);
                $nbond++;
                printf OUT $bondfmt, $nbond, $sorted[1], $sorted[2], $sorted[3]; 
            }
        }
        else
        {
            $nbond++;
            my @tmp2 = split(" ", $bondarray[0]);
            printf OUT $bondfmt, $nbond, $tmp2[1], $tmp2[2], $tmp2[3];
        }
    }
}

close(OUT);

exit;

created 2 years ago

Perl Online Compiler

Write, Run & Share Perl code online using OneCompiler's Perl online compiler for free. It's one of the robust, feature-rich online compilers for Perl language, running on the latest version 5.22.1. Getting started with the OneCompiler's Perl compiler is simple and pretty fast. The editor shows sample boilerplate code when you choose language as Perl and start coding.

Taking inputs (stdin)

OneCompiler's Perl online editor supports stdin and users can give inputs to programs using the STDIN textbox under the I/O tab. Following is a sample Perl program which takes name as input and prints hello message with your name.

my $name = <STDIN>;             
print "Hello $name.\n";

About Perl

Perl(Practical Extraction and Report Language) is especially desined for text processing by Larry Wall.

Key features

Cross-platform
Efficient for mission critical applications.
Open-source
Supports both procedural and object-oriented programming.
Perl interpreter is embeddable with other systems.
Loosely typed language

Syntax help

Data types

There is no need to specify the type of the data in Perl as it is loosely typed language.

Type	Description	Usage
Scalar	Scalar is either a number or a string or an address of a variable(reference)	$var
Arrays	Array is an ordered list of scalars, you can access arrays with indexes which starts from 0	@arr = (1,2,3)
Hash	Hash is an unordered set of key/value pairs	%ul = (1,'foo', 2, 'bar)

Variables

In Perl, there is no need to explicitly declare variables to reserve memory space. When you assign a value to a variable, declaration happens automatically.

$var-name =value; #scalar-variable
@arr-name = (values); #Array-variables
%hashes = (key-value pairs); # Hash-variables

Loops

1. If family:

If, If-else, Nested-Ifs are used when you want to perform a certain set of operations based on conditional expressions.

If

if(conditional-expression){    
//code    
}

If-else

if(conditional-expression){  
//code if condition is true  
}else{  
//code if condition is false  
}

Nested-If-else

if(condition-expression1){  
//code if above condition is true  
}else if(condition-expression2){  
//code if above condition is true  
}  
else if(condition-expression3){  
//code if above condition is true  
}  
...  
else{  
//code if all the conditions are false  
}

2. Switch:

There is no case or switch in perl, instead we use given and when to check the code for multiple conditions.

given(expr){    
when (value1)  
{//code if above value is matched;}    
when (value2)  
{//code if above value is matched;}   
when (value3)  
{//code if above value is matched;}  
default  
{//code if all the above cases are not matched.}     
}

3. For:

For loop is used to iterate a set of statements based on a condition.

for(Initialization; Condition; Increment/decrement){  
  // code  
}

4. While:

While is also used to iterate a set of statements based on a condition. Usually while is preferred when number of iterations are not known in advance.

while(condition) {  
 // code 
}

5. Do-While:

Do-while is also used to iterate a set of statements based on a condition. It is mostly used when you need to execute the statements atleast once.

do {
  // code 
} while (condition);

Sub-routines

Sub-routines are similar to functions which contains set of statements. Usually sub-routines are written when multiple calls are required to same set of statements which increases re-usuability and modularity.

How to define a sub-routine

sub subroutine_name 
{
	# set of Statements
}

How to call a sub-routine

subroutine_name();
subroutine_name(arguments-list); // if arguments are present