#!/usr/bin/perl

use warnings;
use strict;

# ein paar hundert zeilen code dazwischen.....

SKIPFRAG: while(.....)
eval {

        # extract Primary Structure 1 Letter-Code
    
        $primaryStructureSubStr = substr($primaryStructure1L, $k, $fragmentLength);
        
        # extract quartary structure chain
    
        $quartaryStructureSubStr = substr($quartaryStructureChainS, $k, $fragmentLength);
    
        # create secondary structure substring
        
        $secondaryStructureSubStr = substr($secondaryStructureS, $k, $fragmentLength);
    
    };
    if($@) {
        print "skipping fragment \n";
        $k++;    
        next SKIPFRAG;    
    }