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The select function provides an excellent way of handling the data input and output from a number of filehandles concurrently, but this is where the comparison ends It s not possible, in any way, to use select for anything other than communicating with filehandles, and this limits its effectiveness for concurrent processing On the other hand, with threads you can create a new thread to handle any aspect of your process s execution, including, but not limited to, communication with filehandles For example, with a multidiscipline calculation you might create new threads to handle the different parts of the calculation

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Threads have been heavily updated in Perl 56 to form a significant, if still largely experimental, part of the Perl language In fact, in some circumstances, threads actually form a core part of the language s new architecture, and on the Windows platform threads are used to emulate the operation for fork, a function that is missing from the operating system itself Within Perl, the thread system is controlled using the Thread module, which provides an object-oriented interface for the creation and control of individual threads To create a new thread, you create a new Thread object and supply the name of a predefined subroutine, which forms the basis of the thread s execution sequence Once started, a thread can be paused, stopped, split into other threads, or bonded with other threads to create a superthread In all instances, the threads remain attached to the parent process it s not possible to convert a thread into a new process, although there s potentially no reason why you couldn t call fork!

of the first mutation For example, if the first mutation decreased the protein stability by removing a hydrogen-bond donor, a second mutation that changes the acceptor may result in a protein with two mutations that is just as stable as the native protein The second mutation is called a suppressor mutation

To create a new thread, import the Thread module and then create a new Thread object For example, to create a new thread that uses the subroutine process_queue:

use Thread; $thread = new Thread \&process_queue,"/usr/local/queue";

This is also a compromise (Fig 2-5) The specificity of the interaction between a protein and a small molecule or another protein is also a compromise We ve just said that charge charge and hydrogen-bond interactions don t contribute a lot to the stability of a protein because their interaction in the folded protein simply replaces their individual interaction with water The same may be said of the interaction between an enzyme and its substrate or one protein and another However, there is a huge amount of specificity to be gained in these kinds of interactions For tight binding, the protein and its ligand must be complementary in every way size, shape, charge, and hydrogen-bond donor and acceptor sites Both the protein and the ligand are solvated by water when they are separated As the two surfaces interact, water is excluded, hydrogen bonds are broken and formed, hydrophobic interactions occur, and the protein and ligand stick to each other As in protein folding and for the same reasons, the hydrophobic interaction provides much of the free energy for the association reaction, but polar groups that are removed

The object accepts the name of the subroutine to execute, and any further arguments are supplied as arguments to that subroutine The $thread variable in the preceding example contains a reference to the newly created thread and will provide a link from the main program to the thread The thread can obtain a reference to itself with the self method:

$me = Thread->self;

15:

Figure 2-5

Each thread is given its own unique thread ID The main program has a thread ID of 0, and subsequent threads are given a sequential thread number up to a current maximum of 232 1 You can discover the thread ID using the tid method,

$tid = $thread->tid;

The ASSOCIATION of two molecules uses the same interactions that stabilize a protein s structure: hydrophobic interactions, van der Waals interactions, hydrogen bonds, and ionic interactions To get the most out of the interaction, the two molecules must be complementary

or for a thread to find its own ID:

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