/**

@page  energy_evaluation    Free Energy of Secondary Structures
@brief                      A description on how secondary structures are decomposed
                            into individual loops to eventually evaluate their stability
                            in terms of free energy.
                            
@tableofcontents

@section  sec_loop_decomposition  Secondary Structure Loop Decomposition

Each base pair in a secondary structure closes a loop, thereby directly
enclosing unpaired nucleotides, and/or further base pairs. Our implementation
distinguishes four basic types of loops:

- hairpin loops
- interior loops
- multibranch loops
- exterior loop

While the exterior loop is a special case without a closing pair, the other
loops are determined by the number of base pairs involved in the loop formation,
i.e. hairpin loops are 1-loops, since only a single base pair delimits the loop.
interior loops are 2-loops due to their enclosing, and enclosed base pair. All
loops where more than two base pairs are involved, are termed multibranch loops.

@image html loop_types.png
@image latex loop_types.eps

Any secondary structure can be decomposed into its loops. Each of the loops then
can be scored in terms of free energy, and the free energy of an entire secondary
structure is simply the sum of free energies of its loops.

@image html loop_decomposition.png
@image latex loop_decomposition.eps

@subsection   sec_loop_decomposition_api   Free Energy Evaluation API

While we implement some functions that decompose a secondary structure into
its individual loops, the majority of methods provided in @b RNAlib are dedicated
to free energy evaluation. The corresponding modules are:

@see @ref eval, @ref eval_loops


@section  sec_energy_parameters       Free Energy Parameters

For secondary structure free energy evaluation we usually utilize the set of
Nearest Neighbor Parameters also used in other software, such as @em UNAfold
and @em RNAstructure. While the @em RNAlib already contains a compiled-in set
of the latest <em>Turner 2004 Free Energy Parameters</em>, we defined a file
format that allows to change these parameters at runtime. The <tt>ViennaRNA
Package</tt> already comes with a set of parameter files containing

- Turner 1999 RNA parameters
- Mathews 1999 DNA parameters
- Andronescu 2007 RNA parameters
- Mathews 2004 DNA parameters


@subsection sec_energy_parameters_api Free Energy Parameters Modification API

@see @ref energy_parameters, @ref energy_parameters_rw

@section  sec_model_details           Fine-tuning of the Energy Evaluation Model

@see @ref model_details

@htmlonly
<hr>
Go to the next Chapter <a href="folding_grammar.html">&quot;Secondary Structure Folding Grammar&quot;</a>
@endhtmlonly

*/
