/*
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# General Reference Manual Page Layout                      #
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/**
@page getting_started   Getting Started

- @subpage  install           describes how to install and configure <tt>RNAlib</tt> for your requirements
- @subpage  helloworld        presents some small example programs to get a first impression on how to use this library
- @subpage  helloworld_swig   contains small examples that show how to use RNAlib even without C/C++ programming skills from within your favorite scripting language


@page concepts   Concepts and Algorithms

This is an overview of the concepts and algorithms for which implementations can
be found in this library.

Almost all of them rely on the physics based Nearest
Neighbor Model for RNA secondary structure prediction.

- @subpage  secondary_structures          gives an introduction into the different layers of abstraction for RNA structures
- @subpage  distance_measures             introduces different metrics to allow for the comparison of secondary structures
- @subpage  energy_evaluation             shows how the stability of a secondary structure can be quantified in terms of free energy
- @subpage  folding_grammar               explains the basic recursive decomposition scheme that is applied in secondary structure prediction
- @subpage  secondary_structure_landscape describes how transition paths between secondary structures span a landscape like graph
- @subpage  mfe_algorithm                 compute the most stable conformation in thermodynamic equilibrium
- @subpage  pf_algorithm                  enable one to apply statistical mechanics to derive equilibrium probabilities of structure features
- @subpage  suboptimal_structures         allow for alternative description and enumeration of the structure ensemble
- @subpage  rip                           introduces how to model the interaction between RNA molecules
- @subpage  local_vs_global               offer insights into structuredness of long sequences and entire genomes
- @subpage  consensus_structures          augment structure prediction with evolutionary conservation of homologous sequences
- @subpage  classified_dp                 perform an <em>a priori</em> partitioning of the structure ensemble and compute various properties for the resulting classes.
- @subpage  design                        constitutes the inverse problem of structure prediction
- @subpage  structure_probing_data        can be used to guide structure prediction, for instance using SHAPE reactivity data
- @subpage  ligand_binding                adds more complexity to structure prediction by modelling the interaction between small chemical compounds or proteins and the RNA
- @subpage  structure_motifs              extend the abstraction of secondary structure beyond canonical base pair formation


@page io    I/O Formats

Below, you'll find a listing of different sections that introduce the most common notations
of sequence and structure data, specifications of bioinformatics sequence and structure file
formats, and various output file formats produced by our library.

- @subpage  rna_structure_notations       describes the different notations and representations of RNA secondary structures
- @subpage  file_formats                  gives an overview of the file formats compatible with our library
- @subpage  plots                         shows the different (PostScript) plotting functions for RNA secondary structures, feature probabilities, and multiple sequence alignments


@page data_structures Basic Data Structures

- @subpage  sequence_structure_data       shows the most common types for sequence or structure data
- @subpage  fold_compound_container       is the basic, central container for our implementations of prediction-, evaluation, and other algorithms
- @subpage  model_settings                provides the means to store the different model parameters


@page api_features    API Features

- @subpage  newAPI                        
- @subpage  callbacks                     
- @subpage  wrappers                      


@page utilities       Additional Utilities


@page examples  Examples

- @subpage  examples_c
- @subpage  examples_perl5
- @subpage  examples_python

*/


/*
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# Provide some order for the modules                        #
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*/

/**

@defgroup   eval                      Free Energy Evaluation

@defgroup   eval_loops                Energy Evaluation for Individual Loops
@ingroup    eval

@defgroup   eval_move                 Energy Evaluation for Atomic Moves
@ingroup    eval

@defgroup   eval_deprecated           Deprecated Interface for Free Energy Evaluation
@ingroup    eval

@defgroup   grammar                   The RNA Folding Grammar

@defgroup   model_details             Fine-tuning of the Implemented Models
@ingroup    grammar

@defgroup   energy_parameters         Energy Parameters
@ingroup    grammar

@defgroup   domains                   Extending the Folding Grammar with Additional Domains
@ingroup    grammar

@defgroup   domains_up                Unstructured Domains
@ingroup    domains

@defgroup   domains_struc             Structured Domains
@ingroup    domains

@defgroup   constraints               Constraining the RNA Folding Grammar
@ingroup    grammar

@defgroup   hard_constraints          Hard Constraints
@ingroup    constraints

@defgroup   soft_constraints          Soft Constraints
@ingroup    constraints

@defgroup   landscape                 The RNA Secondary Structure Landscape

@defgroup   mfe                       Minimum Free Energy (MFE) Algorithms

@defgroup   pf_fold                   Partition Function and Equilibrium Properties

@defgroup   mfe_global                Global MFE Prediction
@ingroup    mfe

@defgroup   mfe_window                Local (sliding window) MFE Prediction
@ingroup    mfe

@defgroup   mfe_backtracking          Backtracking MFE structures
@ingroup    mfe

@defgroup   part_func_global          Global Partition Function and Equilibrium Probabilities
@ingroup    pf_fold

@defgroup   part_func_window          Local (sliding window) Partition Function and Equilibrium Probabilities
@ingroup    pf_fold

@defgroup   subopt_and_representatives  Suboptimals and Representative Structures

@defgroup   subopt_zuker              Suboptimal Structures sensu Stiegler et al. 1984 / Zuker et al. 1989
@ingroup    subopt_and_representatives

@defgroup   subopt_wuchty             Suboptimal Structures within an Energy Band around the MFE
@ingroup    subopt_and_representatives

@defgroup   subopt_stochbt            Random Structure Samples from the Ensemble
@ingroup    subopt_and_representatives

@defgroup   mea_fold                  Compute the Structure with Maximum Expected Accuracy (MEA)
@ingroup    subopt_and_representatives

@defgroup   centroid_fold             Compute the Centroid Structure
@ingroup    subopt_and_representatives

@defgroup   cofold                    RNA-RNA Interaction

@defgroup   class_fold                Classified Dynamic Programming Variants

@defgroup   kl_neighborhood           Distance Based Partitioning of the Secondary Structure Space
@ingroup    class_fold

@defgroup   kl_neighborhood_mfe       Computing MFE representatives of a Distance Based Partitioning
@ingroup    kl_neighborhood mfe_global

@defgroup   kl_neighborhood_pf        Computing Partition Functions of a Distance Based Partitioning
@ingroup    kl_neighborhood part_func_global

@defgroup   kl_neighborhood_stochbt   Stochastic Backtracking of Structures from Distance Based Partitioning
@ingroup    kl_neighborhood subopt_stochbt

@defgroup   thermodynamics            Predicting various thermodynamic properties
@ingroup    part_func_global

@defgroup   dos                       Compute the Density of States
@ingroup    class_fold

@defgroup   inverse_fold              Inverse Folding (Design)

@defgroup   neighbors                 Neighborhood Relation and Move Sets for Secondary Structures
@ingroup    landscape

@defgroup   paths                     (Re-)folding Paths, Saddle Points, Energy Barriers, and Local Minima
@ingroup    landscape

@defgroup   paths_direct              Direct Refolding Paths between two Secondary Structures
@ingroup    paths

@defgroup   paths_walk                Folding Paths that start at a single Secondary Structure
@ingroup    paths

@defgroup   probing_data              Experimental Structure Probing Data
@brief                                Include Experimental Structure Probing Data to Guide Structure Predictions

@defgroup   SHAPE_reactivities        SHAPE Reactivity Data
@ingroup    probing_data

@defgroup   perturbation              Generate Soft Constraints from Data
@ingroup    probing_data

@defgroup   ligand_binding            Ligands Binding to RNA Structures
@brief                                Simple Extensions to Model Ligand Binding to RNA Structures

@defgroup   ligands_up                Ligands Binding to Unstructured Domains
@ingroup    ligand_binding

@defgroup   constraints_ligand        Incorporating Ligands Binding to Specific Sequence/Structure Motifs using Soft Constraints
@ingroup    ligand_binding

@defgroup   paired_modules            Structure Modules and Pseudoknots

@defgroup   pseudoknots               Pseudoknots
@ingroup    paired_modules

@defgroup   gquads                    G-Quadruplexes
@ingroup    paired_modules

@defgroup   utils                     Utilities

@defgroup   eval_loops_ext            Exterior Loops
@ingroup    eval_loops

@defgroup   eval_loops_hp             Hairpin Loops
@ingroup    eval_loops

@defgroup   eval_loops_int            Internal Loops
@ingroup    eval_loops

@defgroup   eval_loops_mb             Multibranch Loops
@ingroup    eval_loops

@defgroup   pf_cofold                 Partition Function for Two Hybridized Sequences
@ingroup    cofold

@defgroup   up_cofold                 Partition Function for two Hybridized Sequences as a Stepwise Process
@ingroup    cofold

@defgroup   energy_parameters_rw      Reading/Writing Energy Parameter Sets from/to File
@ingroup    energy_parameters

@defgroup   energy_parameters_convert Converting Energy Parameter Files
@ingroup    energy_parameters_rw

@defgroup   alphabet_utils            Utilities to deal with Nucleotide Alphabets
@ingroup    utils

@defgroup   string_utils              (Nucleic Acid Sequence) String Utilitites
@ingroup    utils

@defgroup   struct_utils              Secondary Structure Utilities
@ingroup    utils

@defgroup   struct_utils_dot_bracket  Dot-Bracket Notation of Secondary Structures
@ingroup    struct_utils

@defgroup   struct_utils_wuss         Washington University Secondary Structure (WUSS) notation
@ingroup    struct_utils

@defgroup   struct_utils_pair_table   Pair Table Representation of Secondary Structures
@ingroup    struct_utils

@defgroup   struct_utils_plist        Pair List Representation of Secondary Structures
@ingroup    struct_utils

@defgroup   struct_utils_abstract_shapes   Abstract Shapes Representation of Secondary Structures
@ingroup    struct_utils

@defgroup   struct_utils_helix_list   Helix List Representation of Secondary Structures
@ingroup    struct_utils

@defgroup   struct_utils_tree         Tree Representation of Secondary Structures
@ingroup    struct_utils

@defgroup   struct_utils_metrics      Distance measures between Secondary Structures
@ingroup    struct_utils

@defgroup   aln_utils                 Multiple Sequence Alignment Utilities
@ingroup    utils

@defgroup   file_utils                Files and I/O
@ingroup    utils

@defgroup   file_formats              Nucleic Acid Sequences and Structures
@ingroup    file_utils

@defgroup   file_formats_msa          Multiple Sequence Alignments
@ingroup    file_utils

@defgroup   command_files             Command Files
@ingroup    file_utils

@defgroup   plotting_utils            Plotting
@ingroup    utils

@defgroup   plot_layout_utils         Layouts and Coordinates
@ingroup    plotting_utils

@defgroup   annotation_utils          Annotation
@ingroup    plotting_utils

@defgroup   alignment_plots           Alignment Plots
@ingroup    plotting_utils

@defgroup   search_utils              Search Algorithms
@ingroup    utils

@defgroup   combinatorics_utils       Combinatorics Algorithms
@ingroup    utils

@defgroup   data_structures           (Abstract) Data Structures
@ingroup    utils

@defgroup   message_utils             Messages
@ingroup    utils

@defgroup   units                     Unit Conversion
@ingroup    utils

@defgroup   fold_compound             The Fold Compound
@ingroup    data_structures

@defgroup   dp_matrices               The Dynamic Programming Matrices
@ingroup    data_structures

@defgroup   hash_table_utils          Hash Tables
@ingroup    data_structures

@defgroup   heap_utils                Heaps
@ingroup    data_structures

@defgroup   buffer_utils              Buffers
@ingroup    data_structures

@defgroup   mfe_global_deprecated     Deprecated Interface for Global MFE Prediction
@ingroup    mfe_global

@defgroup   mfe_window_deprecated     Deprecated Interface for Local (Sliding Window) MFE Prediction
@ingroup    mfe_window

@defgroup   part_func_global_deprecated Deprecated Interface for Global Partition Function Computation
@ingroup    part_func_global

@defgroup   part_func_window_deprecated  Deprecated Interface for Local (Sliding Window) Partition Function Computation
@ingroup    part_func_window

@defgroup   subopt_stochbt_deprecated Deprecated Interface for Stochastic Backtracking
@ingroup    subopt_stochbt

@defgroup   aln_utils_deprecated      Deprecated Interface for Multiple Sequence Alignment Utilities
@ingroup    aln_utils

@defgroup   struct_utils_deprecated   Deprecated Interface for Secondary Structure Utilities
@ingroup    struct_utils

@defgroup   plotting_utils_deprecated Deprecated Interface for Plotting Utilities
@ingroup    plotting_utils

@defgroup   paths_deprecated          Deprecated Interface for (Re-)folding Paths, Saddle Points, and Energy Barriers
@ingroup    paths

*/
