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

/**

@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   soft_constraints_up       Soft Constraints (unpaired positions)
@ingroup    soft_constraints

@defgroup   soft_constraints_bp       Soft Constraints (base pairs)
@ingroup    soft_constraints

@defgroup   soft_constraints_st       Soft Constraints (base pair stacks)
@ingroup    soft_constraints

@defgroup   soft_constraints_generic  Soft Constraints (generic implementation)
@ingroup    soft_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   gquad_eval                Energy Evaluation for G-quadruplexes
@ingroup    gquads

@defgroup   gquad_dp                  Construction of G-quadruplex Dynamic Programming Matrices
@ingroup    gquads

@defgroup   gquad_parse               Parsing of G-quadruplexes
@ingroup    gquads

@defgroup   gquad_backtrack           Backtracking of G-quadruplexes
@ingroup    gquads

@defgroup   gquad_other               Ungrouped functions related to G-quadruplexes
@ingroup    gquads

@defgroup   gquad_deprecated          Depreacted G-Quadruplex API
@ingroup    gquads

@defgroup   modified_bases            Post-transcriptional Modifications
@brief                                Support of modified bases in secondary structure prediction

@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_salt    Salt corrections for energy parameters
@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   struct_utils_benchmark    Benchmark measures for Secondary Structure Predictions
@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   plot_probabilities        Probabilities
@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   data_structures_bt        Backtracking-related Structures
@ingroup    data_structures

@defgroup   hash_table_utils          Hash Tables
@ingroup    data_structures

@defgroup   heap_utils                Heaps
@ingroup    data_structures

@defgroup   strings                   Strings
@ingroup    data_structures

@defgroup   array_utils               Arrays
@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

*/
