RNAlib 2.4.6
  • Index
      • Getting Started
        • Installation and Configuration
          • Installing the ViennaRNA Package
          • Quick-start
          • Installation without root privileges
          • Notes for MacOS X users
          • Configuring RNAlib features
          • Streaming SIMD Extension (SSE) support
          • Scripting Interfaces
          • Cluster Analysis
          • Kinfold
          • RNAforester
          • Kinwalker
          • Link Time Optimization (LTO)
          • OpenMP support
          • POSIX threads (pthread) support
          • Stochastic backtracking using Boustrophedon scheme
          • SVM Z-score filter in RNALfold
          • GNU Scientific Library
          • Disable C11/C++11 feature support
          • Enable warnings for use of deprecated symbols
          • Single precision partition function
          • Help
          • Linking against RNAlib
          • Compiler and Linker flags
          • The pkg-config tool
        • HelloWorld
        • HelloWorld (Perl/Python)
          • Perl5
          • Python
      • Concepts and Algorithms
        • RNA Structure
          • RNA Structures
          • Levels of Structure Abstraction
          • Primary Structure
          • Secondary Structure
          • Tertiary Structure
          • Quarternary Structure
          • Pseudo-Knots
        • Distance Measures
          • Functions for Tree Edit Distances
          • Functions for String Alignment
          • Functions for Comparison of Base Pair Probabilities
        • Free Energy of Secondary Structures
          • Secondary Structure Loop Decomposition
          • Free Energy Evaluation API
          • Free Energy Parameters
          • Free Energy Parameters Modification API
          • Fine-tuning of the Energy Evaluation Model
        • Secondary Structure Folding Grammar
          • Secondary Structure Folding Recurrences
          • Additional Structural Domains
          • Structured Domains
          • Unstructured Domains
          • Domain Extension API
          • Constraints on the Folding Grammar
          • Hard Constraints API
          • Soft Constraints API
        • RNA Secondary Structure Landscapes
          • The Neighborhood of a Secondary Structure
          • The Secondary Structure Landscape API
        • Minimum Free Energy Algorithm(s)
          • Zuker’s Algorithm
          • MFE for circular RNAs
          • MFE Algorithm API
        • Partition Function and Equilibrium Probabilitiy Algorithm(s)
          • Equilibrium Ensemble Statistics
          • Partition Function and Equilibrium Probability API
        • Suboptimals and (other) Representative Structures
          • Suboptimal Secondary Structures
          • Sampling Secondary Structures from the Ensemble
          • Structure Enumeration and Sampling API
        • RNA-RNA Interaction
          • rip_intro
          • rip_intro
          • RNA-RNA interaction as a Stepwise Process
          • RNA-RNA Interaction API
        • Locally Stable Secondary Structures
          • local_intro
          • local_mfe
          • local_pf
          • Locally Stable Secondary Structure API
        • Comparative Structure Prediction
          • Incorporate Evolutionary Information
          • Comparative Structure Prediction API
        • Classified DP variations
          • The Idea of Classified Dynamic Programming
          • Distance Class Partitioning
          • Density of States (DOS)
          • Classified DP API
        • RNA Sequence Design
          • Generate Sequences that fold into particular Secondary Structures
          • RNA Sequence Design API
        • Experimental Structure Probing Data
          • Guide the Structure Prediction using Experimental Data
          • SHAPE reactivities
          • Structure Probing Data API
        • Ligand Binding
          • Small Molecules and Proteins that bind to specific RNA Structures
          • ligand_binding_api
        • (Tertiary) Structure Motifs
          • Incorporating Higher-Order (Tertiary) Structure Motifs
          • RNA G-Quadruplexes
          • (Tertiary) Structure Motif API
      • I/O Formats
        • RNA Structure Notations
          • Representations of Secondary Structures
          • Dot-Bracket Notation (a.k.a. Dot-Parenthesis Notation)
          • Extended Dot-Bracket Notation
          • Washington University Secondary Structure (WUSS) notation
          • Examples for Structure Parsing and Conversion
          • Structure Parsing and Conversion API
        • File Formats
          • File formats for Multiple Sequence Alignments (MSA)
          • ClustalW format
          • Stockholm 1.0 format
          • FASTA (Pearson) format
          • MAF format
          • File formats to manipulate the RNA folding grammar
          • Command Files
          • Constraint commands
          • RNA folding grammar exensions
          • Specification of the loop type context
          • Controlling the orientation of base pairing
          • Sequence coordinates
          • Valid constraint commands
          • Valid domain extensions commands
        • Plotting
          • Producing secondary structure graphs
          • Producing (colored) dot plots for base pair probabilities
          • Producing (colored) alignments
      • Basic Data Structures
        • Sequence and Structure Data
        • The ‘Fold Compound’
        • Model Details
      • API Features
        • RNAlib API v3.0
          • Introduction
          • What are the major changes?
          • How to port your program to the new API
          • Some Examples using RNAlib API v3.0
        • Callback Functions
          • The purpose of Callback mechanisms
          • List of available Callbacks
        • Scripting Language interface(s)
          • Introduction
          • Function renaming scheme
          • Object oriented Interface for data structures
          • Examples
          • SWIG generated Wrapper notes
      • Additional Utilities
      • Examples
        • C Examples
          • Hello World Examples
          • First Steps with the Fold Compound
          • Writing Callback Functions
          • Application of Soft Constraints
          • Other Examples
          • Deprecated Examples
        • Perl5 Examples
        • Python Examples
      • Changelog
      • Deprecated List
      • Bug List
      • Bibliography
      • The RNAlib API
        • Data Structures and Preprocessor Macros
          • The Dynamic Programming Matrices
            • enum vrna_mx_type_e
              • Overview
              • Detailed Documentation
                • Enum Values
            • struct vrna_mx_mfe_s
              • Overview
              • Detailed Documentation
              • Fields
            • struct vrna_mx_pf_s
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
          • The Fold Compound
            • enum vrna_fc_type_e
              • Overview
              • Detailed Documentation
                • Enum Values
            • struct vrna_fc_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
            • Macros
          • struct constrain
          • struct dupVar
          • struct duplexT
          • struct interact
            • Overview
            • Detailed Documentation
            • Fields
          • struct node
          • struct pu_contrib
            • Overview
            • Detailed Documentation
            • Fields
          • struct pu_out
            • Overview
            • Detailed Documentation
            • Fields
          • struct snoopT
          • struct vrna_basepair_s
          • struct vrna_bp_stack_s
          • struct vrna_color_s
          • struct vrna_cpair_s
          • struct vrna_data_linear_s
          • struct vrna_sect_s
          • Overview
          • Detailed Documentation
          • Typedefs
          • Global Functions
        • Utilities
          • Utilities for sequence alignments
            • struct vrna_pinfo_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
            • Macros
          • Functions that provide dynamically buffered stream-like data structures
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
          • Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments
            • enum vrna_command_e
            • struct vrna_command_s
              • Overview
              • Detailed Documentation
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
            • Macros
          • Functions for Creating Secondary Structure Plots, Dot-Plots, and More
            • Functions to generate annotations for Secondary Structure Plots, Dot-Plots, and Others
              • Overview
              • Detailed Documentation
              • Global Functions
            • struct COORDINATE
            • struct vrna_dotplot_auxdata_t
            • Overview
            • Detailed Documentation
            • Global Variables
            • Global Functions
            • Macros
          • Parsing, converting, and comparing sequences
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
          • Parsing, converting, comparing secondary structures
            • struct vrna_elem_prob_s
              • Overview
              • Detailed Documentation
            • struct vrna_hx_s
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Variables
            • Global Functions
            • Macros
          • Functions to convert between various units
            • enum vrna_unit_energy_e
              • Overview
              • Detailed Documentation
                • Enum Values
            • enum vrna_unit_temperature_e
              • Overview
              • Detailed Documentation
                • Enum Values
            • Overview
            • Detailed Documentation
            • Global Functions
          • Overview
          • Detailed Documentation
          • Global Variables
          • Global Functions
          • Macros
        • Classified Dynamic Programming variants
          • Compute the Density of States
            • Overview
            • Detailed Documentation
            • Global Variables
          • Distance based partitioning of the Secondary Structure Space
            • Calculating MFE representatives of a Distance Based Partitioning
              • struct TwoDfold_vars
                • Overview
                • Detailed Documentation
                • Fields
              • struct vrna_sol_TwoD_t
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
            • Calculate Partition Functions of a Distance Based Partitioning
              • struct vrna_sol_TwoD_pf_t
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
            • Stochastic Backtracking of Structures from Distance Based Partitioning
              • Overview
              • Detailed Documentation
              • Global Functions
        • RNA-RNA interaction
          • MFE Structures of two hybridized Sequences
            • Overview
            • Detailed Documentation
            • Global Functions
          • Partition Function for two hybridized Sequences
            • struct vrna_dimer_pf_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Variables
            • Global Functions
          • Partition Function for two hybridized Sequences as a stepwise Process
            • Overview
            • Detailed Documentation
            • Global Functions
        • The RNA folding grammar
          • Constraining the RNA folding grammar
            • Hard constraints
              • struct vrna_hc_s
                • Overview
                • Detailed Documentation
                • Fields
              • struct vrna_hc_up_s
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
              • Macros
            • Soft constraints
              • struct vrna_sc_s
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
          • Extending the folding grammar with additional domains
            • Unstructured domains
              • struct vrna_unstructured_domain_s
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
              • Macros
          • Energy parameters
            • Reading/Writing Energy Parameter Sets from/to File
              • Converting Energy Parameter Files
                • Overview
                • Detailed Documentation
                • Global Functions
                • Macros
              • enum parset
              • Overview
              • Detailed Documentation
              • Global Functions
            • struct vrna_exp_param_s
              • Overview
              • Detailed Documentation
              • Fields
            • struct vrna_param_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
          • Fine-tuning of the implemented models
            • struct vrna_md_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Variables
            • Global Functions
            • Macros
          • struct vrna_gr_aux_s
        • The RNA secondary structure landscape
          • Neighborhood relation and move sets for secondary structures
            • struct vrna_move_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
          • Refolding paths of secondary structures
            • Direct refolding paths between two secondary structures
              • struct vrna_path_s
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
        • Comparative structure prediction
          • MFE Consensus Structures for Sequence Alignment(s)
            • Overview
            • Detailed Documentation
            • Global Functions
          • Partition Function and Base Pair Probabilities for Sequence Alignment(s)
            • Overview
            • Detailed Documentation
            • Global Functions
          • Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)
            • Overview
            • Detailed Documentation
            • Global Functions
          • Local MFE Consensus Structure Prediction for Sequence Alignments
            • Overview
            • Detailed Documentation
            • Global Functions
          • Overview
          • Detailed Documentation
          • Global Variables
          • Global Functions
        • Suboptimals and representative structures
          • Compute the centroid structure
            • Overview
            • Detailed Documentation
            • Global Functions
          • Compute the structure with maximum expected accuracy (MEA)
            • Overview
            • Detailed Documentation
            • Global Functions
          • Structure sampling from the ensemble
            • Overview
            • Detailed Documentation
            • Global Variables
            • Global Functions
          • Suboptimal structures within an energy band arround the MFE
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Variables
            • Global Functions
          • Suboptimal structures sensu Stiegler et al. 1984 / Zuker et al. 1989
            • Overview
            • Detailed Documentation
            • Global Functions
        • Ligands binding to RNA structures
          • Incorporating ligands binding to specific sequence/structure motifs using soft constraints
            • Overview
            • Detailed Documentation
            • Global Functions
        • Experimental structure probing data
          • SHAPE reactivity data
            • Overview
            • Detailed Documentation
            • Global Functions
          • Generate soft constraints from data
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
            • Macros
        • Partition function and equilibrium properties
          • Overview
          • Detailed Documentation
          • Global Functions
        • Free energy evaluation
          • Process and evaluate individual loops
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
          • Overview
          • Detailed Documentation
          • Global Variables
          • Global Functions
        • Minimum Free Energy (MFE) algorithms
          • MFE Structures of single Nucleic Acid Sequences
            • Overview
            • Detailed Documentation
            • Global Functions
          • Overview
          • Detailed Documentation
          • Typedefs
          • Global Functions
        • Complex structured modules
          • G-quadruplexes
            • Overview
            • Detailed Documentation
            • Global Functions
        • Inverse Folding (Design)
          • Overview
          • Detailed Documentation
          • Global Variables
          • Global Functions
        • Locally stable structures
          • Local MFE Structure Prediction and Z-scores
            • Overview
            • Detailed Documentation
            • Global Functions
          • Partition Function and Equilibrium Probabilities for Locally Stable Secondary Structures
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
        • Global Namespace
          • enum MOVE_TYPE
          • enum vrna_hc_type_e
            • Overview
            • Detailed Documentation
              • Enum Values
          • enum vrna_sc_type_e
            • Overview
            • Detailed Documentation
              • Enum Values
          • enum vrna_seq_type_e
            • Overview
            • Detailed Documentation
              • Enum Values
          • struct Postorder_list
          • struct Tree
          • struct TwoDpfold_vars
            • Overview
            • Detailed Documentation
            • Fields
          • struct _struct_en
          • struct swString
          • struct vrna_dimer_conc_s
            • Overview
            • Detailed Documentation
            • Fields
          • struct vrna_hc_bp_storage_t
          • struct vrna_sc_bp_storage_t
          • struct vrna_sc_motif_s
          • struct vrna_sequence_s
            • Overview
            • Detailed Documentation
            • Fields
          • struct vrna_structured_domains_s
          • struct vrna_subopt_sol_s
            • Overview
            • Detailed Documentation
            • Fields
          • struct vrna_unstructured_domain_motif_s
          • Overview
          • Detailed Documentation
          • Typedefs
          • Global Variables
          • Global Functions
          • Macros
  • Page
      • Getting Started
      • Concepts and Algorithms
      • I/O Formats
      • Basic Data Structures
      • API Features
      • Additional Utilities
      • Examples
      • Changelog
      • Deprecated List
      • Bug List
      • Bibliography
      • The RNAlib API
        • Data Structures and Preprocessor Macros
        • Utilities
        • Classified Dynamic Programming variants
        • RNA-RNA interaction
        • The RNA folding grammar
        • The RNA secondary structure landscape
          • Neighborhood relation and move sets for secondary structures
          • Refolding paths of secondary structures
        • Comparative structure prediction
        • Suboptimals and representative structures
        • Ligands binding to RNA structures
        • Experimental structure probing data
        • Partition function and equilibrium properties
        • Free energy evaluation
        • Minimum Free Energy (MFE) algorithms
        • Complex structured modules
        • Inverse Folding (Design)
        • Locally stable structures
        • Global Namespace
  • « struct vrna_gr_aux_s
  • Neighborhood ... »
  • Getting Started
  • Concepts and Algorithms
  • I/O Formats
  • Basic Data Structures
  • API Features
  • Additional Utilities
  • Examples
  • Changelog
  • Deprecated List
  • Bug List
  • Bibliography
  • The RNAlib API
    • Data Structures and Preprocessor Macros
    • Utilities
    • Classified Dynamic Programming variants
    • RNA-RNA interaction
    • The RNA folding grammar
    • The RNA secondary structure landscape
      • Neighborhood relation and move sets for secondary structures
      • Refolding paths of secondary structures
    • Comparative structure prediction
    • Suboptimals and representative structures
    • Ligands binding to RNA structures
    • Experimental structure probing data
    • Partition function and equilibrium properties
    • Free energy evaluation
    • Minimum Free Energy (MFE) algorithms
    • Complex structured modules
    • Inverse Folding (Design)
    • Locally stable structures
    • Global Namespace

The RNA secondary structure landscape¶

Neighborhood relation and move sets for secondary structures
Refolding paths of secondary structures
Direct refolding paths between two secondary structures

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© Copyright 2017, Ronny Lorenz.
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