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
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
enum MOVE_TYPE
enum vrna_hc_type_e
enum vrna_sc_type_e
enum vrna_seq_type_e
struct Postorder_list
struct Tree
struct TwoDpfold_vars
struct _struct_en
struct swString
struct vrna_dimer_conc_s
struct vrna_hc_bp_storage_t
struct vrna_sc_bp_storage_t
struct vrna_sc_motif_s
struct vrna_sequence_s
struct vrna_structured_domains_s
struct vrna_subopt_sol_s
struct vrna_unstructured_domain_motif_s
Overview
Detailed Documentation
Typedefs
Global Variables
Global Functions
Macros
« struct TwoDpfold_vars
struct swString »
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
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
enum MOVE_TYPE
enum vrna_hc_type_e
enum vrna_sc_type_e
enum vrna_seq_type_e
struct Postorder_list
struct Tree
struct TwoDpfold_vars
struct _struct_en
struct swString
struct vrna_dimer_conc_s
struct vrna_hc_bp_storage_t
struct vrna_sc_bp_storage_t
struct vrna_sc_motif_s
struct vrna_sequence_s
struct vrna_structured_domains_s
struct vrna_subopt_sol_s
struct vrna_unstructured_domain_motif_s
Overview
Detailed Documentation
Typedefs
Global Variables
Global Functions
Macros
struct _struct_en
¶
#include
<ViennaRNA/move_set.h>
Data structure for
energy_of_move()
// fields
int
energy
short
*
structure