| ►Free Energy Evaluation | Functions and variables related to free energy evaluation of sequence/structure pairs |
| ►Energy Evaluation for Individual Loops | Functions to evaluate the free energy of particular types of loops |
| Exterior Loops | Functions to evaluate the free energy contributions for exterior loops |
| Hairpin Loops | Functions to evaluate the free energy contributions for hairpin loops |
| Internal Loops | Functions to evaluate the free energy contributions for internal loops |
| Multibranch Loops | Functions to evaluate the free energy contributions for mutlibranch loops |
| Energy Evaluation for Atomic Moves | Functions to evaluate the free energy change of a structure after application of (a set of) atomic moves |
| Deprecated Interface for Free Energy Evaluation | Deprecated Energy Evaluation functions |
| ►The RNA Folding Grammar | The RNA folding grammar as implemented in RNAlib |
| Fine-tuning of the Implemented Models | Functions and data structures to fine-tune the implemented secondary structure evaluation model |
| ►Energy Parameters | All relevant functions to retrieve and copy pre-calculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s) |
| ►Reading/Writing Energy Parameter Sets from/to File | Read and Write energy parameter sets from and to files or strings |
| Converting Energy Parameter Files | Convert energy parameter files into the latest format |
| ►Extending the Folding Grammar with Additional Domains | This module covers simple and straight-forward extensions to the RNA folding grammar |
| Unstructured Domains | Add and modify unstructured domains to the RNA folding grammar |
| Structured Domains | Add and modify structured domains to the RNA folding grammar |
| ►Constraining the RNA Folding Grammar | This module provides general functions that allow for an easy control of constrained secondary structure prediction and evaluation |
| Hard Constraints | This module covers all functionality for hard constraints in secondary structure prediction |
| Soft Constraints | Functions and data structures for secondary structure soft constraints |
| ►The RNA Secondary Structure Landscape | |
| Neighborhood Relation and Move Sets for Secondary Structures | Different functions to generate structural neighbors of a secondary structure according to a particular Move Set |
| ►(Re-)folding Paths, Saddle Points, Energy Barriers, and Local Minima | API for various RNA folding path algorithms |
| Direct Refolding Paths between two Secondary Structures | Heuristics to explore direct, optimal (re-)folding paths between two secondary structures |
| Folding Paths that start at a single Secondary Structure | Implementation of gradient- and random walks starting from a single secondary structure |
| Deprecated Interface for (Re-)folding Paths, Saddle Points, and Energy Barriers | |
| ►Minimum Free Energy (MFE) Algorithms | Predicting the Minimum Free Energy (MFE) and a corresponding (consensus) secondary structure |
| ►Global MFE Prediction | Variations of the global Minimum Free Energy (MFE) prediction algorithm |
| Computing MFE representatives of a Distance Based Partitioning | Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures |
| Deprecated Interface for Global MFE Prediction | |
| ►Local (sliding window) MFE Prediction | Variations of the local (sliding window) Minimum Free Energy (MFE) prediction algorithm |
| Deprecated Interface for Local (Sliding Window) MFE Prediction | |
| Backtracking MFE structures | Backtracking related interfaces |
| ►Partition Function and Equilibrium Properties | Compute the partition function to assess various equilibrium properties |
| ►Global Partition Function and Equilibrium Probabilities | Variations of the global partition function algorithm |
| Computing Partition Functions of a Distance Based Partitioning | Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures |
| Predicting various thermodynamic properties | Compute various thermodynamic properties using the partition function |
| Deprecated Interface for Global Partition Function Computation | |
| ►Local (sliding window) Partition Function and Equilibrium Probabilities | Scanning version using a sliding window approach to compute equilibrium probabilities |
| Deprecated Interface for Local (Sliding Window) Partition Function Computation | |
| ►Suboptimals and Representative Structures | Sample and enumerate suboptimal secondary structures from RNA sequence data |
| Suboptimal Structures sensu Stiegler et al. 1984 / Zuker et al. 1989 | |
| Suboptimal Structures within an Energy Band around the MFE | |
| ►Random Structure Samples from the Ensemble | Functions to draw random structure samples from the ensemble according to their equilibrium probability |
| Stochastic Backtracking of Structures from Distance Based Partitioning | Contains functions related to stochastic backtracking from a specified distance class |
| Deprecated Interface for Stochastic Backtracking | |
| Compute the Structure with Maximum Expected Accuracy (MEA) | |
| Compute the Centroid Structure | |
| ►RNA-RNA Interaction | |
| Partition Function for Two Hybridized Sequences | Partition Function Cofolding |
| Partition Function for two Hybridized Sequences as a Stepwise Process | RNA-RNA interaction as a stepwise process |
| ►Classified Dynamic Programming Variants | |
| ►Distance Based Partitioning of the Secondary Structure Space | |
| Computing MFE representatives of a Distance Based Partitioning | Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures |
| Computing Partition Functions of a Distance Based Partitioning | Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures |
| Stochastic Backtracking of Structures from Distance Based Partitioning | Contains functions related to stochastic backtracking from a specified distance class |
| Compute the Density of States | |
| Inverse Folding (Design) | RNA sequence design |
| ►Experimental Structure Probing Data | Include Experimental Structure Probing Data to Guide Structure Predictions |
| SHAPE Reactivity Data | Incorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints |
| Generate Soft Constraints from Data | Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments |
| ►Ligands Binding to RNA Structures | Simple Extensions to Model Ligand Binding to RNA Structures |
| Ligands Binding to Unstructured Domains | Add ligand binding to loop regions using the Unstructured Domains feature |
| Incorporating Ligands Binding to Specific Sequence/Structure Motifs using Soft Constraints | |
| ►Structure Modules and Pseudoknots | |
| Pseudoknots | Implementations to predict pseudoknotted structures |
| G-Quadruplexes | Various functions related to G-quadruplex computations |
| ►Utilities | |
| Utilities to deal with Nucleotide Alphabets | Functions to cope with various aspects related to the nucleotide sequence alphabet |
| (Nucleic Acid Sequence) String Utilitites | Functions to parse, convert, manipulate, create, and compare (nucleic acid sequence) strings |
| ►Secondary Structure Utilities | Functions to create, parse, convert, manipulate, and compare secondary structure representations |
| Dot-Bracket Notation of Secondary Structures | The Dot-Bracket notation as introduced already in the early times of the ViennaRNA Package denotes base pairs by matching pairs of parenthesis () and unpaired nucleotides by dots . |
| Washington University Secondary Structure (WUSS) notation | The WUSS notation, as frequently used for consensus secondary structures in Stockholm 1.0 format |
| Pair Table Representation of Secondary Structures | |
| Pair List Representation of Secondary Structures | |
| Abstract Shapes Representation of Secondary Structures | Abstract Shapes, introduced by Giegerich et al. in (2004) [10], collapse the secondary structure while retaining the nestedness of helices and hairpin loops |
| Helix List Representation of Secondary Structures | |
| Tree Representation of Secondary Structures | Secondary structures can be readily represented as trees, where internal nodes represent base pairs, and leaves represent unpaired nucleotides. The dot-bracket structure string already is a tree represented by a string of parenthesis (base pairs) and dots for the leaf nodes (unpaired nucleotides) |
| Distance measures between Secondary Structures | |
| Deprecated Interface for Secondary Structure Utilities | |
| ►Multiple Sequence Alignment Utilities | Functions to extract features from and to manipulate multiple sequence alignments |
| Deprecated Interface for Multiple Sequence Alignment Utilities | |
| ►Files and I/O | Functions to parse, write, and convert various file formats and to deal with file system related issues |
| Nucleic Acid Sequences and Structures | Functions to read/write different file formats for nucleic acid sequences and secondary structures |
| Multiple Sequence Alignments | Functions to read/write multiple sequence alignments (MSA) in various file formats |
| Command Files | Functions to parse and interpret the content of Command Files |
| ►Plotting | Functions for Creating Secondary Structure Plots, Dot-Plots, and More |
| Layouts and Coordinates | Functions to compute coordinate layouts for secondary structure plots |
| Annotation | Functions to generate annotations for Secondary Structure Plots, Dot-Plots, and Others |
| Alignment Plots | Functions to generate Alignment plots with annotated consensus structure |
| Deprecated Interface for Plotting Utilities | |
| Search Algorithms | Implementations of various search algorithms to detect strings of objects within other strings of objects |
| Combinatorics Algorithms | Implementations to solve various combinatorial aspects for strings of objects |
| ►(Abstract) Data Structures | All datastructures and typedefs shared among the ViennaRNA Package can be found here |
| The Fold Compound | This module provides interfaces that deal with the most basic data structure used in structure predicting and energy evaluating function of the RNAlib |
| The Dynamic Programming Matrices | This module provides interfaces that deal with creation and destruction of dynamic programming matrices used within the RNAlib |
| Hash Tables | Various implementations of hash table functions |
| Heaps | Interface for an abstract implementation of a heap data structure |
| Buffers | Functions that provide dynamically buffered stream-like data structures |
| Messages | Functions to print various kind of messages |
| Unit Conversion | Functions to convert between various physical units |
1.9.1