|
| file | 1.8.4_epars.h [code] |
| | Free energy parameters for parameter file conversion.
|
| |
| file | 1.8.4_intloops.h [code] |
| | Free energy parameters for interior loop contributions needed by the parameter file conversion functions.
|
| |
| file | 2Dfold.h [code] |
| | MFE structures for base pair distance classes.
|
| |
| file | 2Dpfold.h [code] |
| | Partition function implementations for base pair distance classes.
|
| |
| file | alifold.h [code] |
| | Functions for comparative structure prediction using RNA sequence alignments.
|
| |
| file | aln_util.h [code] |
| | Various utility- and helper-functions for sequence alignments and comparative structure prediction.
|
| |
| file | alphabet.h [code] |
| | Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets.
|
| |
| file | boltzmann_sampling.h [code] |
| | Boltzmann Sampling of secondary structures from the ensemble.
|
| |
| file | centroid.h [code] |
| | Centroid structure computation.
|
| |
| file | cofold.h [code] |
| | MFE implementations for RNA-RNA interaction.
|
| |
| file | combinatorics.h [code] |
| | Various implementations that deal with combinatorial aspects of RNA/DNA folding.
|
| |
| file | commands.h [code] |
| | Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation.
|
| |
| file | constraints.h [code] |
| | Functions and data structures for constraining secondary structure predictions and evaluation.
|
| |
| file | constraints_hard.h [code] |
| | Functions and data structures for handling of secondary structure hard constraints.
|
| |
| file | constraints_ligand.h [code] |
| | Functions for incorporation of ligands binding to hairpin and interior loop motifs using the soft constraints framework.
|
| |
| file | constraints_SHAPE.h [code] |
| | This module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints.
|
| |
| file | constraints_soft.h [code] |
| | Functions and data structures for secondary structure soft constraints.
|
| |
| file | convert_epars.h [code] |
| | Functions and definitions for energy parameter file format conversion.
|
| |
| file | data_structures.h [code] |
| | Various data structures and pre-processor macros.
|
| |
| file | dist_vars.h [code] |
| | Global variables for Distance-Package.
|
| |
| file | dp_matrices.h [code] |
| | Functions to deal with standard dynamic programming (DP) matrices.
|
| |
| file | duplex.h [code] |
| | Functions for simple RNA-RNA duplex interactions.
|
| |
| file | edit_cost.h [code] |
| | global variables for Edit Costs included by treedist.c and stringdist.c
|
| |
| file | energy_const.h [code] |
| | Energy parameter constants.
|
| |
| file | equilibrium_probs.h [code] |
| | Equilibrium Probability implementations.
|
| |
| file | eval.h [code] |
| | Functions and variables related to energy evaluation of sequence/structure pairs.
|
| |
| file | exterior_loops.h [code] |
| | Energy evaluation of exterior loops for MFE and partition function calculations.
|
| |
| file | file_formats.h [code] |
| | Read and write different file formats for RNA sequences, structures.
|
| |
| file | file_formats_msa.h [code] |
| | Functions dealing with file formats for Multiple Sequence Alignments (MSA)
|
| |
| file | file_utils.h [code] |
| | Several utilities for file handling.
|
| |
| file | findpath.h [code] |
| | A breadth-first search heuristic for optimal direct folding paths.
|
| |
| file | fold.h [code] |
| | MFE calculations for single RNA sequences.
|
| |
| file | fold_vars.h [code] |
| | Here all all declarations of the global variables used throughout RNAlib.
|
| |
| file | gquad.h [code] |
| | G-quadruplexes.
|
| |
| file | grammar.h [code] |
| | Implementations for the RNA folding grammar.
|
| |
| file | hairpin_loops.h [code] |
| | Energy evaluation of hairpin loops for MFE and partition function calculations.
|
| |
| file | interior_loops.h [code] |
| | Energy evaluation of interior loops for MFE and partition function calculations.
|
| |
| file | inverse.h [code] |
| | Inverse folding routines.
|
| |
| file | Lfold.h [code] |
| | Functions for locally optimal MFE structure prediction.
|
| |
| file | loop_energies.h [code] |
| | Energy evaluation for MFE and partition function calculations.
|
| |
| file | LPfold.h [code] |
| | Partition function implementation for the Lfold algorithm.
|
| |
| file | MEA.h [code] |
| | Computes a MEA (maximum expected accuracy) structure.
|
| |
| file | mfe.h [code] |
| | MFE calculations for single RNA sequences.
|
| |
| file | mm.h [code] |
| | Several Maximum Matching implementations.
|
| |
| file | model.h [code] |
| | The model details data structure and its corresponding modifiers.
|
| |
| file | multibranch_loops.h [code] |
| | Energy evaluation of multibranch loops for MFE and partition function calculations.
|
| |
| file | naview.h [code] |
| |
| file | neighbor.h [code] |
| | Methods to compute the neighbors of an RNA secondary structure.
|
| |
| file | params.h [code] |
| | Functions to deal with sets of energy parameters.
|
| |
| file | part_func.h [code] |
| | Partition function implementations.
|
| |
| file | part_func_co.h [code] |
| | Partition function for two RNA sequences.
|
| |
| file | part_func_up.h [code] |
| | Implementations for accessibility and RNA-RNA interaction as a stepwise process.
|
| |
| file | perturbation_fold.h [code] |
| | Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments.
|
| |
| file | plot_aln.h [code] |
| | Various functions for plotting Sequence / Structure Alignments.
|
| |
| file | plot_layouts.h [code] |
| | Secondary structure plot layout algorithms.
|
| |
| file | plot_structure.h [code] |
| | Various functions for plotting RNA secondary structures.
|
| |
| file | profiledist.h [code] |
| |
| file | PS_dot.h [code] |
| | Various functions for plotting RNA secondary structures, dot-plots and other visualizations.
|
| |
| file | read_epars.h [code] |
| | Read and write energy parameter files.
|
| |
| file | ribo.h [code] |
| | Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.
|
| |
| file | RNAstruct.h [code] |
| | Parsing and Coarse Graining of Structures.
|
| |
| file | string_utils.h [code] |
| | General utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package.
|
| |
| file | stringdist.h [code] |
| | Functions for String Alignment.
|
| |
| file | structure_utils.h [code] |
| | Various utility- and helper-functions for secondary structure parsing, converting, etc.
|
| |
| file | structured_domains.h [code] |
| | This module provides interfaces that deal with additional structured domains in the folding grammar.
|
| |
| file | subopt.h [code] |
| | RNAsubopt and density of states declarations.
|
| |
| file | treedist.h [code] |
| | Functions for Tree Edit Distances.
|
| |
| file | units.h [code] |
| | Physical Units and Functions to convert them into each other.
|
| |
| file | unstructured_domains.h [code] |
| | Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.
|
| |
| file | utils.h [code] |
| | General utility- and helper-functions used throughout the ViennaRNA Package.
|
| |
| file | walk.h [code] |
| | Methods to generate particular paths such as gradient or random walks through the energy landscape of an RNA sequence.
|
| |