RNAlib-2.3.1
ViennaRNA Directory Reference

Files

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  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.