RNAlib-2.3.1
File List
Here is a list of all documented files with brief descriptions:
[detail level 12]
  ViennaRNA
 1.8.4_epars.hFree energy parameters for parameter file conversion
 1.8.4_intloops.hFree energy parameters for interior loop contributions needed by the parameter file conversion functions
 2Dfold.hMFE structures for base pair distance classes
 2Dpfold.hPartition function implementations for base pair distance classes
 ali_plex.h
 alifold.hFunctions for comparative structure prediction using RNA sequence alignments
 aln_util.hVarious utility- and helper-functions for sequence alignments and comparative structure prediction
 alphabet.hFunctions to process, convert, and generally handle different nucleotide and/or base pair alphabets
 boltzmann_sampling.hBoltzmann Sampling of secondary structures from the ensemble
 centroid.hCentroid structure computation
 cofold.hMFE implementations for RNA-RNA interaction
 combinatorics.hVarious implementations that deal with combinatorial aspects of RNA/DNA folding
 commands.hParse and apply different commands that alter the behavior of secondary structure prediction and evaluation
 constraints.hFunctions and data structures for constraining secondary structure predictions and evaluation
 constraints_hard.hFunctions and data structures for handling of secondary structure hard constraints
 constraints_ligand.hFunctions for incorporation of ligands binding to hairpin and interior loop motifs using the soft constraints framework
 constraints_SHAPE.hThis module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints
 constraints_soft.hFunctions and data structures for secondary structure soft constraints
 convert_epars.hFunctions and definitions for energy parameter file format conversion
 data_structures.hVarious data structures and pre-processor macros
 dist_vars.hGlobal variables for Distance-Package
 dp_matrices.hFunctions to deal with standard dynamic programming (DP) matrices
 duplex.hFunctions for simple RNA-RNA duplex interactions
 edit_cost.hGlobal variables for Edit Costs included by treedist.c and stringdist.c
 energy_const.hEnergy parameter constants
 energy_par.h
 equilibrium_probs.hEquilibrium Probability implementations
 eval.hFunctions and variables related to energy evaluation of sequence/structure pairs
 exterior_loops.hEnergy evaluation of exterior loops for MFE and partition function calculations
 file_formats.hRead and write different file formats for RNA sequences, structures
 file_formats_msa.hFunctions dealing with file formats for Multiple Sequence Alignments (MSA)
 file_utils.hSeveral utilities for file handling
 findpath.hA breadth-first search heuristic for optimal direct folding paths
 fold.hMFE calculations for single RNA sequences
 fold_vars.hHere all all declarations of the global variables used throughout RNAlib
 gquad.hG-quadruplexes
 grammar.hImplementations for the RNA folding grammar
 hairpin_loops.hEnergy evaluation of hairpin loops for MFE and partition function calculations
 interior_loops.hEnergy evaluation of interior loops for MFE and partition function calculations
 intl11.h
 intl11dH.h
 intl21.h
 intl21dH.h
 intl22.h
 intl22dH.h
 inverse.hInverse folding routines
 Lfold.hFunctions for locally optimal MFE structure prediction
 loop_energies.hEnergy evaluation for MFE and partition function calculations
 LPfold.hPartition function implementation for the Lfold algorithm
 MEA.hComputes a MEA (maximum expected accuracy) structure
 mfe.hMFE calculations for single RNA sequences
 mm.hSeveral Maximum Matching implementations
 model.hThe model details data structure and its corresponding modifiers
 move_set.h
 multibranch_loops.hEnergy evaluation of multibranch loops for MFE and partition function calculations
 naview.h
 pair_mat.h
 params.hFunctions to deal with sets of energy parameters
 part_func.hPartition function implementations
 part_func_co.hPartition function for two RNA sequences
 part_func_up.hImplementations for accessibility and RNA-RNA interaction as a stepwise process
 perturbation_fold.hFind a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments
 PKplex.h
 plex.h
 plot_aln.hVarious functions for plotting Sequence / Structure Alignments
 plot_layouts.hSecondary structure plot layout algorithms
 plot_structure.hVarious functions for plotting RNA secondary structures
 ProfileAln.h
 profiledist.h
 PS_dot.hVarious functions for plotting RNA secondary structures, dot-plots and other visualizations
 read_epars.hRead and write energy parameter files
 ribo.hParse RiboSum Scoring Matrices for Covariance Scoring of Alignments
 RNAstruct.hParsing and Coarse Graining of Structures
 snofold.h
 snoop.h
 string_utils.hGeneral utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package
 stringdist.hFunctions for String Alignment
 structure_utils.hVarious utility- and helper-functions for secondary structure parsing, converting, etc
 structured_domains.hThis module provides interfaces that deal with additional structured domains in the folding grammar
 subopt.hRNAsubopt and density of states declarations
 svm_utils.h
 treedist.hFunctions for Tree Edit Distances
 units.hPhysical Units and Functions to convert them into each other
 unstructured_domains.hFunctions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches
 utils.hGeneral utility- and helper-functions used throughout the ViennaRNA Package