RNAlib-2.6.3
 
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ViennaRNA Directory Reference
+ Directory dependency graph for ViennaRNA:

Directories

 constraints
 
 datastructures
 
 io
 
 landscape
 
 loops
 
 params
 
 plotting
 
 search
 
 utils
 

Files

 2Dfold.h
 MFE structures for base pair distance classes.
 
 2Dpfold.h
 Partition function implementations for base pair distance classes.
 
 ali_plex.h
 
 alifold.h
 Functions for comparative structure prediction using RNA sequence alignments.
 
 aln_util.h
 Use ViennaRNA/utils/alignments.h instead.
 
 alphabet.h
 Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets.
 
 boltzmann_sampling.h
 Boltzmann Sampling of secondary structures from the ensemble.
 
 centroid.h
 Centroid structure computation.
 
 char_stream.h
 Use ViennaRNA/datastructures/char_stream.h instead.
 
 cofold.h
 MFE implementations for RNA-RNA interaction.
 
 combinatorics.h
 Various implementations that deal with combinatorial aspects of objects.
 
 commands.h
 Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation.
 
 concentrations.h
 Concentration computations for RNA-RNA interactions.
 
 constraints.h
 Use ViennaRNA/constraints/basic.h instead.
 
 constraints_hard.h
 Use ViennaRNA/constraints/hard.h instead.
 
 constraints_ligand.h
 Use ViennaRNA/constraints/ligand.h instead.
 
 constraints_SHAPE.h
 Use ViennaRNA/constraints/SHAPE.h instead.
 
 constraints_soft.h
 Use ViennaRNA/constraints/soft.h instead.
 
 convert_epars.h
 Use ViennaRNA/params/convert.h instead.
 
 data_structures.h
 Use ViennaRNA/datastructures/basic.h instead.
 
 dist_vars.h
 Global variables for Distance-Package.
 
 dp_matrices.h
 Functions to deal with standard dynamic programming (DP) matrices.
 
 duplex.h
 Functions for simple RNA-RNA duplex interactions.
 
 edit_cost.h
 global variables for Edit Costs included by treedist.c and stringdist.c
 
 energy_const.h
 Use ViennaRNA/params/constants.h instead.
 
 energy_par.h
 Use ViennaRNA/params/default.h instead.
 
 equilibrium_probs.h
 Equilibrium Probability implementations.
 
 eval.h
 Functions and variables related to energy evaluation of sequence/structure pairs.
 
 exterior_loops.h
 Use ViennaRNA/loops/external.h instead.
 
 file_formats.h
 Use ViennaRNA/io/file_formats.h instead.
 
 file_formats_msa.h
 Use ViennaRNA/io/file_formats_msa.h instead.
 
 file_utils.h
 Use ViennaRNA/io/utils.h instead.
 
 findpath.h
 Use ViennaRNA/landscape/findpath.h instead.
 
 fold.h
 MFE calculations for single RNA sequences.
 
 fold_compound.h
 The Basic Fold Compound API.
 
 fold_vars.h
 Here all all declarations of the global variables used throughout RNAlib.
 
 gquad.h
 G-quadruplexes.
 
 grammar.h
 Implementations for the RNA folding grammar.
 
 hairpin_loops.h
 Use ViennaRNA/loops/hairpin.h instead.
 
 heat_capacity.h
 Compute heat capacity for an RNA.
 
 interior_loops.h
 Use ViennaRNA/loops/internal.h instead.
 
 inverse.h
 Inverse folding routines.
 
 Lfold.h
 Functions for locally optimal MFE structure prediction.
 
 loop_energies.h
 Use ViennaRNA/loops/all.h instead.
 
 LPfold.h
 Partition function and equilibrium probability implementation for the sliding window algorithm.
 
 MEA.h
 Computes a MEA (maximum expected accuracy) structure.
 
 mfe.h
 Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence data.
 
 mfe_window.h
 Compute local Minimum Free Energy (MFE) using a sliding window approach and backtrace corresponding secondary structures.
 
 mm.h
 Several Maximum Matching implementations.
 
 model.h
 The model details data structure and its corresponding modifiers.
 
 move_set.h
 
 multibranch_loops.h
 Use ViennaRNA/loops/multibranch.h instead.
 
 naview.h
 Use ViennaRNA/plotting/naview/naview.h instead.
 
 neighbor.h
 Use ViennaRNA/landscape/neighbor.h instead.
 
 pair_mat.h
 
 params.h
 Use ViennaRNA/params/basic.h instead.
 
 part_func.h
 Partition function implementations.
 
 part_func_co.h
 Partition function for two RNA sequences.
 
 part_func_up.h
 Implementations for accessibility and RNA-RNA interaction as a stepwise process.
 
 part_func_window.h
 Partition function and equilibrium probability implementation for the sliding window algorithm.
 
 perturbation_fold.h
 Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments.
 
 pf_multifold.h
 
 pk_plex.h
 Heuristics for two-step pseudoknot forming interaction predictions.
 
 PKplex.h
 
 plex.h
 
 plot_aln.h
 Use ViennaRNA/plotting/alignments.h instead.
 
 plot_layouts.h
 Use ViennaRNA/plotting/layouts.h instead.
 
 plot_structure.h
 Use ViennaRNA/plotting/structures.h instead.
 
 plot_utils.h
 Use ViennaRNA/plotting/utils.h instead.
 
 ProfileAln.h
 
 profiledist.h
 
 PS_dot.h
 Use ViennaRNA/plotting/probabilities.h instead.
 
 read_epars.h
 Use ViennaRNA/params/io.h instead.
 
 ribo.h
 Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.
 
 RNAstruct.h
 Parsing and Coarse Graining of Structures.
 
 sequence.h
 Functions and data structures related to sequence representations ,.
 
 snofold.h
 
 snoop.h
 
 special_const.h
 
 stream_output.h
 Use ViennaRNA/datastructures/stream_output.h instead.
 
 string_utils.h
 Use ViennaRNA/utils/strings.h instead.
 
 stringdist.h
 Functions for String Alignment.
 
 structure_utils.h
 Use ViennaRNA/utils/structures.h instead.
 
 structured_domains.h
 This module provides interfaces that deal with additional structured domains in the folding grammar.
 
 subopt.h
 RNAsubopt and density of states declarations.
 
 subopt_zuker.h
 
 svm_utils.h
 Use ViennaRNA/utils/svm.h instead.
 
 treedist.h
 Functions for Tree Edit Distances.
 
 ugly_bt.h
 
 units.h
 Use ViennaRNA/utils/units.h instead.
 
 unstructured_domains.h
 Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.
 
 utils.h
 Use ViennaRNA/utils/basic.h instead.
 
 vrna_config.h
 
 walk.h
 Use ViennaRNA/landscape/walk.h instead.
 
 wrap_dlib.h
 
 zscore.h