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 | |