ViennaRNA Directory Reference

Directory dependency graph for ViennaRNA:

Directories

Files
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]
	Use ViennaRNA/utils/alignments.h instead.
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	char_stream.h [code]
	Use ViennaRNA/datastructures/char_stream.h instead.
file	cofold.h [code]
	MFE implementations for RNA-RNA interaction.
file	combinatorics.h [code]
	Various implementations that deal with combinatorial aspects of objects.
file	commands.h [code]
	Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation.
file	concentrations.h [code]
	Concentration computations for RNA-RNA interactions.
file	constraints.h [code]
	Use ViennaRNA/constraints/basic.h instead.
file	constraints_hard.h [code]
	Use ViennaRNA/constraints/hard.h instead.
file	constraints_ligand.h [code]
	Use ViennaRNA/constraints/ligand.h instead.
file	constraints_SHAPE.h [code]
	Use ViennaRNA/constraints/SHAPE.h instead.
file	constraints_soft.h [code]
	Use ViennaRNA/constraints/soft.h instead.
file	convert_epars.h [code]
	Use ViennaRNA/params/convert.h instead.
file	data_structures.h [code]
	Use ViennaRNA/datastructures/basic.h instead.
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]
	Use ViennaRNA/params/constants.h instead.
file	energy_par.h [code]
	Use ViennaRNA/params/default.h instead.
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]
	Use ViennaRNA/loops/external.h instead.
file	file_formats.h [code]
	Use ViennaRNA/io/file_formats.h instead.
file	file_formats_msa.h [code]
	Use ViennaRNA/io/file_formats_msa.h instead.
file	file_utils.h [code]
	Use ViennaRNA/io/utils.h instead.
file	findpath.h [code]
	Use ViennaRNA/landscape/findpath.h instead.
file	fold.h [code]
	MFE calculations for single RNA sequences.
file	fold_compound.h [code]
	The Basic Fold Compound API.
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]
	Use ViennaRNA/loops/hairpin.h instead.
file	interior_loops.h [code]
	Use ViennaRNA/loops/internal.h instead.
file	inverse.h [code]
	Inverse folding routines.
file	Lfold.h [code]
	Functions for locally optimal MFE structure prediction.
file	loop_energies.h [code]
	Use ViennaRNA/loops/all.h instead.
file	LPfold.h [code]
	Partition function and equilibrium probability implementation for the sliding window algorithm.
file	MEA.h [code]
	Computes a MEA (maximum expected accuracy) structure.
file	mfe.h [code]
	Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence data.
file	mfe_window.h [code]
	Compute local Minimum Free Energy (MFE) using a sliding window approach and backtrace corresponding secondary structures.
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]
	Use ViennaRNA/loops/multibranch.h instead.
file	naview.h [code]
	Use ViennaRNA/plotting/naview.h instead.
file	neighbor.h [code]
	Use ViennaRNA/landscape/neighbor.h instead.
file	params.h [code]
	Use ViennaRNA/params/basic.h instead.
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	part_func_window.h [code]
	Partition function and equilibrium probability implementation for the sliding window algorithm.
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]
	Use ViennaRNA/plotting/alignments.h instead.
file	plot_layouts.h [code]
	Use ViennaRNA/plotting/layouts.h instead.
file	plot_structure.h [code]
	Use ViennaRNA/plotting/structures.h instead.
file	plot_utils.h [code]
	Use ViennaRNA/plotting/utils.h instead.
file	profiledist.h [code]
file	PS_dot.h [code]
	Use ViennaRNA/plotting/probabilities.h instead.
file	read_epars.h [code]
	Use ViennaRNA/params/io.h instead.
file	ribo.h [code]
	Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.
file	RNAstruct.h [code]
	Parsing and Coarse Graining of Structures.
file	sequence.h [code]
	Functions and data structures related to sequence representations ,.
file	stream_output.h [code]
	Use ViennaRNA/datastructures/stream_output.h instead.
file	string_utils.h [code]
	Use ViennaRNA/utils/strings.h instead.
file	stringdist.h [code]
	Functions for String Alignment.
file	structure_utils.h [code]
	Use ViennaRNA/utils/structures.h instead.
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	svm_utils.h [code]
	Use ViennaRNA/utils/svm.h instead.
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]
	Use ViennaRNA/utils/basic.h instead.
file	walk.h [code]
	Use ViennaRNA/landscape/walk.h instead.