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RNAlib-2.4.17
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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 | heat_capacity.h [code] |
| Compute heat capacity for an RNA. | |
| 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] |
| Use ViennaRNA/utils/units.h instead. | |
| 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. | |