RNAlib-2.3.1
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Files | |
file | 1.8.4_epars.h [code] |
Free energy parameters for parameter file conversion. | |
file | 1.8.4_intloops.h [code] |
Free energy parameters for interior loop contributions needed by the parameter file conversion functions. | |
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] |
Various utility- and helper-functions for sequence alignments and comparative structure prediction. | |
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 | cofold.h [code] |
MFE implementations for RNA-RNA interaction. | |
file | combinatorics.h [code] |
Various implementations that deal with combinatorial aspects of RNA/DNA folding. | |
file | commands.h [code] |
Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation. | |
file | constraints.h [code] |
Functions and data structures for constraining secondary structure predictions and evaluation. | |
file | constraints_hard.h [code] |
Functions and data structures for handling of secondary structure hard constraints. | |
file | constraints_ligand.h [code] |
Functions for incorporation of ligands binding to hairpin and interior loop motifs using the soft constraints framework. | |
file | constraints_SHAPE.h [code] |
This module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints. | |
file | constraints_soft.h [code] |
Functions and data structures for secondary structure soft constraints. | |
file | convert_epars.h [code] |
Functions and definitions for energy parameter file format conversion. | |
file | data_structures.h [code] |
Various data structures and pre-processor macros. | |
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] |
Energy parameter constants. | |
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] |
Energy evaluation of exterior loops for MFE and partition function calculations. | |
file | file_formats.h [code] |
Read and write different file formats for RNA sequences, structures. | |
file | file_formats_msa.h [code] |
Functions dealing with file formats for Multiple Sequence Alignments (MSA) | |
file | file_utils.h [code] |
Several utilities for file handling. | |
file | findpath.h [code] |
A breadth-first search heuristic for optimal direct folding paths. | |
file | fold.h [code] |
MFE calculations for single RNA sequences. | |
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] |
Energy evaluation of hairpin loops for MFE and partition function calculations. | |
file | interior_loops.h [code] |
Energy evaluation of interior loops for MFE and partition function calculations. | |
file | inverse.h [code] |
Inverse folding routines. | |
file | Lfold.h [code] |
Functions for locally optimal MFE structure prediction. | |
file | loop_energies.h [code] |
Energy evaluation for MFE and partition function calculations. | |
file | LPfold.h [code] |
Partition function implementation for the Lfold algorithm. | |
file | MEA.h [code] |
Computes a MEA (maximum expected accuracy) structure. | |
file | mfe.h [code] |
MFE calculations for single RNA sequences. | |
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] |
Energy evaluation of multibranch loops for MFE and partition function calculations. | |
file | naview.h [code] |
file | params.h [code] |
Functions to deal with sets of energy parameters. | |
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 | 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] |
Various functions for plotting Sequence / Structure Alignments. | |
file | plot_layouts.h [code] |
Secondary structure plot layout algorithms. | |
file | plot_structure.h [code] |
Various functions for plotting RNA secondary structures. | |
file | profiledist.h [code] |
file | PS_dot.h [code] |
Various functions for plotting RNA secondary structures, dot-plots and other visualizations. | |
file | read_epars.h [code] |
Read and write energy parameter files. | |
file | ribo.h [code] |
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments. | |
file | RNAstruct.h [code] |
Parsing and Coarse Graining of Structures. | |
file | string_utils.h [code] |
General utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package. | |
file | stringdist.h [code] |
Functions for String Alignment. | |
file | structure_utils.h [code] |
Various utility- and helper-functions for secondary structure parsing, converting, etc. | |
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 | 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] |
General utility- and helper-functions used throughout the ViennaRNA Package. | |