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file | 1.8.4_epars.h [code] |
| Free energy parameters for parameter file conversion.
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file | 1.8.4_intloops.h [code] |
| Free energy parameters for interior loop contributions needed by the parameter file conversion functions.
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file | 2Dfold.h [code] |
| MFE structures for base pair distance classes.
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file | 2Dpfold.h [code] |
| Partition function implementations for base pair distance classes.
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file | alifold.h [code] |
| Functions for comparative structure prediction using RNA sequence alignments.
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file | aln_util.h [code] |
| Various utility- and helper-functions for sequence alignments and comparative structure prediction.
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file | alphabet.h [code] |
| Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets.
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file | boltzmann_sampling.h [code] |
| Boltzmann Sampling of secondary structures from the ensemble.
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file | centroid.h [code] |
| Centroid structure computation.
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file | cofold.h [code] |
| MFE implementations for RNA-RNA interaction.
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file | combinatorics.h [code] |
| Various implementations that deal with combinatorial aspects of RNA/DNA folding.
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file | commands.h [code] |
| Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation.
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file | constraints.h [code] |
| Functions and data structures for constraining secondary structure predictions and evaluation.
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file | constraints_hard.h [code] |
| Functions and data structures for handling of secondary structure hard constraints.
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file | constraints_ligand.h [code] |
| Functions for incorporation of ligands binding to hairpin and interior loop motifs using the soft constraints framework.
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file | constraints_SHAPE.h [code] |
| This module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints.
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file | constraints_soft.h [code] |
| Functions and data structures for secondary structure soft constraints.
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file | convert_epars.h [code] |
| Functions and definitions for energy parameter file format conversion.
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file | data_structures.h [code] |
| Various data structures and pre-processor macros.
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file | dist_vars.h [code] |
| Global variables for Distance-Package.
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file | dp_matrices.h [code] |
| Functions to deal with standard dynamic programming (DP) matrices.
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file | duplex.h [code] |
| Functions for simple RNA-RNA duplex interactions.
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file | edit_cost.h [code] |
| global variables for Edit Costs included by treedist.c and stringdist.c
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file | energy_const.h [code] |
| Energy parameter constants.
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file | equilibrium_probs.h [code] |
| Equilibrium Probability implementations.
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file | eval.h [code] |
| Functions and variables related to energy evaluation of sequence/structure pairs.
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file | exterior_loops.h [code] |
| Energy evaluation of exterior loops for MFE and partition function calculations.
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file | file_formats.h [code] |
| Read and write different file formats for RNA sequences, structures.
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file | file_formats_msa.h [code] |
| Functions dealing with file formats for Multiple Sequence Alignments (MSA)
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file | file_utils.h [code] |
| Several utilities for file handling.
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file | findpath.h [code] |
| A breadth-first search heuristic for optimal direct folding paths.
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file | fold.h [code] |
| MFE calculations for single RNA sequences.
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file | fold_vars.h [code] |
| Here all all declarations of the global variables used throughout RNAlib.
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file | gquad.h [code] |
| G-quadruplexes.
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file | grammar.h [code] |
| Implementations for the RNA folding grammar.
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file | hairpin_loops.h [code] |
| Energy evaluation of hairpin loops for MFE and partition function calculations.
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file | interior_loops.h [code] |
| Energy evaluation of interior loops for MFE and partition function calculations.
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file | inverse.h [code] |
| Inverse folding routines.
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file | Lfold.h [code] |
| Functions for locally optimal MFE structure prediction.
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file | loop_energies.h [code] |
| Energy evaluation for MFE and partition function calculations.
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file | LPfold.h [code] |
| Partition function implementation for the Lfold algorithm.
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file | MEA.h [code] |
| Computes a MEA (maximum expected accuracy) structure.
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file | mfe.h [code] |
| MFE calculations for single RNA sequences.
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file | mm.h [code] |
| Several Maximum Matching implementations.
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file | model.h [code] |
| The model details data structure and its corresponding modifiers.
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file | multibranch_loops.h [code] |
| Energy evaluation of multibranch loops for MFE and partition function calculations.
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file | naview.h [code] |
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file | neighbor.h [code] |
| Methods to compute the neighbors of an RNA secondary structure.
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file | params.h [code] |
| Functions to deal with sets of energy parameters.
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file | part_func.h [code] |
| Partition function implementations.
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file | part_func_co.h [code] |
| Partition function for two RNA sequences.
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file | part_func_up.h [code] |
| Implementations for accessibility and RNA-RNA interaction as a stepwise process.
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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.
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file | plot_aln.h [code] |
| Various functions for plotting Sequence / Structure Alignments.
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file | plot_layouts.h [code] |
| Secondary structure plot layout algorithms.
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file | plot_structure.h [code] |
| Various functions for plotting RNA secondary structures.
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file | profiledist.h [code] |
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file | PS_dot.h [code] |
| Various functions for plotting RNA secondary structures, dot-plots and other visualizations.
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file | read_epars.h [code] |
| Read and write energy parameter files.
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file | ribo.h [code] |
| Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.
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file | RNAstruct.h [code] |
| Parsing and Coarse Graining of Structures.
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file | string_utils.h [code] |
| General utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package.
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file | stringdist.h [code] |
| Functions for String Alignment.
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file | structure_utils.h [code] |
| Various utility- and helper-functions for secondary structure parsing, converting, etc.
|
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file | structured_domains.h [code] |
| This module provides interfaces that deal with additional structured domains in the folding grammar.
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file | subopt.h [code] |
| RNAsubopt and density of states declarations.
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file | treedist.h [code] |
| Functions for Tree Edit Distances.
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file | units.h [code] |
| Physical Units and Functions to convert them into each other.
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file | unstructured_domains.h [code] |
| Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.
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file | utils.h [code] |
| General utility- and helper-functions used throughout the ViennaRNA Package.
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file | walk.h [code] |
| Methods to generate particular paths such as gradient or random walks through the energy landscape of an RNA sequence.
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