# File List

Here is a list of all documented files with brief descriptions:

mainpage.h [code] |
H/2Dfold.h [code] | Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures
H/2Dpfold.h [code] | Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures
H/ali_plex.h [code] |
H/alifold.h [code] | Compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples,
H/aln_util.h [code] |
H/cofold.h [code] | MFE version of cofolding routines
H/convert_epars.h [code] | Functions and definitions for energy parameter file format conversion
H/data_structures.h [code] | All datastructures and typedefs shared among the Vienna RNA Package can be found here
H/dist_vars.h [code] | Global variables for Distance-Package
H/duplex.h [code] | Duplex folding function declarations
H/edit_cost.h [code] | Global variables for Edit Costs included by treedist.c and stringdist.c
H/energy_const.h [code] | Energy constants
H/energy_par.h [code] |
H/findpath.h [code] | Compute direct refolding paths between two secondary structures
H/fold.h [code] | MFE calculations and energy evaluations for single RNA sequences
H/fold_vars.h [code] | Here all all declarations of the global variables used throughout RNAlib
H/inverse.h [code] | Inverse folding routines
H/Lfold.h [code] | Predicting local MFE structures of large sequences
H/loop_energies.h [code] | Energy evaluation for MFE and partition function calculations
H/LPfold.h [code] | Function declarations of partition function variants of the Lfold algorithm
H/MEA.h [code] | Computes a MEA (maximum expected accuracy) structure
H/mm.h [code] | Several Maximum Matching implementations
H/naview.h [code] |
H/pair_mat.h [code] |
H/params.h [code] | Several functions to obtain (pre)scaled energy parameter data containers
H/part_func.h [code] | Partition function of single RNA sequences
H/part_func_co.h [code] | Partition function for two RNA sequences
H/part_func_up.h [code] | Partition Function Cofolding as stepwise process
H/PKplex.h [code] |
H/plex.h [code] |
H/plot_layouts.h [code] | Secondary structure plot layout algorithms
H/ProfileAln.h [code] |
H/profiledist.h [code] |
H/PS_dot.h [code] | Various functions for plotting RNA secondary structures, dot-plots and other visualizations
H/read_epars.h [code] | Functions to read and write energy parameter sets from/to files
H/ribo.h [code] |
H/RNAstruct.h [code] | Parsing and Coarse Graining of Structures
H/snofold.h [code] |
H/snoop.h [code] |
H/stringdist.h [code] | Functions for String Alignment
H/subopt.h [code] | RNAsubopt and density of states declarations
H/svm_utils.h [code] |
H/treedist.h [code] | Functions for Tree Edit Distances
H/utils.h [code] | Various utility- and helper-functions used throughout the Vienna RNA package
lib/1.8.4_epars.h [code] | Free energy parameters for parameter file conversion
lib/1.8.4_intloops.h [code] | Free energy parameters for interior loop contributions needed by the parameter file conversion functions
lib/intl11.h [code] |
lib/intl11dH.h [code] |
lib/intl21.h [code] |
lib/intl21dH.h [code] |
lib/intl22.h [code] |
lib/intl22dH.h [code] |
lib/list.h [code] |