### RNAlib-2.1.2

ViennaRNA Package core - RNAlib

Parsing and Comparing - Functions to Manipulate Structures

Utilities - Odds and Ends

Example - A Small Example Program

Deprecated List

Modules

RNA Secondary Structure Folding

Calculating Minimum Free Energy (MFE) Structures

MFE Structures of two hybridized Sequences

MFE Consensus Structures for Sequence Alignment(s)

Local MFE structure Prediction and Z-scores

Calculating MFE representatives of a Distance Based Partitioning

Calculating Partition Functions and Pair Probabilities

Compute the structure with maximum expected accuracy (MEA)

Compute the centroid structure

Partition Function for two hybridized Sequences

Partition Function for two hybridized Sequences as a stepwise Process

Partition Function and Base Pair Probabilities for Sequence Alignment(s)

Partition functions for locally stable secondary structures

Calculate Partition Functions of a Distance Based Partitioning

Enumerating Suboptimal Structures

Suboptimal structures according to Zuker et al. 1989

Suboptimal structures within an energy band arround the MFE

Stochastic backtracking in the Ensemble

Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)

Stochastic Backtracking of Structures from Distance Based Partitioning

Calculate Secondary Structures of two RNAs upon Dimerization

MFE Structures of two hybridized Sequences

Partition Function for two hybridized Sequences

Partition Function for two hybridized Sequences as a stepwise Process

Predicting Consensus Structures from Alignment(s)

MFE Consensus Structures for Sequence Alignment(s)

Partition Function and Base Pair Probabilities for Sequence Alignment(s)

Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)

Local MFE consensus structures for Sequence Alignments

Predicting Locally stable structures of large sequences

Local MFE structure Prediction and Z-scores

Partition functions for locally stable secondary structures

Local MFE consensus structures for Sequence Alignments

Change and Precalculate Energy Parameter Sets and Boltzmann Factors

Reading/Writing energy parameter sets from/to File

Converting energy parameter files

Energy evaluation

Searching Sequences for Predefined Structures

Classified Dynamic Programming

Distance based partitioning of the Secondary Structure Space

Calculating MFE representatives of a Distance Based Partitioning

Calculate Partition Functions of a Distance Based Partitioning

Stochastic Backtracking of Structures from Distance Based Partitioning

Compute the Density of States

Parsing and Comparing - Functions to Manipulate Structures

Data Structures

bondT

bondTEn

cofoldF

ConcEnt

constrain

COORDINATE

cpair

duplexT

dupVar

folden

interact

intermediate_t

INTERVAL

LIST

LST_BUCKET

model_detailsT

move_t

PAIR

pair_info

pairpro

paramT

path_t

pf_paramT

plist

Postorder_list

pu_contrib

pu_out

sect

snoopT

SOLUTION

struct_en

svm_model

swString

Tree

TwoDfold_solution

TwoDfold_vars

TwoDpfold_solution

TwoDpfold_vars

Data Fields

File List

mainpage.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dfold.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ali_plex.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/aln_util.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert_epars.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data_structures.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist_vars.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/duplex.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/edit_cost.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy_const.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy_par.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold_vars.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/inverse.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/Lfold.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/loop_energies.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/LPfold.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/MEA.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/mm.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/move_set.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/naview.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/pair_mat.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func_co.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func_up.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PKplex.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plex.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot_layouts.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ProfileAln.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/profiledist.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PS_dot.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/read_epars.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ribo.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/RNAstruct.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/snofold.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/snoop.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/stringdist.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/subopt.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/svm_utils.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/treedist.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/utils.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4_epars.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4_intloops.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/intl11.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/intl11dH.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/intl21.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/intl21dH.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/intl22.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/intl22dH.h

/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/list.h

Globals