1#ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H
2#define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H
47#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
125 unsigned int position;
217 double energy_backtrack;
218 double opening_backtrack_x;
219 double opening_backtrack_y;
264 float fullStemEnergy;
326#ifndef VRNA_DISABLE_C11_FEATURES
Energy parameter constants.
Functions to deal with standard dynamic programming (DP) matrices.
The Basic Fold Compound API.
Implementations for the RNA folding grammar.
int l
j<l in shorter seq
Definition: basic.h:179
double ** M
multi loops
Definition: basic.h:161
double * Pi
probabilities of interaction
Definition: basic.h:171
int len
sequence length
Definition: basic.h:187
int length
length of the input sequence
Definition: basic.h:163
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: basic.h:191
int w
longest unpaired region
Definition: basic.h:164
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: basic.h:175
double * Gi
free energies of interaction
Definition: basic.h:172
int k
k<i in longer seq
Definition: basic.h:177
int contribs
[-c "SHIME"]
Definition: basic.h:189
int j
j<l in shorter seq
Definition: basic.h:178
int u_vals
number of different -u values
Definition: basic.h:188
double ** I
interior loops
Definition: basic.h:160
int i
k<i in longer seq
Definition: basic.h:176
double ** H
hairpin loops
Definition: basic.h:159
char ** header
header line
Definition: basic.h:190
int length
length of longer sequence
Definition: basic.h:180
double ** E
exterior loop
Definition: basic.h:162
double Gikjl
full free energy for interaction between [k,i] k<i in longer seq and [j,l] j<l in shorter seq
Definition: basic.h:173
void vrna_C11_features(void)
Dummy symbol to check whether the library was build using C11/C++11 features.
struct interact interact
interaction data structure for RNAup
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
struct node folden
Data structure for RNAsnoop (fold energy list)
struct constrain constrain
constraints for cofolding
struct pu_contrib pu_contrib
contributions to p_u
struct dupVar dupVar
Data structure used in RNApkplex.
struct pu_out pu_out
Collection of all free_energy of beeing unpaired values for output.
constraints for cofolding
Definition: basic.h:197
Data structure used in RNApkplex.
Definition: basic.h:277
Data structure for RNAduplex.
Definition: basic.h:211
interaction data structure for RNAup
Definition: basic.h:170
Data structure for RNAsnoop (fold energy list)
Definition: basic.h:239
contributions to p_u
Definition: basic.h:158
Collection of all free_energy of beeing unpaired values for output.
Definition: basic.h:186
Data structure for RNAsnoop.
Definition: basic.h:248
Base pair data structure used in subopt.c.
Definition: basic.h:104
Base pair stack element.
Definition: basic.h:143
this datastructure is used as input parameter in functions of PS_dot.c
Definition: basic.h:112
Stack of partial structures for backtracking.
Definition: basic.h:134
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:482
Functions and data structures for handling of secondary structure hard constraints.
The model details data structure and its corresponding modifiers.
Functions to deal with sets of energy parameters.
Functions and data structures for secondary structure soft constraints.
This module provides interfaces that deal with additional structured domains in the folding grammar.
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.
Various utility- and helper-functions for secondary structure parsing, converting,...