Go to the documentation of this file. 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
The model details data structure and its corresponding modifiers.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:453
Functions and data structures for handling of secondary structure hard constraints.
Data structure used in RNApkplex.
Definition: basic.h:277
Implementations for the RNA folding grammar.
Base pair data structure used in subopt.c.
Definition: basic.h:104
int u_vals
number of different -u values
Definition: basic.h:188
struct pu_out pu_out
Collection of all free_energy of beeing unpaired values for output.
int contribs
[-c "SHIME"]
Definition: basic.h:189
Data structure for RNAsnoop.
Definition: basic.h:248
char ** header
header line
Definition: basic.h:190
struct constrain constrain
constraints for cofolding
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: basic.h:191
struct pu_contrib pu_contrib
contributions to p_u
Functions to deal with standard dynamic programming (DP) matrices.
int length
length of longer sequence
Definition: basic.h:180
this datastructure is used as input parameter in functions of PS_dot.c
Definition: basic.h:112
Base pair stack element.
Definition: basic.h:143
This module provides interfaces that deal with additional structured domains in the folding grammar.
Functions and data structures for secondary structure soft constraints.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
Stack of partial structures for backtracking.
Definition: basic.h:134
int l
j<l in shorter seq
Definition: basic.h:179
Data structure for RNAsnoop (fold energy list)
Definition: basic.h:239
double ** M
multi loops
Definition: basic.h:161
int w
longest unpaired region
Definition: basic.h:164
double ** H
hairpin loops
Definition: basic.h:159
double ** E
exterior loop
Definition: basic.h:162
interaction data structure for RNAup
Definition: basic.h:170
int i
k<i in longer seq
Definition: basic.h:176
int len
sequence length
Definition: basic.h:187
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.
double ** I
interior loops
Definition: basic.h:160
struct dupVar dupVar
Data structure used in RNApkplex.
int length
length of the input sequence
Definition: basic.h:163
void vrna_C11_features(void)
Dummy symbol to check whether the library was build using C11/C++11 features.
contributions to p_u
Definition: basic.h:158
Energy parameter constants.
Data structure for RNAduplex.
Definition: basic.h:211
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
double * Gi
free energies of interaction
Definition: basic.h:172
The Basic Fold Compound API.
struct node folden
Data structure for RNAsnoop (fold energy list)
int j
j<l in shorter seq
Definition: basic.h:178
int k
k<i in longer seq
Definition: basic.h:177
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: basic.h:175
double * Pi
probabilities of interaction
Definition: basic.h:171
Collection of all free_energy of beeing unpaired values for output.
Definition: basic.h:186
constraints for cofolding
Definition: basic.h:197
Functions to deal with sets of energy parameters.
struct interact interact
interaction data structure for RNAup
Various utility- and helper-functions for secondary structure parsing, converting,...