1 #ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 2 #define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 47 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 124 unsigned int position;
216 double energy_backtrack;
217 double opening_backtrack_x;
218 double opening_backtrack_y;
263 float fullStemEnergy;
325 #ifndef VRNA_DISABLE_C11_FEATURES int l
j<l in shorter seq
Definition: basic.h:178
double ** M
multi loops
Definition: basic.h:160
Functions and data structures for secondary structure soft constraints.
void vrna_C11_features(void)
Dummy symbol to check whether the library was build using C11/C++11 features.
Functions to deal with standard dynamic programming (DP) matrices.
double ** H
hairpin loops
Definition: basic.h:158
struct dupVar dupVar
Data structure used in RNApkplex.
struct constrain constrain
constraints for cofolding
int u_vals
number of different -u values
Definition: basic.h:187
Data structure used in RNApkplex.
Definition: basic.h:276
Energy parameter constants.
struct pu_contrib pu_contrib
contributions to p_u
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
int j
j<l in shorter seq
Definition: basic.h:177
Data structure for RNAsnoop (fold energy list)
Definition: basic.h:238
contributions to p_u
Definition: basic.h:157
int contribs
[-c "SHIME"]
Definition: basic.h:188
The model details data structure and its corresponding modifiers.
int i
k<i in longer seq
Definition: basic.h:175
Data structure for RNAsnoop.
Definition: basic.h:247
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: basic.h:190
Stack of partial structures for backtracking.
Definition: basic.h:133
this datastructure is used as input parameter in functions of PS_dot.c
Definition: basic.h:112
Base pair data structure used in subopt.c.
Definition: basic.h:104
int w
longest unpaired region
Definition: basic.h:163
struct pu_out pu_out
Collection of all free_energy of beeing unpaired values for output.
int k
k<i in longer seq
Definition: basic.h:176
Functions and data structures for handling of secondary structure hard constraints.
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches...
interaction data structure for RNAup
Definition: basic.h:169
double * Pi
probabilities of interaction
Definition: basic.h:170
constraints for cofolding
Definition: basic.h:196
double ** I
interior loops
Definition: basic.h:159
struct node folden
Data structure for RNAsnoop (fold energy list)
int len
sequence length
Definition: basic.h:186
int length
length of the input sequence
Definition: basic.h:162
char ** header
header line
Definition: basic.h:189
int length
length of longer sequence
Definition: basic.h:179
struct interact interact
interaction data structure for RNAup
Collection of all free_energy of beeing unpaired values for output.
Definition: basic.h:185
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:172
Base pair stack element.
Definition: basic.h:142
Functions to deal with sets of energy parameters.
double * Gi
free energies of interaction
Definition: basic.h:171
This module provides interfaces that deal with additional structured domains in the folding grammar...
Various utility- and helper-functions for secondary structure parsing, converting, etc.
Data structure for RNAduplex.
Definition: basic.h:210
The Basic Fold Compound API.
Implementations for the RNA folding grammar.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:358
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: basic.h:174
double ** E
exterior loop
Definition: basic.h:161