7 #ifndef VIENNA_RNA_PACKAGE_TWO_D_FOLD_H
8 #define VIENNA_RNA_PACKAGE_TWO_D_FOLD_H
11 #define VRNA_BACKWARD_COMPAT
13 #ifdef DEPRECATION_WARNINGS
15 # define DEPRECATED(func) func __attribute__ ((deprecated))
17 # define DEPRECATED(func) func
20 # define DEPRECATED(func) func
127 #ifdef VRNA_BACKWARD_COMPAT
129 #define TwoDfold_solution vrna_sol_TwoD_t
159 short *reference_pt1;
160 short *reference_pt2;
163 unsigned int seq_length;
182 int **l_min_values_m;
183 int **l_max_values_m;
187 int **l_min_values_m1;
188 int **l_max_values_m1;
189 int *k_min_values_m1;
190 int *k_max_values_m1;
192 int **l_min_values_f;
193 int **l_max_values_f;
197 int **l_min_values_f3;
198 int **l_max_values_f3;
199 int *k_min_values_f3;
200 int *k_max_values_f3;
202 int **l_min_values_m2;
203 int **l_max_values_m2;
204 int *k_min_values_m2;
205 int *k_max_values_m2;
207 int *l_min_values_fc;
208 int *l_max_values_fc;
212 int *l_min_values_fcH;
213 int *l_max_values_fcH;
214 int k_min_values_fcH;
215 int k_max_values_fcH;
217 int *l_min_values_fcI;
218 int *l_max_values_fcI;
219 int k_min_values_fcI;
220 int k_max_values_fcI;
222 int *l_min_values_fcM;
223 int *l_max_values_fcM;
224 int k_min_values_fcM;
225 int k_max_values_fcM;
241 unsigned long ***N_F5;
242 unsigned long ***N_C;
243 unsigned long ***N_M;
244 unsigned long ***N_M1;
270 const char *structure1,
271 const char *structure2,
312 DEPRECATED(TwoDfold_solution *
345 DEPRECATED(TwoDfold_solution **TwoDfold(
TwoDfold_vars *our_variables,
Solution element returned from vrna_mfe_TwoD()
Definition: 2Dfold.h:62
struct TwoDfold_vars TwoDfold_vars
Variables compound for 2Dfold MFE folding.
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: 2Dfold.h:149
Variables compound for 2Dfold MFE folding.
Definition: 2Dfold.h:138
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
char * TwoDfold_backtrack_f5(unsigned int j, int k, int l, TwoDfold_vars *vars)
Backtrack a minimum free energy structure from a 5' section of specified length.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: 2Dfold.h:148
void destroy_TwoDfold_variables(TwoDfold_vars *our_variables)
Destroy a TwoDfold_vars datastructure without memory loss.
int l
Distance to second reference.
Definition: 2Dfold.h:64
char * s
MFE representative structure in dot-bracket notation.
Definition: 2Dfold.h:66
char * vrna_backtrack5_TwoD(vrna_fold_compound_t *vc, int k, int l, unsigned int j)
Backtrack a minimum free energy structure from a 5' section of specified length.
int do_backtrack
Flag whether to do backtracing of the structure(s) or not.
Definition: 2Dfold.h:140
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: 2Dfold.h:156
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: 2Dfold.h:155
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition: 2Dfold.h:151
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: 2Dfold.h:144
vrna_sol_TwoD_t * TwoDfoldList(TwoDfold_vars *vars, int distance1, int distance2)
Compute MFE's and representative for distance partitioning.
struct vrna_sol_TwoD_t vrna_sol_TwoD_t
Solution element returned from vrna_mfe_TwoD()
int k
Distance to first reference.
Definition: 2Dfold.h:63
vrna_sol_TwoD_t * vrna_mfe_TwoD(vrna_fold_compound_t *vc, int distance1, int distance2)
Compute MFE's and representative for distance partitioning.
char * ptype
Precomputed array of pair types.
Definition: 2Dfold.h:141
vrna_param_t * P
Precomputed energy parameters and model details.
Definition: 2Dfold.h:139
short * S1
The input sequences in numeric form.
Definition: 2Dfold.h:143
char * sequence
The input sequence.
Definition: 2Dfold.h:142
TwoDfold_vars * get_TwoDfold_variables(const char *seq, const char *structure1, const char *structure2, int circ)
Get a structure of type TwoDfold_vars prefilled with current global settings.
float en
Free energy in kcal/mol.
Definition: 2Dfold.h:65
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: 2Dfold.h:145
int circ
backward compatibility variable.. this does not effect anything
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: 2Dfold.h:157