7 #ifndef VIENNA_RNA_PACKAGE_TWO_D_FOLD_H
8 #define VIENNA_RNA_PACKAGE_TWO_D_FOLD_H
11 #define VRNA_BACKWARD_COMPAT
14 #define DEPRECATED(func) func __attribute__ ((deprecated))
16 #define DEPRECATED(func) func
123 #ifdef VRNA_BACKWARD_COMPAT
125 #define TwoDfold_solution vrna_sol_TwoD_t
155 short *reference_pt1;
156 short *reference_pt2;
159 unsigned int seq_length;
178 int **l_min_values_m;
179 int **l_max_values_m;
183 int **l_min_values_m1;
184 int **l_max_values_m1;
185 int *k_min_values_m1;
186 int *k_max_values_m1;
188 int **l_min_values_f;
189 int **l_max_values_f;
193 int **l_min_values_f3;
194 int **l_max_values_f3;
195 int *k_min_values_f3;
196 int *k_max_values_f3;
198 int **l_min_values_m2;
199 int **l_max_values_m2;
200 int *k_min_values_m2;
201 int *k_max_values_m2;
203 int *l_min_values_fc;
204 int *l_max_values_fc;
208 int *l_min_values_fcH;
209 int *l_max_values_fcH;
210 int k_min_values_fcH;
211 int k_max_values_fcH;
213 int *l_min_values_fcI;
214 int *l_max_values_fcI;
215 int k_min_values_fcI;
216 int k_max_values_fcI;
218 int *l_min_values_fcM;
219 int *l_max_values_fcM;
220 int k_min_values_fcM;
221 int k_max_values_fcM;
237 unsigned long ***N_F5;
238 unsigned long ***N_C;
239 unsigned long ***N_M;
240 unsigned long ***N_M1;
266 const char *structure1,
267 const char *structure2,
308 DEPRECATED(TwoDfold_solution *
341 DEPRECATED(TwoDfold_solution **TwoDfold(
TwoDfold_vars *our_variables,
char * s
MFE representative structure in dot-bracket notation.
Definition: 2Dfold.h:62
int l
Distance to second reference.
Definition: 2Dfold.h:60
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: 2Dfold.h:144
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: 2Dfold.h:141
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: 2Dfold.h:151
int circ
backward compatibility variable.. this does not effect anything
short * S1
The input sequences in numeric form.
Definition: 2Dfold.h:139
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition: 2Dfold.h:147
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.
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
void destroy_TwoDfold_variables(TwoDfold_vars *our_variables)
Destroy a TwoDfold_vars datastructure without memory loss.
int k
Distance to first reference.
Definition: 2Dfold.h:59
float en
Free energy in kcal/mol.
Definition: 2Dfold.h:61
char * ptype
Precomputed array of pair types.
Definition: 2Dfold.h:137
struct vrna_param_t * P
Precomputed energy parameters and model details.
Definition: 2Dfold.h:135
vrna_sol_TwoD_t * vrna_TwoD_fold(vrna_fold_compound *vc, int distance1, int distance2)
Compute MFE's and representative for distance partitioning.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:698
Solution element returned from vrna_TwoD_fold()
Definition: 2Dfold.h:58
vrna_sol_TwoD_t * TwoDfoldList(TwoDfold_vars *vars, int distance1, int distance2)
Compute MFE's and representative for distance partitioning.
Variables compound for 2Dfold MFE folding.
Definition: 2Dfold.h:134
char * sequence
The input sequence.
Definition: 2Dfold.h:138
double temperature
Temperature used for loop contribution scaling.
Definition: params.h:77
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:41
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: 2Dfold.h:145
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.
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: 2Dfold.h:153
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: 2Dfold.h:152
int do_backtrack
Flag whether to do backtracing of the structure(s) or not.
Definition: 2Dfold.h:136
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: 2Dfold.h:140
char * vrna_TwoD_backtrack5(vrna_fold_compound *vc, int k, int l, unsigned int j)
Backtrack a minimum free energy structure from a 5' section of specified length.