7 #ifndef VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H
8 #define VIENNA_RNA_PACKAGE_TWO_D_PF_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
133 unsigned int length);
140 #ifdef VRNA_BACKWARD_COMPAT
142 #define TwoDpfold_solution vrna_sol_TwoD_pf_t
169 short *reference_pt1;
170 short *reference_pt2;
181 unsigned int seq_length;
199 int **l_min_values_b;
200 int **l_max_values_b;
204 int **l_min_values_m;
205 int **l_max_values_m;
209 int **l_min_values_m1;
210 int **l_max_values_m1;
211 int *k_min_values_m1;
212 int *k_max_values_m1;
214 int **l_min_values_m2;
215 int **l_max_values_m2;
216 int *k_min_values_m2;
217 int *k_max_values_m2;
219 int *l_min_values_qc;
220 int *l_max_values_qc;
224 int *l_min_values_qcH;
225 int *l_max_values_qcH;
226 int k_min_values_qcH;
227 int k_max_values_qcH;
229 int *l_min_values_qcI;
230 int *l_max_values_qcI;
231 int k_min_values_qcI;
232 int k_max_values_qcI;
234 int *l_min_values_qcM;
235 int *l_max_values_qcM;
236 int k_min_values_qcM;
237 int k_max_values_qcM;
274 const char *structure1,
318 DEPRECATED(TwoDpfold_solution *
376 unsigned int length));
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
char * ptype
Precomputed array of pair types.
Definition: 2Dpfold.h:154
Solution element returned from vrna_pf_TwoD()
Definition: 2Dpfold.h:47
double temperature
Rescale energy parameters to a temperature in degC.
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: 2Dpfold.h:172
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: 2Dpfold.h:158
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition: 2Dpfold.h:166
FLT_OR_DBL q
partition function
Definition: 2Dpfold.h:50
TwoDpfold_vars * get_TwoDpfold_variables(const char *seq, const char *structure1, char *structure2, int circ)
Get a datastructure containing all necessary attributes and global folding switches.
char * TwoDpfold_pbacktrack5(TwoDpfold_vars *vars, int d1, int d2, unsigned int length)
Sample secondary structure representatives with a specified length from a set of distance classes acc...
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: 2Dpfold.h:174
void destroy_TwoDpfold_variables(TwoDpfold_vars *vars)
Free all memory occupied by a TwoDpfold_vars datastructure.
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: 2Dpfold.h:157
char * TwoDpfold_pbacktrack(TwoDpfold_vars *vars, int d1, int d2)
Sample secondary structure representatives from a set of distance classes according to their Boltzman...
struct vrna_sol_TwoD_pf_t vrna_sol_TwoD_pf_t
Solution element returned from vrna_pf_TwoD()
int l
Distance to second reference.
Definition: 2Dpfold.h:49
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: 2Dpfold.h:176
char * vrna_pbacktrack5_TwoD(vrna_fold_compound_t *vc, int d1, int d2, unsigned int length)
Sample secondary structure representatives with a specified length from a set of distance classes acc...
vrna_sol_TwoD_pf_t * TwoDpfoldList(TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)
Compute the partition function for all distance classes.
int * jindx
Index for moving in the triangular matrix qm1.
Definition: 2Dpfold.h:167
char * vrna_pbacktrack_TwoD(vrna_fold_compound_t *vc, int d1, int d2)
Sample secondary structure representatives from a set of distance classes according to their Boltzman...
short * S1
The input sequences in numeric form.
Definition: 2Dpfold.h:156
int circ
backward compatibility variable.. this does not effect anything
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
char * sequence
The input sequence.
Definition: 2Dpfold.h:155
vrna_sol_TwoD_pf_t * vrna_pf_TwoD(vrna_fold_compound_t *vc, int maxDistance1, int maxDistance2)
Compute the partition function for all distance classes.
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: 2Dpfold.h:177
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: 2Dpfold.h:173
int k
Distance to first reference.
Definition: 2Dpfold.h:48
Variables compound for 2Dfold partition function folding.
Definition: 2Dpfold.h:151