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
14 #define DEPRECATED(func) func __attribute__ ((deprecated))
16 #define DEPRECATED(func) func
129 unsigned int length);
136 #ifdef VRNA_BACKWARD_COMPAT
138 #define TwoDpfold_solution vrna_sol_TwoD_pf_t
165 short *reference_pt1;
166 short *reference_pt2;
177 unsigned int seq_length;
195 int **l_min_values_b;
196 int **l_max_values_b;
200 int **l_min_values_m;
201 int **l_max_values_m;
205 int **l_min_values_m1;
206 int **l_max_values_m1;
207 int *k_min_values_m1;
208 int *k_max_values_m1;
210 int **l_min_values_m2;
211 int **l_max_values_m2;
212 int *k_min_values_m2;
213 int *k_max_values_m2;
215 int *l_min_values_qc;
216 int *l_max_values_qc;
220 int *l_min_values_qcH;
221 int *l_max_values_qcH;
222 int k_min_values_qcH;
223 int k_max_values_qcH;
225 int *l_min_values_qcI;
226 int *l_max_values_qcI;
227 int k_min_values_qcI;
228 int k_max_values_qcI;
230 int *l_min_values_qcM;
231 int *l_max_values_qcM;
232 int k_min_values_qcM;
233 int k_max_values_qcM;
239 FLT_OR_DBL *Q_M1_rem;
240 FLT_OR_DBL *Q_M2_rem;
270 const char *structure1,
314 DEPRECATED(TwoDpfold_solution *
372 unsigned int length));
388 DEPRECATED(FLT_OR_DBL **TwoDpfold_circ(
vrna_sol_TwoD_pf_t * vrna_TwoD_pf_fold(vrna_fold_compound *vc, int maxDistance1, int maxDistance2)
Compute the partition function for all distance classes.
char * vrna_TwoD_pbacktrack5(vrna_fold_compound *vc, int d1, int d2, unsigned int length)
Sample secondary structure representatives with a specified length from a set of distance classes acc...
int circ
backward compatibility variable.. this does not effect anything
char * ptype
Precomputed array of pair types.
Definition: 2Dpfold.h:150
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: 2Dpfold.h:168
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: 2Dpfold.h:154
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition: 2Dpfold.h:162
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:698
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...
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: 2Dpfold.h:170
void destroy_TwoDpfold_variables(TwoDpfold_vars *vars)
Free all memory occupied by a TwoDpfold_vars datastructure.
Solution element returned from vrna_TwoD_pf_fold()
Definition: 2Dpfold.h:43
int k
Distance to first reference.
Definition: 2Dpfold.h:44
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: 2Dpfold.h:153
char * TwoDpfold_pbacktrack(TwoDpfold_vars *vars, int d1, int d2)
Sample secondary structure representatives from a set of distance classes according to their Boltzman...
char * vrna_TwoD_pbacktrack(vrna_fold_compound *vc, int d1, int d2)
Sample secondary structure representatives from a set of distance classes according to their Boltzman...
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: 2Dpfold.h:172
double temperature
Rescale energy parameters to a temperature in degC.
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
vrna_sol_TwoD_pf_t * TwoDpfoldList(TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)
Compute the partition function for all distance classes.
int l
Distance to second reference.
Definition: 2Dpfold.h:45
int * jindx
Index for moving in the triangular matrix qm1.
Definition: 2Dpfold.h:163
short * S1
The input sequences in numeric form.
Definition: 2Dpfold.h:152
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:86
char * sequence
The input sequence.
Definition: 2Dpfold.h:151
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: 2Dpfold.h:173
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: 2Dpfold.h:169
FLT_OR_DBL q
partition function
Definition: 2Dpfold.h:46
Variables compound for 2Dfold partition function folding.
Definition: 2Dpfold.h:147