1 #ifndef VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H 2 #define VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H 5 #define VRNA_BACKWARD_COMPAT 7 #ifdef VRNA_WARN_DEPRECATED 9 # define DEPRECATED(func) func __attribute__ ((deprecated)) 11 # define DEPRECATED(func) func 14 # define DEPRECATED(func) func 135 unsigned int length);
143 #ifdef VRNA_BACKWARD_COMPAT 145 #define TwoDpfold_solution vrna_sol_TwoD_pf_t 171 short *reference_pt1;
172 short *reference_pt2;
183 unsigned int seq_length;
201 int **l_min_values_b;
202 int **l_max_values_b;
206 int **l_min_values_m;
207 int **l_max_values_m;
211 int **l_min_values_m1;
212 int **l_max_values_m1;
213 int *k_min_values_m1;
214 int *k_max_values_m1;
216 int **l_min_values_m2;
217 int **l_max_values_m2;
218 int *k_min_values_m2;
219 int *k_max_values_m2;
221 int *l_min_values_qc;
222 int *l_max_values_qc;
226 int *l_min_values_qcH;
227 int *l_max_values_qcH;
228 int k_min_values_qcH;
229 int k_max_values_qcH;
231 int *l_min_values_qcI;
232 int *l_max_values_qcI;
233 int k_min_values_qcI;
234 int k_max_values_qcI;
236 int *l_min_values_qcM;
237 int *l_max_values_qcM;
238 int k_min_values_qcM;
239 int k_max_values_qcM;
276 const char *structure1,
320 DEPRECATED(TwoDpfold_solution *
378 unsigned int length));
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:130
char * ptype
Precomputed array of pair types.
Definition: 2Dpfold.h:156
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:174
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: 2Dpfold.h:160
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition: 2Dpfold.h:168
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.
Various data structures and pre-processor macros.
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 data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:102
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:176
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:159
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:178
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:169
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...
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:157
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:179
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: 2Dpfold.h:175
int k
Distance to first reference.
Definition: 2Dpfold.h:48
Variables compound for 2Dfold partition function folding.
Definition: 2Dpfold.h:154