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:48
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
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:101
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...
short * S1
The input sequences in numeric form.
Definition: 2Dpfold.h:158
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