1 #ifndef VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H 2 #define VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H 4 #ifdef VRNA_WARN_DEPRECATED 5 # if defined(__clang__) 6 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 7 # elif defined(__GNUC__) 8 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 10 # define DEPRECATED(func, msg) func 13 # define DEPRECATED(func, msg) func 137 unsigned int length);
144 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 146 #define TwoDpfold_solution vrna_sol_TwoD_pf_t 172 short *reference_pt1;
173 short *reference_pt2;
184 unsigned int seq_length;
202 int **l_min_values_b;
203 int **l_max_values_b;
207 int **l_min_values_m;
208 int **l_max_values_m;
212 int **l_min_values_m1;
213 int **l_max_values_m1;
214 int *k_min_values_m1;
215 int *k_max_values_m1;
217 int **l_min_values_m2;
218 int **l_max_values_m2;
219 int *k_min_values_m2;
220 int *k_max_values_m2;
222 int *l_min_values_qc;
223 int *l_max_values_qc;
227 int *l_min_values_qcH;
228 int *l_max_values_qcH;
229 int k_min_values_qcH;
230 int k_max_values_qcH;
232 int *l_min_values_qcI;
233 int *l_max_values_qcI;
234 int k_min_values_qcI;
235 int k_max_values_qcI;
237 int *l_min_values_qcM;
238 int *l_max_values_qcM;
239 int k_min_values_qcM;
240 int k_max_values_qcM;
277 const char *structure1,
280 "Use the new API and vrna_fold_compound_TwoD() instead");
297 "Use the new API and vrna_fold_compound_free() instead");
323 DEPRECATED(TwoDpfold_solution *
327 "Use the new API and vrna_pf_TwoD() instead");
354 "Use the new API and vrna_pbacktrack_TwoD() instead");
383 unsigned int length),
384 "Use the new API and vrna_pbacktrack5_TwoD() instead");
394 "Use the new API and vrna_pf_TwoD() instead");
404 "Use the new API and vrna_pf_TwoD() instead");
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
char * ptype
Precomputed array of pair types.
Definition: 2Dpfold.h:157
Solution element returned from vrna_pf_TwoD()
Definition: 2Dpfold.h:49
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:175
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: 2Dpfold.h:161
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition: 2Dpfold.h:169
FLT_OR_DBL q
partition function
Definition: 2Dpfold.h:52
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: basic.h:103
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,...
Definition: 2Dpfold.h:177
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:160
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:51
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: 2Dpfold.h:179
Functions to deal with sets of energy parameters.
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:170
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...
The Basic Fold Compound API.
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:158
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:180
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: 2Dpfold.h:176
int k
Distance to first reference.
Definition: 2Dpfold.h:50
Variables compound for 2Dfold partition function folding.
Definition: 2Dpfold.h:155