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
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
138 unsigned int length);
145#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
147#define TwoDpfold_solution vrna_sol_TwoD_pf_t
173 short *reference_pt1;
174 short *reference_pt2;
185 unsigned int seq_length;
203 int **l_min_values_b;
204 int **l_max_values_b;
208 int **l_min_values_m;
209 int **l_max_values_m;
213 int **l_min_values_m1;
214 int **l_max_values_m1;
215 int *k_min_values_m1;
216 int *k_max_values_m1;
218 int **l_min_values_m2;
219 int **l_max_values_m2;
220 int *k_min_values_m2;
221 int *k_max_values_m2;
223 int *l_min_values_qc;
224 int *l_max_values_qc;
228 int *l_min_values_qcH;
229 int *l_max_values_qcH;
230 int k_min_values_qcH;
231 int k_max_values_qcH;
233 int *l_min_values_qcI;
234 int *l_max_values_qcI;
235 int k_min_values_qcI;
236 int k_max_values_qcI;
238 int *l_min_values_qcM;
239 int *l_max_values_qcM;
240 int k_min_values_qcM;
241 int k_max_values_qcM;
278 const char *structure1,
281 "Use the new API and vrna_fold_compound_TwoD() instead");
298 "Use the new API and vrna_fold_compound_free() instead");
324DEPRECATED(TwoDpfold_solution *
328 "Use the new API and vrna_pf_TwoD() instead");
355 "Use the new API and vrna_pbacktrack_TwoD() instead");
385 unsigned int length),
386 "Use the new API and vrna_pbacktrack5_TwoD() instead");
396 "Use the new API and vrna_pf_TwoD() instead");
406 "Use the new API and vrna_pf_TwoD() instead");
char * TwoDpfold_pbacktrack(TwoDpfold_vars *vars, int d1, int d2)
Sample secondary structure representatives from a set of distance classes according to their Boltzman...
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.
TwoDpfold_solution * TwoDpfoldList(TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)
Compute the partition function for all distance classes.
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...
void destroy_TwoDpfold_variables(TwoDpfold_vars *vars)
Free all memory occupied by a TwoDpfold_vars datastructure.
Various data structures and pre-processor macros.
The Basic Fold Compound API.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition basic.h:43
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition basic.h:110
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
int l
Distance to second reference.
Definition 2Dpfold.h:51
FLT_OR_DBL q
partition function
Definition 2Dpfold.h:52
int k
Distance to first reference.
Definition 2Dpfold.h:50
vrna_sol_TwoD_pf_t * vrna_pf_TwoD(vrna_fold_compound_t *fc, int maxDistance1, int maxDistance2)
Compute the partition function for all distance classes.
Solution element returned from vrna_pf_TwoD()
Definition 2Dpfold.h:49
char * vrna_pbacktrack_TwoD(vrna_fold_compound_t *fc, int d1, int d2)
Sample secondary structure representatives from a set of distance classes according to their Boltzman...
char * vrna_pbacktrack5_TwoD(vrna_fold_compound_t *fc, int d1, int d2, unsigned int length)
Sample secondary structure representatives with a specified length from a set of distance classes acc...
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
double temperature
Rescale energy parameters to a temperature in degC.
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
int circ
backward compatibility variable.. this does not effect anything
Functions to deal with sets of energy parameters.
Variables compound for 2Dfold partition function folding.
Definition 2Dpfold.h:156
int * jindx
Index for moving in the triangular matrix qm1.
Definition 2Dpfold.h:171
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition 2Dpfold.h:177
short * S1
The input sequences in numeric form.
Definition 2Dpfold.h:160
char * sequence
The input sequence
Definition 2Dpfold.h:159
char * ptype
Precomputed array of pair types.
Definition 2Dpfold.h:158
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition 2Dpfold.h:161
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition 2Dpfold.h:180
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition 2Dpfold.h:162
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition 2Dpfold.h:170
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,...
Definition 2Dpfold.h:178
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition 2Dpfold.h:176
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition 2Dpfold.h:181