RNAlib-2.4.14
2Dfold.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_TWO_D_FOLD_H
2 #define VIENNA_RNA_PACKAGE_TWO_D_FOLD_H
3 
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)))
9 # else
10 # define DEPRECATED(func, msg) func
11 # endif
12 #else
13 # define DEPRECATED(func, msg) func
14 #endif
15 
35 #include <ViennaRNA/fold_compound.h>
36 #include <ViennaRNA/datastructures/basic.h>
37 #include <ViennaRNA/params/basic.h>
38 
53 typedef struct vrna_sol_TwoD_t {
54  int k;
55  int l;
56  float en;
57  char *s;
58 } vrna_sol_TwoD_t;
59 
60 
88 vrna_sol_TwoD_t *
89 vrna_mfe_TwoD(vrna_fold_compound_t *vc,
90  int distance1,
91  int distance2);
92 
93 
112 char *
113 vrna_backtrack5_TwoD(vrna_fold_compound_t *vc,
114  int k,
115  int l,
116  unsigned int j);
117 
118 
119 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
120 
121 #define TwoDfold_solution vrna_sol_TwoD_t /* restore compatibility of struct rename */
122 
130 typedef struct TwoDfold_vars {
131  vrna_param_t *P;
132  int do_backtrack;
133  char *ptype;
134  char *sequence;
135  short *S, *S1;
136  unsigned int maxD1;
137  unsigned int maxD2;
140  unsigned int *mm1;
141  unsigned int *mm2;
143  int *my_iindx;
145  double temperature;
146 
147  unsigned int *referenceBPs1;
148  unsigned int *referenceBPs2;
149  unsigned int *bpdist;
151  short *reference_pt1;
152  short *reference_pt2;
153  int circ;
154  int dangles;
155  unsigned int seq_length;
156 
157  int ***E_F5;
158  int ***E_F3;
159  int ***E_C;
160  int ***E_M;
161  int ***E_M1;
162  int ***E_M2;
163 
164  int **E_Fc;
165  int **E_FcH;
166  int **E_FcI;
167  int **E_FcM;
168 
169  int **l_min_values;
170  int **l_max_values;
171  int *k_min_values;
172  int *k_max_values;
173 
174  int **l_min_values_m;
175  int **l_max_values_m;
176  int *k_min_values_m;
177  int *k_max_values_m;
178 
179  int **l_min_values_m1;
180  int **l_max_values_m1;
181  int *k_min_values_m1;
182  int *k_max_values_m1;
183 
184  int **l_min_values_f;
185  int **l_max_values_f;
186  int *k_min_values_f;
187  int *k_max_values_f;
188 
189  int **l_min_values_f3;
190  int **l_max_values_f3;
191  int *k_min_values_f3;
192  int *k_max_values_f3;
193 
194  int **l_min_values_m2;
195  int **l_max_values_m2;
196  int *k_min_values_m2;
197  int *k_max_values_m2;
198 
199  int *l_min_values_fc;
200  int *l_max_values_fc;
201  int k_min_values_fc;
202  int k_max_values_fc;
203 
204  int *l_min_values_fcH;
205  int *l_max_values_fcH;
206  int k_min_values_fcH;
207  int k_max_values_fcH;
208 
209  int *l_min_values_fcI;
210  int *l_max_values_fcI;
211  int k_min_values_fcI;
212  int k_max_values_fcI;
213 
214  int *l_min_values_fcM;
215  int *l_max_values_fcM;
216  int k_min_values_fcM;
217  int k_max_values_fcM;
218 
219  /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */
220  int *E_F5_rem;
221  int *E_F3_rem;
222  int *E_C_rem;
223  int *E_M_rem;
224  int *E_M1_rem;
225  int *E_M2_rem;
226 
227  int E_Fc_rem;
228  int E_FcH_rem;
229  int E_FcI_rem;
230  int E_FcM_rem;
231 
232 #ifdef COUNT_STATES
233  unsigned long ***N_F5;
234  unsigned long ***N_C;
235  unsigned long ***N_M;
236  unsigned long ***N_M1;
237 #endif
238 
239  vrna_fold_compound_t *compatibility;
240 } TwoDfold_vars;
241 
260 DEPRECATED(TwoDfold_vars *
261  get_TwoDfold_variables(const char *seq,
262  const char *structure1,
263  const char *structure2,
264  int circ),
265  "Use the new API and corresponding functions vrna_fold_compound_TwoD(), etc. instead");
266 
277 DEPRECATED(void
278  destroy_TwoDfold_variables(TwoDfold_vars *our_variables),
279  "Use the new API and vrna_fold_compound_free() instead");
280 
306 DEPRECATED(TwoDfold_solution *
307  TwoDfoldList(TwoDfold_vars *vars,
308  int distance1,
309  int distance2),
310  "Use the new API and vrna_mfe_TwoD() instead");
311 
332 DEPRECATED(char *TwoDfold_backtrack_f5(unsigned int j,
333  int k,
334  int l,
335  TwoDfold_vars *vars),
336  "Use the new API and vrna_backtrack5_TwoD() instead");
337 
341 DEPRECATED(TwoDfold_solution **TwoDfold(TwoDfold_vars *our_variables,
342  int distance1,
343  int distance2),
344  "Use the new API and vrna_mfe_TwoD() instead");
345 
346 
347 #endif
348 
353 #endif
vrna_sol_TwoD_t
Solution element returned from vrna_mfe_TwoD()
Definition: 2Dfold.h:53
TwoDfold_vars
struct TwoDfold_vars TwoDfold_vars
Variables compound for 2Dfold MFE folding.
TwoDfold_vars::mm2
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: 2Dfold.h:141
TwoDfold_vars
Variables compound for 2Dfold MFE folding.
Definition: 2Dfold.h:130
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
temperature
double temperature
Rescale energy parameters to a temperature in degC.
TwoDfold_backtrack_f5
char * TwoDfold_backtrack_f5(unsigned int j, int k, int l, TwoDfold_vars *vars)
Backtrack a minimum free energy structure from a 5&#39; section of specified length.
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
TwoDfold_vars::mm1
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: 2Dfold.h:140
destroy_TwoDfold_variables
void destroy_TwoDfold_variables(TwoDfold_vars *our_variables)
Destroy a TwoDfold_vars datastructure without memory loss.
vrna_sol_TwoD_t::l
int l
Distance to second reference.
Definition: 2Dfold.h:55
vrna_sol_TwoD_t::s
char * s
MFE representative structure in dot-bracket notation.
Definition: 2Dfold.h:57
vrna_backtrack5_TwoD
char * vrna_backtrack5_TwoD(vrna_fold_compound_t *vc, int k, int l, unsigned int j)
Backtrack a minimum free energy structure from a 5&#39; section of specified length.
basic.h
Various data structures and pre-processor macros.
TwoDfold_vars::do_backtrack
int do_backtrack
Flag whether to do backtracing of the structure(s) or not.
Definition: 2Dfold.h:132
TwoDfold_vars::referenceBPs2
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: 2Dfold.h:148
TwoDfold_vars::referenceBPs1
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: 2Dfold.h:147
TwoDfold_vars::my_iindx
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition: 2Dfold.h:143
TwoDfold_vars::maxD1
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: 2Dfold.h:136
TwoDfoldList
vrna_sol_TwoD_t * TwoDfoldList(TwoDfold_vars *vars, int distance1, int distance2)
Compute MFE&#39;s and representative for distance partitioning.
vrna_sol_TwoD_t
struct vrna_sol_TwoD_t vrna_sol_TwoD_t
Solution element returned from vrna_mfe_TwoD()
vrna_sol_TwoD_t::k
int k
Distance to first reference.
Definition: 2Dfold.h:54
vrna_mfe_TwoD
vrna_sol_TwoD_t * vrna_mfe_TwoD(vrna_fold_compound_t *vc, int distance1, int distance2)
Compute MFE&#39;s and representative for distance partitioning.
TwoDfold_vars::ptype
char * ptype
Precomputed array of pair types.
Definition: 2Dfold.h:133
TwoDfold_vars::P
vrna_param_t * P
Precomputed energy parameters and model details.
Definition: 2Dfold.h:131
TwoDfold_vars::S1
short * S1
The input sequences in numeric form.
Definition: 2Dfold.h:135
TwoDfold_vars::sequence
char * sequence
The input sequence.
Definition: 2Dfold.h:134
get_TwoDfold_variables
TwoDfold_vars * get_TwoDfold_variables(const char *seq, const char *structure1, const char *structure2, int circ)
Get a structure of type TwoDfold_vars prefilled with current global settings.
basic.h
Functions to deal with sets of energy parameters.
vrna_sol_TwoD_t::en
float en
Free energy in kcal/mol.
Definition: 2Dfold.h:56
TwoDfold_vars::maxD2
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: 2Dfold.h:137
fold_compound.h
The Basic Fold Compound API.
circ
int circ
backward compatibility variable.. this does not effect anything
dangles
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
TwoDfold_vars::bpdist
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: 2Dfold.h:149