RNAlib-2.2.0RC0
structure_utils.h
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1 #ifndef __VIENNA_RNA_PACKAGE_STRUCT_UTILS_H__
2 #define __VIENNA_RNA_PACKAGE_STRUCT_UTILS_H__
3 
9 #include <stdio.h>
10 
12 
13 #ifdef __GNUC__
14 #define DEPRECATED(func) func __attribute__ ((deprecated))
15 #else
16 #define DEPRECATED(func) func
17 #endif
18 
30 char *vrna_pack_structure(const char *struc);
31 
44 DEPRECATED(char *pack_structure(const char *struc));
45 
55 char *vrna_unpack_structure(const char *packed);
56 
67 DEPRECATED(char *unpack_structure(const char *packed));
68 
78 short *vrna_pt_get(const char *structure);
79 
91 DEPRECATED(short *make_pair_table(const char *structure));
92 
93 
106 short *vrna_pt_pk_get(const char *structure);
107 
108 DEPRECATED(short *make_pair_table_pk(const char *structure));
109 
116 short *vrna_pt_copy(const short *pt);
117 
126 DEPRECATED(short *copy_pair_table(const short *pt));
127 
132 short *vrna_pt_ali_get(const char *structure);
133 
139 DEPRECATED(short *alimake_pair_table(const char *structure));
140 
148 short *vrna_pt_snoop_get(const char *structure);
149 
156 DEPRECATED(short *make_pair_table_snoop(const char *structure));
157 
158 
162 int *vrna_get_loop_index(const short *pt);
163 
164 DEPRECATED(int *make_loop_index_pt(short *pt));
165 
172 char *vrna_pt_to_db(short *pt);
173 
174 
186 int vrna_bp_distance( const char *str1,
187  const char *str2);
188 
201 DEPRECATED(int bp_distance(const char *str1, const char *str2));
202 
203 
210 unsigned int *vrna_refBPcnt_matrix(const short *reference_pt,
211  unsigned int turn);
212 
221 DEPRECATED(unsigned int *make_referenceBP_array(short *reference_pt,
222  unsigned int turn));
223 
224 
232 unsigned int *vrna_refBPdist_matrix( const short *pt1,
233  const short *pt2,
234  unsigned int turn);
235 
244 DEPRECATED(unsigned int *compute_BPdifferences( short *pt1,
245  short *pt2,
246  unsigned int turn));
247 
264 plist *vrna_get_plist_from_pr(vrna_fold_compound *vc, double cut_off);
265 
285 DEPRECATED(void assign_plist_from_pr( plist **pl,
286  FLT_OR_DBL *probs,
287  int length,
288  double cutoff));
289 
293 void bppm_to_structure(char *structure,
294  FLT_OR_DBL *pr,
295  unsigned int length);
296 
300 char bppm_symbol(const float *x);
301 
306 void vrna_parenthesis_structure( char *structure,
307  bondT *bp,
308  int length);
309 
317 DEPRECATED(void parenthesis_structure(char *structure,
318  bondT *bp,
319  int length));
320 
327 void vrna_parenthesis_zuker(char *structure,
328  bondT *bp,
329  int length);
330 
339 DEPRECATED(void parenthesis_zuker(char *structure,
340  bondT *bp,
341  int length));
342 
343 void vrna_letter_structure( char *structure,
344  bondT *bp,
345  int length);
346 
347 DEPRECATED(void letter_structure( char *structure,
348  bondT *bp,
349  int length));
350 
366 plist *vrna_get_plist_from_db(const char *struc, float pr);
367 
385 DEPRECATED(void assign_plist_from_db(plist **pl, const char *struc, float pr));
386 
387 #endif
unsigned int * vrna_refBPcnt_matrix(const short *reference_pt, unsigned int turn)
Make a reference base pair count matrix.
short * alimake_pair_table(const char *structure)
short * vrna_pt_pk_get(const char *structure)
Create a pair table of a secondary structure (pseudo-knot version)
void assign_plist_from_db(plist **pl, const char *struc, float pr)
Create a plist from a dot-bracket string.
plist * vrna_get_plist_from_pr(vrna_fold_compound *vc, double cut_off)
Create a plist from base pair probability matrix.
short * make_pair_table_snoop(const char *structure)
void parenthesis_zuker(char *structure, bondT *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calcul...
char bppm_symbol(const float *x)
Get a pseudo dot bracket notation for a given probability information.
short * make_pair_table(const char *structure)
Create a pair table of a secondary structure.
short * vrna_pt_get(const char *structure)
Create a pair table of a secondary structure.
void vrna_parenthesis_zuker(char *structure, bondT *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calcul...
Definition: data_structures.h:359
char * pack_structure(const char *struc)
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
int * vrna_get_loop_index(const short *pt)
Get a loop index representation of a structure.
short * vrna_pt_snoop_get(const char *structure)
Create a pair table of a secondary structure (snoop version)
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
int bp_distance(const char *str1, const char *str2)
Compute the "base pair" distance between two secondary structures s1 and s2.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:94
unsigned int * compute_BPdifferences(short *pt1, short *pt2, unsigned int turn)
Make a reference base pair distance matrix.
void assign_plist_from_pr(plist **pl, FLT_OR_DBL *probs, int length, double cutoff)
Create a plist from a probability matrix.
short * vrna_pt_ali_get(const char *structure)
Create a pair table of a secondary structure (snoop align version)
char * unpack_structure(const char *packed)
Unpack secondary structure previously packed with pack_structure()
char * vrna_pt_to_db(short *pt)
Convert a pair table into dot-parenthesis notation.
short * copy_pair_table(const short *pt)
Get an exact copy of a pair table.
Base pair.
Definition: data_structures.h:122
void bppm_to_structure(char *structure, FLT_OR_DBL *pr, unsigned int length)
Create a dot-bracket like structure string from base pair probability matrix.
unsigned int * make_referenceBP_array(short *reference_pt, unsigned int turn)
Make a reference base pair count matrix.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
plist * vrna_get_plist_from_db(const char *struc, float pr)
Create a plist from a dot-bracket string.
void vrna_parenthesis_structure(char *structure, bondT *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack.
void parenthesis_structure(char *structure, bondT *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack.
char * vrna_unpack_structure(const char *packed)
Unpack secondary structure previously packed with pack_structure()
char * vrna_pack_structure(const char *struc)
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
unsigned int * vrna_refBPdist_matrix(const short *pt1, const short *pt2, unsigned int turn)
Make a reference base pair distance matrix.
short * vrna_pt_copy(const short *pt)
Get an exact copy of a pair table.
int vrna_bp_distance(const char *str1, const char *str2)
Compute the "base pair" distance between two secondary structures s1 and s2.