1 #ifndef VIENNA_RNA_PACKAGE_STRUCT_UTILS_H
2 #define VIENNA_RNA_PACKAGE_STRUCT_UTILS_H
5 #define VRNA_BACKWARD_COMPAT
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
10 #define DEPRECATED(func) func
161 unsigned int length);
174 unsigned int length);
184 unsigned int length);
186 void vrna_letter_structure(
char *structure,
188 unsigned int length);
241 #ifdef VRNA_BACKWARD_COMPAT
305 DEPRECATED(
short *make_pair_table_pk(
const char *structure));
332 DEPRECATED(
int *make_loop_index_pt(
short *pt));
346 DEPRECATED(
int bp_distance(
const char *str1,
const char *str2));
417 DEPRECATED(
void letter_structure(
char *structure,
plist * vrna_pl_get_from_pr(vrna_fold_compound *vc, double cut_off)
Create a plist from base pair probability matrix.
char vrna_bpp_symbol(const float *x)
Get a pseudo dot bracket notation for a given probability information.
void vrna_parenthesis_structure(char *structure, bondT *bp, unsigned int length)
Create a dot-backet/parenthesis structure from backtracking stack.
void vrna_parenthesis_zuker(char *structure, bondT *bp, unsigned int length)
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calcul...
int vrna_bp_distance(const char *str1, const char *str2)
Compute the "base pair" distance between two secondary structures s1 and s2.
int * vrna_get_loop_index(const short *pt)
Get a loop index representation of a structure.
int bp_distance(const char *str1, const char *str2)
Compute the "base pair" distance between two secondary structures s1 and s2.
char * vrna_db_pack(const char *struc)
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
void parenthesis_zuker(char *structure, bondT *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calcul...
void parenthesis_structure(char *structure, bondT *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack.
char * vrna_pt_to_db(short *pt)
Convert a pair table into dot-parenthesis notation.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:689
void assign_plist_from_db(plist **pl, const char *struc, float pr)
Create a plist from a dot-bracket string.
short * vrna_pt_pk_get(const char *structure)
Create a pair table of a secondary structure (pseudo-knot version)
short * make_pair_table(const char *structure)
Create a pair table of a secondary structure.
char bppm_symbol(const float *x)
Get a pseudo dot bracket notation for a given probability information.
unsigned int * compute_BPdifferences(short *pt1, short *pt2, unsigned int turn)
Make a reference base pair distance matrix.
unsigned int * vrna_refBPdist_matrix(const short *pt1, const short *pt2, unsigned int turn)
Make a reference base pair distance matrix.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:45
char * vrna_db_unpack(const char *packed)
Unpack secondary structure previously packed with vrna_db_pack()
void assign_plist_from_pr(plist **pl, FLT_OR_DBL *probs, int length, double cutoff)
Create a plist from a probability matrix.
short * copy_pair_table(const short *pt)
Get an exact copy of a pair table.
short * vrna_pt_copy(const short *pt)
Get an exact copy of a pair table.
short * vrna_pt_ali_get(const char *structure)
Create a pair table of a secondary structure (snoop align version)
char * vrna_db_get_from_pr(const FLT_OR_DBL *pr, unsigned int length)
Create a dot-bracket like structure string from base pair probability matrix.
Base pair.
Definition: data_structures.h:73
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.
plist * vrna_pl_get(const char *struc, float pr)
Create a plist from a dot-bracket string.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
char * unpack_structure(const char *packed)
Unpack secondary structure previously packed with pack_structure()
char * pack_structure(const char *struc)
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
short * alimake_pair_table(const char *structure)
char * vrna_pl_to_db(plist *pairs, unsigned int n)
Convert a list of base pairs into dot-bracket notation.
short * vrna_pt_snoop_get(const char *structure)
Create a pair table of a secondary structure (snoop version)
short * make_pair_table_snoop(const char *structure)
int pairs
contains the number of base pairs in the last parsed structure.
short * vrna_pt_get(const char *structure)
Create a pair table of a secondary structure.
Definition: structure_utils.h:26
unsigned int * vrna_refBPcnt_matrix(const short *reference_pt, unsigned int turn)
Make a reference base pair count matrix.
unsigned int * make_referenceBP_array(short *reference_pt, unsigned int turn)
Make a reference base pair count matrix.