1 #ifndef VIENNA_RNA_PACKAGE_STRUCT_UTILS_H
2 #define VIENNA_RNA_PACKAGE_STRUCT_UTILS_H
5 #define VRNA_BACKWARD_COMPAT
7 #ifdef DEPRECATION_WARNINGS
9 # define DEPRECATED(func) func __attribute__ ((deprecated))
11 # define DEPRECATED(func) func
14 # define DEPRECATED(func) func
167 unsigned int length);
186 unsigned int length);
188 void vrna_letter_structure(
char *structure,
190 unsigned int length);
239 vrna_hx_t *vrna_hx_from_ptable(
short *pt);
242 #ifdef VRNA_BACKWARD_COMPAT
306 DEPRECATED(
short *make_pair_table_pk(
const char *structure));
333 DEPRECATED(
int *make_loop_index_pt(
short *pt));
347 DEPRECATED(
int bp_distance(
const char *str1,
const char *str2));
418 DEPRECATED(
void letter_structure(
char *structure,
char vrna_bpp_symbol(const float *x)
Get a pseudo dot bracket notation for a given probability information.
int * vrna_loopidx_from_ptable(const short *pt)
Get a loop index representation of a structure.
int vrna_bp_distance(const char *str1, const char *str2)
Compute the "base pair" distance between two secondary structures s1 and s2.
vrna_plist_t * vrna_plist(const char *struc, float pr)
Create a vrna_plist_t from a dot-bracket string.
char * vrna_db_from_plist(vrna_plist_t *pairs, unsigned int n)
Convert a list of base pairs into dot-bracket notation.
char * vrna_db_from_bp_stack(vrna_bp_stack_t *bp, unsigned int length)
Create a dot-backet/parenthesis structure from backtracking stack.
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.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
vrna_plist_t * vrna_plist_from_probs(vrna_fold_compound_t *vc, double cut_off)
Create a vrna_plist_t from base pair probability matrix.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
short * vrna_ptable(const char *structure)
Create a pair table of a secondary structure.
char * vrna_db_from_probs(const FLT_OR_DBL *pr, unsigned int length)
Create a dot-bracket like structure string from base pair probability matrix.
void parenthesis_zuker(char *structure, vrna_bp_stack_t *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calcul...
char * vrna_db_from_ptable(short *pt)
Convert a pair table into dot-parenthesis notation.
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.
Definition: structure_utils.h:32
char * vrna_db_unpack(const char *packed)
Unpack secondary structure previously packed with vrna_db_pack()
short * copy_pair_table(const short *pt)
Get an exact copy of a pair table.
void assign_plist_from_db(vrna_plist_t **pl, const char *struc, float pr)
Create a vrna_plist_t from a dot-bracket string.
short * vrna_pt_ali_get(const char *structure)
Create a pair table of a secondary structure (snoop align version)
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
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.
void parenthesis_structure(char *structure, vrna_bp_stack_t *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack.
Base pair stack element.
Definition: data_structures.h:192
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)
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)
short * vrna_ptable_copy(const short *pt)
Get an exact copy of a pair table.
void assign_plist_from_pr(vrna_plist_t **pl, FLT_OR_DBL *probs, int length, double cutoff)
Create a vrna_plist_t from a probability matrix.
int pairs
contains the number of base pairs in the last parsed structure.
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.