Go to the documentation of this file. 1 #ifndef VIENNA_RNA_PACKAGE_RNASTRUCT_H
2 #define VIENNA_RNA_PACKAGE_RNASTRUCT_H
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)))
10 # define DEPRECATED(func, msg) func
13 # define DEPRECATED(func, msg) func
52 DEPRECATED(
char *
b2HIT(
const char *structure),
53 "Use vrna_db_to_tree_string() instead!");
66 DEPRECATED(
char *
b2C(
const char *structure),
67 "Use vrna_db_to_tree_string() instead!");
81 DEPRECATED(
char *
b2Shapiro(
const char *structure),
82 "Use vrna_db_to_tree_string() instead!");
91 DEPRECATED(
char *
add_root(
const char *structure),
103 "Use vrna_db_to_tree_string() instead!");
114 DEPRECATED(
char *
expand_Full(
const char *structure),
115 "Use vrna_db_to_tree_string() instead!");
126 "Use vrna_tree_string_to_db() instead!");
135 DEPRECATED(
char *
unweight(
const char *wcoarse),
136 "Use vrna_tree_string_unweight() instead!");
188 DEPRECATED(
extern int loops,
200 DEPRECATED(
extern int pairs,
int loop_degree[2000]
contains the corresponding list of loop degrees.
char * expand_Full(const char *structure)
Convert the full structure from bracket notation to the expanded notation including root.
char * expand_Shapiro(const char *coarse)
Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C().
char * b2C(const char *structure)
Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' ...
int loops
contains the number of loops ( and therefore of stacks ).
void parse_structure(const char *structure)
Collects a statistic of structure elements of the full structure in bracket notation.
int unpaired
contains the number of unpaired bases.
char * b2HIT(const char *structure)
Converts the full structure from bracket notation to the HIT notation including root.
int helix_size[2000]
contains a list of all stack sizes.
int pairs
contains the number of base pairs in the last parsed structure.
char * unexpand_Full(const char *ffull)
Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifi...
char * b2Shapiro(const char *structure)
Converts the full structure from bracket notation to the weighted coarse grained notation using the '...
char * add_root(const char *structure)
Adds a root to an un-rooted tree in any except bracket notation.
void unexpand_aligned_F(char *align[2])
Converts two aligned structures in expanded notation.
char * unweight(const char *wcoarse)
Strip weights from any weighted tree.
int loop_size[2000]
contains a list of all loop sizes. loop_size[0] contains the number of external bases.