RNAstruct.h
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#ifndef VIENNA_RNA_PACKAGE_RNASTRUCT_H
#define VIENNA_RNA_PACKAGE_RNASTRUCT_H
#define STRUC 2000
char *b2HIT(const char *structure); /* Full -> HIT [incl. root] */
char *b2C(const char *structure); /* Full -> Coarse [incl. root] */
char *b2Shapiro(const char *structure); /* Full -> weighted Shapiro [i.r.] */
char *add_root(const char *structure); /* {Tree} -> ({Tree}R) */
char *expand_Shapiro(const char *coarse);
/* add S for stacks to coarse struct */
char *expand_Full(const char *structure); /* Full -> FFull */
char *unexpand_Full(const char *ffull); /* FFull -> Full */
char *unweight(const char *wcoarse); /* remove weights from coarse struct */
void unexpand_aligned_F(char *align[2]);
void parse_structure(const char *structure); /* make structure statistics */
extern int loop_size[STRUC]; /* loop sizes of a structure */
extern int helix_size[STRUC]; /* helix sizes of a structure */
extern int loop_degree[STRUC]; /* loop degrees of a structure */
extern int loops; /* n of loops and stacks */
extern int unpaired;
extern int pairs; /* n of unpaired digits and pairs */
#endif
unweight
char * unweight(const char *wcoarse)
Strip weights from any weighted tree.
parse_structure
void parse_structure(const char *structure)
Collects a statistic of structure elements of the full structure in bracket notation.
expand_Full
char * expand_Full(const char *structure)
Convert the full structure from bracket notation to the expanded notation including root...
unexpand_Full
char * unexpand_Full(const char *ffull)
Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifi...
unexpand_aligned_F
void unexpand_aligned_F(char *align[2])
Converts two aligned structures in expanded notation.
expand_Shapiro
char * expand_Shapiro(const char *coarse)
Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C()...
helix_size
int helix_size[STRUC]
contains a list of all stack sizes.
b2C
char * b2C(const char *structure)
Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' ...
b2HIT
char * b2HIT(const char *structure)
Converts the full structure from bracket notation to the HIT notation including root.
unpaired
int unpaired
contains the number of unpaired bases.
loop_size
int loop_size[STRUC]
contains a list of all loop sizes. loop_size[0] contains the number of external bases.
add_root
char * add_root(const char *structure)
Adds a root to an un-rooted tree in any except bracket notation.
loop_degree
int loop_degree[STRUC]
contains the corresponding list of loop degrees.
b2Shapiro
char * b2Shapiro(const char *structure)
Converts the full structure from bracket notation to the weighted coarse grained notation using the '...
loops
int loops
contains the number of loops ( and therefore of stacks ).
pairs
int pairs
contains the number of base pairs in the last parsed structure.