RNAlib-2.1.9h
RNAstruct.h
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1 #ifndef __VIENNA_RNA_PACKAGE_RNASTRUCT_H__
2 #define __VIENNA_RNA_PACKAGE_RNASTRUCT_H__
3 
24 #define STRUC 2000
25 
33 char *b2HIT(const char *structure); /* Full -> HIT [incl. root] */
34 
42 char *b2C(const char *structure); /* Full -> Coarse [incl. root] */
43 
52 char *b2Shapiro(const char *structure); /* Full -> weighted Shapiro [i.r.] */
53 
60 char *add_root(const char *structure); /* {Tree} -> ({Tree}R) */
61 
69 char *expand_Shapiro(const char *coarse);
70 
71 /* add S for stacks to coarse struct */
79 char *expand_Full(const char *structure); /* Full -> FFull */
80 
88 char *unexpand_Full(const char *ffull); /* FFull -> Full */
89 
96 char *unweight(const char *wcoarse); /* remove weights from coarse struct */
97 
107 void unexpand_aligned_F(char *align[2]);
108 
119 void parse_structure(const char *structure); /* make structure statistics */
120 
125 extern int loop_size[STRUC]; /* loop sizes of a structure */
126 
130 extern int helix_size[STRUC]; /* helix sizes of a structure */
131 
135 extern int loop_degree[STRUC]; /* loop degrees of a structure */
136 
140 extern int loops; /* n of loops and stacks */
141 
145 extern int unpaired;
146 
150 extern int pairs; /* n of unpaired digits and pairs */
151 
152 #endif
void parse_structure(const char *structure)
Collects a statistic of structure elements of the full structure in bracket notation.
char * b2C(const char *structure)
Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' ...
char * unweight(const char *wcoarse)
Strip weights from any weighted tree.
char * add_root(const char *structure)
Adds a root to an un-rooted tree in any except bracket notation.
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 * unexpand_Full(const char *ffull)
Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifi...
void unexpand_aligned_F(char *align[2])
Converts two aligned structures in expanded notation.
int pairs
contains the number of base pairs in the last parsed structure.
char * b2HIT(const char *structure)
Converts the full structure from bracket notation to the HIT notation including root.
int loops
contains the number of loops ( and therefore of stacks ).
int loop_size[STRUC]
contains a list of all loop sizes. loop_size[0] contains the number of external bases.
int unpaired
contains the number of unpaired bases.
char * b2Shapiro(const char *structure)
Converts the full structure from bracket notation to the weighted coarse grained notation using the '...
int loop_degree[STRUC]
contains the corresponding list of loop degrees.
int helix_size[STRUC]
contains a list of all stack sizes.