RNAlib-2.2.7
RNAstruct.h
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1 #ifndef VIENNA_RNA_PACKAGE_RNASTRUCT_H
2 #define VIENNA_RNA_PACKAGE_RNASTRUCT_H
3 
28 #define STRUC 2000
29 
37 char *b2HIT(const char *structure); /* Full -> HIT [incl. root] */
38 
46 char *b2C(const char *structure); /* Full -> Coarse [incl. root] */
47 
56 char *b2Shapiro(const char *structure); /* Full -> weighted Shapiro [i.r.] */
57 
64 char *add_root(const char *structure); /* {Tree} -> ({Tree}R) */
65 
73 char *expand_Shapiro(const char *coarse);
74 
75 /* add S for stacks to coarse struct */
83 char *expand_Full(const char *structure); /* Full -> FFull */
84 
92 char *unexpand_Full(const char *ffull); /* FFull -> Full */
93 
100 char *unweight(const char *wcoarse); /* remove weights from coarse struct */
101 
111 void unexpand_aligned_F(char *align[2]);
112 
123 void parse_structure(const char *structure); /* make structure statistics */
124 
129 extern int loop_size[STRUC]; /* loop sizes of a structure */
130 
134 extern int helix_size[STRUC]; /* helix sizes of a structure */
135 
139 extern int loop_degree[STRUC]; /* loop degrees of a structure */
140 
144 extern int loops; /* n of loops and stacks */
145 
149 extern int unpaired;
150 
154 extern int pairs; /* n of unpaired digits and pairs */
155 
160 #endif
char * unweight(const char *wcoarse)
Strip weights from any weighted tree.
void parse_structure(const char *structure)
Collects a statistic of structure elements of the full structure in bracket notation.
char * expand_Full(const char *structure)
Convert the full structure from bracket notation to the expanded notation including root...
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.
char * expand_Shapiro(const char *coarse)
Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C()...
int helix_size[STRUC]
contains a list of all stack sizes.
char * b2C(const char *structure)
Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' ...
char * b2HIT(const char *structure)
Converts the full structure from bracket notation to the HIT notation including root.
int unpaired
contains the number of unpaired bases.
int loop_size[STRUC]
contains a list of all loop sizes. loop_size[0] contains the number of external bases.
char * add_root(const char *structure)
Adds a root to an un-rooted tree in any except bracket notation.
int loop_degree[STRUC]
contains the corresponding list of loop degrees.
char * b2Shapiro(const char *structure)
Converts the full structure from bracket notation to the weighted coarse grained notation using the '...
int loops
contains the number of loops ( and therefore of stacks ).
int pairs
contains the number of base pairs in the last parsed structure.