RNAlib-2.2.9

- Main Page
- Related Pages
- Modules
- Data Structures
- Files

- File List
- Globals

RNAstruct.h
Go to the documentation of this file.
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
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 &#39;S&#39; 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 &#39;H&#39; &#39;B&#39; ...
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 &#39;...
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.