RNAstruct.h File Reference

Parsing and Coarse Graining of Structures. More...

Go to the source code of this file.

Functions
char *	b2HIT (const char *structure)
	Converts the full structure from bracket notation to the HIT notation including root. More...
char *	b2C (const char *structure)
	Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers. More...
char *	b2Shapiro (const char *structure)
	Converts the full structure from bracket notation to the weighted coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers. More...
char *	add_root (const char *structure)
	Adds a root to an un-rooted tree in any except bracket notation. More...
char *	expand_Shapiro (const char *coarse)
	Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C(). More...
char *	expand_Full (const char *structure)
	Convert the full structure from bracket notation to the expanded notation including root. More...
char *	unexpand_Full (const char *ffull)
	Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifiers 'U' 'P' and 'R'. More...
char *	unweight (const char *wcoarse)
	Strip weights from any weighted tree. More...
void	unexpand_aligned_F (char *align[2])
	Converts two aligned structures in expanded notation. More...
void	parse_structure (const char *structure)
	Collects a statistic of structure elements of the full structure in bracket notation. More...

Variables
int	loop_size [STRUC]
	contains a list of all loop sizes. loop_size[0] contains the number of external bases.
int	helix_size [STRUC]
	contains a list of all stack sizes.
int	loop_degree [STRUC]
	contains the corresponding list of loop degrees.
int	loops
	contains the number of loops ( and therefore of stacks ).
int	unpaired
	contains the number of unpaired bases.
int	pairs
	contains the number of base pairs in the last parsed structure.

Detailed Description

Parsing and Coarse Graining of Structures.

Example:

*   .((..(((...)))..((..)))).   is the bracket or full tree
*   becomes expanded:   - expand_Full() -
*   ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R)
*   HIT:                - b2HIT() -
*   ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R)
*   Coarse:             - b2C() -
*   ((H)((H)M)R)
*   becomes expanded:   - expand_Shapiro() -
*   (((((H)S)((H)S)M)S)R)
*   weighted Shapiro:   - b2Shapiro() -
*   ((((((H3)S3)((H2)S2)M4)S2)E2)R)
*  

Function Documentation

char* b2HIT

(

const char *

structure

)

Converts the full structure from bracket notation to the HIT notation including root.

Parameters

structure

Returns

char* b2C

(

const char *

structure

)

Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers.

Parameters

structure

Returns

char* b2Shapiro

(

const char *

structure

)

Converts the full structure from bracket notation to the weighted coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers.

Parameters

structure

Returns

char* add_root

(

const char *

structure

)

Adds a root to an un-rooted tree in any except bracket notation.

Parameters

structure

Returns

char* expand_Shapiro

(

const char *

coarse

)

Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C().

Parameters

coarse

Returns

char* expand_Full

(

const char *

structure

)

Convert the full structure from bracket notation to the expanded notation including root.

Parameters

structure

Returns

char* unexpand_Full

(

const char *

ffull

)

Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifiers 'U' 'P' and 'R'.

Parameters

ffull

Returns

char* unweight

(

const char *

wcoarse

)

Strip weights from any weighted tree.

Parameters

wcoarse

Returns

void unexpand_aligned_F

(

char *

align[2]

)

Converts two aligned structures in expanded notation.

Takes two aligned structures as produced by tree_edit_distance() function back to bracket notation with '_' as the gap character. The result overwrites the input.

Parameters

align

void parse_structure

(

const char *

structure

)

Collects a statistic of structure elements of the full structure in bracket notation.

The function writes to the following global variables: loop_size, loop_degree, helix_size, loops, pairs, unpaired

Parameters

structure

Returns