H/RNAstruct.h File Reference

Parsing and Coarse Graining of Structures. More...

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Functions
char *	b2HIT (const char *structure)
	Converts the full structure from bracket notation to the HIT notation including root.
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.
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.
char *	add_root (const char *structure)
	Adds a root to an un-rooted tree in any except bracket notation.
char *	expand_Shapiro (const char *coarse)
	Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C().
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 identifiers 'U' 'P' and 'R'.
char *	unweight (const char *wcoarse)
	Strip weights from any weighted tree.
void	unexpand_aligned_F (char *align[2])
	Converts two aligned structures in expanded notation.
void	parse_structure (const char *structure)
	Collects a statistic of structure elements of the full structure in bracket notation.
Variables
int	loop_size [STRUC]
	contains a list of all loop sizes.
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.

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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:

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Variable Documentation

int loop_size[STRUC]

contains a list of all loop sizes.

loop_size[0] contains the number of external bases.