Detailed Description

Collaboration diagram for Deprecated Interface for Secondary Structure Utilities:

Files
file	RNAstruct.h
	Parsing and Coarse Graining of Structures.

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...

char *	pack_structure (const char *struc)
	Pack secondary secondary structure, 5:1 compression using base 3 encoding. More...

char *	unpack_structure (const char *packed)
	Unpack secondary structure previously packed with pack_structure() More...

short *	make_pair_table (const char *structure)
	Create a pair table of a secondary structure. More...

short *	copy_pair_table (const short *pt)
	Get an exact copy of a pair table. More...

short *	alimake_pair_table (const char *structure)

short *	make_pair_table_snoop (const char *structure)

int	bp_distance (const char str1, const char str2)
	Compute the "base pair" distance between two secondary structures s1 and s2. More...

unsigned int *	make_referenceBP_array (short *reference_pt, unsigned int turn)
	Make a reference base pair count matrix. More...

unsigned int *	compute_BPdifferences (short pt1, short pt2, unsigned int turn)
	Make a reference base pair distance matrix. More...

void	parenthesis_structure (char structure, vrna_bp_stack_t bp, int length)
	Create a dot-backet/parenthesis structure from backtracking stack. More...

void	parenthesis_zuker (char structure, vrna_bp_stack_t bp, int length)
	Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c. More...

void	bppm_to_structure (char structure, FLT_OR_DBL pr, unsigned int length)
	Create a dot-bracket like structure string from base pair probability matrix. More...

char	bppm_symbol (const float *x)
	Get a pseudo dot bracket notation for a given probability information. More...

Variables
int	loop_size [2000]
	contains a list of all loop sizes. loop_size[0] contains the number of external bases.

int	helix_size [2000]
	contains a list of all stack sizes.

int	loop_degree [2000]
	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.

Function Documentation

char* b2HIT ( const char * structure )

#include <ViennaRNA/RNAstruct.h>

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

Deprecated:: See vrna_db_to_tree_string() and VRNA_STRUCTURE_TREE_HIT for a replacement

Parameters

structure

Returns

char* b2C ( const char * structure )

#include <ViennaRNA/RNAstruct.h>

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

Deprecated:: See vrna_db_to_tree_string() and VRNA_STRUCTURE_TREE_SHAPIRO_SHORT for a replacement

Parameters

structure

Returns

char* b2Shapiro ( const char * structure )

#include <ViennaRNA/RNAstruct.h>

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

Deprecated:: See vrna_db_to_tree_string() and VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT for a replacement

Parameters

structure

Returns

char* add_root ( const char * structure )

#include <ViennaRNA/RNAstruct.h>

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

Parameters

structure

Returns

char* expand_Shapiro ( const char * coarse )

#include <ViennaRNA/RNAstruct.h>

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

Parameters

coarse

Returns

char* expand_Full ( const char * structure )

#include <ViennaRNA/RNAstruct.h>

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

Parameters

structure

Returns

char* unexpand_Full ( const char * ffull )

#include <ViennaRNA/RNAstruct.h>

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 )

#include <ViennaRNA/RNAstruct.h>

Strip weights from any weighted tree.

Parameters

wcoarse

Returns

void unexpand_aligned_F ( char * align[2] )

#include <ViennaRNA/RNAstruct.h>

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 )

#include <ViennaRNA/RNAstruct.h>

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

char* pack_structure ( const char * struc )

#include <ViennaRNA/utils/structures.h>

Pack secondary secondary structure, 5:1 compression using base 3 encoding.

Returns a binary string encoding of the secondary structure using a 5:1 compression scheme. The string is NULL terminated and can therefore be used with standard string functions such as strcmp(). Useful for programs that need to keep many structures in memory.

Deprecated:: Use vrna_db_pack() as a replacement

Parameters

struc The secondary structure in dot-bracket notation

Returns: The binary encoded structure

char* unpack_structure ( const char * packed )

#include <ViennaRNA/utils/structures.h>

Unpack secondary structure previously packed with pack_structure()

Translate a compressed binary string produced by pack_structure() back into the familiar dot-bracket notation.

Deprecated:: Use vrna_db_unpack() as a replacement

Parameters

packed The binary encoded packed secondary structure

Returns: The unpacked secondary structure in dot-bracket notation

short* make_pair_table ( const char * structure )

#include <ViennaRNA/utils/structures.h>

Create a pair table of a secondary structure.

Returns a newly allocated table, such that table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure.

Deprecated:: Use vrna_ptable() instead

Parameters

structure The secondary structure in dot-bracket notation

Returns: A pointer to the created pair_table

short* copy_pair_table ( const short * pt )

#include <ViennaRNA/utils/structures.h>

Get an exact copy of a pair table.

Deprecated:: Use vrna_ptable_copy() instead

Parameters

pt	The pair table to be copied

Returns: A pointer to the copy of 'pt'

short* alimake_pair_table ( const char * structure )

#include <ViennaRNA/utils/structures.h>

Pair table for snoop align

Deprecated:: Use vrna_pt_ali_get() instead!

short* make_pair_table_snoop ( const char * structure )

#include <ViennaRNA/utils/structures.h>

returns a newly allocated table, such that: table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure. The special pseudoknotted H/ACA-mRNA structure is taken into account.

Deprecated:: Use vrna_pt_snoop_get() instead!

int bp_distance	(	const char *	str1,
		const char *	str2
	)

#include <ViennaRNA/utils/structures.h>

Compute the "base pair" distance between two secondary structures s1 and s2.

The sequences should have the same length. dist = number of base pairs in one structure but not in the other same as edit distance with open-pair close-pair as move-set

Deprecated:: Use vrna_bp_distance instead

Parameters

str1	First structure in dot-bracket notation
str2	Second structure in dot-bracket notation

Returns: The base pair distance between str1 and str2

unsigned int* make_referenceBP_array	(	short *	reference_pt,
		unsigned int	turn
	)

#include <ViennaRNA/utils/structures.h>

Make a reference base pair count matrix.

Get an upper triangular matrix containing the number of basepairs of a reference structure for each interval [i,j] with i<j. Access it via iindx!!!

Deprecated:: Use vrna_refBPcnt_matrix() instead

unsigned int* compute_BPdifferences	(	short *	pt1,
		short *	pt2,
		unsigned int	turn
	)

#include <ViennaRNA/utils/structures.h>

Make a reference base pair distance matrix.

Get an upper triangular matrix containing the base pair distance of two reference structures for each interval [i,j] with i<j. Access it via iindx!!!

Deprecated:: Use vrna_refBPdist_matrix() instead

void parenthesis_structure	(	char *	structure,
		vrna_bp_stack_t *	bp,
		int	length
	)

#include <ViennaRNA/utils/structures.h>

Create a dot-backet/parenthesis structure from backtracking stack.

Deprecated:: use vrna_parenthesis_structure() instead

Note: This function is threadsafe

void parenthesis_zuker	(	char *	structure,
		vrna_bp_stack_t *	bp,
		int	length
	)

#include <ViennaRNA/utils/structures.h>

Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c.

Deprecated:: use vrna_parenthesis_zuker instead

Note: This function is threadsafe

void bppm_to_structure	(	char *	structure,
		FLT_OR_DBL *	pr,
		unsigned int	length
	)

#include <ViennaRNA/utils/structures.h>

Create a dot-bracket like structure string from base pair probability matrix.

Deprecated:: Use vrna_db_from_probs() instead!

char bppm_symbol ( const float * x )

#include <ViennaRNA/utils/structures.h>

Get a pseudo dot bracket notation for a given probability information.

Deprecated:: Use vrna_bpp_symbol() instead!

Detailed Description

Files

Functions

Variables

Function Documentation