Functions and data structures for handling of secondary structure hard constraints. More...

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Data Structures
struct	vrna_hc_bp_storage_t
	A base pair hard constraint. More...

struct	vrna_hc_s
	The hard constraints data structure. More...

struct	vrna_hc_up_s
	A single hard constraint for a single nucleotide. More...

Macros
#define	VRNA_CONSTRAINT_NO_HEADER 0
	do not print the header information line More...

#define	VRNA_CONSTRAINT_DB 16384U
	Flag for vrna_constraints_add() to indicate that constraint is passed in pseudo dot-bracket notation. More...

#define	VRNA_CONSTRAINT_DB_ENFORCE_BP 32768U
	Switch for dot-bracket structure constraint to enforce base pairs. More...

#define	VRNA_CONSTRAINT_DB_PIPE 65536U
	Flag that is used to indicate the pipe '\|' sign in pseudo dot-bracket notation of hard constraints. More...

#define	VRNA_CONSTRAINT_DB_DOT 131072U
	dot '.' switch for structure constraints (no constraint at all) More...

#define	VRNA_CONSTRAINT_DB_X 262144U
	'x' switch for structure constraint (base must not pair) More...

#define	VRNA_CONSTRAINT_DB_ANG_BRACK 524288U
	angle brackets '<', '>' switch for structure constraint (paired downstream/upstream) More...

#define	VRNA_CONSTRAINT_DB_RND_BRACK 1048576U
	round brackets '(',')' switch for structure constraint (base i pairs base j) More...

#define	VRNA_CONSTRAINT_DB_INTRAMOL 2097152U
	Flag that is used to indicate the character 'l' in pseudo dot-bracket notation of hard constraints. More...

#define	VRNA_CONSTRAINT_DB_INTERMOL 4194304U
	Flag that is used to indicate the character 'e' in pseudo dot-bracket notation of hard constraints. More...

#define	VRNA_CONSTRAINT_DB_GQUAD 8388608U
	'+' switch for structure constraint (base is involved in a gquad) More...

#define	VRNA_CONSTRAINT_DB_WUSS 33554432U
	Flag to indicate Washington University Secondary Structure (WUSS) notation of the hard constraint string. More...

#define	VRNA_CONSTRAINT_DB_DEFAULT
	Switch for dot-bracket structure constraint with default symbols. More...

#define	VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (unsigned char)0x01
	Hard constraints flag, base pair in the exterior loop.

#define	VRNA_CONSTRAINT_CONTEXT_HP_LOOP (unsigned char)0x02
	Hard constraints flag, base pair encloses hairpin loop.

#define	VRNA_CONSTRAINT_CONTEXT_INT_LOOP (unsigned char)0x04
	Hard constraints flag, base pair encloses an interior loop.

#define	VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (unsigned char)0x08
	Hard constraints flag, base pair encloses a multi branch loop.

#define	VRNA_CONSTRAINT_CONTEXT_MB_LOOP (unsigned char)0x10
	Hard constraints flag, base pair is enclosed in an interior loop.

#define	VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (unsigned char)0x20
	Hard constraints flag, base pair is enclosed in a multi branch loop.

#define	VRNA_CONSTRAINT_CONTEXT_ENFORCE (unsigned char)0x40
	Hard constraint flag to indicate enforcement of constraints.

#define	VRNA_CONSTRAINT_CONTEXT_NO_REMOVE (unsigned char)0x80
	Hard constraint flag to indicate not to remove base pairs that conflict with a given constraint.

#define	VRNA_CONSTRAINT_CONTEXT_NONE (unsigned char)0
	Constraint context flag that forbids any loop.

#define	VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS
	Constraint context flag indicating base pairs that close any loop.

#define	VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS
	Constraint context flag indicating base pairs enclosed by any loop.

#define	VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS
	Constraint context flag indicating any loop context.

Typedefs
typedef struct vrna_hc_s	vrna_hc_t
	Typename for the hard constraints data structure vrna_hc_s.

typedef struct vrna_hc_up_s	vrna_hc_up_t
	Typename for the single nucleotide hard constraint data structure vrna_hc_up_s.

typedef unsigned char(	vrna_callback_hc_evaluate) (int i, int j, int k, int l, unsigned char d, void *data)
	Callback to evaluate whether or not a particular decomposition step is contributing to the solution space. More...

Enumerations

Functions
void	vrna_message_constraint_options (unsigned int option)
	Print a help message for pseudo dot-bracket structure constraint characters to stdout. (constraint support is specified by option parameter) More...

void	vrna_message_constraint_options_all (void)
	Print structure constraint characters to stdout (full constraint support) More...

void	vrna_hc_init (vrna_fold_compound_t *vc)
	Initialize/Reset hard constraints to default values. More...

void	vrna_hc_add_up (vrna_fold_compound_t *vc, int i, unsigned char option)
	Make a certain nucleotide unpaired. More...

int	vrna_hc_add_up_batch (vrna_fold_compound_t vc, vrna_hc_up_t constraints)
	Apply a list of hard constraints for single nucleotides. More...

void	vrna_hc_add_bp (vrna_fold_compound_t *vc, int i, int j, unsigned char option)
	Favorize/Enforce a certain base pair (i,j) More...

void	vrna_hc_add_bp_nonspecific (vrna_fold_compound_t *vc, int i, int d, unsigned char option)
	Enforce a nucleotide to be paired (upstream/downstream) More...

void	vrna_hc_free (vrna_hc_t *hc)
	Free the memory allocated by a vrna_hc_t data structure. More...

void	vrna_hc_add_f (vrna_fold_compound_t vc, vrna_callback_hc_evaluate f)
	Add a function pointer pointer for the generic hard constraint feature.

void	vrna_hc_add_data (vrna_fold_compound_t vc, void data, vrna_callback_free_auxdata *f)
	Add an auxiliary data structure for the generic hard constraints callback function. More...

int	vrna_hc_add_from_db (vrna_fold_compound_t vc, const char constraint, unsigned int options)
	Add hard constraints from pseudo dot-bracket notation. More...

void	print_tty_constraint (unsigned int option)
	Print structure constraint characters to stdout. (constraint support is specified by option parameter) More...

void	print_tty_constraint_full (void)
	Print structure constraint characters to stdout (full constraint support) More...

void	constrain_ptypes (const char constraint, unsigned int length, char ptype, int *BP, int min_loop_size, unsigned int idx_type)
	Insert constraining pair types according to constraint structure string. More...

Detailed Description

Functions and data structures for handling of secondary structure hard constraints.

Macro Definition Documentation

#define VRNA_CONSTRAINT_NO_HEADER 0

do not print the header information line

Deprecated:: This mode is not supported anymore!

#define VRNA_CONSTRAINT_DB_ANG_BRACK 524288U

angle brackets '<', '>' switch for structure constraint (paired downstream/upstream)

See also: vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(), vrna_message_constraint_options_all()

Enumeration Type Documentation

enum vrna_hc_type_e

The hard constraints type.

Global and local structure prediction methods use a slightly different way to handle hard constraints internally. This enum is used to distinguish both types.

Enumerator

VRNA_HC_DEFAULT

Default Hard Constraints.

VRNA_HC_WINDOW

Hard Constraints suitable for local structure prediction using window approach.

See also: vrna_mfe_window(), vrna_mfe_window_zscore(), pfl_fold()

Function Documentation

void vrna_hc_add_data	(	vrna_fold_compound_t *	vc,
		void *	data,
		vrna_callback_free_auxdata *	f
	)

Add an auxiliary data structure for the generic hard constraints callback function.

See also: vrna_hc_add_f()

Parameters

vc	The fold compound the generic hard constraint function should be bound to
data	A pointer to the data structure that holds required data for function 'f'
f	A pointer to a function that free's the memory occupied by `data` (Maybe `NULL`)

void print_tty_constraint ( unsigned int option )

Print structure constraint characters to stdout. (constraint support is specified by option parameter)

Deprecated:: Use vrna_message_constraints() instead!

Parameters

option Option switch that tells which constraint help will be printed

void print_tty_constraint_full ( void )

Print structure constraint characters to stdout (full constraint support)

Deprecated:: Use vrna_message_constraint_options_all() instead!

void constrain_ptypes	(	const char *	constraint,
		unsigned int	length,
		char *	ptype,
		int *	BP,
		int	min_loop_size,
		unsigned int	idx_type
	)

Insert constraining pair types according to constraint structure string.

Deprecated:: Do not use this function anymore! Structure constraints are now handled through vrna_hc_t and related functions.

Parameters

constraint	The structure constraint string
length	The actual length of the sequence (constraint may be shorter)
ptype	A pointer to the basepair type array
BP	(not used anymore)
min_loop_size	The minimal loop size (usually TURN )
idx_type	Define the access type for base pair type array (0 = indx, 1 = iindx)

Data Structures

Macros

Typedefs

Enumerations

Functions

Detailed Description

Macro Definition Documentation

Enumeration Type Documentation

Function Documentation