This module covers all functionality for hard constraints in secondary structure prediction. More...

Detailed Description

This module covers all functionality for hard constraints in secondary structure prediction.

Collaboration diagram for Hard Constraints:

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

Data Structures
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_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_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_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...

Functions
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...

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...

Data Structure Documentation

struct vrna_hc_s

The hard constraints data structure.

The content of this data structure determines the decomposition pattern used in the folding recursions. Attribute 'matrix' is used as source for the branching pattern of the decompositions during all folding recursions. Any entry in matrix[i,j] consists of the 6 LSB that allows one to distinguish the following types of base pairs:

in the exterior loop (VRNA_CONSTRAINT_CONTEXT_EXT_LOOP)
enclosing a hairpin (VRNA_CONSTRAINT_CONTEXT_HP_LOOP)
enclosing an interior loop (VRNA_CONSTRAINT_CONTEXT_INT_LOOP)
enclosed by an exterior loop (VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC)
enclosing a multi branch loop (VRNA_CONSTRAINT_CONTEXT_MB_LOOP)
enclosed by a multi branch loop (VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)

The four linear arrays 'up_xxx' provide the number of available unpaired nucleotides (including position i) 3' of each position in the sequence.

See also: vrna_hc_init(), vrna_hc_free(), VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, VRNA_CONSTRAINT_CONTEXT_HP_LOOP, VRNA_CONSTRAINT_CONTEXT_INT_LOOP, VRNA_CONSTRAINT_CONTEXT_MB_LOOP, VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC

Collaboration diagram for vrna_hc_s:

Data Fields
int *	up_ext
	A linear array that holds the number of allowed unpaired nucleotides in an exterior loop.

int *	up_hp
	A linear array that holds the number of allowed unpaired nucleotides in a hairpin loop.

int *	up_int
	A linear array that holds the number of allowed unpaired nucleotides in an interior loop.

int *	up_ml
	A linear array that holds the number of allowed unpaired nucleotides in a multi branched loop.

vrna_callback_hc_evaluate *	f
	A function pointer that returns whether or not a certain decomposition may be evaluated.

void *	data
	A pointer to some structure where the user may store necessary data to evaluate its generic hard constraint function.

vrna_callback_free_auxdata *	free_data
	A pointer to a function to free memory occupied by auxiliary data. More...

unsigned char *	matrix
	Upper triangular matrix that encodes where a base pair or unpaired nucleotide is allowed.

Field Documentation

vrna_callback_free_auxdata* vrna_hc_s::free_data

A pointer to a function to free memory occupied by auxiliary data.

The function this pointer is pointing to will be called upon destruction of the vrna_hc_s, and provided with the vrna_hc_s.data pointer that may hold auxiliary data. Hence, to avoid leaking memory, the user may use this pointer to free memory occupied by auxiliary data.

struct vrna_hc_up_s

A single hard constraint for a single nucleotide.

Data Fields
int	position
	The sequence position (1-based)

unsigned char	options
	The hard constraint option.

Macro Definition Documentation

#define VRNA_CONSTRAINT_DB 16384U

#include <ViennaRNA/constraints/hard.h>

Flag for vrna_constraints_add() to indicate that constraint is passed in pseudo dot-bracket notation.

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

#define VRNA_CONSTRAINT_DB_ENFORCE_BP 32768U

#include <ViennaRNA/constraints/hard.h>

Switch for dot-bracket structure constraint to enforce base pairs.

This flag should be used to really enforce base pairs given in dot-bracket constraint rather than just weakly-enforcing them.

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

#define VRNA_CONSTRAINT_DB_PIPE 65536U

#include <ViennaRNA/constraints/hard.h>

Flag that is used to indicate the pipe '|' sign in pseudo dot-bracket notation of hard constraints.

Use this definition to indicate the pipe sign '|' (paired with another base)

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

#define VRNA_CONSTRAINT_DB_DOT 131072U

#include <ViennaRNA/constraints/hard.h>

dot '.' switch for structure constraints (no constraint at all)

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

#define VRNA_CONSTRAINT_DB_X 262144U

#include <ViennaRNA/constraints/hard.h>

'x' switch for structure constraint (base must not pair)

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

#define VRNA_CONSTRAINT_DB_RND_BRACK 1048576U

#include <ViennaRNA/constraints/hard.h>

round brackets '(',')' switch for structure constraint (base i pairs base j)

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

#define VRNA_CONSTRAINT_DB_INTRAMOL 2097152U

#include <ViennaRNA/constraints/hard.h>

Flag that is used to indicate the character 'l' in pseudo dot-bracket notation of hard constraints.

Use this definition to indicate the usage of 'l' character (intramolecular pairs only)

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

#define VRNA_CONSTRAINT_DB_INTERMOL 4194304U

#include <ViennaRNA/constraints/hard.h>

Flag that is used to indicate the character 'e' in pseudo dot-bracket notation of hard constraints.

Use this definition to indicate the usage of 'e' character (intermolecular pairs only)

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

#define VRNA_CONSTRAINT_DB_GQUAD 8388608U

#include <ViennaRNA/constraints/hard.h>

'+' switch for structure constraint (base is involved in a gquad)

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

Warning: This flag is for future purposes only! No implementation recognizes it yet.

#define VRNA_CONSTRAINT_DB_WUSS 33554432U

#include <ViennaRNA/constraints/hard.h>

Flag to indicate Washington University Secondary Structure (WUSS) notation of the hard constraint string.

This secondary structure notation for RNAs is usually used as consensus secondary structure (SS_cons) entry in Stockholm formatted files

#define VRNA_CONSTRAINT_DB_DEFAULT

#include <ViennaRNA/constraints/hard.h>

Value:

(VRNA_CONSTRAINT_DB \
   | VRNA_CONSTRAINT_DB_PIPE \
   | VRNA_CONSTRAINT_DB_DOT \
   | VRNA_CONSTRAINT_DB_X \
   | VRNA_CONSTRAINT_DB_ANG_BRACK \
   | VRNA_CONSTRAINT_DB_RND_BRACK \
   | VRNA_CONSTRAINT_DB_INTRAMOL \
   | VRNA_CONSTRAINT_DB_INTERMOL \
   | VRNA_CONSTRAINT_DB_GQUAD \
  )

Switch for dot-bracket structure constraint with default symbols.

This flag conveniently combines all possible symbols in dot-bracket notation for hard constraints and VRNA_CONSTRAINT_DB

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

Typedef Documentation

typedef unsigned char( vrna_callback_hc_evaluate) (int i, int j, int k, int l, unsigned char d, void *data)

#include <ViennaRNA/constraints/hard.h>

Callback to evaluate whether or not a particular decomposition step is contributing to the solution space.

This is the prototype for callback functions used by the folding recursions to evaluate generic hard constraints. The first four parameters passed indicate the delimiting nucleotide positions of the decomposition, and the parameter denotes the decomposition step. The last parameter data is the auxiliary data structure associated to the hard constraints via vrna_hc_add_data(), or NULL if no auxiliary data was added.

Notes on Callback Functions:: This callback enables one to over-rule default hard constraints in secondary structure decompositions.

See also: VRNA_DECOMP_PAIR_HP, VRNA_DECOMP_PAIR_IL, VRNA_DECOMP_PAIR_ML, VRNA_DECOMP_ML_ML_ML, VRNA_DECOMP_ML_STEM, VRNA_DECOMP_ML_ML, VRNA_DECOMP_ML_UP, VRNA_DECOMP_ML_ML_STEM, VRNA_DECOMP_ML_COAXIAL, VRNA_DECOMP_EXT_EXT, VRNA_DECOMP_EXT_UP, VRNA_DECOMP_EXT_STEM, VRNA_DECOMP_EXT_EXT_EXT, VRNA_DECOMP_EXT_STEM_EXT, VRNA_DECOMP_EXT_EXT_STEM, VRNA_DECOMP_EXT_EXT_STEM1, vrna_hc_add_f(), vrna_hc_add_data()

Parameters

i	Left (5') delimiter position of substructure
j	Right (3') delimiter position of substructure
k	Left delimiter of decomposition
l	Right delimiter of decomposition
d	Decomposition step indicator
data	Auxiliary data

Returns: A non-zero value if the decomposition is valid, 0 otherwise

Function Documentation

void vrna_hc_init ( vrna_fold_compound_t * vc )

#include <ViennaRNA/constraints/hard.h>

Initialize/Reset hard constraints to default values.

This function resets the hard constraints to their default values, i.e. all positions may be unpaired in all contexts, and base pairs are allowed in all contexts, if they resemble canonical pairs. Previously set hard constraints will be removed before initialization.

See also: vrna_hc_add_bp(), vrna_hc_add_bp_nonspecific(), vrna_hc_add_up()

Parameters

vc	The fold compound

SWIG Wrapper Notes:: This function is attached as method hc_init() to objects of type fold_compound

void vrna_hc_add_up	(	vrna_fold_compound_t *	vc,
		int	i,
		unsigned char	option
	)

#include <ViennaRNA/constraints/hard.h>

Make a certain nucleotide unpaired.

See also: vrna_hc_add_bp(), vrna_hc_add_bp_nonspecific(), vrna_hc_init(), VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, VRNA_CONSTRAINT_CONTEXT_HP_LOOP, VRNA_CONSTRAINT_CONTEXT_INT_LOOP, VRNA_CONSTRAINT_CONTEXT_MB_LOOP, VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS

Parameters

vc	The vrna_fold_compound_t the hard constraints are associated with
i	The position that needs to stay unpaired (1-based)
option	The options flag indicating how/where to store the hard constraints

int vrna_hc_add_up_batch	(	vrna_fold_compound_t *	vc,
		vrna_hc_up_t *	constraints
	)

#include <ViennaRNA/constraints/hard.h>

Apply a list of hard constraints for single nucleotides.

Parameters

vc	The vrna_fold_compound_t the hard constraints are associated with
constraints	The list off constraints to apply, last entry must have position attribute set to 0

void vrna_hc_add_bp	(	vrna_fold_compound_t *	vc,
		int	i,
		int	j,
		unsigned char	option
	)

#include <ViennaRNA/constraints/hard.h>

Favorize/Enforce a certain base pair (i,j)

See also: vrna_hc_add_bp_nonspecific(), vrna_hc_add_up(), vrna_hc_init(), VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, VRNA_CONSTRAINT_CONTEXT_HP_LOOP, VRNA_CONSTRAINT_CONTEXT_INT_LOOP, VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC, VRNA_CONSTRAINT_CONTEXT_MB_LOOP, VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC, VRNA_CONSTRAINT_CONTEXT_ENFORCE, VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS

Parameters

vc	The vrna_fold_compound_t the hard constraints are associated with
i	The 5' located nucleotide position of the base pair (1-based)
j	The 3' located nucleotide position of the base pair (1-based)
option	The options flag indicating how/where to store the hard constraints

void vrna_hc_add_bp_nonspecific	(	vrna_fold_compound_t *	vc,
		int	i,
		int	d,
		unsigned char	option
	)

#include <ViennaRNA/constraints/hard.h>

Enforce a nucleotide to be paired (upstream/downstream)

See also: vrna_hc_add_bp(), vrna_hc_add_up(), vrna_hc_init(), VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, VRNA_CONSTRAINT_CONTEXT_HP_LOOP, VRNA_CONSTRAINT_CONTEXT_INT_LOOP, VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC, VRNA_CONSTRAINT_CONTEXT_MB_LOOP, VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC, VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS

Parameters

vc	The vrna_fold_compound_t the hard constraints are associated with
i	The position that needs to stay unpaired (1-based)
d	The direction of base pairing ( : pairs upstream, : pairs downstream, : no direction)
option	The options flag indicating in which loop type context the pairs may appear

void vrna_hc_free ( vrna_hc_t * hc )

#include <ViennaRNA/constraints/hard.h>

Free the memory allocated by a vrna_hc_t data structure.

Use this function to free all memory that was allocated for a data structure of type vrna_hc_t .

See also: get_hard_constraints(), vrna_hc_t

int vrna_hc_add_from_db	(	vrna_fold_compound_t *	vc,
		const char *	constraint,
		unsigned int	options
	)

#include <ViennaRNA/constraints/hard.h>

Add hard constraints from pseudo dot-bracket notation.

This function allows one to apply hard constraints from a pseudo dot-bracket notation. The options parameter controls, which characters are recognized by the parser. Use the VRNA_CONSTRAINT_DB_DEFAULT convenience macro, if you want to allow all known characters

See also: VRNA_CONSTRAINT_DB_PIPE, VRNA_CONSTRAINT_DB_DOT, VRNA_CONSTRAINT_DB_X, VRNA_CONSTRAINT_DB_ANG_BRACK, VRNA_CONSTRAINT_DB_RND_BRACK, VRNA_CONSTRAINT_DB_INTRAMOL, VRNA_CONSTRAINT_DB_INTERMOL, VRNA_CONSTRAINT_DB_GQUAD

Parameters

vc	The fold compound
constraint	A pseudo dot-bracket notation of the hard constraint.
options	The option flags

SWIG Wrapper Notes:: This function is attached as method hc_add_from_db() to objects of type fold_compound

Detailed Description

Files

Data Structures

Macros

Typedefs

Functions

Data Structure Documentation

Data Fields

Field Documentation

Data Fields

Macro Definition Documentation

Typedef Documentation

Function Documentation