fold.h File Reference

MFE calculations and energy evaluations for single RNA sequences. More...

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Functions
float	fold_par (const char *sequence, char *structure, paramT *parameters, int is_constrained, int is_circular)
	Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
float	fold (const char *sequence, char *structure)
	Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
float	circfold (const char *sequence, char *structure)
	Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence.
float	energy_of_structure (const char *string, const char *structure, int verbosity_level)
	Calculate the free energy of an already folded RNA using global model detail settings.
float	energy_of_struct_par (const char *string, const char *structure, paramT *parameters, int verbosity_level)
	Calculate the free energy of an already folded RNA.
float	energy_of_circ_structure (const char *string, const char *structure, int verbosity_level)
	Calculate the free energy of an already folded circular RNA.
float	energy_of_circ_struct_par (const char *string, const char *structure, paramT *parameters, int verbosity_level)
	Calculate the free energy of an already folded circular RNA.
int	energy_of_structure_pt (const char *string, short *ptable, short *s, short *s1, int verbosity_level)
	Calculate the free energy of an already folded RNA.
int	energy_of_struct_pt_par (const char *string, short *ptable, short *s, short *s1, paramT *parameters, int verbosity_level)
	Calculate the free energy of an already folded RNA.
void	free_arrays (void)
	Free arrays for mfe folding.
void	parenthesis_structure (char *structure, bondT *bp, int length)
	Create a dot-backet/parenthesis structure from backtracking stack.
void	parenthesis_zuker (char *structure, bondT *bp, int length)
	Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c.
void	update_fold_params (void)
	Recalculate energy parameters.
float	energy_of_move (const char *string, const char *structure, int m1, int m2)
	Calculate energy of a move (closing or opening of a base pair)
int	energy_of_move_pt (short *pt, short *s, short *s1, int m1, int m2)
	Calculate energy of a move (closing or opening of a base pair)
int	loop_energy (short *ptable, short *s, short *s1, int i)
	Calculate energy of a loop.
void	assign_plist_from_db (plist **pl, const char *struc, float pr)
	Create a plist from a dot-bracket string.
int	LoopEnergy (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)
int	HairpinE (int size, int type, int si1, int sj1, const char *string)
void	initialize_fold (int length)
float	energy_of_struct (const char *string, const char *structure)
int	energy_of_struct_pt (const char *string, short *ptable, short *s, short *s1)
float	energy_of_circ_struct (const char *string, const char *structure)

Variables
int	logML
	if nonzero use logarithmic ML energy in energy_of_struct
int	uniq_ML
	do ML decomposition uniquely (for subopt)
int	cut_point
	set to first pos of second seq for cofolding
int	eos_debug
	verbose info from energy_of_struct

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Detailed Description

MFE calculations and energy evaluations for single RNA sequences.

This file includes (almost) all function declarations within the RNAlib that are related to MFE folding...

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Function Documentation

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

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

Note:

This function is threadsafe

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

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

Note:

This function is threadsafe

float energy_of_move	(	const char *	string,
		const char *	structure,
		int	m1,
		int	m2
	)

Calculate energy of a move (closing or opening of a base pair)

If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).

See also:

make_pair_table(), energy_of_move()

Parameters:

string	RNA sequence
structure	secondary structure in dot-bracket notation
m1	first coordinate of base pair
m2	second coordinate of base pair

Returns:

energy change of the move in kcal/mol

int energy_of_move_pt	(	short *	pt,
		short *	s,
		short *	s1,
		int	m1,
		int	m2
	)

Calculate energy of a move (closing or opening of a base pair)

If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).

See also:

make_pair_table(), energy_of_move()

Parameters:

pt	the pair table of the secondary structure
s	encoded RNA sequence
s1	encoded RNA sequence
m1	first coordinate of base pair
m2	second coordinate of base pair

Returns:

energy change of the move in 10cal/mol

int loop_energy	(	short *	ptable,
		short *	s,
		short *	s1,
		int	i
	)

Calculate energy of a loop.

Parameters:

ptable	the pair table of the secondary structure
s	encoded RNA sequence
s1	encoded RNA sequence
i	position of covering base pair

Returns:

free energy of the loop in 10cal/mol

void assign_plist_from_db	(	plist **	pl,
		const char *	struc,
		float	pr
	)

Create a plist from a dot-bracket string.

The dot-bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.

The end of the plist is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries

This function is threadsafe

Parameters:

pl	A pointer to the plist that is to be created
struc	The secondary structure in dot-bracket notation
pr	The probability for each base pair

int LoopEnergy	(	int	n1,
		int	n2,
		int	type,
		int	type_2,
		int	si1,
		int	sj1,
		int	sp1,
		int	sq1
	)

Deprecated:

{This function is deprecated and will be removed soon. Use E_IntLoop() instead!}

int HairpinE	(	int	size,
		int	type,
		int	si1,
		int	sj1,
		const char *	string
	)

Deprecated:

{This function is deprecated and will be removed soon. Use E_Hairpin() instead!}

void initialize_fold

(

int

length

)

Allocate arrays for folding

Deprecated:

{This function is deprecated and will be removed soon!}

float energy_of_struct	(	const char *	string,
		const char *	structure
	)

Calculate the free energy of an already folded RNA

Note:

This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...

Deprecated:

This function is deprecated and should not be used in future programs! Use energy_of_structure() instead!

See also:

energy_of_structure, energy_of_circ_struct(), energy_of_struct_pt()

Parameters:

string	RNA sequence
structure	secondary structure in dot-bracket notation

Returns:

the free energy of the input structure given the input sequence in kcal/mol

int energy_of_struct_pt	(	const char *	string,
		short *	ptable,
		short *	s,
		short *	s1
	)

Calculate the free energy of an already folded RNA

Note:

This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...

Deprecated:

This function is deprecated and should not be used in future programs! Use energy_of_structure_pt() instead!

See also:

make_pair_table(), energy_of_structure()

Parameters:

string	RNA sequence
ptable	the pair table of the secondary structure
s	encoded RNA sequence
s1	encoded RNA sequence

Returns:

the free energy of the input structure given the input sequence in 10kcal/mol

float energy_of_circ_struct	(	const char *	string,
		const char *	structure
	)

Calculate the free energy of an already folded circular RNA

Note:

This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...

Deprecated:

This function is deprecated and should not be used in future programs Use energy_of_circ_structure() instead!

See also:

energy_of_circ_structure(), energy_of_struct(), energy_of_struct_pt()

Parameters:

string	RNA sequence
structure	secondary structure in dot-bracket notation

Returns:

the free energy of the input structure given the input sequence in kcal/mol