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. More...
float	fold (const char *sequence, char *structure)
	Compute minimum free energy and an appropriate secondary structure of an RNA sequence. More...
float	circfold (const char *sequence, char *structure)
	Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence. More...
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. More...
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. More...
float	energy_of_circ_structure (const char *string, const char *structure, int verbosity_level)
	Calculate the free energy of an already folded circular RNA. More...
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. More...
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. More...
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. More...
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. More...
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. More...
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) More...
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) More...
int	loop_energy (short *ptable, short *s, short *s1, int i)
	Calculate energy of a loop. More...
void	assign_plist_from_db (plist **pl, const char *struc, float pr)
	Create a plist from a dot-bracket string. More...
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

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...

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