H/fold.h File Reference

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

Include dependency graph for fold.h:

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.
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)
	Allocate arrays for folding .
float	energy_of_struct (const char string, const char structure)
	Calculate the free energy of an already folded RNA.
int	energy_of_struct_pt (const char string, short ptable, short s, short s1)
	Calculate the free energy of an already folded RNA.
float	energy_of_circ_struct (const char string, const char structure)
	Calculate the free energy of an already folded circular RNA.
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
	brief set to first pos of second seq for cofolding
int	eos_debug
	brief 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

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.

The first parameter given, the RNA sequence, must be uppercase and should only contain an alphabet $\Sigma$ that is understood by the RNAlib
(e.g. $\Sigma = \{A,U,C,G\}$ )

The second parameter, structure, must always point to an allocated block of memory with a size of at least $\mathrm{strlen}(\mathrm{sequence})+1$

If the third parameter is NULL, global model detail settings are assumed for the folding recursions. Otherwise, the provided parameters are used.

The fourth parameter indicates whether a secondary structure constraint in enhanced dot-bracket notation is passed through the structure parameter or not. If so, the characters " | x < > " are recognized to mark bases that are paired, unpaired, paired upstream, or downstream, respectively. Matching brackets " ( ) " denote base pairs, dots "." are used for unconstrained bases.

To indicate that the RNA sequence is circular and thus has to be post-processed, set the last parameter to non-zero

After a successful call of fold_par(), a backtracked secondary structure (in dot-bracket notation) that exhibits the minimum of free energy will be written to the memory structure is pointing to. The function returns the minimum of free energy for any fold of the sequence given.

Note:: OpenMP: Passing NULL to the 'parameters' argument involves access to several global model detail variables and thus is not to be considered threadsafe

See also:: fold(), circfold(), model_detailsT, set_energy_model(), get_scaled_parameters()

Parameters:

	sequence	RNA sequence
	structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to
	parameters	A data structure containing the prescaled energy contributions and the model details. (NULL may be passed, see OpenMP notes above)
	is_constrained	Switch to indicate that a structure contraint is passed via the structure argument (0==off)
	is_circular	Switch to (de-)activate postprocessing steps in case RNA sequence is circular (0==off)

Returns:: the minimum free energy (MFE) in kcal/mol

float fold	(	const char *	sequence,
		char *	structure
	)

Compute minimum free energy and an appropriate secondary structure of an RNA sequence.

This function essentially does the same thing as fold_par(). However, it takes its model details, i.e. temperature, dangles, tetra_loop, noGU, no_closingGU, fold_constrained, noLonelyPairs from the current global settings within the library

Use fold_par() for a completely threadsafe variant

See also:: fold_par(), circfold()

Parameters:

	sequence	RNA sequence
	structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns:: the minimum free energy (MFE) in kcal/mol

float circfold	(	const char *	sequence,
		char *	structure
	)

Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence.

This function essentially does the same thing as fold_par(). However, it takes its model details, i.e. temperature, dangles, tetra_loop, noGU, no_closingGU, fold_constrained, noLonelyPairs from the current global settings within the library

Use fold_par() for a completely threadsafe variant

See also:: fold_par(), circfold()

Parameters:

	sequence	RNA sequence
	structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns:: the minimum free energy (MFE) in kcal/mol

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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

Note:: OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_struct_par() for a completely threadsafe implementation.

See also:: energy_of_struct_par(), energy_of_circ_structure()

Parameters:

	string	RNA sequence
	structure	secondary structure in dot-bracket notation
	verbosity_level	a flag to turn verbose output on/off

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

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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

See also:: energy_of_circ_structure(), energy_of_structure_pt(), get_scaled_parameters()

Parameters:

	string	RNA sequence in uppercase letters
	structure	Secondary structure in dot-bracket notation
	parameters	A data structure containing the prescaled energy contributions and the model details.
	verbosity_level	A flag to turn verbose output on/off

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

float energy_of_circ_structure	(	const char *	string,
		const char *	structure,
		int	verbosity_level
	)

Calculate the free energy of an already folded circular RNA.

Note:: OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_circ_struct_par() for a completely threadsafe implementation.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

See also:: energy_of_circ_struct_par(), energy_of_struct_par()

Parameters:

	string	RNA sequence
	structure	Secondary structure in dot-bracket notation
	verbosity_level	A flag to turn verbose output on/off

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

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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

See also:: energy_of_struct_par(), get_scaled_parameters()

Parameters:

	string	RNA sequence
	structure	Secondary structure in dot-bracket notation
	parameters	A data structure containing the prescaled energy contributions and the model details.
	verbosity_level	A flag to turn verbose output on/off

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

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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

Note:: OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_struct_pt_par() for a completely threadsafe implementation.

See also:: make_pair_table(), energy_of_struct_pt_par()

Parameters:

	string	RNA sequence
	ptable	the pair table of the secondary structure
	s	encoded RNA sequence
	s1	encoded RNA sequence
	verbosity_level	a flag to turn verbose output on/off

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

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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

See also:: make_pair_table(), energy_of_struct_par(), get_scaled_parameters()

Parameters:

	string	RNA sequence in uppercase letters
	ptable	The pair table of the secondary structure
	s	Encoded RNA sequence
	s1	Encoded RNA sequence
	parameters	A data structure containing the prescaled energy contributions and the model details.
	verbosity_level	A flag to turn verbose output on/off

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

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

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

H/fold.h File Reference

Functions

Variables

Detailed Description

Function Documentation