Energy evaluation
[RNA Secondary Structure Folding]

This module contains all functions and variables related to energy evaluation of sequence/structure pairs. More...

Collaboration diagram for Energy evaluation:

Functions
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.
Variables
int	eos_debug
	verbose info from energy_of_struct

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Detailed Description

This module contains all functions and variables related to energy evaluation of sequence/structure pairs.

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Function Documentation

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