Deprecated Energy Evaluation functions. More...

Detailed Description

Deprecated Energy Evaluation functions.

Using the functions below is discouraged as they have been marked deprecated and will be removed from the library in the (near) future!

Collaboration diagram for Deprecated Interface for Free 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. More...

float	energy_of_struct_par (const char string, const char structure, vrna_param_t *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, vrna_param_t *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, vrna_param_t *parameters, int verbosity_level)
	Calculate the free energy of an already folded RNA. More...

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...

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)

int	E_Stem (int type, int si1, int sj1, int extLoop, vrna_param_t *P)
	Compute the energy contribution of a stem branching off a loop-region. More...

FLT_OR_DBL	exp_E_ExtLoop (int type, int si1, int sj1, vrna_exp_param_t *P)

FLT_OR_DBL	exp_E_Stem (int type, int si1, int sj1, int extLoop, vrna_exp_param_t *P)

PRIVATE int	E_IntLoop (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, vrna_param_t *P)

PRIVATE FLT_OR_DBL	exp_E_IntLoop (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, vrna_exp_param_t *P)

Variables
int	cut_point
	first pos of second seq for cofolding

int	eos_debug
	verbose info from energy_of_struct

Function Documentation

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

#include <ViennaRNA/eval.h>

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.

Deprecated:: Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!

See also: vrna_eval_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,
		vrna_param_t *	parameters,
		int	verbosity_level
	)

#include <ViennaRNA/eval.h>

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

Deprecated:: Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!

See also: vrna_eval_structure()

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
	)

#include <ViennaRNA/eval.h>

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

Deprecated:: Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!

See also: vrna_eval_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_circ_struct_par	(	const char *	string,
		const char *	structure,
		vrna_param_t *	parameters,
		int	verbosity_level
	)

#include <ViennaRNA/eval.h>

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

Deprecated:: Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!

See also: vrna_eval_structure()

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
	)

#include <ViennaRNA/eval.h>

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.

Deprecated:: Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!

See also: vrna_eval_structure_pt()

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,
		vrna_param_t *	parameters,
		int	verbosity_level
	)

#include <ViennaRNA/eval.h>

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

Deprecated:: Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!

See also: vrna_eval_structure_pt()

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

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

#include <ViennaRNA/eval.h>

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).

Deprecated:: Use vrna_eval_move() instead!

See also: vrna_eval_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
	)

#include <ViennaRNA/eval.h>

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).

Deprecated:: Use vrna_eval_move_pt() instead!

See also: vrna_eval_move_pt()

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
	)

#include <ViennaRNA/eval.h>

Calculate energy of a loop.

Deprecated:: Use vrna_eval_loop_pt() instead!

See also: vrna_eval_loop_pt()

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

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

#include <ViennaRNA/eval.h>

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
	)

#include <ViennaRNA/eval.h>

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
	)

#include <ViennaRNA/eval.h>

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

int E_Stem	(	int	type,
		int	si1,
		int	sj1,
		int	extLoop,
		vrna_param_t *	P
	)

#include <ViennaRNA/loops/external.h>

Compute the energy contribution of a stem branching off a loop-region.

This function computes the energy contribution of a stem that branches off a loop region. This can be the case in multiloops, when a stem branching off increases the degree of the loop but also immediately interior base pairs of an exterior loop contribute free energy. To switch the behavior of the function according to the evaluation of a multiloop- or exterior-loop-stem, you pass the flag 'extLoop'. The returned energy contribution consists of a TerminalAU penalty if the pair type is greater than 2, dangling end contributions of mismatching nucleotides adjacent to the stem if only one of the si1, sj1 parameters is greater than 0 and mismatch energies if both mismatching nucleotides are positive values. Thus, to avoid incorporating dangling end or mismatch energies just pass a negative number, e.g. -1 to the mismatch argument.

This is an illustration of how the energy contribution is assembled:

      3'  5'
      |   |
      X - Y
5'-si1     sj1-3'

Here, (X,Y) is the base pair that closes the stem that branches off a loop region. The nucleotides si1 and sj1 are the 5'- and 3'- mismatches, respectively. If the base pair type of (X,Y) is greater than 2 (i.e. an A-U or G-U pair, the TerminalAU penalty will be included in the energy contribution returned. If si1 and sj1 are both nonnegative numbers, mismatch energies will also be included. If one of si1 or sj1 is a negative value, only 5' or 3' dangling end contributions are taken into account. To prohibit any of these mismatch contributions to be incorporated, just pass a negative number to both, si1 and sj1. In case the argument extLoop is 0, the returned energy contribution also includes the internal-loop-penalty of a multiloop stem with closing pair type.

See also: E_MLstem(); E_ExtLoop()

Note: This function is threadsafe

Deprecated:: Please use one of the functions vrna_E_ext_stem() and E_MLstem() instead! Use the former for cases where extLoop != 0 and the latter otherwise.

Parameters

type	The pair type of the first base pair un the stem
si1	The 5'-mismatching nucleotide
sj1	The 3'-mismatching nucleotide
extLoop	A flag that indicates whether the contribution reflects the one of an exterior loop or not
P	The data structure containing scaled energy parameters

Returns: The Free energy of the branch off the loop in dcal/mol

FLT_OR_DBL exp_E_ExtLoop	(	int	type,
		int	si1,
		int	sj1,
		vrna_exp_param_t *	P
	)

#include <ViennaRNA/loops/external.h>

This is the partition function variant of E_ExtLoop()

Deprecated:: Use vrna_exp_E_ext_stem() instead!

See also: E_ExtLoop()

Returns: The Boltzmann weighted energy contribution of the introduced exterior-loop stem

FLT_OR_DBL exp_E_Stem	(	int	type,
		int	si1,
		int	sj1,
		int	extLoop,
		vrna_exp_param_t *	P
	)

#include <ViennaRNA/loops/external.h>

Compute the Boltzmann weighted energy contribution of a stem branching off a loop-region

This is the partition function variant of E_Stem()

See also: E_Stem()

Note: This function is threadsafe

Returns: The Boltzmann weighted energy contribution of the branch off the loop

PRIVATE int E_IntLoop	(	int	n1,
		int	n2,
		int	type,
		int	type_2,
		int	si1,
		int	sj1,
		int	sp1,
		int	sq1,
		vrna_param_t *	P
	)

#include <ViennaRNA/loops/internal.h>

Compute the Energy of an interior-loop

This function computes the free energy $\Delta G$ of an interior-loop with the following structure:

      3'  5'
      |   |
      U - V
  a_n       b_1
   .        .
   .        .
   .        .
  a_1       b_m
      X - Y
      |   |
      5'  3'

This general structure depicts an interior-loop that is closed by the base pair (X,Y). The enclosed base pair is (V,U) which leaves the unpaired bases a_1-a_n and b_1-b_n that constitute the loop. In this example, the length of the interior-loop is $(n+m)$ where n or m may be 0 resulting in a bulge-loop or base pair stack. The mismatching nucleotides for the closing pair (X,Y) are:
5'-mismatch: a_1
3'-mismatch: b_m
and for the enclosed base pair (V,U):
5'-mismatch: b_1
3'-mismatch: a_n

Note: Base pairs are always denoted in 5'->3' direction. Thus the enclosed base pair must be 'turned arround' when evaluating the free energy of the interior-loop

See also: scale_parameters(); vrna_param_t

Note: This function is threadsafe

Parameters

n1	The size of the 'left'-loop (number of unpaired nucleotides)
n2	The size of the 'right'-loop (number of unpaired nucleotides)
type	The pair type of the base pair closing the interior loop
type_2	The pair type of the enclosed base pair
si1	The 5'-mismatching nucleotide of the closing pair
sj1	The 3'-mismatching nucleotide of the closing pair
sp1	The 3'-mismatching nucleotide of the enclosed pair
sq1	The 5'-mismatching nucleotide of the enclosed pair
P	The datastructure containing scaled energy parameters

Returns: The Free energy of the Interior-loop in dcal/mol

PRIVATE FLT_OR_DBL exp_E_IntLoop	(	int	u1,
		int	u2,
		int	type,
		int	type2,
		short	si1,
		short	sj1,
		short	sp1,
		short	sq1,
		vrna_exp_param_t *	P
	)

#include <ViennaRNA/loops/internal.h>

Compute Boltzmann weight $e^{-\Delta G/kT}$ of interior loop

multiply by scale[u1+u2+2] for scaling

See also: get_scaled_pf_parameters(); vrna_exp_param_t; E_IntLoop()

Note: This function is threadsafe

Parameters

u1	The size of the 'left'-loop (number of unpaired nucleotides)
u2	The size of the 'right'-loop (number of unpaired nucleotides)
type	The pair type of the base pair closing the interior loop
type2	The pair type of the enclosed base pair
si1	The 5'-mismatching nucleotide of the closing pair
sj1	The 3'-mismatching nucleotide of the closing pair
sp1	The 3'-mismatching nucleotide of the enclosed pair
sq1	The 5'-mismatching nucleotide of the enclosed pair
P	The datastructure containing scaled Boltzmann weights of the energy parameters

Returns: The Boltzmann weight of the Interior-loop

Detailed Description

Functions

Variables

Function Documentation

Compute the Boltzmann weighted energy contribution of a stem branching off a loop-region

Compute the Energy of an interior-loop

Compute Boltzmann weight of interior loop

Compute Boltzmann weight $e^{-\Delta G/kT}$ of interior loop