Energy Evaluation for Individual Loops

Functions to evaluate the free energy of particular types of loops. More...

Detailed Description

Functions to evaluate the free energy of particular types of loops.

To assess the free energy contribution of a particular loop within a secondary structure, two variants are provided:

• The bare free energy (usually in deka-calories, i.e. multiples of ), and
• The Boltzmann weight of the free energy (with , gas constant and temperature )

The latter is usually required for partition function computations.

Collaboration diagram for Energy Evaluation for Individual Loops:

Modules
	Exterior Loops
	Functions to evaluate the free energy contributions for exterior loops.
	Hairpin Loops
	Functions to evaluate the free energy contributions for hairpin loops.
	Internal Loops
	Functions to evaluate the free energy contributions for internal loops.
	Multibranch Loops
	Functions to evaluate the free energy contributions for mutlibranch loops.

Files
file	all.h
	Energy evaluation for MFE and partition function calculations.
file	external.h
	Energy evaluation of exterior loops for MFE and partition function calculations.
file	hairpin.h
	Energy evaluation of hairpin loops for MFE and partition function calculations.
file	internal.h
	Energy evaluation of interior loops for MFE and partition function calculations.
file	multibranch.h
	Energy evaluation of multibranch loops for MFE and partition function calculations.

Functions
int	vrna_eval_loop_pt (vrna_fold_compound_t *vc, int i, const short *pt)
	Calculate energy of a loop. More...
int	vrna_eval_loop_pt_v (vrna_fold_compound_t *vc, int i, const short *pt, int verbosity_level)
	Calculate energy of a loop. More...

Function Documentation

int vrna_eval_loop_pt	(	vrna_fold_compound_t *	vc,
		int	i,
		const short *	pt
	)

#include <ViennaRNA/eval.h>

Calculate energy of a loop.

Parameters

vc	A vrna_fold_compound_t containing the energy parameters and model details
i	position of covering base pair
pt	the pair table of the secondary structure

Returns

free energy of the loop in 10cal/mol

SWIG Wrapper Notes:

This function is attached as method eval_loop_pt() to objects of type fold_compound

int vrna_eval_loop_pt_v	(	vrna_fold_compound_t *	vc,
		int	i,
		const short *	pt,
		int	verbosity_level
	)

#include <ViennaRNA/eval.h>

Calculate energy of a loop.

Parameters

vc	A vrna_fold_compound_t containing the energy parameters and model details
i	position of covering base pair
pt	the pair table of the secondary structure
verbosity_level	The level of verbosity of this function

Returns

free energy of the loop in 10cal/mol