Functions to evaluate the free energy contributions for mutlibranch loops. More...

Detailed Description

Functions to evaluate the free energy contributions for mutlibranch loops.

Collaboration diagram for Multibranch Loops:

Files
file	multibranch.h
	Energy evaluation of multibranch loops for MFE and partition function calculations.

Basic free energy interface
int	vrna_E_mb_loop_stack (vrna_fold_compound_t *fc, int i, int j)
	Evaluate energy of a multi branch helices stacking onto closing pair (i,j) More...

int	vrna_E_mb_loop_fast (vrna_fold_compound_t fc, int i, int j, int dmli1, int *dmli2)

int	E_ml_rightmost_stem (int i, int j, vrna_fold_compound_t *fc)

int	vrna_E_ml_stems_fast (vrna_fold_compound_t fc, int i, int j, int fmi, int *dmli)

Boltzmann weight (partition function) interface
typedef struct vrna_mx_pf_aux_ml_s *	vrna_mx_pf_aux_ml_t
	Auxiliary helper arrays for fast exterior loop computations. More...

FLT_OR_DBL	vrna_exp_E_mb_loop_fast (vrna_fold_compound_t *fc, int i, int j, vrna_mx_pf_aux_ml_t aux_mx)

vrna_mx_pf_aux_ml_t	vrna_exp_E_ml_fast_init (vrna_fold_compound_t *fc)

void	vrna_exp_E_ml_fast_rotate (vrna_mx_pf_aux_ml_t aux_mx)

void	vrna_exp_E_ml_fast_free (vrna_mx_pf_aux_ml_t aux_mx)

const FLT_OR_DBL *	vrna_exp_E_ml_fast_qqm (struct vrna_mx_pf_aux_ml_s *aux_mx)

const FLT_OR_DBL *	vrna_exp_E_ml_fast_qqm1 (struct vrna_mx_pf_aux_ml_s *aux_mx)

FLT_OR_DBL	vrna_exp_E_ml_fast (vrna_fold_compound_t *fc, int i, int j, vrna_mx_pf_aux_ml_t aux_mx)

Typedef Documentation

typedef struct vrna_mx_pf_aux_ml_s* vrna_mx_pf_aux_ml_t

Auxiliary helper arrays for fast exterior loop computations.

See also: vrna_exp_E_ml_fast_init(), vrna_exp_E_ml_fast_rotate(), vrna_exp_E_ml_fast_free(), vrna_exp_E_ml_fast()

Evaluate energy of a multi branch helices stacking onto closing pair (i,j)

Computes total free energy for coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1)