Energy Evaluation for Atomic Moves

Functions to evaluate the free energy change of a structure after application of (a set of) atomic moves. More...

Detailed Description

Functions to evaluate the free energy change of a structure after application of (a set of) atomic moves.

Here, atomic moves are not to be confused with moves of actual physical atoms. Instead, an atomic move is considered the smallest conformational change a secondary structure can undergo to form another, distinguishable structure. We currently support the following moves

Atomic Moves:

• Opening (dissociation) of a single base pair
• Closing (formation) of a single base pair
• Shifting one pairing partner of an existing pair to a different location

Collaboration diagram for Energy Evaluation for Atomic Moves:

Functions
float	vrna_eval_move (vrna_fold_compound_t *vc, const char *structure, int m1, int m2)
	Calculate energy of a move (closing or opening of a base pair) More...
int	vrna_eval_move_pt (vrna_fold_compound_t *vc, short *pt, int m1, int m2)
	Calculate energy of a move (closing or opening of a base pair) More...

Function Documentation

float vrna_eval_move	(	vrna_fold_compound_t *	vc,
		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).

See also

vrna_eval_move_pt()

Parameters

vc	A vrna_fold_compound_t containing the energy parameters and model details
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 (INF / 100. upon any error)

SWIG Wrapper Notes:

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

int vrna_eval_move_pt	(	vrna_fold_compound_t *	vc,
		short *	pt,
		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).

See also

vrna_eval_move()

Parameters

vc	A vrna_fold_compound_t containing the energy parameters and model details
pt	the pair table of the secondary structure
m1	first coordinate of base pair
m2	second coordinate of base pair

Returns

energy change of the move in 10cal/mol

SWIG Wrapper Notes:

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