RNAlib-2.1.9h
+ Collaboration diagram for MFE Structures of two hybridized Sequences:

Files

file  cofold.h
 MFE version of cofolding routines.
 

Functions

float cofold (const char *sequence, char *structure)
 Compute the minimum free energy of two interacting RNA molecules.
 
float cofold_par (const char *string, char *structure, paramT *parameters, int is_constrained)
 Compute the minimum free energy of two interacting RNA molecules.
 
void free_co_arrays (void)
 Free memory occupied by cofold()
 
void update_cofold_params (void)
 Recalculate parameters.
 
void export_cofold_arrays_gq (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)
 Export the arrays of partition function cofold (with gquadruplex support)
 
void export_cofold_arrays (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)
 Export the arrays of partition function cofold.
 

Detailed Description

Function Documentation

◆ cofold()

float cofold ( const char *  sequence,
char *  structure 
)

Compute the minimum free energy of two interacting RNA molecules.

The code is analog to the fold() function. If cut_point ==-1 results should be the same as with fold().

Parameters
sequenceThe two sequences concatenated
structureWill hold the barcket dot structure of the dimer molecule
Returns
minimum free energy of the structure

◆ cofold_par()

float cofold_par ( const char *  string,
char *  structure,
paramT parameters,
int  is_constrained 
)

Compute the minimum free energy of two interacting RNA molecules.

◆ export_cofold_arrays_gq()

void export_cofold_arrays_gq ( int **  f5_p,
int **  c_p,
int **  fML_p,
int **  fM1_p,
int **  fc_p,
int **  ggg_p,
int **  indx_p,
char **  ptype_p 
)

Export the arrays of partition function cofold (with gquadruplex support)

Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking

Parameters
f5_pA pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
c_pA pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
fML_pA pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem
fM1_pA pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
fc_pA pointer to the 'fc' array, i.e. array ...
ggg_pA pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j]
indx_pA pointer to the indexing array used for accessing the energy matrices
ptype_pA pointer to the ptype array containing the base pair types for each possibility (i,j)

◆ export_cofold_arrays()

void export_cofold_arrays ( int **  f5_p,
int **  c_p,
int **  fML_p,
int **  fM1_p,
int **  fc_p,
int **  indx_p,
char **  ptype_p 
)

Export the arrays of partition function cofold.

Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking

Parameters
f5_pA pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
c_pA pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
fML_pA pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem
fM1_pA pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
fc_pA pointer to the 'fc' array, i.e. array ...
indx_pA pointer to the indexing array used for accessing the energy matrices
ptype_pA pointer to the ptype array containing the base pair types for each possibility (i,j)