RNAlib-2.2.0-RC3
+ 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. More...
 
float cofold_par (const char *string, char *structure, vrna_param_t *parameters, int is_constrained)
 Compute the minimum free energy of two interacting RNA molecules. More...
 
float vrna_cofold (vrna_fold_compound *vc, char *structure)
 Compute the minimum free energy of two interacting RNA molecules. More...
 
char * vrna_cut_point_insert (const char *string, int cp)
 Add a separating '&' character into a string according to cut-point position. More...
 
char * vrna_cut_point_remove (const char *string, int *cp)
 Remove a separating '&' character from a string. More...
 
void free_co_arrays (void)
 Free memory occupied by cofold() More...
 
void update_cofold_params (void)
 Recalculate parameters.
 
void update_cofold_params_par (vrna_param_t *parameters)
 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) More...
 
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. More...
 

Detailed Description

Function Documentation

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().

Deprecated:
use vrna_cofold() instead
Parameters
sequenceThe two sequences concatenated
structureWill hold the barcket dot structure of the dimer molecule
Returns
minimum free energy of the structure
float cofold_par ( const char *  string,
char *  structure,
vrna_param_t parameters,
int  is_constrained 
)

Compute the minimum free energy of two interacting RNA molecules.

Deprecated:
use vrna_cofold() instead
float vrna_cofold ( vrna_fold_compound vc,
char *  structure 
)

Compute the minimum free energy of two interacting RNA molecules.

The code is analog to the vrna_fold() function.

Parameters
vcfold compound
structureWill hold the barcket dot structure of the dimer molecule
Returns
minimum free energy of the structure
char* vrna_cut_point_insert ( const char *  string,
int  cp 
)

Add a separating '&' character into a string according to cut-point position.

If the cut-point position is less or equal to zero, this function just returns a copy of the provided string. Otherwise, the cut-point character is set at the corresponding position

Parameters
stringThe original string
cpThe cut-point position
Returns
A copy of the provided string including the cut-point character
char* vrna_cut_point_remove ( const char *  string,
int *  cp 
)

Remove a separating '&' character from a string.

This function removes the cut-point indicating '&' character from a string and memorizes its position in a provided integer variable. If not '&' is found in the input, the integer variable is set to -1. The function returns a copy of the input string with the '&' being sliced out.

Parameters
stringThe original string
cpThe cut-point position
Returns
A copy of the input string with the '&' being sliced out
void free_co_arrays ( void  )

Free memory occupied by cofold()

Deprecated:
This function will only free memory allocated by a prior call of cofold() or cofold_par(). See vrna_cofold() for how to use the new API
Note
folding matrices now reside in the fold compound, and should be free'd there
See also
vrna_fc_destroy(), vrna_cofold()
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

Deprecated:
folding matrices now reside within the fold compound. Thus, this function will only work in conjunction with a prior call to cofold() or cofold_par()
See also
vrna_cofold() for the new API
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)
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

Deprecated:
folding matrices now reside within the fold compound. Thus, this function will only work in conjunction with a prior call to cofold() or cofold_par()
See also
vrna_cofold() for the new API
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)