RNAlib-2.2.0-RC3
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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... | |
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().
sequence | The two sequences concatenated |
structure | Will hold the barcket dot structure of the dimer molecule |
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.
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.
vc | fold compound |
structure | Will hold the barcket dot structure of the dimer molecule |
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
string | The original string |
cp | The cut-point position |
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.
string | The original string |
cp | The cut-point position |
void free_co_arrays | ( | void | ) |
Free memory occupied by 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
f5_p | A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j] |
c_p | A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j |
fML_p | A 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_p | A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem |
fc_p | A pointer to the 'fc' array, i.e. array ... |
ggg_p | A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j] |
indx_p | A pointer to the indexing array used for accessing the energy matrices |
ptype_p | A 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
f5_p | A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j] |
c_p | A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j |
fML_p | A 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_p | A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem |
fc_p | A pointer to the 'fc' array, i.e. array ... |
indx_p | A pointer to the indexing array used for accessing the energy matrices |
ptype_p | A pointer to the ptype array containing the base pair types for each possibility (i,j) |