RNAlib-2.2.7
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Files | |
file | cofold.h |
MFE version of cofolding routines. | |
Functions | |
float | vrna_cofold (const char *string, char *structure) |
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences. More... | |
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... | |
void | free_co_arrays (void) |
Free memory occupied by cofold() More... | |
void | update_cofold_params (void) |
Recalculate parameters. More... | |
void | update_cofold_params_par (vrna_param_t *parameters) |
Recalculate parameters. More... | |
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... | |
void | get_monomere_mfes (float *e1, float *e2) |
get_monomer_free_energies More... | |
void | initialize_cofold (int length) |
float | vrna_mfe_dimer (vrna_fold_compound_t *vc, char *structure) |
Compute the minimum free energy of two interacting RNA molecules. More... | |
float vrna_cofold | ( | const char * | string, |
char * | structure | ||
) |
#include <ViennaRNA/cofold.h>
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences.
This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for two RNA sequences upon dimerization using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.
sequence | two RNA sequences separated by the '&' character |
structure | A pointer to the character array where the secondary structure in dot-bracket notation will be written to |
float cofold | ( | const char * | sequence, |
char * | structure | ||
) |
#include <ViennaRNA/cofold.h>
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 | ||
) |
#include <ViennaRNA/cofold.h>
Compute the minimum free energy of two interacting RNA molecules.
void free_co_arrays | ( | void | ) |
#include <ViennaRNA/cofold.h>
Free memory occupied by cofold()
void update_cofold_params | ( | void | ) |
#include <ViennaRNA/cofold.h>
Recalculate parameters.
void update_cofold_params_par | ( | vrna_param_t * | parameters | ) |
#include <ViennaRNA/cofold.h>
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 | ||
) |
#include <ViennaRNA/cofold.h>
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 | ||
) |
#include <ViennaRNA/cofold.h>
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) |
void get_monomere_mfes | ( | float * | e1, |
float * | e2 | ||
) |
#include <ViennaRNA/cofold.h>
get_monomer_free_energies
Export monomer free energies out of cofold arrays
e1 | A pointer to a variable where the energy of molecule A will be written to |
e2 | A pointer to a variable where the energy of molecule B will be written to |
void initialize_cofold | ( | int | length | ) |
#include <ViennaRNA/cofold.h>
allocate arrays for folding
float vrna_mfe_dimer | ( | vrna_fold_compound_t * | vc, |
char * | structure | ||
) |
#include <ViennaRNA/mfe.h>
Compute the minimum free energy of two interacting RNA molecules.
The code is analog to the vrna_mfe() function.
vc | fold compound |
structure | Will hold the barcket dot structure of the dimer molecule |