RNAlib-2.3.1
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MFE version of cofolding routines This file includes (almost) all function declarations within the RNAlib that are related to MFE Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines. More...
Functions | |
float | vrna_cofold (const char *sequence, 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... | |
MFE version of cofolding routines This file includes (almost) all function declarations within the RNAlib that are related to MFE Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines.
float vrna_cofold | ( | const char * | sequence, |
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 |