MFE version of cofolding routines. More...
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Functions | |
float | cofold (const char *sequence, char *structure) |
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. | |
SOLUTION * | zukersubopt (const char *string) |
Compute Zuker type suboptimal structures. | |
void | get_monomere_mfes (float *e1, float *e2) |
get_monomer_free_energies | |
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. | |
void | initialize_cofold (int length) |
allocate arrays for folding |
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 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
|
SOLUTION* zukersubopt | ( | const char * | string | ) |
Compute Zuker type suboptimal structures.
Compute Suboptimal structures according to M. Zuker, i.e. for every possible base pair the minimum energy structure containing the resp. base pair. Returns a list of these structures and their energies.
string | RNA sequence
|
void get_monomere_mfes | ( | float * | e1, | |
float * | e2 | |||
) |
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
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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]
|
void initialize_cofold | ( | int | length | ) |
allocate arrays for folding