Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures. More…
// typedefs typedef struct vrna_sol_TwoD_pf_t vrna_sol_TwoD_pf_t // structs struct vrna_sol_TwoD_pf_t // global functions vrna_sol_TwoD_pf_t* vrna_pf_TwoD ( vrna_fold_compound_t* vc, int maxDistance1, int maxDistance2 )
typedef struct vrna_sol_TwoD_pf_t vrna_sol_TwoD_pf_t
This element contains the partition function for the appropriate kappa (k), lambda (l) neighborhood The datastructure contains two integer attributes ‘k’ and ‘l’ as well as an attribute ‘q’ of type FLT_OR_DBL
A value of INF in k denotes the end of a list
See also:
vrna_sol_TwoD_pf_t* vrna_pf_TwoD ( vrna_fold_compound_t* vc, int maxDistance1, int maxDistance2 )
This function computes the partition functions for all distance classes according the two reference structures specified in the datastructure ‘vars’. Similar to vrna_mfe_TwoD() the arguments maxDistance1 and maxDistance2 specify the maximum distance to both reference structures. A value of ‘-1’ in either of them makes the appropriate distance restrictionless, i.e. all basepair distancies to the reference are taken into account during computation. In case there is a restriction, the returned solution contains an entry where the attribute k=l=-1 contains the partition function for all structures exceeding the restriction. A value of INF in the attribute ‘k’ of the returned list denotes the end of the list
Parameters:
vc | The datastructure containing all necessary folding attributes and matrices |
maxDistance1 | The maximum basepair distance to reference1 (may be -1) |
maxDistance2 | The maximum basepair distance to reference2 (may be -1) |
Returns:
A list of partition funtions for the corresponding distance classes