RNAlib-2.2.0-RC2

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...

+ Collaboration diagram for Calculate Partition Functions of a Distance Based Partitioning:

Files

file  2Dpfold.h
 

Data Structures

struct  vrna_sol_TwoD_pf_t
 Solution element returned from vrna_TwoD_pf_fold() More...
 

Functions

vrna_sol_TwoD_pf_tvrna_TwoD_pf_fold (vrna_fold_compound *vc, int maxDistance1, int maxDistance2)
 Compute the partition function for all distance classes. More...
 

Detailed Description

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.

Function Documentation

vrna_sol_TwoD_pf_t* vrna_TwoD_pf_fold ( vrna_fold_compound vc,
int  maxDistance1,
int  maxDistance2 
)

Compute the partition function for all distance classes.

This function computes the partition functions for all distance classes according the two reference structures specified in the datastructure 'vars'. Similar to vrna_TwoD_fold() 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

See also
vrna_get_fold_compound_2D(), vrna_free_fold_compound(), vrna_fold_compound vrna_sol_TwoD_pf_t
Parameters
vcThe datastructure containing all necessary folding attributes and matrices
maxDistance1The maximum basepair distance to reference1 (may be -1)
maxDistance2The maximum basepair distance to reference2 (may be -1)
Returns
A list of partition funtions for the corresponding distance classes