RNAlib-2.2.0RC0
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Energy evaluation of interior loops for MFE and partition function calculations. More...
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Functions | |
PRIVATE int | E_IntLoop (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, paramT *P) |
PRIVATE double | exp_E_IntLoop (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, pf_paramT *P) |
PRIVATE int | E_stack (int i, int j, vrna_fold_compound *vc) |
Evaluate energy of a base pair stack closed by (i,j) | |
Energy evaluation of interior loops for MFE and partition function calculations.
PRIVATE int E_IntLoop | ( | int | n1, |
int | n2, | ||
int | type, | ||
int | type_2, | ||
int | si1, | ||
int | sj1, | ||
int | sp1, | ||
int | sq1, | ||
paramT * | P | ||
) |
This function computes the free energy of an interior-loop with the following structure:
3' 5' | | U - V a_n b_1 . . . . . . a_1 b_m X - Y | | 5' 3'
This general structure depicts an interior-loop that is closed by the base pair (X,Y). The enclosed base pair is (V,U) which leaves the unpaired bases a_1-a_n and b_1-b_n that constitute the loop. In this example, the length of the interior-loop is where n or m may be 0 resulting in a bulge-loop or base pair stack. The mismatching nucleotides for the closing pair (X,Y) are:
5'-mismatch: a_1
3'-mismatch: b_m
and for the enclosed base pair (V,U):
5'-mismatch: b_1
3'-mismatch: a_n
n1 | The size of the 'left'-loop (number of unpaired nucleotides) |
n2 | The size of the 'right'-loop (number of unpaired nucleotides) |
type | The pair type of the base pair closing the interior loop |
type_2 | The pair type of the enclosed base pair |
si1 | The 5'-mismatching nucleotide of the closing pair |
sj1 | The 3'-mismatching nucleotide of the closing pair |
sp1 | The 3'-mismatching nucleotide of the enclosed pair |
sq1 | The 5'-mismatching nucleotide of the enclosed pair |
P | The datastructure containing scaled energy parameters |
PRIVATE double exp_E_IntLoop | ( | int | u1, |
int | u2, | ||
int | type, | ||
int | type2, | ||
short | si1, | ||
short | sj1, | ||
short | sp1, | ||
short | sq1, | ||
pf_paramT * | P | ||
) |
multiply by scale[u1+u2+2] for scaling
u1 | The size of the 'left'-loop (number of unpaired nucleotides) |
u2 | The size of the 'right'-loop (number of unpaired nucleotides) |
type | The pair type of the base pair closing the interior loop |
type2 | The pair type of the enclosed base pair |
si1 | The 5'-mismatching nucleotide of the closing pair |
sj1 | The 3'-mismatching nucleotide of the closing pair |
sp1 | The 3'-mismatching nucleotide of the enclosed pair |
sq1 | The 5'-mismatching nucleotide of the enclosed pair |
P | The datastructure containing scaled Boltzmann weights of the energy parameters |