RNAlib-2.2.0RC0
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Energy evaluation of hairpin loops for MFE and partition function calculations. More...
Go to the source code of this file.
Functions | |
PRIVATE int | E_Hairpin (int size, int type, int si1, int sj1, const char *string, paramT *P) |
Compute the Energy of a hairpin-loop. More... | |
PRIVATE double | exp_E_Hairpin (int u, int type, short si1, short sj1, const char *string, pf_paramT *P) |
Compute Boltzmann weight ![]() | |
PRIVATE int | E_hp_loop (int i, int j, vrna_fold_compound *vc) |
High-Level function for hairpin loop energy evaluation. | |
PRIVATE double | exp_E_hp_loop (int i, int j, vrna_fold_compound *vc) |
High-Level function for hairpin loop energy evaluation (partition function variant) More... | |
Energy evaluation of hairpin loops for MFE and partition function calculations.
PRIVATE int E_Hairpin | ( | int | size, |
int | type, | ||
int | si1, | ||
int | sj1, | ||
const char * | string, | ||
paramT * | P | ||
) |
Compute the Energy of a hairpin-loop.
To evaluate the free energy of a hairpin-loop, several parameters have to be known. A general hairpin-loop has this structure:
a3 a4 a2 a5 a1 a6 X - Y | | 5' 3'
where X-Y marks the closing pair [e.g. a (G,C) pair]. The length of this loop is 6 as there are six unpaired nucleotides (a1-a6) enclosed by (X,Y). The 5' mismatching nucleotide is a1 while the 3' mismatch is a6. The nucleotide sequence of this loop is "a1.a2.a3.a4.a5.a6"
size | The size of the loop (number of unpaired nucleotides) |
type | The pair type of the base pair closing the hairpin |
si1 | The 5'-mismatching nucleotide |
sj1 | The 3'-mismatching nucleotide |
string | The sequence of the loop |
P | The datastructure containing scaled energy parameters |
PRIVATE double exp_E_Hairpin | ( | int | u, |
int | type, | ||
short | si1, | ||
short | sj1, | ||
const char * | string, | ||
pf_paramT * | P | ||
) |
Compute Boltzmann weight of a hairpin loop.
multiply by scale[u+2]
u | The size of the loop (number of unpaired nucleotides) |
type | The pair type of the base pair closing the hairpin |
si1 | The 5'-mismatching nucleotide |
sj1 | The 3'-mismatching nucleotide |
string | The sequence of the loop |
P | The datastructure containing scaled Boltzmann weights of the energy parameters |
PRIVATE double exp_E_hp_loop | ( | int | i, |
int | j, | ||
vrna_fold_compound * | vc | ||
) |
High-Level function for hairpin loop energy evaluation (partition function variant)