RNAlib-2.2.0RC0
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Energy evaluation of exterior loops for MFE and partition function calculations. More...
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Functions | |
PRIVATE int | E_ExtLoop (int type, int si1, int sj1, paramT *P) |
PRIVATE double | exp_E_ExtLoop (int type, int si1, int sj1, pf_paramT *P) |
PRIVATE int | E_Stem (int type, int si1, int sj1, int extLoop, paramT *P) |
PRIVATE double | exp_E_Stem (int type, int si1, int sj1, int extLoop, pf_paramT *P) |
Energy evaluation of exterior loops for MFE and partition function calculations.
PRIVATE int E_ExtLoop | ( | int | type, |
int | si1, | ||
int | sj1, | ||
paramT * | P | ||
) |
This definition is a wrapper for the E_Stem() funtion. It is substituted by an E_Stem() funtion call with argument extLoop=1, so the energy contribution returned reflects a stem introduced in an exterior-loop.
As for the parameters si1 and sj1 of the substituted E_Stem() function, you can inhibit to take 5'-, 3'-dangles or mismatch contributions to be taken into account by passing -1 to these parameters.
type | The pair type of the stem-closing pair |
si1 | The 5'-mismatching nucleotide |
sj1 | The 3'-mismatching nucleotide |
P | The datastructure containing scaled energy parameters |
PRIVATE double exp_E_ExtLoop | ( | int | type, |
int | si1, | ||
int | sj1, | ||
pf_paramT * | P | ||
) |
This is the partition function variant of E_ExtLoop()
PRIVATE int E_Stem | ( | int | type, |
int | si1, | ||
int | sj1, | ||
int | extLoop, | ||
paramT * | P | ||
) |
This function computes the energy contribution of a stem that branches off a loop region. This can be the case in multiloops, when a stem branching off increases the degree of the loop but also immediately interior base pairs of an exterior loop contribute free energy. To switch the bahavior of the function according to the evaluation of a multiloop- or exterior-loop-stem, you pass the flag 'extLoop'. The returned energy contribution consists of a TerminalAU penalty if the pair type is greater than 2, dangling end contributions of mismatching nucleotides adjacent to the stem if only one of the si1, sj1 parameters is greater than 0 and mismatch energies if both mismatching nucleotides are positive values. Thus, to avoid incooperating dangling end or mismatch energies just pass a negative number, e.g. -1 to the mismatch argument.
This is an illustration of how the energy contribution is assembled:
3' 5' | | X - Y 5'-si1 sj1-3'
Here, (X,Y) is the base pair that closes the stem that branches off a loop region. The nucleotides si1 and sj1 are the 5'- and 3'- mismatches, respectively. If the base pair type of (X,Y) is greater than 2 (i.e. an A-U or G-U pair, the TerminalAU penalty will be included in the energy contribution returned. If si1 and sj1 are both nonnegative numbers, mismatch energies will also be included. If one of sij or sj1 is a negtive value, only 5' or 3' dangling end contributions are taken into account. To prohibit any of these mismatch contributions to be incoorporated, just pass a negative number to both, si1 and sj1. In case the argument extLoop is 0, the returned energy contribution also includes the internal-loop-penalty of a multiloop stem with closing pair type.
type | The pair type of the first base pair un the stem |
si1 | The 5'-mismatching nucleotide |
sj1 | The 3'-mismatching nucleotide |
extLoop | A flag that indicates whether the contribution reflects the one of an exterior loop or not |
P | The datastructure containing scaled energy parameters |
PRIVATE double exp_E_Stem | ( | int | type, |
int | si1, | ||
int | sj1, | ||
int | extLoop, | ||
pf_paramT * | P | ||
) |