RNAlib-2.4.0
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Files | |
file | exterior_loops.h |
Energy evaluation of exterior loops for MFE and partition function calculations. | |
file | hairpin_loops.h |
Energy evaluation of hairpin loops for MFE and partition function calculations. | |
file | interior_loops.h |
Energy evaluation of interior loops for MFE and partition function calculations. | |
file | loop_energies.h |
Energy evaluation for MFE and partition function calculations. | |
file | multibranch_loops.h |
Energy evaluation of multibranch loops for MFE and partition function calculations. | |
Data Structures | |
struct | vrna_mx_pf_aux_el_t |
Auxiliary helper arrays for fast exterior loop computations. More... | |
struct | vrna_mx_pf_aux_ml_t |
Auxiliary helper arrays for fast exterior loop computations. More... | |
PRIVATE int | E_Hairpin (int size, int type, int si1, int sj1, const char *string, vrna_param_t *P) |
Compute the Energy of a hairpin-loop. More... | |
int | vrna_eval_ext_hp_loop (vrna_fold_compound_t *vc, int i, int j) |
Evaluate free energy of an exterior hairpin loop. | |
int | vrna_eval_hp_loop (vrna_fold_compound_t *vc, int i, int j) |
Evaluate free energy of a hairpin loop. More... | |
PRIVATE FLT_OR_DBL | exp_E_Hairpin (int u, int type, short si1, short sj1, const char *string, vrna_exp_param_t *P) |
Compute Boltzmann weight ![]() | |
int | vrna_E_hp_loop (vrna_fold_compound_t *vc, int i, int j) |
Evaluate the free energy of a hairpin loop and consider hard constraints if they apply. More... | |
int | vrna_E_ext_hp_loop (vrna_fold_compound_t *vc, int i, int j) |
Evaluate the free energy of an exterior hairpin loop and consider possible hard constraints. More... | |
FLT_OR_DBL | vrna_exp_E_hp_loop (vrna_fold_compound_t *vc, int i, int j) |
High-Level function for hairpin loop energy evaluation (partition function variant) More... | |
int | vrna_BT_hp_loop (vrna_fold_compound_t *vc, int i, int j, int en, vrna_bp_stack_t *bp_stack, int *stack_count) |
Backtrack a hairpin loop closed by ![]() | |
PRIVATE int | E_IntLoop (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, vrna_param_t *P) |
PRIVATE FLT_OR_DBL | exp_E_IntLoop (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, vrna_exp_param_t *P) |
int | vrna_eval_int_loop (vrna_fold_compound_t *vc, int i, int j, int k, int l) |
int | vrna_BT_stack (vrna_fold_compound_t *vc, int *i, int *j, int *en, vrna_bp_stack_t *bp_stack, int *stack_count) |
Backtrack a stacked pair closed by ![]() | |
int | vrna_BT_int_loop (vrna_fold_compound_t *vc, int *i, int *j, int en, vrna_bp_stack_t *bp_stack, int *stack_count) |
Backtrack an interior loop closed by ![]() | |
struct vrna_mx_pf_aux_el_t |
Auxiliary helper arrays for fast exterior loop computations.
struct vrna_mx_pf_aux_ml_t |
Auxiliary helper arrays for fast exterior loop computations.
PRIVATE int E_Hairpin | ( | int | size, |
int | type, | ||
int | si1, | ||
int | sj1, | ||
const char * | string, | ||
vrna_param_t * | P | ||
) |
#include <ViennaRNA/hairpin_loops.h>
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 |
int vrna_eval_hp_loop | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
int | j | ||
) |
#include <ViennaRNA/hairpin_loops.h>
Evaluate free energy of a hairpin loop.
vc | The vrna_fold_compound_t for the particular energy evaluation |
i | 5'-position of the base pair |
j | 3'-position of the base pair |
PRIVATE int E_IntLoop | ( | int | n1, |
int | n2, | ||
int | type, | ||
int | type_2, | ||
int | si1, | ||
int | sj1, | ||
int | sp1, | ||
int | sq1, | ||
vrna_param_t * | P | ||
) |
#include <ViennaRNA/interior_loops.h>
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 FLT_OR_DBL exp_E_Hairpin | ( | int | u, |
int | type, | ||
short | si1, | ||
short | sj1, | ||
const char * | string, | ||
vrna_exp_param_t * | P | ||
) |
#include <ViennaRNA/hairpin_loops.h>
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 |
int vrna_E_hp_loop | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
int | j | ||
) |
#include <ViennaRNA/hairpin_loops.h>
Evaluate the free energy of a hairpin loop and consider hard constraints if they apply.
This function evaluates the free energy of a hairpin loop
In case the base pair is not allowed due to a constraint conflict, this function returns INF.
vc | The vrna_fold_compound_t that stores all relevant model settings |
i | The 5' nucleotide of the base pair (3' to evaluate the pair as exterior hairpin loop) |
j | The 3' nucleotide of the base pair (5' to evaluate the pair as exterior hairpin loop) |
int vrna_E_ext_hp_loop | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
int | j | ||
) |
#include <ViennaRNA/hairpin_loops.h>
Evaluate the free energy of an exterior hairpin loop and consider possible hard constraints.
FLT_OR_DBL vrna_exp_E_hp_loop | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
int | j | ||
) |
#include <ViennaRNA/hairpin_loops.h>
High-Level function for hairpin loop energy evaluation (partition function variant)
int vrna_BT_hp_loop | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
int | j, | ||
int | en, | ||
vrna_bp_stack_t * | bp_stack, | ||
int * | stack_count | ||
) |
#include <ViennaRNA/hairpin_loops.h>
Backtrack a hairpin loop closed by .
PRIVATE FLT_OR_DBL exp_E_IntLoop | ( | int | u1, |
int | u2, | ||
int | type, | ||
int | type2, | ||
short | si1, | ||
short | sj1, | ||
short | sp1, | ||
short | sq1, | ||
vrna_exp_param_t * | P | ||
) |
#include <ViennaRNA/interior_loops.h>
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 |
int vrna_eval_int_loop | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
int | j, | ||
int | k, | ||
int | l | ||
) |
#include <ViennaRNA/interior_loops.h>