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RNAlib-2.3.4
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Collaboration diagram for Process and evaluate individual loops: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 of a hairpin loop. More... | |
| 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 . More... | |
| 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 |
in deka-kal/mol| 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
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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>
of interior loopmultiply 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>