RNAlib-2.2.7
Processing and Evaluating Decomposed Loops

Files

file  exterior_loops.h
 Energy evaluation of exterior loops for MFE and partition function calculations.
 
file  gquad.h
 Various functions related to G-quadruplex computations.
 
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.
 

Functions

int E_ExtLoop (int type, int si1, int sj1, vrna_param_t *P)
 
FLT_OR_DBL exp_E_ExtLoop (int type, int si1, int sj1, vrna_exp_param_t *P)
 
int E_Stem (int type, int si1, int sj1, int extLoop, vrna_param_t *P)
 
FLT_OR_DBL exp_E_Stem (int type, int si1, int sj1, int extLoop, vrna_exp_param_t *P)
 
int * get_gquad_matrix (short *S, vrna_param_t *P)
 Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes. More...
 
int parse_gquad (const char *struc, int *L, int l[3])
 
PRIVATE int backtrack_GQuad_IntLoop (int c, int i, int j, int type, short *S, int *ggg, int *index, int *p, int *q, vrna_param_t *P)
 
PRIVATE int backtrack_GQuad_IntLoop_L (int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, vrna_param_t *P)
 
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...
 
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 $e^{-\Delta G/kT} $ 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 possible hard constraints. 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 $ (i,j) $. 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 E_stack (int i, int j, vrna_fold_compound_t *vc)
 Evaluate energy of a base pair stack closed by (i,j)
 
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 $ (i,j) $.
 
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 $ (i,j) $.
 
int E_mb_loop_stack (int i, int j, vrna_fold_compound_t *vc)
 Evaluate energy of a multi branch helices stacking onto closing pair (i,j) More...
 
int vrna_BT_mb_loop (vrna_fold_compound_t *vc, int *i, int *j, int *k, int en, int *component1, int *component2)
 Backtrack the decomposition of a multi branch loop closed by $ (i,j) $. More...
 

Detailed Description

Function Documentation

int E_ExtLoop ( int  type,
int  si1,
int  sj1,
vrna_param_t P 
)

#include <ViennaRNA/exterior_loops.h>

Compute the Energy contribution of an Exterior loop stem

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.

See also
E_Stem()
Parameters
typeThe pair type of the stem-closing pair
si1The 5'-mismatching nucleotide
sj1The 3'-mismatching nucleotide
PThe datastructure containing scaled energy parameters
Returns
The energy contribution of the introduced exterior-loop stem
FLT_OR_DBL exp_E_ExtLoop ( int  type,
int  si1,
int  sj1,
vrna_exp_param_t P 
)

#include <ViennaRNA/exterior_loops.h>

This is the partition function variant of E_ExtLoop()

See also
E_ExtLoop()
Returns
The Boltzmann weighted energy contribution of the introduced exterior-loop stem
int E_Stem ( int  type,
int  si1,
int  sj1,
int  extLoop,
vrna_param_t P 
)

#include <ViennaRNA/exterior_loops.h>

Compute the energy contribution of a stem branching off a loop-region

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.

See also
E_MLstem()
E_ExtLoop()
Note
This function is threadsafe
Parameters
typeThe pair type of the first base pair un the stem
si1The 5'-mismatching nucleotide
sj1The 3'-mismatching nucleotide
extLoopA flag that indicates whether the contribution reflects the one of an exterior loop or not
PThe datastructure containing scaled energy parameters
Returns
The Free energy of the branch off the loop in dcal/mol
FLT_OR_DBL exp_E_Stem ( int  type,
int  si1,
int  sj1,
int  extLoop,
vrna_exp_param_t P 
)

#include <ViennaRNA/exterior_loops.h>

Compute the Boltzmann weighted energy contribution of a stem branching off a loop-region

This is the partition function variant of E_Stem()

See also
E_Stem()
Note
This function is threadsafe
Returns
The Boltzmann weighted energy contribution of the branch off the loop
int* get_gquad_matrix ( short *  S,
vrna_param_t P 
)

#include <ViennaRNA/gquad.h>

Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes.

At each position ij in the matrix, the minimum free energy of any G-quadruplex delimited by i and j is stored. If no G-quadruplex formation is possible, the matrix element is set to INF. Access the elements in the matrix via matrix[indx[j]+i]. To get the integer array indx see get_jindx().

See also
get_jindx(), encode_sequence()
Parameters
SThe encoded sequence
PA pointer to the data structure containing the precomputed energy contributions
Returns
A pointer to the G-quadruplex contribution matrix
int parse_gquad ( const char *  struc,
int *  L,
int  l[3] 
)

#include <ViennaRNA/gquad.h>

given a dot-bracket structure (possibly) containing gquads encoded by '+' signs, find first gquad, return end position or 0 if none found Upon return L and l[] contain the number of stacked layers, as well as the lengths of the linker regions. To parse a string with many gquads, call parse_gquad repeatedly e.g. end1 = parse_gquad(struc, &L, l); ... ; end2 = parse_gquad(struc+end1, &L, l); end2+=end1; ... ; end3 = parse_gquad(struc+end2, &L, l); end3+=end2; ... ;

PRIVATE int backtrack_GQuad_IntLoop ( int  c,
int  i,
int  j,
int  type,
short *  S,
int *  ggg,
int *  index,
int *  p,
int *  q,
vrna_param_t P 
)

#include <ViennaRNA/gquad.h>

backtrack an interior loop like enclosed g-quadruplex with closing pair (i,j)

Parameters
cThe total contribution the loop should resemble
iposition i of enclosing pair
jposition j of enclosing pair
typebase pair type of enclosing pair (must be reverse type)
Sinteger encoded sequence
gggtriangular matrix containing g-quadruplex contributions
indexthe index for accessing the triangular matrix
phere the 5' position of the gquad is stored
qhere the 3' position of the gquad is stored
Pthe datastructure containing the precalculated contibutions
Returns
1 on success, 0 if no gquad found
PRIVATE int backtrack_GQuad_IntLoop_L ( int  c,
int  i,
int  j,
int  type,
short *  S,
int **  ggg,
int  maxdist,
int *  p,
int *  q,
vrna_param_t P 
)

#include <ViennaRNA/gquad.h>

backtrack an interior loop like enclosed g-quadruplex with closing pair (i,j) with underlying Lfold matrix

Parameters
cThe total contribution the loop should resemble
iposition i of enclosing pair
jposition j of enclosing pair
typebase pair type of enclosing pair (must be reverse type)
Sinteger encoded sequence
gggtriangular matrix containing g-quadruplex contributions
phere the 5' position of the gquad is stored
qhere the 3' position of the gquad is stored
Pthe datastructure containing the precalculated contibutions
Returns
1 on success, 0 if no gquad found
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"

Note
The parameter sequence should contain the sequence of the loop in capital letters of the nucleic acid alphabet if the loop size is below 7. This is useful for unusually stable tri-, tetra- and hexa-loops which are treated differently (based on experimental data) if they are tabulated.
See also
scale_parameters()
vrna_param_t
Warning
Not (really) thread safe! A threadsafe implementation will replace this function in a future release!
Energy evaluation may change due to updates in global variable "tetra_loop"
Parameters
sizeThe size of the loop (number of unpaired nucleotides)
typeThe pair type of the base pair closing the hairpin
si1The 5'-mismatching nucleotide
sj1The 3'-mismatching nucleotide
stringThe sequence of the loop
PThe datastructure containing scaled energy parameters
Returns
The Free energy of the Hairpin-loop in dcal/mol
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 $e^{-\Delta G/kT} $ of a hairpin loop.

multiply by scale[u+2]

See also
get_scaled_pf_parameters()
vrna_exp_param_t
E_Hairpin()
Warning
Not (really) thread safe! A threadsafe implementation will replace this function in a future release!
Energy evaluation may change due to updates in global variable "tetra_loop"
Parameters
uThe size of the loop (number of unpaired nucleotides)
typeThe pair type of the base pair closing the hairpin
si1The 5'-mismatching nucleotide
sj1The 3'-mismatching nucleotide
stringThe sequence of the loop
PThe datastructure containing scaled Boltzmann weights of the energy parameters
Returns
The Boltzmann weight of the Hairpin-loop
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 possible hard constraints.

Note
This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_VC_TYPE_SINGLE or VRNA_VC_TYPE_ALIGNMENT
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.

Note
This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_VC_TYPE_SINGLE or VRNA_VC_TYPE_ALIGNMENT
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)

See also
vrna_E_hp_loop() for it's free energy counterpart
Note
This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_VC_TYPE_SINGLE or VRNA_VC_TYPE_ALIGNMENT
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 $ (i,j) $.

Note
This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_VC_TYPE_SINGLE or VRNA_VC_TYPE_ALIGNMENT
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>

Compute the Energy of an interior-loop

This function computes the free energy $\Delta G$ 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 $(n+m)$ 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

Note
Base pairs are always denoted in 5'->3' direction. Thus the enclosed base pair must be 'turned arround' when evaluating the free energy of the interior-loop
See also
scale_parameters()
vrna_param_t
Note
This function is threadsafe
Parameters
n1The size of the 'left'-loop (number of unpaired nucleotides)
n2The size of the 'right'-loop (number of unpaired nucleotides)
typeThe pair type of the base pair closing the interior loop
type_2The pair type of the enclosed base pair
si1The 5'-mismatching nucleotide of the closing pair
sj1The 3'-mismatching nucleotide of the closing pair
sp1The 3'-mismatching nucleotide of the enclosed pair
sq1The 5'-mismatching nucleotide of the enclosed pair
PThe datastructure containing scaled energy parameters
Returns
The Free energy of the Interior-loop in dcal/mol
PUBLIC 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>

Compute Boltzmann weight $e^{-\Delta G/kT} $ of interior loop

multiply by scale[u1+u2+2] for scaling

See also
get_scaled_pf_parameters()
vrna_exp_param_t
E_IntLoop()
Note
This function is threadsafe
Parameters
u1The size of the 'left'-loop (number of unpaired nucleotides)
u2The size of the 'right'-loop (number of unpaired nucleotides)
typeThe pair type of the base pair closing the interior loop
type2The pair type of the enclosed base pair
si1The 5'-mismatching nucleotide of the closing pair
sj1The 3'-mismatching nucleotide of the closing pair
sp1The 3'-mismatching nucleotide of the enclosed pair
sq1The 5'-mismatching nucleotide of the enclosed pair
PThe datastructure containing scaled Boltzmann weights of the energy parameters
Returns
The Boltzmann weight of the Interior-loop
int E_mb_loop_stack ( int  i,
int  j,
vrna_fold_compound_t vc 
)

#include <ViennaRNA/multibranch_loops.h>

Evaluate energy of a multi branch helices stacking onto closing pair (i,j)

Computes total free energy for coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1)

int vrna_BT_mb_loop ( vrna_fold_compound_t vc,
int *  i,
int *  j,
int *  k,
int  en,
int *  component1,
int *  component2 
)

#include <ViennaRNA/multibranch_loops.h>

Backtrack the decomposition of a multi branch loop closed by $ (i,j) $.

Parameters
vcThe vrna_fold_compound_t filled with all relevant data for backtracking
i5' position of base pair closing the loop (will be set to 5' position of leftmost decomposed block upon successful backtracking)
j3' position of base pair closing the loop (will be set to 3' position of rightmost decomposed block upon successful backtracking)
kSplit position that delimits leftmost from rightmost block, [i,k] and [k+1, j], respectively. (Will be set upon successful backtracking)
enThe energy contribution of the substructure enclosed by $ (i,j) $
component1Type of leftmost block (1 = ML, 2 = C)
component2Type of rightmost block (1 = ML, 2 = C)
Returns
1, if backtracking succeeded, 0 otherwise.