RNAlib-2.2.5
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Add and modify unstructured domains to the RNA folding grammar. More...
Files | |
file | unstructured_domains.h |
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches. | |
Data Structures | |
struct | vrna_unstructured_domain_s |
Data structure to store all functionality for ligand binding. More... | |
Macros | |
#define | VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP 1U |
Flag to indicate ligand bound to unpiared stretch in the exterior loop. | |
#define | VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP 2U |
Flag to indicate ligand bound to unpaired stretch in a hairpin loop. | |
#define | VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP 4U |
Flag to indicate ligand bound to unpiared stretch in an interior loop. | |
#define | VRNA_UNSTRUCTURED_DOMAIN_ML_LOOP 8U |
Flag to indicate ligand bound to unpiared stretch in a multibranch loop. | |
#define | VRNA_UNSTRUCTURED_DOMAIN_MOTIF 16U |
Flag to indicate ligand binding without additional unbound nucleotides (motif-only) | |
#define | VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS (VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_ML_LOOP) |
Flag to indicate ligand bound to unpiared stretch in any loop (convenience macro) | |
Typedefs | |
typedef struct vrna_unstructured_domain_s | vrna_ud_t |
Typename for the ligand binding extension data structure vrna_unstructured_domain_s. | |
typedef int( | vrna_callback_ud_energy) (vrna_fold_compound_t *vc, int i, int j, unsigned int looptype, void *data) |
Callback to retrieve binding free energy of a ligand bound to an unpaired sequence segment. | |
typedef FLT_OR_DBL( | vrna_callback_ud_exp_energy) (vrna_fold_compound_t *vc, int i, int j, unsigned int looptype, void *data) |
Callback to retrieve Boltzmann factor of the binding free energy of a ligand bound to an unpaired sequence segment. | |
typedef void( | vrna_callback_ud_production) (vrna_fold_compound_t *vc, void *data) |
Callback for pre-processing the production rule of the ligand binding to unpaired stretches feature. | |
typedef void( | vrna_callback_ud_exp_production) (vrna_fold_compound_t *vc, void *data) |
Callback for pre-processing the production rule of the ligand binding to unpaired stretches feature (partition function variant) | |
Functions | |
void | vrna_ud_add_motif (vrna_fold_compound_t *vc, const char *motif, double motif_en, unsigned int loop_type) |
Add a ligand binding motif. More... | |
void | vrna_ud_remove (vrna_fold_compound_t *vc) |
Remove ligand binding to unpaired stretches. More... | |
void | vrna_ud_set_data (vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *free) |
Attach an auxiliary data structure. More... | |
void | vrna_ud_set_prod_rule (vrna_fold_compound_t *vc, vrna_callback_ud_production *rule) |
Attach production rule for free energies. More... | |
void | vrna_ud_set_exp_prod_rule (vrna_fold_compound_t *vc, vrna_callback_ud_exp_production *rule) |
Attach production rule for partition function. More... | |
void | vrna_ud_set_energy (vrna_fold_compound_t *vc, vrna_callback_ud_energy *e) |
Attach evaluation function for free energies. More... | |
void | vrna_ud_set_exp_energy (vrna_fold_compound_t *vc, vrna_callback_ud_exp_energy *exp_e) |
Attach evaluation function for Boltzmann factors. More... | |
Add and modify unstructured domains to the RNA folding grammar.
This module provides the tools to add and modify unstructured domains to the production rules of the RNA folding grammar. Usually this functionality is utilized for incorporating ligand binding to unpaired stretches of an RNA.
Unstructured domains appear in the production rules of the RNA folding grammar whereever new unpaired nucleotides are attached to a growing substructure (see also [11]):
The white boxes represent the stretch of RNA bound to the ligand and represented by a more or less specific sequence motif. The motif itself is considered unable to form basepairs. The additional production rule U is used to precompute the contribution of unpaired stretches possibly bound by one or more ligands. The auxiliary DP matrix for this production rule is filled right before processing the other (regular) production rules of the RNA folding grammar.
In a context with Structured domains the grammar is extended as follows:
A default implementation allows to readily use this feature by simply adding sequence motifs and correpsonding binding free energies with the function vrna_ud_add_motif() (see also Ligands binding to unstructured domains).
The grammar extension is realized using a callback function that
The callback is passed the segment positions, the loop context, and which of the two above mentioned evaluations are required. A second callback implements the pre-processing step that prepares the U DP matrix by evaluating all possible cases of the additional production rule. Both callbacks have a default implementation in RNAlib, but may be over-written by a user-implementation, making it fully user-customizable.
struct vrna_unstructured_domain_s |
Data structure to store all functionality for ligand binding.
Data Fields | |
int | motif_count |
Number of distinguished motifs. | |
char ** | motif |
Motif sequences. | |
unsigned int * | motif_size |
Motif lengths. | |
double * | motif_en |
Ligand binding free energy contribution. | |
unsigned int * | motif_type |
Type of motif, i.e. loop type the ligand binds to. | |
vrna_callback_ud_production * | prod_cb |
Callback to ligand binding production rule, i.e. create/fill DP free energy matrices. More... | |
vrna_callback_ud_exp_production * | exp_prod_cb |
Callback to ligand binding production rule, i.e. create/fill DP partition function matrices. | |
vrna_callback_ud_energy * | energy_cb |
Callback to evaluate free energy of ligand binding to a particular unpaired stretch. | |
vrna_callback_ud_exp_energy * | exp_energy_cb |
Callback to evaluate Boltzmann factor of ligand binding to a particular unpaired stretch. | |
void * | data |
Auxiliary data structure passed to energy evaluation callbacks. | |
vrna_callback_free_auxdata * | free_data |
Callback to free auxiliary data structure. | |
vrna_callback_ud_production* vrna_unstructured_domain_s::prod_cb |
Callback to ligand binding production rule, i.e. create/fill DP free energy matrices.
This callback will be executed right before the actual secondary structure decompositions, and, therefore, any implementation must not interleave with the regular DP matrices.
void vrna_ud_add_motif | ( | vrna_fold_compound_t * | vc, |
const char * | motif, | ||
double | motif_en, | ||
unsigned int | loop_type | ||
) |
#include <ViennaRNA/unstructured_domains.h>
Add a ligand binding motif.
This function adds a ligand binding motif and the associated binding free energy to the vrna_ud_t attribute of a vrna_fold_compound_t. The motif data will then be used in subsequent secondary structure predictions. Multiple calls to this function with different motifs append all additional data to a list of ligands, which all will be evaluated. Ligand motif data can be removed from the vrna_fold_compound_t again using the vrna_ud_remove() function. The loop type parameter allows one to limit the ligand binding to particular loop type, such as the exterior loop, hairpin loops, interior loops, or multibranch loops.
vc | The vrna_fold_compound_t data structure the ligand motif should be bound to |
motif | The sequence motif the ligand binds to |
motif_en | The binding free energy of the ligand in kcal/mol |
loop_type | The loop type the ligand binds to |
void vrna_ud_remove | ( | vrna_fold_compound_t * | vc | ) |
#include <ViennaRNA/unstructured_domains.h>
Remove ligand binding to unpaired stretches.
This function removes all ligand motifs that were bound to a vrna_fold_compound_t using the vrna_ud_add_motif() function.
vc | The vrna_fold_compound_t data structure the ligand motif data should be removed from |
void vrna_ud_set_data | ( | vrna_fold_compound_t * | vc, |
void * | data, | ||
vrna_callback_free_auxdata * | free | ||
) |
#include <ViennaRNA/unstructured_domains.h>
Attach an auxiliary data structure.
This function binds an arbitrary, auxiliary data structure for user-implemented ligand binding. The optional callback free
will be passed the bound data structure whenever the vrna_fold_compound_t is removed from memory to avoid memory leaks.
vc | The vrna_fold_compound_t data structure the auxiliary data structure should be bound to |
data | A pointer to the auxiliary data structure |
free | A pointer to a callback function that free's memory occupied by data |
void vrna_ud_set_prod_rule | ( | vrna_fold_compound_t * | vc, |
vrna_callback_ud_production * | rule | ||
) |
#include <ViennaRNA/unstructured_domains.h>
Attach production rule for free energies.
Use this function to supply a user-implemented production rule B
. This callback will be executed as a pre-processing step right before the regular secondary structure rules. Usually one would use this callback to fill the dynamic processing matrices B
and preparations of the auxiliary data structure vrna_unstructured_domain_s.data
vc | The vrna_fold_compound_t data structure the callback should be bound to |
rule | A pointer to a callback function for the B production rule |
void vrna_ud_set_exp_prod_rule | ( | vrna_fold_compound_t * | vc, |
vrna_callback_ud_exp_production * | rule | ||
) |
#include <ViennaRNA/unstructured_domains.h>
Attach production rule for partition function.
This function is the partition function companion of vrna_ud_set_prod_rule(). Use it to bind a callback to fill the B
production rule dynamic programming matrices and/or prepare the vrna_unstructured_domain_s.data.
vc | The vrna_fold_compound_t data structure the callback should be bound to |
rule | A pointer to a callback function for the B production rule |
void vrna_ud_set_energy | ( | vrna_fold_compound_t * | vc, |
vrna_callback_ud_energy * | e | ||
) |
#include <ViennaRNA/unstructured_domains.h>
Attach evaluation function for free energies.
Use this function to bind a user-implemented binding free energy evaluation callback. The callback has to evaluate the free energy contribution of the unpaired segment
and is executed in each of the regular secondary structure production rules. Whenever the callback is passed the VRNA_UNSTRUCTURED_DOMAIN_MOTIF flag via its
loop_type
parameter the contribution of any ligand that consecutively binds from position to
(the white box) is requested. Otherwise, the callback usually performs a lookup in the precomputed
B
matrices. Which B
matrix is addressed will be indicated by the flags VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP, VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP, and VRNA_UNSTRUCTURED_DOMAIN_ML_LOOP. As their names already imply, they specify exterior loops (F
production rule), hairpin loops and interior loops (C
production rule), and multibranch loops (M
and M1
production rule).
vc | The vrna_fold_compound_t data structure the callback should be bound to |
e | A pointer to a callback function for free energy evaluation |
void vrna_ud_set_exp_energy | ( | vrna_fold_compound_t * | vc, |
vrna_callback_ud_exp_energy * | exp_e | ||
) |
#include <ViennaRNA/unstructured_domains.h>
Attach evaluation function for Boltzmann factors.
This is the partition function variant of vrna_ud_set_energy().
vc | The vrna_fold_compound_t data structure the callback should be bound to |
e | A pointer to callback that compute the partition function for a segment ![]() |