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RNAlib-2.4.17
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Collaboration diagram for Pair List Representation of Secondary Structures:Data Structures | |
| struct | vrna_elem_prob_s |
| Data structure representing a single entry of an element probability list (e.g. list of pair probabilities) More... | |
Macros | |
| #define | VRNA_PLIST_TYPE_BASEPAIR 0 |
| A Base Pair element. | |
| #define | VRNA_PLIST_TYPE_GQUAD 1 |
| A G-Quadruplex element. | |
| #define | VRNA_PLIST_TYPE_H_MOTIF 2 |
| A Hairpin loop motif element. | |
| #define | VRNA_PLIST_TYPE_I_MOTIF 3 |
| An Internal loop motif element. | |
| #define | VRNA_PLIST_TYPE_UD_MOTIF 4 |
| An Unstructured Domain motif element. | |
| #define | VRNA_PLIST_TYPE_STACK 5 |
| A Base Pair stack element. | |
Typedefs | |
| typedef struct vrna_elem_prob_s | vrna_ep_t |
| Convenience typedef for data structure vrna_elem_prob_s. | |
Functions | |
| vrna_ep_t * | vrna_plist (const char *struc, float pr) |
| Create a vrna_ep_t from a dot-bracket string. More... | |
| struct vrna_elem_prob_s |
Data structure representing a single entry of an element probability list (e.g. list of pair probabilities)
Data Fields | |
| int | i |
| Start position (usually 5' nucleotide that starts the element, e.g. base pair) | |
| int | j |
| End position (usually 3' nucleotide that ends the element, e.g. base pair) | |
| float | p |
| Probability of the element. | |
| int | type |
| Type of the element. | |
| vrna_ep_t* vrna_plist | ( | const char * | struc, |
| float | pr | ||
| ) |
#include <ViennaRNA/utils/structures.h>
Create a vrna_ep_t from a dot-bracket string.
The dot-bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.
The end of the plist is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries
| struc | The secondary structure in dot-bracket notation |
| pr | The probability for each base pair used in the plist |