Functions to create, parse, convert, manipulate, and compare secondary structure representations. More...
Detailed Description
Functions to create, parse, convert, manipulate, and compare secondary structure representations.
Collaboration diagram for Secondary Structure Utilities:Files | |
| file | structures.h |
| Various utility- and helper-functions for secondary structure parsing, converting, etc. | |
Functions | |
| int * | vrna_loopidx_from_ptable (const short *pt) |
| Get a loop index representation of a structure. | |
| int | vrna_bp_distance (const char *str1, const char *str2) |
| Compute the "base pair" distance between two secondary structures s1 and s2. More... | |
| unsigned int * | vrna_refBPcnt_matrix (const short *reference_pt, unsigned int turn) |
| Make a reference base pair count matrix. More... | |
| unsigned int * | vrna_refBPdist_matrix (const short *pt1, const short *pt2, unsigned int turn) |
| Make a reference base pair distance matrix. More... | |
| char * | vrna_db_from_probs (const FLT_OR_DBL *pr, unsigned int length) |
| Create a dot-bracket like structure string from base pair probability matrix. | |
| char | vrna_bpp_symbol (const float *x) |
| Get a pseudo dot bracket notation for a given probability information. | |
| char * | vrna_db_from_bp_stack (vrna_bp_stack_t *bp, unsigned int length) |
| Create a dot-backet/parenthesis structure from backtracking stack. More... | |
Function Documentation
| int vrna_bp_distance | ( | const char * | str1, |
| const char * | str2 | ||
| ) |
#include <ViennaRNA/utils/structures.h>
Compute the "base pair" distance between two secondary structures s1 and s2.
The sequences should have the same length. dist = number of base pairs in one structure but not in the other same as edit distance with open-pair close-pair as move-set
- Parameters
-
str1 First structure in dot-bracket notation str2 Second structure in dot-bracket notation
- Returns
- The base pair distance between str1 and str2
| unsigned int* vrna_refBPcnt_matrix | ( | const short * | reference_pt, |
| unsigned int | turn | ||
| ) |
#include <ViennaRNA/utils/structures.h>
Make a reference base pair count matrix.
Get an upper triangular matrix containing the number of basepairs of a reference structure for each interval [i,j] with i<j. Access it via iindx!!!
| unsigned int* vrna_refBPdist_matrix | ( | const short * | pt1, |
| const short * | pt2, | ||
| unsigned int | turn | ||
| ) |
#include <ViennaRNA/utils/structures.h>
Make a reference base pair distance matrix.
Get an upper triangular matrix containing the base pair distance of two reference structures for each interval [i,j] with i<j. Access it via iindx!!!
| char* vrna_db_from_bp_stack | ( | vrna_bp_stack_t * | bp, |
| unsigned int | length | ||
| ) |
#include <ViennaRNA/utils/structures.h>
Create a dot-backet/parenthesis structure from backtracking stack.
This function is capable to create dot-bracket structures from suboptimal structure prediction sensu M. Zuker
- Parameters
-
bp Base pair stack containing the traced base pairs length The length of the structure
- Returns
- The secondary structure in dot-bracket notation as provided in the input
