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RNAlib-2.4.17
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Functions to create, parse, convert, manipulate, and compare secondary structure representations. More...
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... | |
| 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
| str1 | First structure in dot-bracket notation |
| str2 | Second structure in dot-bracket notation |
| 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
| bp | Base pair stack containing the traced base pairs |
| length | The length of the structure |