Various functions related to G-quadruplex computations. +More...
+
Include dependency graph for gquad.h:
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++Functions | |
| int * | get_gquad_matrix (short *S, paramT *P) |
| Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes. | |
| 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, paramT *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, paramT *P) |
Detailed Description
+Various functions related to G-quadruplex computations.
+Function Documentation
+ +| int* get_gquad_matrix | +( | +short * | +S, | +
| + | + | paramT * | +P | +
| + | ) | ++ |
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:
-
+
+
+S The encoded sequence P A 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] | +
| + | ) | ++ |
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, | +
| + | + | paramT * | +P | +
| + | ) | ++ |
backtrack an interior loop like enclosed g-quadruplex with closing pair (i,j)
+- Parameters:
-
+
+
+c The total contribution the loop should resemble i position i of enclosing pair j position j of enclosing pair type base pair type of enclosing pair (must be reverse type) S integer encoded sequence ggg triangular matrix containing g-quadruplex contributions index the index for accessing the triangular matrix p here the 5' position of the gquad is stored q here the 3' position of the gquad is stored P the 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, | +
| + | + | paramT * | +P | +
| + | ) | ++ |
backtrack an interior loop like enclosed g-quadruplex with closing pair (i,j) with underlying Lfold matrix
+- Parameters:
-
+
+
+c The total contribution the loop should resemble i position i of enclosing pair j position j of enclosing pair type base pair type of enclosing pair (must be reverse type) S integer encoded sequence ggg triangular matrix containing g-quadruplex contributions p here the 5' position of the gquad is stored q here the 3' position of the gquad is stored P the datastructure containing the precalculated contibutions
+
- Returns:
- 1 on success, 0 if no gquad found
