RNAlib-2.2.0-RC3
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Data Structures | |
struct | vrna_hc_t |
The hard constraints data structure. More... | |
Macros | |
#define | VRNA_CONSTRAINT_MULTILINE 32U |
constraint may span over several lines | |
#define | VRNA_CONSTRAINT_NO_HEADER 64U |
do not print the header information line | |
#define | VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (char)0x01 |
Hard constraints flag, base pair in the exterior loop. | |
#define | VRNA_CONSTRAINT_CONTEXT_HP_LOOP (char)0x02 |
Hard constraints flag, base pair encloses hairpin loop. | |
#define | VRNA_CONSTRAINT_CONTEXT_INT_LOOP (char)0x04 |
Hard constraints flag, base pair encloses an interior loop. | |
#define | VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (char)0x08 |
Hard constraints flag, base pair encloses a multi branch loop. | |
#define | VRNA_CONSTRAINT_CONTEXT_MB_LOOP (char)0x10 |
Hard constraints flag, base pair is enclosed in an interior loop. | |
#define | VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (char)0x20 |
Hard constraints flag, base pair is enclosed in a multi branch loop. | |
#define | VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS |
Hard constraints flag, shortcut for all base pairs. | |
Functions | |
void | vrna_hc_init (vrna_fold_compound *vc) |
Initialize/Reset hard constraints to default values. More... | |
void | vrna_hc_add_up (vrna_fold_compound *vc, int i, char option) |
Make a certain nucleotide unpaired. More... | |
void | vrna_hc_add_bp (vrna_fold_compound *vc, int i, int j, char option) |
Favorize/Enforce a certain base pair (i,j) More... | |
void | vrna_hc_add_bp_nonspecific (vrna_fold_compound *vc, int i, int d, char option) |
Enforce a nucleotide to be paired (upstream/downstream) More... | |
void | vrna_hc_free (vrna_hc_t *hc) |
Free the memory allocated by a vrna_hc_t data structure. More... | |
void vrna_hc_init | ( | vrna_fold_compound * | vc | ) |
Initialize/Reset hard constraints to default values.
This function resets the hard constraints to their default values, i.e. all positions may be unpaired in all contexts, and base pairs are allowed in all contexts, if they resemble canonical pairs. Previously set hard constraints will be removed vefore initialization.
vc | The fold compound |
void vrna_hc_add_up | ( | vrna_fold_compound * | vc, |
int | i, | ||
char | option | ||
) |
Make a certain nucleotide unpaired.
vc | The vrna_fold_compound the hard constraints are associated with |
i | The position that needs to stay unpaired (1-based) |
option | The options flag indicating how/where to store the hard constraints |
void vrna_hc_add_bp | ( | vrna_fold_compound * | vc, |
int | i, | ||
int | j, | ||
char | option | ||
) |
Favorize/Enforce a certain base pair (i,j)
vc | The vrna_fold_compound the hard constraints are associated with |
i | The 5' located nucleotide position of the base pair (1-based) |
j | The 3' located nucleotide position of the base pair (1-based) |
option | The options flag indicating how/where to store the hard constraints |
void vrna_hc_add_bp_nonspecific | ( | vrna_fold_compound * | vc, |
int | i, | ||
int | d, | ||
char | option | ||
) |
Enforce a nucleotide to be paired (upstream/downstream)
vc | The vrna_fold_compound the hard constraints are associated with |
i | The position that needs to stay unpaired (1-based) |
d | The direction of base pairing ( ![]() ![]() ![]() |
option | The options flag indicating in which loop type context the pairs may appear |