RNAlib-2.2.7
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Functions and data structures for handling of secondary structure hard constraints. More...
Go to the source code of this file.
Data Structures | |
struct | vrna_hc_s |
The hard constraints data structure. More... | |
struct | vrna_hc_up_s |
A single hard constraint for a single nucleotide. More... | |
Macros | |
#define | VRNA_CONSTRAINT_NO_HEADER 0 |
do not print the header information line More... | |
#define | VRNA_CONSTRAINT_DB 16384U |
Flag for vrna_constraints_add() to indicate that constraint is passed in pseudo dot-bracket notation. More... | |
#define | VRNA_CONSTRAINT_DB_ENFORCE_BP 32768U |
Switch for dot-bracket structure constraint to enforce base pairs. More... | |
#define | VRNA_CONSTRAINT_DB_PIPE 65536U |
Flag that is used to indicate the pipe '|' sign in pseudo dot-bracket notation of hard constraints. More... | |
#define | VRNA_CONSTRAINT_DB_DOT 131072U |
dot '.' switch for structure constraints (no constraint at all) More... | |
#define | VRNA_CONSTRAINT_DB_X 262144U |
'x' switch for structure constraint (base must not pair) More... | |
#define | VRNA_CONSTRAINT_DB_ANG_BRACK 524288U |
angle brackets '<', '>' switch for structure constraint (paired downstream/upstream) More... | |
#define | VRNA_CONSTRAINT_DB_RND_BRACK 1048576U |
round brackets '(',')' switch for structure constraint (base i pairs base j) More... | |
#define | VRNA_CONSTRAINT_DB_INTRAMOL 2097152U |
Flag that is used to indicate the character 'l' in pseudo dot-bracket notation of hard constraints. More... | |
#define | VRNA_CONSTRAINT_DB_INTERMOL 4194304U |
Flag that is used to indicate the character 'e' in pseudo dot-bracket notation of hard constraints. More... | |
#define | VRNA_CONSTRAINT_DB_GQUAD 8388608U |
'+' switch for structure constraint (base is involved in a gquad) More... | |
#define | VRNA_CONSTRAINT_DB_DEFAULT |
Switch for dot-bracket structure constraint with default symbols. More... | |
#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. | |
Typedefs | |
typedef struct vrna_hc_s | vrna_hc_t |
Typename for the hard constraints data structure vrna_hc_s. | |
typedef struct vrna_hc_up_s | vrna_hc_up_t |
Typename for the single nucleotide hard constraint data structure vrna_hc_up_s. | |
typedef char( | vrna_callback_hc_evaluate) (int i, int j, int k, int l, char d, void *data) |
Callback to evaluate whether or not a particular decomposition step is contributing to the solution space. More... | |
Functions | |
void | vrna_message_constraint_options (unsigned int option) |
Print a help message for pseudo dot-bracket structure constraint characters to stdout. (constraint support is specified by option parameter) More... | |
void | vrna_message_constraint_options_all (void) |
Print structure constraint characters to stdout (full constraint support) More... | |
void | vrna_hc_init (vrna_fold_compound_t *vc) |
Initialize/Reset hard constraints to default values. More... | |
void | vrna_hc_add_up (vrna_fold_compound_t *vc, int i, char option) |
Make a certain nucleotide unpaired. More... | |
int | vrna_hc_add_up_batch (vrna_fold_compound_t *vc, vrna_hc_up_t *constraints) |
Apply a list of hard constraints for single nucleotides. More... | |
void | vrna_hc_add_bp (vrna_fold_compound_t *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_t *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... | |
int | vrna_hc_add_from_db (vrna_fold_compound_t *vc, const char *constraint, unsigned int options) |
Add hard constraints from pseudo dot-bracket notation. More... | |
void | print_tty_constraint (unsigned int option) |
Print structure constraint characters to stdout. (constraint support is specified by option parameter) More... | |
void | print_tty_constraint_full (void) |
Print structure constraint characters to stdout (full constraint support) More... | |
void | constrain_ptypes (const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type) |
Insert constraining pair types according to constraint structure string. More... | |
Functions and data structures for handling of secondary structure hard constraints.
#define VRNA_CONSTRAINT_NO_HEADER 0 |
do not print the header information line
#define VRNA_CONSTRAINT_DB_ANG_BRACK 524288U |
angle brackets '<', '>' switch for structure constraint (paired downstream/upstream)
void print_tty_constraint | ( | unsigned int | option | ) |
Print structure constraint characters to stdout. (constraint support is specified by option parameter)
option | Option switch that tells which constraint help will be printed |
void print_tty_constraint_full | ( | void | ) |
Print structure constraint characters to stdout (full constraint support)
void constrain_ptypes | ( | const char * | constraint, |
unsigned int | length, | ||
char * | ptype, | ||
int * | BP, | ||
int | min_loop_size, | ||
unsigned int | idx_type | ||
) |
Insert constraining pair types according to constraint structure string.
constraint | The structure constraint string |
length | The actual length of the sequence (constraint may be shorter) |
ptype | A pointer to the basepair type array |
BP | (not used anymore) |
min_loop_size | The minimal loop size (usually TURN ) |
idx_type | Define the access type for base pair type array (0 = indx, 1 = iindx) |