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RNAlib-2.4.17
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Functions and data structures for handling of secondary structure hard constraints. More...
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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_WUSS 33554432U |
| Flag to indicate Washington University Secondary Structure (WUSS) notation of the hard constraint string. More... | |
| #define | VRNA_CONSTRAINT_DB_DEFAULT |
| Switch for dot-bracket structure constraint with default symbols. More... | |
| #define | VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (unsigned char)0x01 |
| Hard constraints flag, base pair in the exterior loop. | |
| #define | VRNA_CONSTRAINT_CONTEXT_HP_LOOP (unsigned char)0x02 |
| Hard constraints flag, base pair encloses hairpin loop. | |
| #define | VRNA_CONSTRAINT_CONTEXT_INT_LOOP (unsigned char)0x04 |
| Hard constraints flag, base pair encloses an interior loop. | |
| #define | VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (unsigned char)0x08 |
| Hard constraints flag, base pair encloses a multi branch loop. | |
| #define | VRNA_CONSTRAINT_CONTEXT_MB_LOOP (unsigned char)0x10 |
| Hard constraints flag, base pair is enclosed in an interior loop. | |
| #define | VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (unsigned char)0x20 |
| Hard constraints flag, base pair is enclosed in a multi branch loop. | |
| #define | VRNA_CONSTRAINT_CONTEXT_ENFORCE (unsigned char)0x40 |
| Hard constraint flag to indicate enforcement of constraints. | |
| #define | VRNA_CONSTRAINT_CONTEXT_NO_REMOVE (unsigned char)0x80 |
| Hard constraint flag to indicate not to remove base pairs that conflict with a given constraint. | |
| #define | VRNA_CONSTRAINT_CONTEXT_NONE (unsigned char)0 |
| Constraint context flag that forbids any loop. | |
| #define | VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS |
| Constraint context flag indicating base pairs that close any loop. | |
| #define | VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS |
| Constraint context flag indicating base pairs enclosed by any loop. | |
| #define | VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS |
| Constraint context flag indicating any loop context. | |
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 unsigned char() | vrna_callback_hc_evaluate(int i, int j, int k, int l, unsigned char d, void *data) |
| Callback to evaluate whether or not a particular decomposition step is contributing to the solution space. More... | |
Enumerations | |
| enum | vrna_hc_type_e { VRNA_HC_DEFAULT, VRNA_HC_WINDOW } |
| The hard constraints type. 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, unsigned 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... | |
| int | vrna_hc_add_bp (vrna_fold_compound_t *vc, int i, int j, unsigned 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, unsigned 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_add_f (vrna_fold_compound_t *vc, vrna_callback_hc_evaluate *f) |
| Add a function pointer pointer for the generic hard constraint feature. | |
| void | vrna_hc_add_data (vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *f) |
| Add an auxiliary data structure for the generic hard constraints callback function. 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)
| enum vrna_hc_type_e |
The hard constraints type.
Global and local structure prediction methods use a slightly different way to handle hard constraints internally. This enum is used to distinguish both types.
| Enumerator | |
|---|---|
| VRNA_HC_DEFAULT | Default Hard Constraints. |
| VRNA_HC_WINDOW | Hard Constraints suitable for local structure prediction using window approach. |
| void vrna_hc_add_data | ( | vrna_fold_compound_t * | vc, |
| void * | data, | ||
| vrna_callback_free_auxdata * | f | ||
| ) |
Add an auxiliary data structure for the generic hard constraints callback function.
| vc | The fold compound the generic hard constraint function should be bound to |
| data | A pointer to the data structure that holds required data for function 'f' |
| f | A pointer to a function that free's the memory occupied by data (Maybe NULL) |
| 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) |