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#define | VRNA_CONSTRAINT_DB_PIPE 1U |
| Flag that is used to indicate the pipe '|' sign in pseudo dot-bracket notation of hard constraints. More...
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#define | VRNA_CONSTRAINT_DB_DOT 2U |
| dot '.' switch for structure constraints (no constraint at all) More...
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#define | VRNA_CONSTRAINT_DB_X 4U |
| 'x' switch for structure constraint (base must not pair) More...
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#define | VRNA_CONSTRAINT_DB_ANG_BRACK 8U |
| angle brackets '<', '>' switch for structure constraint (paired downstream/upstream) More...
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#define | VRNA_CONSTRAINT_DB_RND_BRACK 16U |
| round brackets '(',')' switch for structure constraint (base i pairs base j) More...
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#define | VRNA_CONSTRAINT_DB_INTRAMOL 2048U |
| Flag that is used to indicate the character 'l' in pseudo dot-bracket notation of hard constraints. More...
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#define | VRNA_CONSTRAINT_DB_INTERMOL 4096U |
| Flag that is used to indicate the character 'e' in pseudo dot-bracket notation of hard constraints. More...
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#define | VRNA_CONSTRAINT_DB_GQUAD 8192U |
| '+' switch for structure constraint (base is involved in a gquad) More...
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#define | VRNA_CONSTRAINT_DB_ENFORCE_BP 16384U |
| Switch for dot-bracket structure constraint to enforce base pairs. More...
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#define | VRNA_CONSTRAINT_MULTILINE 32U |
| constraint may span over several lines
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#define | VRNA_CONSTRAINT_NO_HEADER 64U |
| do not print the header information line
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#define | VRNA_CONSTRAINT_ALL 128U |
| placeholder for all constraining characters
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#define | VRNA_CONSTRAINT_DB 256U |
| Flag for vrna_constraints_add() to indicate that constraint is passed in pseudo dot-bracket notation. More...
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#define | VRNA_CONSTRAINT_FILE 512U |
| Flag for vrna_constraints_add() to indicate that constraints are present in a text file. More...
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#define | VRNA_CONSTRAINT_SOFT_MFE 8192U |
| Soft constraints flag, apply constraints for MFE calculations.
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#define | VRNA_CONSTRAINT_SOFT_PF 16384U |
| Soft constraints flag, apply constraints for partition function calculations.
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#define | VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (char)0x01 |
| Hard constraints flag, base pair in the exterior loop.
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#define | VRNA_CONSTRAINT_CONTEXT_HP_LOOP (char)0x02 |
| Hard constraints flag, base pair encloses hairpin loop.
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#define | VRNA_CONSTRAINT_CONTEXT_INT_LOOP (char)0x04 |
| Hard constraints flag, base pair encloses an interior loop.
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#define | VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (char)0x08 |
| Hard constraints flag, base pair encloses a multi branch loop.
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#define | VRNA_CONSTRAINT_CONTEXT_MB_LOOP (char)0x10 |
| Hard constraints flag, base pair is enclosed in an interior loop.
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#define | VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (char)0x20 |
| Hard constraints flag, base pair is enclosed in a multi branch loop.
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#define | VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS |
| Hard constraints flag, shortcut for all base pairs.
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#define | VRNA_DECOMP_PAIR_HP 1 |
| Generalized constraint folding flag indicating hairpin loop decomposition step.
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#define | VRNA_DECOMP_PAIR_IL 2 |
| Generalized constraint folding flag indicating interior loop decomposition step.
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typedef struct vrna_hc_s | vrna_hc_t |
| Typename for the hard constraints data structure vrna_hc_s.
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typedef struct vrna_sc_s | vrna_sc_t |
| Typename for the soft constraints data structure vrna_sc_s.
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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...
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typedef int( | vrna_callback_sc_energy) (int i, int j, int k, int l, char d, void *data) |
| Callback to retrieve pseudo energy contribution for soft constraint feature. More...
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typedef FLT_OR_DBL( | vrna_callback_sc_exp_energy) (int i, int j, int k, int l, char d, void *data) |
| Callback to retrieve pseudo energy contribution as Boltzmann Factors for soft constraint feature. More...
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typedef vrna_basepair_t *( | vrna_callback_sc_backtrack) (int i, int j, int k, int l, char d, void *data) |
| Callback to retrieve auxiliary base pairs for soft constraint feature. More...
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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...
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void | vrna_message_constraint_options_all (void) |
| Print structure constraint characters to stdout (full constraint support) More...
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void | vrna_constraints_add (vrna_fold_compound_t *vc, const char *constraint, unsigned int options) |
| Add constraints to a vrna_fold_compound_t data structure. More...
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void | vrna_hc_init (vrna_fold_compound_t *vc) |
| Initialize/Reset hard constraints to default values. More...
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void | vrna_hc_add_up (vrna_fold_compound_t *vc, int i, char option) |
| Make a certain nucleotide unpaired. More...
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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...
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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...
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void | vrna_hc_free (vrna_hc_t *hc) |
| Free the memory allocated by a vrna_hc_t data structure. More...
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void | vrna_sc_init (vrna_fold_compound_t *vc) |
| Initialize an empty soft constraints data structure within a vrna_fold_compound_t. More...
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void | vrna_sc_add_bp (vrna_fold_compound_t *vc, const FLT_OR_DBL **constraints, unsigned int options) |
| Add soft constraints for paired nucleotides. More...
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void | vrna_sc_add_up (vrna_fold_compound_t *vc, const FLT_OR_DBL *constraints, unsigned int options) |
| Add soft constraints for unpaired nucleotides. More...
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void | vrna_sc_remove (vrna_fold_compound_t *vc) |
| Remove soft constraints from vrna_fold_compound_t. More...
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void | vrna_sc_free (vrna_sc_t *sc) |
| Free memory occupied by a vrna_sc_t data structure. More...
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int | vrna_sc_add_SHAPE_deigan (vrna_fold_compound_t *vc, const double *reactivities, double m, double b, unsigned int options) |
| Add SHAPE reactivity data as soft constraints (Deigan et al. method) More...
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int | vrna_sc_add_SHAPE_deigan_ali (vrna_fold_compound_t *vc, const char **shape_files, const int *shape_file_association, double m, double b, unsigned int options) |
| Add SHAPE reactivity data from files as soft constraints for consensus structure prediction (Deigan et al. method) More...
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int | vrna_sc_add_SHAPE_zarringhalam (vrna_fold_compound_t *vc, const double *reactivities, double b, double default_value, const char *shape_conversion, unsigned int options) |
| Add SHAPE reactivity data as soft constraints (Zarringhalam et al. method) More...
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int | vrna_sc_SHAPE_parse_method (const char *method_string, char *method, float *param_1, float *param_2) |
| Parse a character string and extract the encoded SHAPE reactivity conversion method and possibly the parameters for conversion into pseudo free energies. More...
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int | vrna_sc_SHAPE_to_pr (const char *shape_conversion, double *values, int length, double default_value) |
| Convert SHAPE reactivity values to probabilities for being unpaired. More...
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void | vrna_sc_add_f (vrna_fold_compound_t *vc, vrna_callback_sc_energy *f) |
| Bind a function pointer for generalized soft constraint feature (MFE version) More...
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void | vrna_sc_add_bt (vrna_fold_compound_t *vc, vrna_callback_sc_backtrack *f) |
| Bind a backtracking function pointer for generalized soft constraint feature. More...
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void | vrna_sc_add_exp_f (vrna_fold_compound_t *vc, vrna_callback_sc_exp_energy *exp_f) |
| Bind a function pointer for generalized soft constraint feature (PF version) More...
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void | print_tty_constraint (unsigned int option) |
| Print structure constraint characters to stdout. (constraint support is specified by option parameter) More...
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void | print_tty_constraint_full (void) |
| Print structure constraint characters to stdout (full constraint support) More...
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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...
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