eval.h File Reference
Functions and variables related to energy evaluation of sequence/structure pairs. More...
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Macros | |
| #define | VRNA_VERBOSITY_QUIET -1 |
| Quiet level verbosity setting. | |
| #define | VRNA_VERBOSITY_DEFAULT 1 |
| Default level verbosity setting. | |
Functions | |
| int | vrna_eval_loop_pt (vrna_fold_compound_t *vc, int i, const short *pt) |
| Calculate energy of a loop. More... | |
| int | vrna_eval_loop_pt_v (vrna_fold_compound_t *vc, int i, const short *pt, int verbosity_level) |
| Calculate energy of a loop. More... | |
| float | vrna_eval_move (vrna_fold_compound_t *vc, const char *structure, int m1, int m2) |
| Calculate energy of a move (closing or opening of a base pair) More... | |
| int | vrna_eval_move_pt (vrna_fold_compound_t *vc, short *pt, int m1, int m2) |
| Calculate energy of a move (closing or opening of a base pair) More... | |
| float | energy_of_structure (const char *string, const char *structure, int verbosity_level) |
| Calculate the free energy of an already folded RNA using global model detail settings. More... | |
| float | energy_of_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level) |
| Calculate the free energy of an already folded RNA. More... | |
| float | energy_of_circ_structure (const char *string, const char *structure, int verbosity_level) |
| Calculate the free energy of an already folded circular RNA. More... | |
| float | energy_of_circ_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level) |
| Calculate the free energy of an already folded circular RNA. More... | |
| int | energy_of_structure_pt (const char *string, short *ptable, short *s, short *s1, int verbosity_level) |
| Calculate the free energy of an already folded RNA. More... | |
| int | energy_of_struct_pt_par (const char *string, short *ptable, short *s, short *s1, vrna_param_t *parameters, int verbosity_level) |
| Calculate the free energy of an already folded RNA. More... | |
| float | energy_of_move (const char *string, const char *structure, int m1, int m2) |
| Calculate energy of a move (closing or opening of a base pair) More... | |
| int | energy_of_move_pt (short *pt, short *s, short *s1, int m1, int m2) |
| Calculate energy of a move (closing or opening of a base pair) More... | |
| int | loop_energy (short *ptable, short *s, short *s1, int i) |
| Calculate energy of a loop. More... | |
| float | energy_of_struct (const char *string, const char *structure) |
| int | energy_of_struct_pt (const char *string, short *ptable, short *s, short *s1) |
| float | energy_of_circ_struct (const char *string, const char *structure) |
Basic Energy Evaluation Interface with Dot-Bracket Structure String | |
| float | vrna_eval_structure (vrna_fold_compound_t *vc, const char *structure) |
| Calculate the free energy of an already folded RNA. More... | |
| float | vrna_eval_covar_structure (vrna_fold_compound_t *vc, const char *structure) |
| Calculate the pseudo energy derived by the covariance scores of a set of aligned sequences. More... | |
| float | vrna_eval_structure_verbose (vrna_fold_compound_t *vc, const char *structure, FILE *file) |
| Calculate the free energy of an already folded RNA and print contributions on a per-loop base. More... | |
| float | vrna_eval_structure_v (vrna_fold_compound_t *vc, const char *structure, int verbosity_level, FILE *file) |
| Calculate the free energy of an already folded RNA and print contributions on a per-loop base. More... | |
| float | vrna_eval_structure_cstr (vrna_fold_compound_t *vc, const char *structure, int verbosity_level, vrna_cstr_t output_stream) |
Basic Energy Evaluation Interface with Structure Pair Table | |
| int | vrna_eval_structure_pt (vrna_fold_compound_t *vc, const short *pt) |
| Calculate the free energy of an already folded RNA. More... | |
| int | vrna_eval_structure_pt_verbose (vrna_fold_compound_t *vc, const short *pt, FILE *file) |
| Calculate the free energy of an already folded RNA. More... | |
| int | vrna_eval_structure_pt_v (vrna_fold_compound_t *vc, const short *pt, int verbosity_level, FILE *file) |
| Calculate the free energy of an already folded RNA. More... | |
Simplified Energy Evaluation with Sequence and Dot-Bracket Strings | |
| float | vrna_eval_structure_simple (const char *string, const char *structure) |
| Calculate the free energy of an already folded RNA. More... | |
| float | vrna_eval_circ_structure (const char *string, const char *structure) |
| Evaluate the free energy of a sequence/structure pair where the sequence is circular. More... | |
| float | vrna_eval_gquad_structure (const char *string, const char *structure) |
| Evaluate the free energy of a sequence/structure pair where the structure may contain G-Quadruplexes. More... | |
| float | vrna_eval_circ_gquad_structure (const char *string, const char *structure) |
| Evaluate the free energy of a sequence/structure pair where the sequence is circular and the structure may contain G-Quadruplexes. More... | |
| float | vrna_eval_structure_simple_verbose (const char *string, const char *structure, FILE *file) |
| Calculate the free energy of an already folded RNA and print contributions per loop. More... | |
| float | vrna_eval_structure_simple_v (const char *string, const char *structure, int verbosity_level, FILE *file) |
| Calculate the free energy of an already folded RNA and print contributions per loop. More... | |
| float | vrna_eval_circ_structure_v (const char *string, const char *structure, int verbosity_level, FILE *file) |
| Evaluate free energy of a sequence/structure pair, assume sequence to be circular and print contributions per loop. More... | |
| float | vrna_eval_gquad_structure_v (const char *string, const char *structure, int verbosity_level, FILE *file) |
| Evaluate free energy of a sequence/structure pair, allow for G-Quadruplexes in the structure and print contributions per loop. More... | |
| float | vrna_eval_circ_gquad_structure_v (const char *string, const char *structure, int verbosity_level, FILE *file) |
| Evaluate free energy of a sequence/structure pair, assume sequence to be circular, allow for G-Quadruplexes in the structure, and print contributions per loop. More... | |
Simplified Energy Evaluation with Sequence Alignments and Consensus Structure Dot-Bracket String | |
| float | vrna_eval_consensus_structure_simple (const char **alignment, const char *structure) |
| Calculate the free energy of an already folded RNA sequence alignment. More... | |
| float | vrna_eval_circ_consensus_structure (const char **alignment, const char *structure) |
| Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the sequences are circular. More... | |
| float | vrna_eval_gquad_consensus_structure (const char **alignment, const char *structure) |
| Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the structure may contain G-Quadruplexes. More... | |
| float | vrna_eval_circ_gquad_consensus_structure (const char **alignment, const char *structure) |
| Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the sequence is circular and the structure may contain G-Quadruplexes. More... | |
| float | vrna_eval_consensus_structure_simple_verbose (const char **alignment, const char *structure, FILE *file) |
| Evaluate the free energy of a consensus structure for an RNA sequence alignment and print contributions per loop. More... | |
| float | vrna_eval_consensus_structure_simple_v (const char **alignment, const char *structure, int verbosity_level, FILE *file) |
| Evaluate the free energy of a consensus structure for an RNA sequence alignment and print contributions per loop. More... | |
| float | vrna_eval_circ_consensus_structure_v (const char **alignment, const char *structure, int verbosity_level, FILE *file) |
| Evaluate the free energy of a consensus structure for an alignment of circular RNA sequences and print contributions per loop. More... | |
| float | vrna_eval_gquad_consensus_structure_v (const char **alignment, const char *structure, int verbosity_level, FILE *file) |
| Evaluate the free energy of a consensus structure for an RNA sequence alignment, allow for annotated G-Quadruplexes in the structure and print contributions per loop. More... | |
| float | vrna_eval_circ_gquad_consensus_structure_v (const char **alignment, const char *structure, int verbosity_level, FILE *file) |
| Evaluate the free energy of a consensus structure for an alignment of circular RNA sequences, allow for annotated G-Quadruplexes in the structure and print contributions per loop. More... | |
Simplified Energy Evaluation with Sequence String and Structure Pair Table | |
| int | vrna_eval_structure_pt_simple (const char *string, const short *pt) |
| Calculate the free energy of an already folded RNA. More... | |
| int | vrna_eval_structure_pt_simple_verbose (const char *string, const short *pt, FILE *file) |
| Calculate the free energy of an already folded RNA. More... | |
| int | vrna_eval_structure_pt_simple_v (const char *string, const short *pt, int verbosity_level, FILE *file) |
| Calculate the free energy of an already folded RNA. More... | |
Simplified Energy Evaluation with Sequence Alignment and Consensus Structure Pair Table | |
| int | vrna_eval_consensus_structure_pt_simple (const char **alignment, const short *pt) |
| Evaluate the Free Energy of a Consensus Secondary Structure given a Sequence Alignment. More... | |
| int | vrna_eval_consensus_structure_pt_simple_verbose (const char **alignment, const short *pt, FILE *file) |
| int | vrna_eval_consensus_structure_pt_simple_v (const char **alignment, const short *pt, int verbosity_level, FILE *file) |
Variables | |
| int | cut_point |
| first pos of second seq for cofolding | |
| int | eos_debug |
| verbose info from energy_of_struct | |
Detailed Description
Functions and variables related to energy evaluation of sequence/structure pairs.
