1 #ifndef VIENNA_RNA_PACKAGE_EVAL_H 2 #define VIENNA_RNA_PACKAGE_EVAL_H 10 #ifdef VRNA_WARN_DEPRECATED 11 # if defined(__clang__) 12 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 13 # elif defined(__GNUC__) 14 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 16 # define DEPRECATED(func, msg) func 19 # define DEPRECATED(func, msg) func 57 #define VRNA_VERBOSITY_QUIET -1 63 #define VRNA_VERBOSITY_DEFAULT 1 93 const char *structure);
117 const char *structure);
134 const char *structure,
164 const char *structure,
171 const char *structure,
173 vrna_cstr_t output_stream);
280 const char *structure);
294 const char *structure);
315 const char *structure);
337 const char *structure);
355 const char *structure,
383 const char *structure,
404 const char *structure,
432 const char *structure,
458 const char *structure,
494 const char *structure);
513 const char *structure);
539 const char *structure);
565 const char *structure);
588 const char *structure,
617 const char *structure,
642 const char *structure,
674 const char *structure,
706 const char *structure,
812 int vrna_eval_consensus_structure_pt_simple_verbose(
const char **alignment,
818 vrna_eval_consensus_structure_pt_simple_v(
const char **alignment,
872 int verbosity_level);
910 const char *structure,
935 int vrna_eval_move_pt_simple(
const char *
string,
951 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 992 const char *structure,
993 int verbosity_level),
994 "Use vrna_eval_structure_simple() and vrna_eval_structure() instead");
1012 const char *structure,
1014 int verbosity_level),
1015 "Use vrna_eval_structure() instead");
1036 const char *structure,
1037 int verbosity_level),
1038 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
1056 const char *structure,
1058 int verbosity_level),
1059 "Use vrna_eval_structure() instead");
1062 DEPRECATED(
float energy_of_gquad_structure(
const char *
string,
1063 const char *structure,
1064 int verbosity_level),
1065 "Use vrna_eval_structure_simple() instead");
1067 DEPRECATED(
float energy_of_gquad_struct_par(
const char *
string,
1068 const char *structure,
1070 int verbosity_level),
1071 "Use vrna_eval_structure() instead");
1098 int verbosity_level),
1099 "Use vrna_eval_structure_pt_simple() and vrna_eval_structure_pt() instead");
1123 int verbosity_level),
1124 "Use vrna_eval_structure_pt() instead");
1144 const char *structure,
1147 "Use vrna_eval_move() instead");
1173 "Use vrna_eval_move_pt_simple() and vrna_eval_move_pt() instead");
1192 "Use vrna_eval_loop_pt() instead");
1209 const char *structure),
1210 "Use vrna_eval_structure_simple() instead");
1232 "Use vrna_eval_structure_pt_simple() instead");
1249 const char *structure),
1250 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
float vrna_eval_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the free energy of an already folded RNA.
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.
int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)
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 prin...
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.
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...
int vrna_eval_loop_pt_v(vrna_fold_compound_t *vc, int i, const short *pt, int verbosity_level)
Calculate energy of a loop.
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.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
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.
int eos_debug
verbose info from energy_of_struct
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:56
float energy_of_circ_struct(const char *string, const char *structure)
int loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a loop.
float vrna_eval_structure_simple(const char *string, const char *structure)
Calculate the free energy of an already folded RNA.
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.
Methods to compute the neighbors of an RNA secondary structure.
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)
int cut_point
first pos of second seq for cofolding
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.
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 ...
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 contribut...
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)
Various data structures and pre-processor macros.
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.
int vrna_eval_loop_pt(vrna_fold_compound_t *vc, int i, const short *pt)
Calculate energy of a loop.
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 contributio...
float vrna_eval_consensus_structure_simple(const char **alignment, const char *structure)
Calculate the free energy of an already folded RNA sequence alignment.
float energy_of_circ_structure(const char *string, const char *structure, int verbosity_level)
Calculate the free energy of an already folded circular RNA.
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.
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)
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.
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 structur...
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...
float energy_of_struct(const char *string, const char *structure)
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)
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 structur...
int vrna_eval_structure_pt_simple_verbose(const char *string, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
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.
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.
int vrna_eval_structure_pt_simple(const char *string, const short *pt)
Calculate the free energy of an already folded RNA.
Implementation of a dynamic, buffered character stream.
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...
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...
Functions to deal with sets of energy parameters.
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.
int vrna_eval_structure_pt(vrna_fold_compound_t *vc, const short *pt)
Calculate the free energy of an already folded RNA.
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 sequence...
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 contributio...
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 prin...
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.
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...
An atomic representation of the transition / move from one structure to its neighbor.
Definition: neighbor.h:156
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.