1#ifndef VIENNA_RNA_PACKAGE_EVAL_H
2#define VIENNA_RNA_PACKAGE_EVAL_H
11#ifdef VRNA_WARN_DEPRECATED
12# if defined(__clang__)
13# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
14# elif defined(__GNUC__)
15# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
17# define DEPRECATED(func, msg) func
20# define DEPRECATED(func, msg) func
58#define VRNA_VERBOSITY_QUIET -1
64#define VRNA_VERBOSITY_DEFAULT 1
95 const char *structure);
120 const char *structure);
138 const char *structure,
169 const char *structure,
176 const char *structure,
178 vrna_cstr_t output_stream);
290 const char *structure);
305 const char *structure);
327 const char *structure);
350 const char *structure);
369 const char *structure,
398 const char *structure,
420 const char *structure,
449 const char *structure,
476 const char *structure,
513 const char *structure);
533 const char *structure);
560 const char *structure);
587 const char *structure);
611 const char *structure,
641 const char *structure,
667 const char *structure,
700 const char *structure,
733 const char *structure,
906 int verbosity_level);
946 const char *structure,
974vrna_eval_move_pt_simple(
const char *
string,
990#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
1031 const char *structure,
1032 int verbosity_level),
1033 "Use vrna_eval_structure_simple() and vrna_eval_structure() instead");
1051 const char *structure,
1053 int verbosity_level),
1054 "Use vrna_eval_structure() instead");
1075 const char *structure,
1076 int verbosity_level),
1077 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
1095 const char *structure,
1097 int verbosity_level),
1098 "Use vrna_eval_structure() instead");
1101DEPRECATED(
float energy_of_gquad_structure(
const char *
string,
1102 const char *structure,
1103 int verbosity_level),
1104 "Use vrna_eval_structure_simple() instead");
1106DEPRECATED(
float energy_of_gquad_struct_par(
const char *
string,
1107 const char *structure,
1109 int verbosity_level),
1110 "Use vrna_eval_structure() instead");
1137 int verbosity_level),
1138 "Use vrna_eval_structure_pt_simple() and vrna_eval_structure_pt() instead");
1162 int verbosity_level),
1163 "Use vrna_eval_structure_pt() instead");
1183 const char *structure,
1186 "Use vrna_eval_move() instead");
1212 "Use vrna_eval_move_pt_simple() and vrna_eval_move_pt() instead");
1231 "Use vrna_eval_loop_pt() instead");
1249 const char *structure),
1250 "Use vrna_eval_structure_simple() instead");
1273 "Use vrna_eval_structure_pt_simple() instead");
1291 const char *structure),
1292 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
Various data structures and pre-processor macros.
Implementation of a dynamic, buffered character stream.
The Basic Fold Compound API.
The datastructure that contains temperature scaled energy parameters.
Definition basic.h:57
int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)
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_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.
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)
int loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a loop.
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)
int eos_debug
verbose info from energy_of_struct
float energy_of_circ_struct(const char *string, const char *structure)
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 cut_point
first pos of second seq for cofolding
float energy_of_struct(const char *string, const char *structure)
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 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 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.
int vrna_eval_loop_pt(vrna_fold_compound_t *fc, int i, const short *pt)
Calculate energy of a loop.
int vrna_eval_loop_pt_v(vrna_fold_compound_t *fc, int i, const short *pt, int verbosity_level)
Calculate energy of a loop.
int vrna_eval_move_pt(vrna_fold_compound_t *fc, short *pt, int m1, int m2)
Calculate energy of a move (closing or opening of a base pair)
float vrna_eval_move(vrna_fold_compound_t *fc, const char *structure, int m1, int m2)
Calculate energy of a move (closing or opening of a base pair)
float vrna_eval_structure(vrna_fold_compound_t *fc, const char *structure)
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.
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...
int vrna_eval_structure_pt_v(vrna_fold_compound_t *fc, const short *pt, int verbosity_level, FILE *file)
Calculate the free energy of an already folded RNA.
int vrna_eval_consensus_structure_pt_simple_verbose(const char **alignment, const short *pt, FILE *file)
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.
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 vrna_eval_structure_verbose(vrna_fold_compound_t *fc, 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_covar_structure(vrna_fold_compound_t *fc, const char *structure)
Calculate the pseudo energy derived by the covariance scores of a set of aligned sequences.
int vrna_eval_structure_pt_simple_verbose(const char *string, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
float vrna_eval_consensus_structure_simple(const char **alignment, const char *structure)
Calculate the free energy of an already folded RNA sequence alignment.
float vrna_eval_structure_simple(const char *string, const char *structure)
Calculate the free energy of an already folded RNA.
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_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_verbose(vrna_fold_compound_t *fc, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
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,...
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_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_structure_pt_simple_v(const char *string, const short *pt, int verbosity_level, FILE *file)
Calculate the free energy of an already folded RNA.
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...
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_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_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_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_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...
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 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_structure_v(vrna_fold_compound_t *fc, 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.
int vrna_eval_consensus_structure_pt_simple_v(const char **alignment, const short *pt, int verbosity_level, FILE *file)
int vrna_eval_structure_pt(vrna_fold_compound_t *fc, const short *pt)
Calculate the free energy of an already folded RNA.
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.
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
An atomic representation of the transition / move from one structure to its neighbor.
Definition move.h:78
Methods to operate with structural neighbors of RNA secondary structures.
Functions to deal with sets of energy parameters.