1 #ifndef VIENNA_RNA_PACKAGE_EVAL_H 2 #define VIENNA_RNA_PACKAGE_EVAL_H 9 #ifdef VRNA_WARN_DEPRECATED 10 # if defined(__clang__) 11 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 12 # elif defined(__GNUC__) 13 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 15 # define DEPRECATED(func, msg) func 18 # define DEPRECATED(func, msg) func 56 #define VRNA_VERBOSITY_QUIET -1 62 #define VRNA_VERBOSITY_DEFAULT 1 92 const char *structure);
116 const char *structure);
133 const char *structure,
163 const char *structure,
273 const char *structure);
287 const char *structure);
308 const char *structure);
330 const char *structure);
348 const char *structure,
376 const char *structure,
397 const char *structure,
425 const char *structure,
451 const char *structure,
487 const char *structure);
506 const char *structure);
532 const char *structure);
558 const char *structure);
581 const char *structure,
610 const char *structure,
635 const char *structure,
667 const char *structure,
699 const char *structure,
805 int vrna_eval_consensus_structure_pt_simple_verbose(
const char **alignment,
811 vrna_eval_consensus_structure_pt_simple_v(
const char **alignment,
865 int verbosity_level);
903 const char *structure,
928 int vrna_eval_move_pt_simple(
const char *
string,
944 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 985 const char *structure,
986 int verbosity_level),
987 "Use vrna_eval_structure_simple() and vrna_eval_structure() instead");
1005 const char *structure,
1007 int verbosity_level),
1008 "Use vrna_eval_structure() instead");
1029 const char *structure,
1030 int verbosity_level),
1031 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
1049 const char *structure,
1051 int verbosity_level),
1052 "Use vrna_eval_structure() instead");
1055 DEPRECATED(
float energy_of_gquad_structure(
const char *
string,
1056 const char *structure,
1057 int verbosity_level),
1058 "Use vrna_eval_structure_simple() instead");
1060 DEPRECATED(
float energy_of_gquad_struct_par(
const char *
string,
1061 const char *structure,
1063 int verbosity_level),
1064 "Use vrna_eval_structure() instead");
1091 int verbosity_level),
1092 "Use vrna_eval_structure_pt_simple() and vrna_eval_structure_pt() instead");
1116 int verbosity_level),
1117 "Use vrna_eval_structure_pt() instead");
1137 const char *structure,
1140 "Use vrna_eval_move() instead");
1166 "Use vrna_eval_move_pt_simple() and vrna_eval_move_pt() instead");
1185 "Use vrna_eval_loop_pt() instead");
1202 const char *structure),
1203 "Use vrna_eval_structure_simple() instead");
1225 "Use vrna_eval_structure_pt_simple() instead");
1242 const char *structure),
1243 "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.
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.