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 22 #define VRNA_VERBOSITY_QUIET -1 23 #define VRNA_VERBOSITY_DEFAULT 1 41 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 78 const char *structure);
102 const char *structure);
119 const char *structure,
149 const char *structure,
259 const char *structure);
273 const char *structure);
294 const char *structure);
316 const char *structure);
334 const char *structure,
362 const char *structure,
383 const char *structure,
411 const char *structure,
437 const char *structure,
473 const char *structure);
492 const char *structure);
518 const char *structure);
544 const char *structure);
567 const char *structure,
596 const char *structure,
621 const char *structure,
653 const char *structure,
685 const char *structure,
791 int vrna_eval_consensus_structure_pt_simple_verbose(
const char **alignment,
797 vrna_eval_consensus_structure_pt_simple_v(
const char **alignment,
837 int verbosity_level);
865 const char *structure,
890 int vrna_eval_move_pt_simple(
const char *
string,
905 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 934 const char *structure,
935 int verbosity_level),
936 "Use vrna_eval_structure_simple() and vrna_eval_structure() instead");
954 const char *structure,
956 int verbosity_level),
957 "Use vrna_eval_structure() instead");
978 const char *structure,
979 int verbosity_level),
980 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
998 const char *structure,
1000 int verbosity_level),
1001 "Use vrna_eval_structure() instead");
1004 DEPRECATED(
float energy_of_gquad_structure(
const char *
string,
1005 const char *structure,
1006 int verbosity_level),
1007 "Use vrna_eval_structure_simple() instead");
1009 DEPRECATED(
float energy_of_gquad_struct_par(
const char *
string,
1010 const char *structure,
1012 int verbosity_level),
1013 "Use vrna_eval_structure() instead");
1040 int verbosity_level),
1041 "Use vrna_eval_structure_pt_simple() and vrna_eval_structure_pt() instead");
1065 int verbosity_level),
1066 "Use vrna_eval_structure_pt() instead");
1086 const char *structure,
1089 "Use vrna_eval_move() instead");
1115 "Use vrna_eval_move_pt_simple() and vrna_eval_move_pt() instead");
1134 "Use vrna_eval_loop_pt() instead");
1151 const char *structure),
1152 "Use vrna_eval_structure_simple() instead");
1174 "Use vrna_eval_structure_pt_simple() instead");
1191 const char *structure),
1192 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
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.
float vrna_eval_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the free energy of an already folded RNA.
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 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.
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...
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.
float energy_of_struct(const char *string, const char *structure)
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:131
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.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:56
float vrna_eval_structure_simple(const char *string, const char *structure)
Calculate the free energy of an already folded RNA.
int cut_point
set to first pos of second seq for cofolding
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)
float energy_of_circ_structure(const char *string, const char *structure, int verbosity_level)
Calculate the free energy of an already folded circular RNA.
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)
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...
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 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_loop_pt_v(vrna_fold_compound_t *vc, int i, const short *pt, int verbosity_level)
Calculate energy of a loop.
Various data structures and pre-processor macros.
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_structure(const char *string, const char *structure, int verbosity_level)
Calculate the free energy of an already folded RNA using global model detail settings.
Functions to deal with sets of energy parameters.
float energy_of_circ_struct(const char *string, const char *structure)
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.
int vrna_eval_loop_pt(vrna_fold_compound_t *vc, int i, const short *pt)
Calculate energy of a loop.
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...
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...
int eos_debug
verbose info from energy_of_struct
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 loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a loop.
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 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.
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.
int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)
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