RNAlib-2.5.1
eval.h
Go to the documentation of this file.
1#ifndef VIENNA_RNA_PACKAGE_EVAL_H
2#define VIENNA_RNA_PACKAGE_EVAL_H
3
4#include <stdio.h>
9#include <ViennaRNA/params/basic.h> /* for deprecated functions */
10
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)))
16# else
17# define DEPRECATED(func, msg) func
18# endif
19#else
20# define DEPRECATED(func, msg) func
21#endif
22
23
58#define VRNA_VERBOSITY_QUIET -1
59
60
64#define VRNA_VERBOSITY_DEFAULT 1
65
66
93float
95 const char *structure);
96
97
118float
120 const char *structure);
121
122
136float
138 const char *structure,
139 FILE *file);
140
141
167float
169 const char *structure,
170 int verbosity_level,
171 FILE *file);
172
173
174float
175vrna_eval_structure_cstr(vrna_fold_compound_t *fc,
176 const char *structure,
177 int verbosity_level,
178 vrna_cstr_t output_stream);
179
180
181/* End basic eval interface */
208int
210 const short *pt);
211
212
226int
228 const short *pt,
229 FILE *file);
230
231
257int
259 const short *pt,
260 int verbosity_level,
261 FILE *file);
262
263
264/* End basic eval interface with pair table */
288float
289vrna_eval_structure_simple(const char *string,
290 const char *structure);
291
292
303float
304vrna_eval_circ_structure(const char *string,
305 const char *structure);
306
307
325float
326vrna_eval_gquad_structure(const char *string,
327 const char *structure);
328
329
348float
350 const char *structure);
351
352
367float
369 const char *structure,
370 FILE *file);
371
372
396float
398 const char *structure,
399 int verbosity_level,
400 FILE *file);
401
402
418float
419vrna_eval_circ_structure_v(const char *string,
420 const char *structure,
421 int verbosity_level,
422 FILE *file);
423
424
447float
449 const char *structure,
450 int verbosity_level,
451 FILE *file);
452
453
474float
476 const char *structure,
477 int verbosity_level,
478 FILE *file);
479
480
481/* End simplified eval interface */
511float
513 const char *structure);
514
515
531float
533 const char *structure);
534
535
558float
560 const char *structure);
561
562
585float
587 const char *structure);
588
589
609float
611 const char *structure,
612 FILE *file);
613
614
639float
641 const char *structure,
642 int verbosity_level,
643 FILE *file);
644
645
665float
667 const char *structure,
668 int verbosity_level,
669 FILE *file);
670
671
698float
700 const char *structure,
701 int verbosity_level,
702 FILE *file);
703
704
731float
733 const char *structure,
734 int verbosity_level,
735 FILE *file);
736
737
738/* End simplified comparative eval interface */
761int
763 const short *pt);
764
765
779int
781 const short *pt,
782 FILE *file);
783
784
809int
811 const short *pt,
812 int verbosity_level,
813 FILE *file);
814
815
816/* End simplified eval interface with pair table */
838int
840 const short *pt);
841
842
843int
845 const short *pt,
846 FILE *file);
847
848
849int
851 const short *pt,
852 int verbosity_level,
853 FILE *file);
854
855
856/* End simplified eval interface with pair table */
887int
889 int i,
890 const short *pt);
891
892
902int
904 int i,
905 const short *pt,
906 int verbosity_level);
907
908
943float
945 const char *structure,
946 int m1,
947 int m2);
948
949
964int
966 short *pt,
967 int m1,
968 int m2);
969
970
971int
972vrna_eval_move_pt_simple(const char *string,
973 short *pt,
974 int m1,
975 int m2);
976
977
978int
979vrna_eval_move_shift_pt(vrna_fold_compound_t *fc,
980 vrna_move_t *m,
981 short *structure);
982
983
988#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
989
1003extern int cut_point;
1004
1008extern int eos_debug;
1009
1028DEPRECATED(float energy_of_structure(const char *string,
1029 const char *structure,
1030 int verbosity_level),
1031 "Use vrna_eval_structure_simple() and vrna_eval_structure() instead");
1032
1048DEPRECATED(float energy_of_struct_par(const char *string,
1049 const char *structure,
1050 vrna_param_t *parameters,
1051 int verbosity_level),
1052 "Use vrna_eval_structure() instead");
1053
1072DEPRECATED(float energy_of_circ_structure(const char *string,
1073 const char *structure,
1074 int verbosity_level),
1075 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
1076
1092DEPRECATED(float energy_of_circ_struct_par(const char *string,
1093 const char *structure,
1094 vrna_param_t *parameters,
1095 int verbosity_level),
1096 "Use vrna_eval_structure() instead");
1097
1098
1099DEPRECATED(float energy_of_gquad_structure(const char *string,
1100 const char *structure,
1101 int verbosity_level),
1102 "Use vrna_eval_structure_simple() instead");
1103
1104DEPRECATED(float energy_of_gquad_struct_par(const char *string,
1105 const char *structure,
1106 vrna_param_t *parameters,
1107 int verbosity_level),
1108 "Use vrna_eval_structure() instead");
1109
1110
1131DEPRECATED(int energy_of_structure_pt(const char *string,
1132 short *ptable,
1133 short *s,
1134 short *s1,
1135 int verbosity_level),
1136 "Use vrna_eval_structure_pt_simple() and vrna_eval_structure_pt() instead");
1137
1155DEPRECATED(int energy_of_struct_pt_par(const char *string,
1156 short *ptable,
1157 short *s,
1158 short *s1,
1159 vrna_param_t *parameters,
1160 int verbosity_level),
1161 "Use vrna_eval_structure_pt() instead");
1162
1163
1180DEPRECATED(float energy_of_move(const char *string,
1181 const char *structure,
1182 int m1,
1183 int m2),
1184 "Use vrna_eval_move() instead");
1185
1186
1205DEPRECATED(int energy_of_move_pt(short *pt,
1206 short *s,
1207 short *s1,
1208 int m1,
1209 int m2),
1210 "Use vrna_eval_move_pt_simple() and vrna_eval_move_pt() instead");
1211
1225DEPRECATED(int loop_energy(short *ptable,
1226 short *s,
1227 short *s1,
1228 int i),
1229 "Use vrna_eval_loop_pt() instead");
1230
1245DEPRECATED(float energy_of_struct(const char *string,
1246 const char *structure),
1247 "Use vrna_eval_structure_simple() instead");
1248
1265DEPRECATED(int energy_of_struct_pt(const char *string,
1266 short *ptable,
1267 short *s,
1268 short *s1),
1269 "Use vrna_eval_structure_pt_simple() instead");
1270
1285DEPRECATED(float energy_of_circ_struct(const char *string,
1286 const char *structure),
1287 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
1288
1289#endif
1290
1295#endif
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:148
An atomic representation of the transition / move from one structure to its neighbor.
Definition: move.h:73
Methods to operate with structural neighbors of RNA secondary structures.
Functions to deal with sets of energy parameters.