RNAlib-2.6.3
 
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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
944float
946 const char *structure,
947 int m1,
948 int m2);
949
950
966int
968 short *pt,
969 int m1,
970 int m2);
971
972
973int
974vrna_eval_move_pt_simple(const char *string,
975 short *pt,
976 int m1,
977 int m2);
978
979
980int
981vrna_eval_move_shift_pt(vrna_fold_compound_t *fc,
982 vrna_move_t *m,
983 short *structure);
984
985
990#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
991
1005extern int cut_point;
1006
1010extern int eos_debug;
1011
1030DEPRECATED(float energy_of_structure(const char *string,
1031 const char *structure,
1032 int verbosity_level),
1033 "Use vrna_eval_structure_simple() and vrna_eval_structure() instead");
1034
1050DEPRECATED(float energy_of_struct_par(const char *string,
1051 const char *structure,
1052 vrna_param_t *parameters,
1053 int verbosity_level),
1054 "Use vrna_eval_structure() instead");
1055
1074DEPRECATED(float energy_of_circ_structure(const char *string,
1075 const char *structure,
1076 int verbosity_level),
1077 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
1078
1094DEPRECATED(float energy_of_circ_struct_par(const char *string,
1095 const char *structure,
1096 vrna_param_t *parameters,
1097 int verbosity_level),
1098 "Use vrna_eval_structure() instead");
1099
1100
1101DEPRECATED(float energy_of_gquad_structure(const char *string,
1102 const char *structure,
1103 int verbosity_level),
1104 "Use vrna_eval_structure_simple() instead");
1105
1106DEPRECATED(float energy_of_gquad_struct_par(const char *string,
1107 const char *structure,
1108 vrna_param_t *parameters,
1109 int verbosity_level),
1110 "Use vrna_eval_structure() instead");
1111
1112
1133DEPRECATED(int energy_of_structure_pt(const char *string,
1134 short *ptable,
1135 short *s,
1136 short *s1,
1137 int verbosity_level),
1138 "Use vrna_eval_structure_pt_simple() and vrna_eval_structure_pt() instead");
1139
1157DEPRECATED(int energy_of_struct_pt_par(const char *string,
1158 short *ptable,
1159 short *s,
1160 short *s1,
1161 vrna_param_t *parameters,
1162 int verbosity_level),
1163 "Use vrna_eval_structure_pt() instead");
1164
1165
1182DEPRECATED(float energy_of_move(const char *string,
1183 const char *structure,
1184 int m1,
1185 int m2),
1186 "Use vrna_eval_move() instead");
1187
1188
1207DEPRECATED(int energy_of_move_pt(short *pt,
1208 short *s,
1209 short *s1,
1210 int m1,
1211 int m2),
1212 "Use vrna_eval_move_pt_simple() and vrna_eval_move_pt() instead");
1213
1227DEPRECATED(int loop_energy(short *ptable,
1228 short *s,
1229 short *s1,
1230 int i),
1231 "Use vrna_eval_loop_pt() instead");
1232
1248DEPRECATED(float energy_of_struct(const char *string,
1249 const char *structure),
1250 "Use vrna_eval_structure_simple() instead");
1251
1269DEPRECATED(int energy_of_struct_pt(const char *string,
1270 short *ptable,
1271 short *s,
1272 short *s1),
1273 "Use vrna_eval_structure_pt_simple() instead");
1274
1290DEPRECATED(float energy_of_circ_struct(const char *string,
1291 const char *structure),
1292 "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
1293
1294#endif
1295
1300#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: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.