RNAlib-2.4.14
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>
5 #include <ViennaRNA/datastructures/basic.h>
6 #include <ViennaRNA/fold_compound.h>
7 #include <ViennaRNA/datastructures/char_stream.h>
8 #include <ViennaRNA/landscape/move.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 
93 float
94 vrna_eval_structure(vrna_fold_compound_t *vc,
95  const char *structure);
96 
97 
118 float
119 vrna_eval_covar_structure(vrna_fold_compound_t *vc,
120  const char *structure);
121 
122 
136 float
137 vrna_eval_structure_verbose(vrna_fold_compound_t *vc,
138  const char *structure,
139  FILE *file);
140 
141 
167 float
168 vrna_eval_structure_v(vrna_fold_compound_t *vc,
169  const char *structure,
170  int verbosity_level,
171  FILE *file);
172 
173 
174 float
175 vrna_eval_structure_cstr(vrna_fold_compound_t *vc,
176  const char *structure,
177  int verbosity_level,
178  vrna_cstr_t output_stream);
179 
180 
181 /* End basic eval interface */
208 int
209 vrna_eval_structure_pt(vrna_fold_compound_t *vc,
210  const short *pt);
211 
212 
226 int
227 vrna_eval_structure_pt_verbose(vrna_fold_compound_t *vc,
228  const short *pt,
229  FILE *file);
230 
231 
257 int
258 vrna_eval_structure_pt_v(vrna_fold_compound_t *vc,
259  const short *pt,
260  int verbosity_level,
261  FILE *file);
262 
263 
264 /* End basic eval interface with pair table */
288 float
289 vrna_eval_structure_simple(const char *string,
290  const char *structure);
291 
292 
303 float
304 vrna_eval_circ_structure(const char *string,
305  const char *structure);
306 
307 
325 float
326 vrna_eval_gquad_structure(const char *string,
327  const char *structure);
328 
329 
348 float
349 vrna_eval_circ_gquad_structure(const char *string,
350  const char *structure);
351 
352 
367 float
368 vrna_eval_structure_simple_verbose(const char *string,
369  const char *structure,
370  FILE *file);
371 
372 
396 float
397 vrna_eval_structure_simple_v(const char *string,
398  const char *structure,
399  int verbosity_level,
400  FILE *file);
401 
402 
418 float
419 vrna_eval_circ_structure_v(const char *string,
420  const char *structure,
421  int verbosity_level,
422  FILE *file);
423 
424 
447 float
448 vrna_eval_gquad_structure_v(const char *string,
449  const char *structure,
450  int verbosity_level,
451  FILE *file);
452 
453 
474 float
475 vrna_eval_circ_gquad_structure_v(const char *string,
476  const char *structure,
477  int verbosity_level,
478  FILE *file);
479 
480 
481 /* End simplified eval interface */
511 float
512 vrna_eval_consensus_structure_simple(const char **alignment,
513  const char *structure);
514 
515 
531 float
532 vrna_eval_circ_consensus_structure(const char **alignment,
533  const char *structure);
534 
535 
558 float
559 vrna_eval_gquad_consensus_structure(const char **alignment,
560  const char *structure);
561 
562 
585 float
586 vrna_eval_circ_gquad_consensus_structure(const char **alignment,
587  const char *structure);
588 
589 
609 float
610 vrna_eval_consensus_structure_simple_verbose(const char **alignment,
611  const char *structure,
612  FILE *file);
613 
614 
639 float
640 vrna_eval_consensus_structure_simple_v(const char **alignment,
641  const char *structure,
642  int verbosity_level,
643  FILE *file);
644 
645 
665 float
666 vrna_eval_circ_consensus_structure_v(const char **alignment,
667  const char *structure,
668  int verbosity_level,
669  FILE *file);
670 
671 
698 float
699 vrna_eval_gquad_consensus_structure_v(const char **alignment,
700  const char *structure,
701  int verbosity_level,
702  FILE *file);
703 
704 
731 float
732 vrna_eval_circ_gquad_consensus_structure_v(const char **alignment,
733  const char *structure,
734  int verbosity_level,
735  FILE *file);
736 
737 
738 /* End simplified comparative eval interface */
761 int
762 vrna_eval_structure_pt_simple(const char *string,
763  const short *pt);
764 
765 
779 int
780 vrna_eval_structure_pt_simple_verbose(const char *string,
781  const short *pt,
782  FILE *file);
783 
784 
809 int
810 vrna_eval_structure_pt_simple_v(const char *string,
811  const short *pt,
812  int verbosity_level,
813  FILE *file);
814 
815 
816 /* End simplified eval interface with pair table */
838 int
839 vrna_eval_consensus_structure_pt_simple(const char **alignment,
840  const short *pt);
841 
842 
843 int
844 vrna_eval_consensus_structure_pt_simple_verbose(const char **alignment,
845  const short *pt,
846  FILE *file);
847 
848 
849 int
850 vrna_eval_consensus_structure_pt_simple_v(const char **alignment,
851  const short *pt,
852  int verbosity_level,
853  FILE *file);
854 
855 
856 /* End simplified eval interface with pair table */
887 int
888 vrna_eval_loop_pt(vrna_fold_compound_t *vc,
889  int i,
890  const short *pt);
891 
892 
902 int
903 vrna_eval_loop_pt_v(vrna_fold_compound_t *vc,
904  int i,
905  const short *pt,
906  int verbosity_level);
907 
908 
943 float
944 vrna_eval_move(vrna_fold_compound_t *vc,
945  const char *structure,
946  int m1,
947  int m2);
948 
949 
964 int
965 vrna_eval_move_pt(vrna_fold_compound_t *vc,
966  short *pt,
967  int m1,
968  int m2);
969 
970 
971 int
972 vrna_eval_move_pt_simple(const char *string,
973  short *pt,
974  int m1,
975  int m2);
976 
977 
978 int
979 vrna_eval_move_shift_pt(vrna_fold_compound_t *vc,
980  vrna_move_t *m,
981  short *structure);
982 
983 
988 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
989 
1003 extern int cut_point;
1004 
1008 extern int eos_debug;
1009 
1028 DEPRECATED(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 
1048 DEPRECATED(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 
1072 DEPRECATED(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 
1092 DEPRECATED(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 
1099 DEPRECATED(float energy_of_gquad_structure(const char *string,
1100  const char *structure,
1101  int verbosity_level),
1102  "Use vrna_eval_structure_simple() instead");
1103 
1104 DEPRECATED(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 
1131 DEPRECATED(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 
1155 DEPRECATED(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 
1180 DEPRECATED(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 
1205 DEPRECATED(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 
1225 DEPRECATED(int loop_energy(short *ptable,
1226  short *s,
1227  short *s1,
1228  int i),
1229  "Use vrna_eval_loop_pt() instead");
1230 
1245 DEPRECATED(float energy_of_struct(const char *string,
1246  const char *structure),
1247  "Use vrna_eval_structure_simple() instead");
1248 
1265 DEPRECATED(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 
1285 DEPRECATED(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
vrna_eval_structure
float vrna_eval_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the free energy of an already folded RNA.
energy_of_circ_struct_par
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.
energy_of_struct_pt
int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)
vrna_eval_circ_consensus_structure_v
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...
vrna_eval_structure_simple_verbose
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.
vrna_eval_circ_gquad_consensus_structure
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...
vrna_eval_loop_pt_v
int vrna_eval_loop_pt_v(vrna_fold_compound_t *vc, int i, const short *pt, int verbosity_level)
Calculate energy of a loop.
vrna_eval_circ_gquad_structure_v
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.
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
vrna_eval_structure_pt_verbose
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.
eos_debug
int eos_debug
verbose info from energy_of_struct
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
energy_of_circ_struct
float energy_of_circ_struct(const char *string, const char *structure)
loop_energy
int loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a loop.
vrna_eval_structure_simple
float vrna_eval_structure_simple(const char *string, const char *structure)
Calculate the free energy of an already folded RNA.
energy_of_struct_pt_par
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.
vrna_eval_move
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)
cut_point
int cut_point
first pos of second seq for cofolding
energy_of_structure
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.
vrna_eval_gquad_consensus_structure_v
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 ...
vrna_eval_circ_structure_v
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...
vrna_eval_move_pt
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)
basic.h
Various data structures and pre-processor macros.
vrna_eval_covar_structure
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.
vrna_eval_loop_pt
int vrna_eval_loop_pt(vrna_fold_compound_t *vc, int i, const short *pt)
Calculate energy of a loop.
vrna_eval_consensus_structure_simple_verbose
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...
vrna_eval_consensus_structure_simple
float vrna_eval_consensus_structure_simple(const char **alignment, const char *structure)
Calculate the free energy of an already folded RNA sequence alignment.
energy_of_circ_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.
vrna_eval_circ_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.
energy_of_move
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)
vrna_eval_structure_simple_v
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.
vrna_eval_gquad_consensus_structure
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...
vrna_eval_circ_gquad_consensus_structure_v
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...
energy_of_struct
float energy_of_struct(const char *string, const char *structure)
energy_of_move_pt
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)
vrna_eval_circ_gquad_structure
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...
move.h
Methods to operate with structural neighbors of RNA secondary structures.
vrna_eval_structure_pt_simple_verbose
int vrna_eval_structure_pt_simple_verbose(const char *string, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
vrna_eval_structure_pt_simple_v
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.
vrna_eval_structure_pt_v
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.
vrna_eval_structure_pt_simple
int vrna_eval_structure_pt_simple(const char *string, const short *pt)
Calculate the free energy of an already folded RNA.
char_stream.h
Implementation of a dynamic, buffered character stream.
vrna_eval_structure_verbose
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...
vrna_eval_gquad_structure
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...
basic.h
Functions to deal with sets of energy parameters.
energy_of_structure_pt
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.
vrna_eval_structure_pt
int vrna_eval_structure_pt(vrna_fold_compound_t *vc, const short *pt)
Calculate the free energy of an already folded RNA.
vrna_eval_circ_consensus_structure
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...
fold_compound.h
The Basic Fold Compound API.
vrna_eval_consensus_structure_simple_v
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...
vrna_eval_gquad_structure_v
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...
vrna_eval_consensus_structure_pt_simple
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.
vrna_eval_structure_v
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...
vrna_move_s
An atomic representation of the transition / move from one structure to its neighbor.
Definition: move.h:73
energy_of_struct_par
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.