RNAlib-2.4.10
eval.h
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1 #ifndef VIENNA_RNA_PACKAGE_EVAL_H
2 #define VIENNA_RNA_PACKAGE_EVAL_H
3 
4 #include <stdio.h>
7 #include "ViennaRNA/neighbor.h"
8 #include <ViennaRNA/params/basic.h> /* for deprecated functions */
9 
10 #ifdef VRNA_WARN_DEPRECATED
11 # if defined(__clang__)
12 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
13 # elif defined(__GNUC__)
14 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
15 # else
16 # define DEPRECATED(func, msg) func
17 # endif
18 #else
19 # define DEPRECATED(func, msg) func
20 #endif
21 
22 
57 #define VRNA_VERBOSITY_QUIET -1
58 
59 
63 #define VRNA_VERBOSITY_DEFAULT 1
64 
65 
93  const char *structure);
94 
95 
117  const char *structure);
118 
119 
134  const char *structure,
135  FILE *file);
136 
137 
164  const char *structure,
165  int verbosity_level,
166  FILE *file);
167 
168 
169 float
170 vrna_eval_structure_cstr(vrna_fold_compound_t *vc,
171  const char *structure,
172  int verbosity_level,
173  vrna_cstr_t output_stream);
174 
175 /* End basic eval interface */
203  const short *pt);
204 
205 
220  const short *pt,
221  FILE *file);
222 
223 
250  const short *pt,
251  int verbosity_level,
252  FILE *file);
253 
254 
255 /* End basic eval interface with pair table */
279 float vrna_eval_structure_simple(const char *string,
280  const char *structure);
281 
282 
293 float vrna_eval_circ_structure(const char *string,
294  const char *structure);
295 
296 
314 float vrna_eval_gquad_structure(const char *string,
315  const char *structure);
316 
317 
336 float vrna_eval_circ_gquad_structure(const char *string,
337  const char *structure);
338 
339 
354 float vrna_eval_structure_simple_verbose(const char *string,
355  const char *structure,
356  FILE *file);
357 
358 
382 float vrna_eval_structure_simple_v(const char *string,
383  const char *structure,
384  int verbosity_level,
385  FILE *file);
386 
387 
403 float vrna_eval_circ_structure_v(const char *string,
404  const char *structure,
405  int verbosity_level,
406  FILE *file);
407 
408 
431 float vrna_eval_gquad_structure_v(const char *string,
432  const char *structure,
433  int verbosity_level,
434  FILE *file);
435 
436 
457 float vrna_eval_circ_gquad_structure_v(const char *string,
458  const char *structure,
459  int verbosity_level,
460  FILE *file);
461 
462 
463 /* End simplified eval interface */
493 float vrna_eval_consensus_structure_simple(const char **alignment,
494  const char *structure);
495 
496 
512 float vrna_eval_circ_consensus_structure(const char **alignment,
513  const char *structure);
514 
515 
538 float vrna_eval_gquad_consensus_structure(const char **alignment,
539  const char *structure);
540 
541 
564 float vrna_eval_circ_gquad_consensus_structure(const char **alignment,
565  const char *structure);
566 
567 
587 float vrna_eval_consensus_structure_simple_verbose(const char **alignment,
588  const char *structure,
589  FILE *file);
590 
591 
616 float vrna_eval_consensus_structure_simple_v(const char **alignment,
617  const char *structure,
618  int verbosity_level,
619  FILE *file);
620 
621 
641 float vrna_eval_circ_consensus_structure_v(const char **alignment,
642  const char *structure,
643  int verbosity_level,
644  FILE *file);
645 
646 
673 float vrna_eval_gquad_consensus_structure_v(const char **alignment,
674  const char *structure,
675  int verbosity_level,
676  FILE *file);
677 
678 
705 float vrna_eval_circ_gquad_consensus_structure_v(const char **alignment,
706  const char *structure,
707  int verbosity_level,
708  FILE *file);
709 
710 
711 /* End simplified comparative eval interface */
734 int vrna_eval_structure_pt_simple(const char *string,
735  const short *pt);
736 
737 
751 int vrna_eval_structure_pt_simple_verbose(const char *string,
752  const short *pt,
753  FILE *file);
754 
755 
780 int vrna_eval_structure_pt_simple_v(const char *string,
781  const short *pt,
782  int verbosity_level,
783  FILE *file);
784 
785 
786 /* End simplified eval interface with pair table */
808 int vrna_eval_consensus_structure_pt_simple(const char **alignment,
809  const short *pt);
810 
811 
812 int vrna_eval_consensus_structure_pt_simple_verbose(const char **alignment,
813  const short *pt,
814  FILE *file);
815 
816 
817 int
818 vrna_eval_consensus_structure_pt_simple_v(const char **alignment,
819  const short *pt,
820  int verbosity_level,
821  FILE *file);
822 
823 
824 /* End simplified eval interface with pair table */
856  int i,
857  const short *pt);
858 
859 
870  int i,
871  const short *pt,
872  int verbosity_level);
873 
874 
910  const char *structure,
911  int m1,
912  int m2);
913 
914 
930  short *pt,
931  int m1,
932  int m2);
933 
934 
935 int vrna_eval_move_pt_simple(const char *string,
936  short *pt,
937  int m1,
938  int m2);
939 
940 
941 int
942 vrna_eval_move_shift_pt(vrna_fold_compound_t *vc,
943  vrna_move_t *m,
944  short *structure);
945 
946 
951 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
952 
966 extern int cut_point;
967 
971 extern int eos_debug;
972 
991 DEPRECATED(float energy_of_structure(const char *string,
992  const char *structure,
993  int verbosity_level),
994  "Use vrna_eval_structure_simple() and vrna_eval_structure() instead");
995 
1011 DEPRECATED(float energy_of_struct_par(const char *string,
1012  const char *structure,
1013  vrna_param_t *parameters,
1014  int verbosity_level),
1015  "Use vrna_eval_structure() instead");
1016 
1035 DEPRECATED(float energy_of_circ_structure(const char *string,
1036  const char *structure,
1037  int verbosity_level),
1038  "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
1039 
1055 DEPRECATED(float energy_of_circ_struct_par(const char *string,
1056  const char *structure,
1057  vrna_param_t *parameters,
1058  int verbosity_level),
1059  "Use vrna_eval_structure() instead");
1060 
1061 
1062 DEPRECATED(float energy_of_gquad_structure(const char *string,
1063  const char *structure,
1064  int verbosity_level),
1065  "Use vrna_eval_structure_simple() instead");
1066 
1067 DEPRECATED(float energy_of_gquad_struct_par(const char *string,
1068  const char *structure,
1069  vrna_param_t *parameters,
1070  int verbosity_level),
1071  "Use vrna_eval_structure() instead");
1072 
1073 
1094 DEPRECATED(int energy_of_structure_pt(const char *string,
1095  short *ptable,
1096  short *s,
1097  short *s1,
1098  int verbosity_level),
1099  "Use vrna_eval_structure_pt_simple() and vrna_eval_structure_pt() instead");
1100 
1118 DEPRECATED(int energy_of_struct_pt_par(const char *string,
1119  short *ptable,
1120  short *s,
1121  short *s1,
1122  vrna_param_t *parameters,
1123  int verbosity_level),
1124  "Use vrna_eval_structure_pt() instead");
1125 
1126 
1143 DEPRECATED(float energy_of_move(const char *string,
1144  const char *structure,
1145  int m1,
1146  int m2),
1147  "Use vrna_eval_move() instead");
1148 
1149 
1168 DEPRECATED(int energy_of_move_pt(short *pt,
1169  short *s,
1170  short *s1,
1171  int m1,
1172  int m2),
1173  "Use vrna_eval_move_pt_simple() and vrna_eval_move_pt() instead");
1174 
1188 DEPRECATED(int loop_energy(short *ptable,
1189  short *s,
1190  short *s1,
1191  int i),
1192  "Use vrna_eval_loop_pt() instead");
1193 
1208 DEPRECATED(float energy_of_struct(const char *string,
1209  const char *structure),
1210  "Use vrna_eval_structure_simple() instead");
1211 
1228 DEPRECATED(int energy_of_struct_pt(const char *string,
1229  short *ptable,
1230  short *s,
1231  short *s1),
1232  "Use vrna_eval_structure_pt_simple() instead");
1233 
1248 DEPRECATED(float energy_of_circ_struct(const char *string,
1249  const char *structure),
1250  "Use vrna_eval_circ_structure_simple() and vrna_eval_structure() instead");
1251 
1252 #endif
1253 
1258 #endif
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.
Implementation of a dynamic, buffered character stream.
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.