1 #ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H
2 #define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H
21 #define FLT_OR_DBL double
23 #define FLT_OR_DBL float
190 typedef struct move {
200 typedef struct intermediate {
210 typedef struct path {
283 double energy_backtrack;
284 double opening_backtrack_x;
285 double opening_backtrack_y;
305 typedef struct node {
330 float fullStemEnergy;
415 #if __STDC_VERSION__ >= 201112L
441 #if __STDC_VERSION__ >= 201112L
526 unsigned long ***N_F5;
527 unsigned long ***N_C;
528 unsigned long ***N_M;
529 unsigned long ***N_M1;
536 #if __STDC_VERSION__ >= 201112L
557 #if __STDC_VERSION__ >= 201112L
584 FLT_OR_DBL *expMLbase;
589 #if __STDC_VERSION__ >= 201112L
659 FLT_OR_DBL *Q_M1_rem;
660 FLT_OR_DBL *Q_M2_rem;
670 #if __STDC_VERSION__ >= 201112L
731 #if __STDC_VERSION__ >= 201112L
748 short *sequence_encoding2;
771 #if __STDC_VERSION__ >= 201112L
804 unsigned short **a2s;
816 #if __STDC_VERSION__ >= 201112L
854 #define VRNA_OPTION_MFE 1
862 #define VRNA_OPTION_PF 2
864 #define VRNA_OPTION_HYBRID 4
866 #define VRNA_OPTION_DIST_CLASS 16
868 #define VRNA_OPTION_LFOLD 32
879 #define VRNA_OPTION_EVAL_ONLY 8
912 unsigned int options);
943 unsigned int options);
950 unsigned int options);
int * f3
Energy of 3' end.
Definition: data_structures.h:427
Definition: data_structures.h:305
unsigned int length
Length of the sequence, therefore an indicator of the size of the DP matrices.
Definition: data_structures.h:410
double FAB
all states with DuplexInit correction
Definition: data_structures.h:131
int * ggg
Energies of g-quadruplexes.
Definition: data_structures.h:432
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: data_structures.h:833
int w
longest unpaired region
Definition: data_structures.h:230
int * c
Energy array, given that i-j pair.
Definition: data_structures.h:425
DP matrices suitable for local structure prediction.
Definition: data_structures.h:393
vrna_fold_compound * vrna_get_fold_compound_ali(const char **sequences, vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound data structure for sequence alignments.
struct vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: data_structures.h:716
int * fM1
Second ML array, only for unique multibrnach loop decomposition.
Definition: data_structures.h:430
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint...
Definition: data_structures.h:712
The hard constraints data structure.
Definition: constraints.h:390
short ** S5
S5[s][i] holds next base 5' of i in sequence s.
Definition: data_structures.h:797
unsigned j
nucleotide position j
Definition: data_structures.h:173
char ** header
header line
Definition: data_structures.h:256
int contribs
[-c "SHIME"]
Definition: data_structures.h:255
Base pair with associated energy.
Definition: data_structures.h:81
int oldAliEn
use old alifold energies (with gaps)
Definition: data_structures.h:128
struct vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: data_structures.h:721
double FcAB
true hybrid states only
Definition: data_structures.h:132
int * jindx
DP matrix accessor.
Definition: data_structures.h:725
int * fML
Multi-loop auxiliary energy array.
Definition: data_structures.h:429
short * S_cons
Numerical encoding of the consensus sequence.
Definition: data_structures.h:791
The model details data structure and its corresponding modifiers.
Definition: data_structures.h:190
double * Gi
free energies of interaction
Definition: data_structures.h:238
float energy
Free Energy of structure in kcal/mol.
Definition: data_structures.h:115
float p
Probability.
Definition: data_structures.h:174
Definition: data_structures.h:681
Default DP matrices.
Definition: data_structures.h:392
Definition: data_structures.h:314
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: data_structures.h:805
double FB
monomer B
Definition: data_structures.h:134
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition: data_structures.h:800
unsigned int n_seq
The number of sequences in the alignment.
Definition: data_structures.h:785
void vrna_exp_params_update(vrna_fold_compound *vc, vrna_exp_param_t *params)
Update the energy parameters for subsequent partition function computations.
int length
length of longer sequence
Definition: data_structures.h:246
Collection of all free_energy of beeing unpaired values for output.
Definition: data_structures.h:252
vrna_fold_compound * vrna_get_fold_compound(const char *sequence, vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound data structure for single sequences and hybridizing sequences...
vrna_mx_pf_t * exp_matrices
The PF DP matrices.
Definition: data_structures.h:719
void vrna_params_update(vrna_fold_compound *vc, vrna_param_t *par)
Update/Reset energy parameters data structure within a vrna_fold_compound.
double Gikjl
full free energy for interaction between [k,i] k
Definition: data_structures.h:239
Definition: data_structures.h:343
double ** I
interior loops
Definition: data_structures.h:226
void vrna_free_mfe_matrices(vrna_fold_compound *vc)
Free memory occupied by the Minimum Free Energy (MFE) Dynamic Programming (DP) matrices.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:698
Solution element from subopt.c.
Definition: data_structures.h:114
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: data_structures.h:837
double ** M
multi loops
Definition: data_structures.h:227
constraints for cofolding
Definition: data_structures.h:263
char ** sequences
The aligned sequences.
Definition: data_structures.h:781
Definition: data_structures.h:277
void vrna_exp_params_rescale(vrna_fold_compound *vc, double *mfe)
Rescale Boltzmann factors for partition function computations.
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: data_structures.h:832
int * fc
Energy from i to cutpoint (and vice versa if i>cut)
Definition: data_structures.h:428
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: data_structures.h:828
A base pair info structure.
Definition: data_structures.h:171
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:45
void vrna_free_fold_compound(vrna_fold_compound *vc)
Free memory occupied by a vrna_fold_compound.
double ** H
hairpin loops
Definition: data_structures.h:225
void vrna_free_pf_matrices(vrna_fold_compound *vc)
Free memory occupied by the Partition Function (PF) Dynamic Programming (DP) matrices.
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: data_structures.h:546
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: data_structures.h:718
double F0AB
Null model without DuplexInit.
Definition: data_structures.h:130
int * iindx
DP matrix accessor.
Definition: data_structures.h:724
int k
k
Definition: data_structures.h:243
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: data_structures.h:788
double A0
start concentration A
Definition: data_structures.h:141
short ** S
Numerical encoding of the sequences in the alignment.
Definition: data_structures.h:794
short * reference_pt2
A pairtable of the second reference structure.
Definition: data_structures.h:830
short * reference_pt1
A pairtable of the first reference structure.
Definition: data_structures.h:829
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: data_structures.h:836
Sequence interval stack element used in subopt.c.
Definition: data_structures.h:105
Definition: data_structures.h:236
unsigned int length
The length of the sequence (or sequence alignment)
Definition: data_structures.h:711
int l
j
Definition: data_structures.h:245
DP matrices suitable for distance class partitioned structure prediction.
Definition: data_structures.h:396
double ABc
End concentration AB.
Definition: data_structures.h:143
vrna_vc_t type
The type of the vrna_fold_compound.
Definition: data_structures.h:704
char * ptype
Pair type array.
Definition: data_structures.h:749
struct vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors.
Definition: data_structures.h:722
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: data_structures.h:257
Base pair.
Definition: data_structures.h:73
Stack of partial structures for backtracking.
Definition: data_structures.h:64
double ** E
exterior loop
Definition: data_structures.h:228
int len
sequence length
Definition: data_structures.h:253
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:41
Definition: data_structures.h:682
The soft constraints data structure.
Definition: constraints.h:413
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:169
this datastructure is used as input parameter in functions of PS_dot.c
Definition: data_structures.h:55
int i
k
Definition: data_structures.h:242
Definition: data_structures.h:210
int length
length of the input sequence
Definition: data_structures.h:229
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: data_structures.h:241
int j
j
Definition: data_structures.h:244
Base pair data structure used in subopt.c.
Definition: data_structures.h:97
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: data_structures.h:744
double * Pi
probabilities of interaction
Definition: data_structures.h:237
struct vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: data_structures.h:763
vrna_vc_t
An enumerator that is used to specify the type of a vrna_fold_compound.
Definition: data_structures.h:680
unsigned i
nucleotide position i
Definition: data_structures.h:172
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: data_structures.h:834
contributions to p_u
Definition: data_structures.h:224
Definition: data_structures.h:153
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:86
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: data_structures.h:827
float ent
Pseudo entropy for .
Definition: data_structures.h:175
double B0
start concentration B
Definition: data_structures.h:142
int * fM2
Energy for a multibranch loop region with exactly two stems, extending to 3' end. ...
Definition: data_structures.h:431
char * ptype_pf_compat
ptype array indexed via iindx
Definition: data_structures.h:758
char * sequence
The input sequence string.
Definition: data_structures.h:741
int Fc
Minimum Free Energy of entire circular RNA.
Definition: data_structures.h:433
vrna_mx_t
An enumerator that is used to specify the type of a polymorphic Dynamic Programming (DP) matrix data ...
Definition: data_structures.h:391
Definition: data_structures.h:140
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: data_structures.h:405
int * f5
Energy of 5' end.
Definition: data_structures.h:426
int u_vals
number of different -u values
Definition: data_structures.h:254
double FA
monomer A
Definition: data_structures.h:133
char * structure
Structure in dot-bracket notation.
Definition: data_structures.h:116
char comp
1 iff pair is in mfe structure
Definition: data_structures.h:177
struct vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: data_structures.h:808