RNAlib-2.1.9h
data_structures.h
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1 #ifndef __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__
2 #define __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__
3 
4 #include "energy_const.h"
10 /* to use floats instead of doubles in pf_fold() comment next line */
11 #define LARGE_PF
12 #ifdef LARGE_PF
13 #define FLT_OR_DBL double
14 #else
15 #define FLT_OR_DBL float
16 #endif
17 
18 #ifndef MAXALPHA
19 
22 #define MAXALPHA 20
23 #endif
24 
28 #define MAXDOS 1000
29 
30 #define VRNA_GQUAD_MAX_STACK_SIZE 7
31 #define VRNA_GQUAD_MIN_STACK_SIZE 2
32 #define VRNA_GQUAD_MAX_LINKER_LENGTH 15
33 #define VRNA_GQUAD_MIN_LINKER_LENGTH 1
34 #define VRNA_GQUAD_MIN_BOX_SIZE ((4*VRNA_GQUAD_MIN_STACK_SIZE)+(3*VRNA_GQUAD_MIN_LINKER_LENGTH))
35 #define VRNA_GQUAD_MAX_BOX_SIZE ((4*VRNA_GQUAD_MAX_STACK_SIZE)+(3*VRNA_GQUAD_MAX_LINKER_LENGTH))
36 
37 
38 /*
39 * ############################################################
40 * Here are the type definitions of various datastructures
41 * shared among the Vienna RNA Package
42 * ############################################################
43 */
44 
48 typedef struct plist {
49  int i;
50  int j;
51  float p;
52  int type;
53 } plist;
54 
58 typedef struct cpair {
59  int i,j,mfe;
60  float p, hue, sat;
61 } cpair;
62 
67 typedef struct {
68  float X; /* X coords */
69  float Y; /* Y coords */
70 } COORDINATE;
71 
75 typedef struct sect {
76  int i;
77  int j;
78  int ml;
79 } sect;
80 
84 typedef struct bondT {
85  unsigned int i;
86  unsigned int j;
87 } bondT;
88 
92 typedef struct bondTEn {
93  int i;
94  int j;
95  int energy;
96 } bondTEn;
97 
102 typedef struct{
103  int dangles;
110  int noLP;
111  int noGU;
113  int logML;
114  int circ;
115  int gquad;
118 
122 typedef struct{
123  int id;
124  double temperature;
125 
126  /* RNA, RNA-DNA, DNA params merged */
127  int stack[NBPAIRS_HYBRID+1][NBPAIRS_HYBRID+1];
134  int dangle5[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID];
135  int dangle3[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID];
139  int MLintern[NBPAIRS_HYBRID+1];
140  int TerminalAU_t[NBPAIRS_HYBRID+1];
141 
142  int gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]
143  [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
144 
145  int TripleC;
146  int MultipleCA;
147  int MultipleCB;
148  int TerminalAU;
149  int DuplexInit;
150 
151  /* RNA params */
152  int hairpin[31];
153  int bulge[MAXLOOP+1];
154  int internal_loop[MAXLOOP+1];
155  int ninio[NNUCLEOTIDES_HYBRID];
156  double lxc;
157  int MLbase;
158  int MLclosing;
159  int Tetraloop_E[200];
160  char Tetraloops[1401];
161  int Triloop_E[40];
162  char Triloops[241];
163  int Hexaloop_E[40];
164  char Hexaloops[1801];
165 
166  /* hybrid params */
167  int hairpin_RD[31];
168  int bulge_RD[MAXLOOP+1];
169  int internal_loop_RD[MAXLOOP+1];
170  int ninio_RD[5];
171  double lxc_RD;
172  int MLbase_RD;
173  int MLclosing_RD;
174  int Tetraloop_E_RD[200];
175  char Tetraloops_RD[1401];
176  int Triloop_E_RD[40];
177  char Triloops_RD[241];
178  int Hexaloop_E_RD[40];
179  char Hexaloops_RD[1801];
180 
181  /* DNA params */
182  int hairpin_D[31];
183  int bulge_D[MAXLOOP+1];
184  int internal_loop_D[MAXLOOP+1];
185  int ninio_D[5];
186  double lxc_D;
187  int MLbase_D;
188  int MLclosing_D;
189  int Tetraloop_E_D[200];
190  char Tetraloops_D[1401];
191  int Triloop_E_D[40];
192  char Triloops_D[241];
193  int Hexaloop_E_D[40];
194  char Hexaloops_D[1801];
195 
198 } paramT;
199 
203 typedef struct{
204  int id;
205  /* RNA, RNA-DNA, DNA params merged */
206  double expstack[NBPAIRS_HYBRID+1][NBPAIRS_HYBRID+1];
207  double expmismatchExt[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID][NNUCLEOTIDES_HYBRID];
208  double expmismatchI[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID][NNUCLEOTIDES_HYBRID];
209  double expmismatch23I[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID][NNUCLEOTIDES_HYBRID];
210  double expmismatch1nI[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID][NNUCLEOTIDES_HYBRID];
211  double expmismatchH[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID][NNUCLEOTIDES_HYBRID];
212  double expmismatchM[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID][NNUCLEOTIDES_HYBRID];
213  double expdangle5[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID];
214  double expdangle3[NBPAIRS_HYBRID+1][NNUCLEOTIDES_HYBRID];
218  double expMLintern[NBPAIRS_HYBRID+1];
219  double expTermAU_t[NBPAIRS_HYBRID+1];
220 
221  double expDuplexInit;
222  double expTermAU;
223 
224  /* RNA params */
225  double exphairpin[31];
226  double expbulge[MAXLOOP+1];
227  double expinternal[MAXLOOP+1];
228  double expninio[5][MAXLOOP+1];
229  double lxc;
230  double expMLbase;
231  double expMLclosing;
232  double exptetra[40];
233  double exptri[40];
234  double exphex[40];
235  char Tetraloops[1401];
236  char Triloops[241];
237  char Hexaloops[1801];
238 
239  /* hybrid params */
240  double exphairpin_RD[31];
241  double expbulge_RD[MAXLOOP+1];
242  double expinternal_RD[MAXLOOP+1];
243  double expninio_RD[5][MAXLOOP+1];
244  double lxc_RD;
245  double expMLbase_RD;
246  double expMLclosing_RD;
247  double exptetra_RD[40];
248  double exptri_RD[40];
249  double exphex_RD[40];
250  char Tetraloops_RD[1401];
251  char Triloops_RD[241];
252  char Hexaloops_RD[1801];
253 
254  /* DNA params */
255  double exphairpin_D[31];
256  double expbulge_D[MAXLOOP+1];
257  double expinternal_D[MAXLOOP+1];
258  double expninio_D[5][MAXLOOP+1];
259  double lxc_D;
260  double expMLbase_D;
261  double expMLclosing_D;
262  double exptetra_D[40];
263  double exptri_D[40];
264  double exphex_D[40];
265  char Tetraloops_D[1401];
266  char Triloops_D[241];
267  char Hexaloops_D[1801];
268 
269  double expTripleC;
270  double expMultipleCA;
271  double expMultipleCB;
272  double expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]
273  [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
274 
275  double kT;
276  double pf_scale;
278  double temperature;
279  double alpha;
287 } pf_paramT;
288 
289 
290 
291 /*
292 * ############################################################
293 * SUBOPT data structures
294 * ############################################################
295 */
296 
297 
301 typedef struct {
302  int i;
303  int j;
304 } PAIR;
305 
309 typedef struct {
310  int i;
311  int j;
312  int array_flag;
313 } INTERVAL;
314 
318 typedef struct {
319  float energy;
320  char *structure;
321 } SOLUTION;
322 
323 /*
324 * ############################################################
325 * COFOLD data structures
326 * ############################################################
327 */
328 
332 typedef struct cofoldF {
333  /* free energies for: */
334  double F0AB;
335  double FAB;
336  double FcAB;
337  double FA;
338  double FB;
339 } cofoldF;
340 
344 typedef struct ConcEnt {
345  double A0;
346  double B0;
347  double ABc;
348  double AAc;
349  double BBc;
350  double Ac;
351  double Bc;
352 } ConcEnt;
353 
357 typedef struct pairpro{
358  struct plist *AB;
359  struct plist *AA;
360  struct plist *A;
361  struct plist *B;
362  struct plist *BB;
363 }pairpro;
364 
375 typedef struct {
376  unsigned i;
377  unsigned j;
378  float p;
379  float ent;
380  short bp[8];
381  char comp;
382 } pair_info;
383 
384 
385 /*
386 * ############################################################
387 * FINDPATH data structures
388 * ############################################################
389 */
390 
394 typedef struct move {
395  int i; /* i,j>0 insert; i,j<0 delete */
396  int j;
397  int when; /* 0 if still available, else resulting distance from start */
398  int E;
399 } move_t;
400 
404 typedef struct intermediate {
405  short *pt;
406  int Sen;
407  int curr_en;
410 
414 typedef struct path {
415  double en;
416  char *s;
417 } path_t;
418 
419 /*
420 * ############################################################
421 * RNAup data structures
422 * ############################################################
423 */
424 
428 typedef struct pu_contrib {
429  double **H;
430  double **I;
431  double **M;
432  double **E;
433  int length;
434  int w;
435 } pu_contrib;
436 
440 typedef struct interact {
441  double *Pi;
442  double *Gi;
443  double Gikjl;
445  double Gikjl_wo;
446  int i;
447  int k;
448  int j;
449  int l;
450  int length;
451 } interact;
452 
456 typedef struct pu_out {
457  int len;
458  int u_vals;
459  int contribs;
460  char **header;
461  double **u_values;
462 } pu_out;
463 
467 typedef struct constrain{
468  int *indx;
469  char *ptype;
470 } constrain;
471 
472 /*
473 * ############################################################
474 * RNAduplex data structures
475 * ############################################################
476 */
477 
481 typedef struct {
482  int i;
483  int j;
484  int end;
485  char *structure;
486  double energy;
487  double energy_backtrack;
488  double opening_backtrack_x;
489  double opening_backtrack_y;
490  int offset;
491  double dG1;
492  double dG2;
493  double ddG;
494  int tb;
495  int te;
496  int qb;
497  int qe;
498 } duplexT;
499 
500 /*
501 * ############################################################
502 * RNAsnoop data structures
503 * ############################################################
504 */
505 
509 typedef struct node {
510  int k;
511  int energy;
512  struct node *next;
513 } folden;
514 
518 typedef struct {
519  int i;
520  int j;
521  int u;
522  char *structure;
523  float energy;
524  float Duplex_El;
525  float Duplex_Er;
526  float Loop_E;
527  float Loop_D;
528  float pscd;
529  float psct;
530  float pscg;
531  float Duplex_Ol;
532  float Duplex_Or;
533  float Duplex_Ot;
534  float fullStemEnergy;
535 } snoopT;
536 
537 
538 
539 
540 
541 
542 
543 /*
544 * ############################################################
545 * PKplex data structures
546 * ############################################################
547 */
548 
552 typedef struct dupVar{
553  int i;
554  int j;
555  int end;
556  char *pk_helix;
557  char *structure;
558  double energy;
559  int offset;
560  double dG1;
561  double dG2;
562  double ddG;
563  int tb;
564  int te;
565  int qb;
566  int qe;
567  int inactive;
568  int processed;
569 } dupVar;
570 
571 
572 
573 /*
574 * ############################################################
575 * 2Dfold data structures
576 * ############################################################
577 */
578 
593 typedef struct{
594  int k;
595  int l;
596  float en;
597  char *s;
599 
605 typedef struct{
608  char *ptype;
609  char *sequence;
610  short *S, *S1;
611  unsigned int maxD1;
612  unsigned int maxD2;
615  unsigned int *mm1;
616  unsigned int *mm2;
618  int *my_iindx;
620  double temperature;
621 
622  unsigned int *referenceBPs1;
623  unsigned int *referenceBPs2;
624  unsigned int *bpdist;
626  short *reference_pt1;
627  short *reference_pt2;
628  int circ;
629  int dangles;
630  unsigned int seq_length;
631 
632  int ***E_F5;
633  int ***E_F3;
634  int ***E_C;
635  int ***E_M;
636  int ***E_M1;
637  int ***E_M2;
638 
639  int **E_Fc;
640  int **E_FcH;
641  int **E_FcI;
642  int **E_FcM;
643 
644  int **l_min_values;
645  int **l_max_values;
646  int *k_min_values;
647  int *k_max_values;
648 
649  int **l_min_values_m;
650  int **l_max_values_m;
651  int *k_min_values_m;
652  int *k_max_values_m;
653 
654  int **l_min_values_m1;
655  int **l_max_values_m1;
656  int *k_min_values_m1;
657  int *k_max_values_m1;
658 
659  int **l_min_values_f;
660  int **l_max_values_f;
661  int *k_min_values_f;
662  int *k_max_values_f;
663 
664  int **l_min_values_f3;
665  int **l_max_values_f3;
666  int *k_min_values_f3;
667  int *k_max_values_f3;
668 
669  int **l_min_values_m2;
670  int **l_max_values_m2;
671  int *k_min_values_m2;
672  int *k_max_values_m2;
673 
674  int *l_min_values_fc;
675  int *l_max_values_fc;
676  int k_min_values_fc;
677  int k_max_values_fc;
678 
679  int *l_min_values_fcH;
680  int *l_max_values_fcH;
681  int k_min_values_fcH;
682  int k_max_values_fcH;
683 
684  int *l_min_values_fcI;
685  int *l_max_values_fcI;
686  int k_min_values_fcI;
687  int k_max_values_fcI;
688 
689  int *l_min_values_fcM;
690  int *l_max_values_fcM;
691  int k_min_values_fcM;
692  int k_max_values_fcM;
693 
694  /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */
695  int *E_F5_rem;
696  int *E_F3_rem;
697  int *E_C_rem;
698  int *E_M_rem;
699  int *E_M1_rem;
700  int *E_M2_rem;
701 
702  int E_Fc_rem;
703  int E_FcH_rem;
704  int E_FcI_rem;
705  int E_FcM_rem;
706 
707 #ifdef COUNT_STATES
708  unsigned long ***N_F5;
709  unsigned long ***N_C;
710  unsigned long ***N_M;
711  unsigned long ***N_M1;
712 #endif
713 } TwoDfold_vars;
714 
727 typedef struct{
728  int k;
729  int l;
730  FLT_OR_DBL q;
732 
739 typedef struct{
740 
741  unsigned int alloc;
742  char *ptype;
743  char *sequence;
744  short *S, *S1;
745  unsigned int maxD1;
746  unsigned int maxD2;
748  double temperature; /* temperature in last call to scale_pf_params */
749  double init_temp; /* temperature in last call to scale_pf_params */
750  FLT_OR_DBL *scale;
751  FLT_OR_DBL pf_scale;
752  pf_paramT *pf_params; /* holds all [unscaled] pf parameters */
753 
754  int *my_iindx;
755  int *jindx;
757  short *reference_pt1;
758  short *reference_pt2;
759 
760  unsigned int *referenceBPs1;
761  unsigned int *referenceBPs2;
762  unsigned int *bpdist;
764  unsigned int *mm1;
765  unsigned int *mm2;
767  int circ;
768  int dangles;
769  unsigned int seq_length;
770 
771  FLT_OR_DBL ***Q;
772  FLT_OR_DBL ***Q_B;
773  FLT_OR_DBL ***Q_M;
774  FLT_OR_DBL ***Q_M1;
775  FLT_OR_DBL ***Q_M2;
776 
777  FLT_OR_DBL **Q_c;
778  FLT_OR_DBL **Q_cH;
779  FLT_OR_DBL **Q_cI;
780  FLT_OR_DBL **Q_cM;
781 
782  int **l_min_values;
783  int **l_max_values;
784  int *k_min_values;
785  int *k_max_values;
786 
787  int **l_min_values_b;
788  int **l_max_values_b;
789  int *k_min_values_b;
790  int *k_max_values_b;
791 
792  int **l_min_values_m;
793  int **l_max_values_m;
794  int *k_min_values_m;
795  int *k_max_values_m;
796 
797  int **l_min_values_m1;
798  int **l_max_values_m1;
799  int *k_min_values_m1;
800  int *k_max_values_m1;
801 
802  int **l_min_values_m2;
803  int **l_max_values_m2;
804  int *k_min_values_m2;
805  int *k_max_values_m2;
806 
807  int *l_min_values_qc;
808  int *l_max_values_qc;
809  int k_min_values_qc;
810  int k_max_values_qc;
811 
812  int *l_min_values_qcH;
813  int *l_max_values_qcH;
814  int k_min_values_qcH;
815  int k_max_values_qcH;
816 
817  int *l_min_values_qcI;
818  int *l_max_values_qcI;
819  int k_min_values_qcI;
820  int k_max_values_qcI;
821 
822  int *l_min_values_qcM;
823  int *l_max_values_qcM;
824  int k_min_values_qcM;
825  int k_max_values_qcM;
826 
827  /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */
828  FLT_OR_DBL *Q_rem;
829  FLT_OR_DBL *Q_B_rem;
830  FLT_OR_DBL *Q_M_rem;
831  FLT_OR_DBL *Q_M1_rem;
832  FLT_OR_DBL *Q_M2_rem;
833 
834  FLT_OR_DBL Q_c_rem;
835  FLT_OR_DBL Q_cH_rem;
836  FLT_OR_DBL Q_cI_rem;
837  FLT_OR_DBL Q_cM_rem;
838 
840 
841 #endif
int l
Distance to second reference.
Definition: data_structures.h:595
int Sen
saddle energy so far
Definition: data_structures.h:406
Definition: data_structures.h:509
double temperature
Temperature used for loop contribution scaling.
Definition: data_structures.h:278
double FAB
all states with DuplexInit correction
Definition: data_structures.h:335
int w
longest unpaired region
Definition: data_structures.h:434
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: data_structures.h:615
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: data_structures.h:612
unsigned j
nucleotide position j
Definition: data_structures.h:377
char ** header
header line
Definition: data_structures.h:460
int contribs
[-c "SHIME"]
Definition: data_structures.h:459
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: data_structures.h:622
#define MAXLOOP
Definition: energy_const.h:28
Base pair with associated energy.
Definition: data_structures.h:92
float en
Free energy in kcal/mol.
Definition: data_structures.h:596
Definition: data_structures.h:404
short * S1
The input sequences in numeric form.
Definition: data_structures.h:610
Definition: data_structures.h:332
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition: data_structures.h:618
paramT * P
Precomputed energy parameters and model details.
Definition: data_structures.h:606
move_t * moves
remaining moves to target
Definition: data_structures.h:408
double FcAB
true hybrid states only
Definition: data_structures.h:336
char * ptype
Precomputed array of pair types.
Definition: data_structures.h:742
int special_hp
Include special hairpin contributions for tri, tetra and hexaloops.
Definition: data_structures.h:109
int circ
backward compatibility variable.. this does not effect anything
Solution element returned from TwoDpfoldList.
Definition: data_structures.h:727
Definition: data_structures.h:394
double * Gi
free energies of interaction
Definition: data_structures.h:442
float energy
Free Energy of structure in kcal/mol.
Definition: data_structures.h:319
The datastructure that contains temperature scaled energy parameters.
Definition: data_structures.h:122
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: data_structures.h:760
float p
Probability.
Definition: data_structures.h:378
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: data_structures.h:746
Definition: data_structures.h:518
int * my_iindx
Index for moving in quadratic distancy dimensions.
Definition: data_structures.h:754
model_detailsT model_details
Model details to be used in the recursions.
Definition: data_structures.h:196
double FB
monomer B
Definition: data_structures.h:338
#define NNUCLEOTIDES_HYBRID
Definition: energy_const.h:36
char * s
MFE representative structure in dot-bracket notation.
Definition: data_structures.h:597
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: data_structures.h:203
char * ptype
Precomputed array of pair types.
Definition: data_structures.h:608
int length
length of longer sequence
Definition: data_structures.h:450
Collection of all free_energy of beeing unpaired values for output.
Definition: data_structures.h:456
double Gikjl
full free energy for interaction between [k,i] k
Definition: data_structures.h:443
int noGU
Do not allow GU pairs.
Definition: data_structures.h:111
Definition: data_structures.h:552
double ** I
interior loops
Definition: data_structures.h:430
Solution element from subopt.c.
Definition: data_structures.h:318
double ** M
multi loops
Definition: data_structures.h:431
constraints for cofolding
Definition: data_structures.h:467
Definition: data_structures.h:481
int canonicalBPonly
remove non-canonical bp's from constraint structures
Definition: data_structures.h:116
int noGUclosure
Do not allow loops to be closed by GU pair.
Definition: data_structures.h:112
int curr_en
current energy
Definition: data_structures.h:407
A base pair info structure.
Definition: data_structures.h:375
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:48
double q
partition function
Definition: data_structures.h:730
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: data_structures.h:762
double ** H
hairpin loops
Definition: data_structures.h:429
int gquad
Include G-quadruplexes in structure prediction.
Definition: data_structures.h:115
int gquad
Allow G-quadruplex formation.
Variables compound for 2Dfold MFE folding.
Definition: data_structures.h:605
double F0AB
Null model without DuplexInit.
Definition: data_structures.h:334
int dangles
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
Definition: data_structures.h:103
int k
k
Definition: data_structures.h:447
char * sequence
The input sequence.
Definition: data_structures.h:609
double A0
start concentration A
Definition: data_structures.h:345
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: data_structures.h:745
Sequence interval stack element used in subopt.c.
Definition: data_structures.h:309
Definition: data_structures.h:440
short * pt
pair table
Definition: data_structures.h:405
int l
j
Definition: data_structures.h:449
double ABc
End concentration AB.
Definition: data_structures.h:347
double alpha
Scaling factor for the thermodynamic temperature.
Definition: data_structures.h:279
#define NBPAIRS_HYBRID
Definition: energy_const.h:34
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: data_structures.h:461
Base pair.
Definition: data_structures.h:84
int l
Distance to second reference.
Definition: data_structures.h:729
int logML
Use logarithmic scaling for multi loops.
Definition: data_structures.h:113
Stack of partial structures for backtracking.
Definition: data_structures.h:75
double ** E
exterior loop
Definition: data_structures.h:432
int len
sequence length
Definition: data_structures.h:457
int k
Distance to first reference.
Definition: data_structures.h:728
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: data_structures.h:616
this datastructure is used as input parameter in functions of PS_dot.c
Definition: data_structures.h:58
int i
k
Definition: data_structures.h:446
Definition: data_structures.h:414
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: data_structures.h:764
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: data_structures.h:624
int length
length of the input sequence
Definition: data_structures.h:433
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: data_structures.h:623
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: data_structures.h:445
int noLP
Only consider canonical structures, i.e. no 'lonely' base pairs.
Definition: data_structures.h:110
int j
j
Definition: data_structures.h:448
The data structure that contains the complete model details used throughout the calculations.
Definition: data_structures.h:102
Base pair data structure used in subopt.c.
Definition: data_structures.h:301
double * Pi
probabilities of interaction
Definition: data_structures.h:441
int * jindx
Index for moving in the triangular matrix qm1.
Definition: data_structures.h:755
int circ
Assume molecule to be circular.
Definition: data_structures.h:114
int do_backtrack
Flag whether to do backtracing of the structure(s) or not.
Definition: data_structures.h:607
unsigned i
nucleotide position i
Definition: data_structures.h:376
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
int k
Distance to first reference.
Definition: data_structures.h:594
short * S1
The input sequences in numeric form.
Definition: data_structures.h:744
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: data_structures.h:611
contributions to p_u
Definition: data_structures.h:428
Definition: data_structures.h:357
double pf_scale
Scaling factor to avoid over-/underflows.
Definition: data_structures.h:276
float ent
Pseudo entropy for .
Definition: data_structures.h:379
char * sequence
The input sequence.
Definition: data_structures.h:743
double B0
start concentration B
Definition: data_structures.h:346
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: data_structures.h:765
model_detailsT model_details
Model details to be used in the recursions.
Definition: data_structures.h:286
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: data_structures.h:761
Definition: data_structures.h:344
Solution element returned from TwoDfoldList.
Definition: data_structures.h:593
int u_vals
number of different -u values
Definition: data_structures.h:458
double temperature
Rescale energy parameters to a temperature in degC.
this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORD...
Definition: data_structures.h:67
double FA
monomer A
Definition: data_structures.h:337
char * structure
Structure in dot-bracket notation.
Definition: data_structures.h:320
char comp
1 iff pair is in mfe structure
Definition: data_structures.h:381
Variables compound for 2Dfold partition function folding.
Definition: data_structures.h:739