1 #ifndef VIENNA_RNA_PACKAGE_INTERIOR_LOOPS_H 2 #define VIENNA_RNA_PACKAGE_INTERIOR_LOOPS_H 5 #include "ViennaRNA/energy_par.h" 11 # define INLINE inline 20 #define ON_SAME_STRAND(I, J, C) (((I) >= (C)) || ((J) < (C))) 118 PRIVATE INLINE
int E_IntLoop_Co(
int type,
150 ubf_eval_int_loop(
int i,
163 unsigned char type_2,
175 if ((cp < 0) || (ON_SAME_STRAND(i, p, cp) && ON_SAME_STRAND(q, j, cp))) {
177 energy =
E_IntLoop(u1, u2, type, type_2, si, sj, sp, sq, P);
181 Si = ON_SAME_STRAND(i, i1, cp) ? si : -1;
182 Sj = ON_SAME_STRAND(j1, j, cp) ? sj : -1;
183 energy = E_IntLoop_Co(rtype[type], rtype[type_2],
229 ubf_eval_ext_int_loop(
int i,
242 unsigned char type_2,
247 int energy, u1, u2, u3;
253 energy =
E_IntLoop(u2, u1 + u3, type, type_2, si, sj, sp, sq, P);
264 if (u1 + u2 + u3 == 0)
290 int nl, ns, u, energy;
303 return P->stack[type][type_2];
307 energy = (nl <=
MAXLOOP) ? P->bulge[nl] :
308 (P->bulge[30] + (
int)(P->lxc * log(nl / 30.)));
310 energy += P->stack[type][type_2];
313 energy += P->TerminalAU;
316 energy += P->TerminalAU;
324 return P->int11[type][type_2][si1][sj1];
329 energy = P->int21[type][type_2][si1][sq1][sj1];
331 energy = P->int21[type_2][type][sq1][si1][sp1];
338 MAXLOOP) ? (P->internal_loop[nl + 1]) : (P->internal_loop[30] +
339 (int)(P->lxc * log((nl + 1) / 30.)));
340 energy +=
MIN2(MAX_NINIO, (nl - ns) * P->ninio[2]);
341 energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type_2][sq1][sp1];
344 }
else if (ns == 2) {
347 return P->int22[type][type_2][si1][sp1][sq1][sj1];
348 }
else if (nl == 3) {
350 energy = P->internal_loop[5] + P->ninio[2];
351 energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type_2][sq1][sp1];
361 MAXLOOP) ? (P->internal_loop[u]) : (P->internal_loop[30] + (int)(P->lxc * log((u) / 30.)));
363 energy +=
MIN2(MAX_NINIO, (nl - ns) * P->ninio[2]);
365 energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type_2][sq1][sp1];
384 int ul, us, no_close = 0;
388 if ((noGUclosure) && ((type2 == 3) || (type2 == 4) || (type == 3) || (type == 4)))
401 z = P->expstack[type][type2];
402 }
else if (!no_close) {
407 z *= P->expstack[type][type2];
417 }
else if (us == 1) {
419 return (
FLT_OR_DBL)(P->expint11[type][type2][si1][sj1]);
424 return (
FLT_OR_DBL)(P->expint21[type][type2][si1][sq1][sj1]);
426 return (
FLT_OR_DBL)(P->expint21[type2][type][sq1][si1][sp1]);
429 z = P->expinternal[ul + us] * P->expmismatch1nI[type][si1][sj1] *
430 P->expmismatch1nI[type2][sq1][sp1];
431 return (
FLT_OR_DBL)(z * P->expninio[2][ul - us]);
433 }
else if (us == 2) {
436 return (
FLT_OR_DBL)(P->expint22[type][type2][si1][sp1][sq1][sj1]);
437 }
else if (ul == 3) {
439 z = P->expinternal[5] * P->expmismatch23I[type][si1][sj1] *
440 P->expmismatch23I[type2][sq1][sp1];
446 z = P->expinternal[ul + us] * P->expmismatchI[type][si1][sj1] *
447 P->expmismatchI[type2][sq1][sp1];
448 return (
FLT_OR_DBL)(z * P->expninio[2][ul - us]);
456 E_IntLoop_Co(
int type,
470 int energy, ci, cj, cp, cq, d3, d5, d5_2, d3_2, tmm, tmm_2;
474 energy += P->TerminalAU;
477 energy += P->TerminalAU;
482 ci = ON_SAME_STRAND(i, i + 1, cutpoint);
483 cj = ON_SAME_STRAND(j - 1, j, cutpoint);
484 cp = ON_SAME_STRAND(p - 1, p, cutpoint);
485 cq = ON_SAME_STRAND(q, q + 1, cutpoint);
487 d3 = ci ? P->dangle3[type][si1] : 0;
488 d5 = cj ? P->dangle5[type][sj1] : 0;
489 d5_2 = cp ? P->dangle5[type_2][sp1] : 0;
490 d3_2 = cq ? P->dangle3[type_2][sq1] : 0;
492 tmm = (cj && ci) ? P->mismatchExt[type][sj1][si1] : d5 + d3;
493 tmm_2 = (cp && cq) ? P->mismatchExt[type_2][sp1][sq1] : d5_2 + d3_2;
496 return energy + tmm + tmm_2;
501 energy += tmm + tmm_2;
503 energy += (cj && cq) ?
MIN2(tmm + d5_2, tmm_2 + d3) : tmm + tmm_2;
506 }
else if (i + 2 == p) {
508 energy += (ci && cp) ?
MIN2(tmm + d3_2, tmm_2 + d5) : tmm + tmm_2;
510 energy +=
MIN2(tmm,
MIN2(tmm_2,
MIN2(d5 + d5_2, d3 + d3_2)));
512 energy +=
MIN2(d3, d5_2);
517 energy +=
MIN2(d5, d3_2);
int dangles
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
Definition: model.h:192
#define MAXLOOP
Definition: energy_const.h:29
vrna_md_t model_details
Model details to be used in the recursions.
Definition: params.h:95
vrna_md_t model_details
Model details to be used in the recursions.
Definition: params.h:151
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:48
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
int noGUclosure
Do not allow loops to be closed by GU pair.
Definition: model.h:219
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:57
int * energy_stack
Pseudo Energy contribution per base pair involved in a stack.
Definition: constraints_soft.h:186
vrna_callback_sc_energy * f
A function pointer used for pseudo energy contribution in MFE calculations.
Definition: constraints_soft.h:190
General utility- and helper-functions used throughout the ViennaRNA Package.
int vrna_eval_int_loop(vrna_fold_compound_t *vc, int i, int j, int k, int l)
Various data structures and pre-processor macros.
The soft constraints data structure.
Definition: constraints_soft.h:154
#define INF
Definition: energy_const.h:17
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:101
int ** energy_up
Energy contribution for stretches of unpaired nucleotides.
Definition: constraints_soft.h:160
#define VRNA_DECOMP_PAIR_IL
Indicator for interior loop decomposition step.
Definition: constraints.h:72
Base pair stack element.
Definition: data_structures.h:229
Functions and data structures for constraining secondary structure predictions and evaluation...
int * energy_bp
Energy contribution for base pairs.
Definition: constraints_soft.h:171
int vrna_BT_stack(vrna_fold_compound_t *vc, int *i, int *j, int *en, vrna_bp_stack_t *bp_stack, int *stack_count)
Backtrack a stacked pair closed by .
PRIVATE int E_IntLoop(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, vrna_param_t *P)
Definition: interior_loops.h:279
#define MIN2(A, B)
Get the minimum of two comparable values.
Definition: utils.h:116
int vrna_BT_int_loop(vrna_fold_compound_t *vc, int *i, int *j, int en, vrna_bp_stack_t *bp_stack, int *stack_count)
Backtrack an interior loop closed by .
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
PRIVATE FLT_OR_DBL exp_E_IntLoop(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, vrna_exp_param_t *P)
Definition: interior_loops.h:374
void * data
A pointer to the data object provided for for pseudo energy contribution functions of the generic sof...
Definition: constraints_soft.h:207